K. C. Nicolaou, Rudolf Hanko, Wolfgang Hartwig Handbook of Combinatorial Chemistry Drugs, Catalysts, Materials 2-Vol. Set PDF

Handbook of
Combinatorial Chemistry
Drugs, Catalysts, Materials
Edited by K. C. Nicolaou,
R. Hanko, and W. Hartwig
Handbook of Combinatorial Chemistry. Drugs, Catalysts, Materials.

Edited by K. C. Nicolaou, R. Hanko, and W. Hartwig
Copyright 8 2002 WILEY-VCH Verlag GmbH, Weinheim
ISBN: 3-527-30509-2
Further Titles of Interest
W. Bannwarth, E. Felder (Eds.)
2000, ISBN 3-527-30186-0
G. Jung (Ed.)
Synthesis, Analysis, Screening
1999, ISBN 3-527-29869-X
F. Zaragoza D
orwald
Organic Synthesis on Solid Phase

Supports, Linkers, Reactions
2000, ISBN 3-527-29950-5
A. Beck-Sickinger, P. Weber
Combinatorial Strategies in Biology and

Chemistry
2002, ISBN 0-471-49726-6
Handbook of Combinatorial Chemistry
Drugs, Catalysts, Materials

Editors 9 This book was carefully produced. Never-
theless, editors, authors and publisher
Prof. Dr. K. C. Nicolaou do not warrant the information contained
Department of Chemistry and the Skaggs therein to be free of errors. Readers are
Institute for Chemical Biology advised to keep in mind that statements,
The Scripps Research Institute data, illustrations, procedural details or
10550 North Torrey other items may inadvertently be
Pines Road inaccurate.
La Jolla, CA 92037
USA Library of Congress Card No.: applied for
A catalogue record for this book is available
Dr. R. Hanko from the British Library.
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( WILEY-VCH Verlag GmbH, D-69469
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Bayer AG 2002
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Printed in the Federal Republic of

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ISBN 3-527-30509-2
v
Contents
Volume 1
Part I General Aspects 1
1 Combinatorial Chemistry in Perspective 3

K. C. Nicolaou, R. Hanko, and W. Hartwig
1.1 Introduction 3
1.2 Brief History of Combinatorial Chemistry 4
1.3 Applications of Combinatorial Chemistry 6
1.4 Outline of the Book 7
Acknowledgments 8
References 8
2 Introduction to Combinatorial Chemistry 10

David L. Coffen and Joachim E. A. Luithle
2.1 Combinatorial Chemistry in Drug Discovery a Perspective 10
2.2 Key Issues 11
2.3 Combinatorial Synthesis 15
2.3.1 Solid-phase Combinatorial Synthesis 16
2.3.1.1 Reagents and Conditions 16
2.3.1.2 Automation 17
2.3.1.3 Split and Combine 17
2.3.1.4 Cost 19
2.3.1.5 The Products from Solid-phase Chemistry 19
2.3.2 Solution-phase Combinatorial Synthesis 19
2.3.2.1 Reagents and Conditions 19
2.3.2.2 Scavenger Resins, Polymer-supported Reagents and Fluorous Tags 20
2.3.2.3 Equipment and Costs 22
2.4 Conclusion 22
References 22
Valuable Internet Links 23
3 Solid Phase and Soluble Polymers for Combinatorial Synthesis 24

Rainer Haag, Andre Hebel, and Jean-Francois Stumbe
3.1 Introduction 24
vi Contents
3.2 Solid-phase Supports 25

3.2.1 Polystyrene-based Resins 25
3.2.1.1 General Aspects 25
3.2.1.2 Macroporous Resins 28
3.2.1.3 Microporous Resins 31
3.2.2 Polystyrene Hybrid Supports 35
3.2.2.1 PEGylated Resins 35
3.2.2.2 High-loading PS Hybrid Supports 36
3.2.3 Other Crosslinked Polymeric Supports 41
3.2.3.1 Crosslinked Acrylamides 41
3.2.3.2 Crosslinked PEGs 44
3.2.4 Inorganic Supports 46
3.3 Soluble Polymeric Supports 46
3.3.1 Separation Techniques for Soluble Polymeric Supports 47
3.3.2 Terminal Functionalized Linear Polymeric Supports 49
3.3.3 Polyfunctional Linear Polymeric Supports 49
3.3.4 Dendritic Polymeric Supports 51
3.3.5 Microgels 54
3.4 Conclusions 54
References 54
4 Linkers for Solid-phase Synthesis 59

Stefan Brase and Stefan Dahmen
4.1 Introduction 59
4.2 General Linker Structures 60
4.2.1 Immobilization of Molecules 60
4.2.2 Spacers 61
4.2.3 Functionalized Linkers as Analytical Constructs 62
4.3 Linker Families 62
4.3.1 Benzyl-type Linkers Including Trityl and Benzhydryl Linkers 63
4.3.2 Allyl-based Linkers 68
4.3.3 Ketal/Acetal-based Linkers 70
4.3.4 Ester-, Amide-, and Carbamate-based Linkers 71
4.3.5 Silyl Linkers 73
4.3.6 Boronate Linkers 76
4.3.7 Sulfur, Stannane- and Selenium-based Linkers 77
4.3.7.1 Sulfur-based Linkers 77
4.3.7.2 Stannane-based Linkers 81
4.3.7.3 Selenium-based Linkers 81
4.3.8 Triazene-based Linkers 83
4.3.9 Orthogonality Between Linkers 88
4.4 Cleavage 88
4.4.1 Electrophilic and Nucleophilic Cleavage 88
4.4.2 Oxidative/Reductive Methods 90
4.4.3 Photocleavable Linkers 91
4.4.4 Metal-assisted Cleavage 93
Contents vii
4.4.4.1 Cleavage with Ensuing Allylic Substitution or Cross-coupling

Reactions 94
4.4.4.2 Cleavage via Alkene Metathesis 97
4.4.5 Unusual Cleavage Methods 98
4.5 Linker and Cleavage Strategies 98
4.5.1 Safety-catch Linkers 99
4.5.2 Cyclative Cleavage (Cyclorelease Strategy) 103
4.5.3 Cleavage-cyclization Cases 105
4.5.4 Fragmentation Strategies 107
4.5.5 Traceless Linkers 110
4.5.6 Multifunctional Cleavage 117
4.5.7 Linkers for Asymmetric Synthesis 120
4.6 Linkers for Functional Groups 121
4.6.1 Linkers for Nitrogen Functionalities 122
4.6.1.1 Linkers for Amines 123
4.6.1.2 Linkers for Primary Amines 123
4.6.1.3 Linkers for Secondary Amines 125
4.6.1.4 Linkers for Tertiary Amines 125
4.6.1.5 Linkers for Hydrazines, Hydrazones and Hydroxylamines 128
4.6.1.6 Linkers for Diazonium Salts 128
4.6.1.7 Linkers for Azides 129
4.6.1.8 Linkers for Nitro Compounds 129
4.6.1.9 Linkers for Azo Compounds 129
4.6.1.10 Linkers for Nitriles 129
4.6.1.11 Linkers for N-Heterocycles 129
4.6.2 Linkers for Carbonyl Functionalities 133
4.6.2.1 Linkers for Carboxylic Acids 133
4.6.2.2 Linkers for Carboxylic Esters, Anhydrides and Lactones 134
4.6.2.3 Linkers for Thiocarboxylic Acids and Esters 135
4.6.2.4 Linkers for Carboxamides and Related Structures 136
4.6.2.5 Linkers for Hydrazides and Semicarbazones 142
4.6.2.6 Linkers for Cyclic Amides and Related Structures 143
4.6.3 Linkers for Ketones and Aldehydes 144
4.6.4 Linkers for Alcohols, Phenols, Ethers, and Ketals 144
4.6.4.1 Linkers for Alcohols 144
4.6.4.2 Linkers for Phenols 146
4.6.5 Linkers for Sulfur Compounds 146
4.6.5.1 Linkers for Thiols and Thioethers 146
4.6.5.2 Linkers for Sulfonamides 147
4.6.5.3 Linkers for Sulfonic Acids 147
4.6.5.4 Linkers for Sulfones and Sulfoxides 148
4.6.5.5 Linkers for Sulfoximines 148
4.6.6 Linkers for Hydrocarbons 148
4.6.6.1 Linkers for Alkanes 149
4.6.6.2 Linkers for Arenes and Heteroarenes 149
4.6.6.3 Linkers for Alkenes 149
viii Contents
4.6.6.4 Linkers for Alkynes 150

4.6.7 Linkers for Aryl and Alkyl Halides 150
4.6.8 Linkers for Heterocycles 151
4.6.9 Linkers for Reactive Intermediates 151
4.6.10 Linkers for Other Functional Groups 152
4.6.10.1 Linkers for Phosphonates 152
4.6.10.2 Linkers for Boronates 152
4.6.10.3 Linkers for Silanes and Silanols 152
4.7 Overview for Linkers for Functional Groups 152
4.8 Conclusion, Summary and Outlook 152
References 153
5 Encoding Technologies 170

Thomas Kramer, Valery V. Antonenko, Reza Mortezaei, Nicolay V. Kulikov
5.1 Introduction 170
5.2 Chemical-encoding Methods 171
5.2.1 Oligonucleotide Tags 171
5.2.2 Peptide Tags 173
5.2.3 Haloaromatic Binary Coding 173
5.2.4 Secondary Amine Binary Coding 175
5.2.5 Mass Encoding 178
5.3 Nonchemical Encoding Methods 180
5.3.1 Positional Encoding 180
5.3.1.1 Light-directed Synthesis 180
5.3.1.2 Microtiter Plate-based Positional Encoding 181
5.3.2 Nonpositional Encoding 183
5.3.2.1 Tea-bag Approach 183
5.3.2.2 Cellulose and Laminar Supports 183
5.3.2.3 Radiofrequency Tags 183
5.3.2.4 Laser Encoding 186
5.4 Conclusion 186
References 187
6 Instrumentation for Combinatorial Chemistry 190

Marcus Bauser and Hubertus Stakemeier
6.1 Automation in Combinatorial Synthesis 190
6.1.1 General Remarks 190
6.1.2 Fully Automated Systems for Solid- and Solution-phase Synthesis 190
6.1.2.1 Robot-arm-based Systems 190
6.1.2.2 Fully Automated Workstation Systems 201
6.1.2.3 Modular Systems 207
6.2 Purication of Combinatorial Libraries 209
6.2.1 Automated LiquidLiquid Extraction 210
6.2.2 Solid-phase Extraction 211
6.2.3 Normal Phase Chromatography 212
6.2.3.1 CombiFlashTM from Isco 212
Contents ix
6.2.3.2 Quad3TM from Biotage 212

6.2.3.3 FlashMaster TM from Jones Chromatography 213
6.2.4 Reversed Phase Chromatography 213
6.2.4.1 Biotage 214
6.2.4.2 Gilson 214
6.2.4.3 Merck 215
6.2.4.4 Varian 215
6.2.4.5 Shimadzu 215
6.2.5 Preparative HPLC-MS 215
6.2.5.1 PE Sciex 215
6.2.5.2 Waters Micromass 216
6.2.5.3 Merck-Hitachi 216
6.2.5.4 Shimadzu 216
6.2.5.5 Gilson ThermoQuest 216
6.3 Analysis of Combinatorial Libraries 216
6.3.1 Purity of Combinatorial Libraries 217
6.3.2 Identity of Combinatorial Libraries 218
6.3.3 Quantication of Combinatorial Libraries 219
6.4 Automated Sample Processing 219
6.4.1 Sample Logistics 219
6.4.2 Evaporation 221
References 222
Part II Synthetic Chemistry 225
7 Radical Reactions in Combinatorial Chemistry 227

A. Ganesan and Mukund P. Sibi
7.2 Intramolecular Radical Additions to sp 2 and sp Carbon 228
7.3 Intermolecular Radical Additions 230
7.4 Functional Group Removal 237
7.5 Polymer-supported Reagents for Radical Chemistry 238
7.5.1 Polymer-supported Tinhydrides 239
7.5.2 Polymer-supported Allyl Stannane 242
7.5.3 Polymer-supported Reagents for Atom-transfer Reactions 242
7.5.4 Photochemical Generation of Radicals 243
7.6 Summary 244
References 244
8 Nucleophilic Substitution in Combinatorial and Solid-phase Synthesis 247

Jan-Gerd Hansel and Stephan Jordan
8.2 Nucleophilic Substitution at Aliphatic Carbons 247
8.2.2 Halogen Nucleophiles 248
8.2.3 Oxygen Nucleophiles 249
x Contents
8.2.4 Sulfur Nucleophiles 251

8.2.5 Nitrogen Nucleophiles 251
8.2.6 Ring-closing Reactions 254
8.3 Nucleophilic Substitution at Aromatic Carbons 254
8.3.2 Nitrogen Nucleophiles 255
8.3.3 Oxygen Nucleophiles 262
8.3.4 Sulfur Nucleophiles 264
8.3.5 Macrocyclization Reactions 265
References 266
9 Electrophilic Substitution in Combinatorial and Solid-phase Synthesis 270

9.2 Electrophilic Substitution at Aliphatic Carbons 271
9.2.1 Halogen Electrophiles 271
9.2.2 Nitrogen Electrophiles 271
9.2.3 Carbon Electrophiles 272
9.3 Electrophilic Substitution at Aromatic Carbons 272
9.3.2 Halogen Electrophiles 273
9.3.3 Nitrogen Electrophiles 274
9.3.4 Carbon Electrophiles 275
References 277
10 Elimination Chemistry in the Solution- and Solid-phase Synthesis of

Combinatorial Libraries 279
Demosthenes Fokas and Carmen Baldino
10.2 b-Eliminations in Combinatorial Chemistry 279
10.2.1 The Hofmann Elimination Solid-phase Synthesis of Tertiary Amines 280
10.2.1.1 Via a Regenerated Michael Acceptor (REM) Resin 280
10.2.1.2 Via a Safety-catch Resin 282
10.2.1.3 Via a Hydroxylamine Resin 283
10.2.1.4 Alternative Cleavage Techniques 284
10.2.2 b-Elimination on Selenyl Resins 286
10.2.3 b-Elimination on Sulfone Resins 288
10.2.4 b-Elimination on Silyl Resins 289
10.2.5 b-Elimination on Fluorenyl Resins 291
10.2.6 b-Elimination on 2-(2-Nitrophenyl)ethyl Resins 291
10.2.7 Radical-based b-Eliminations 292
10.2.7.1 b-C,O Bond Scission 292
10.2.7.2 b-C,Se Bond Scission-release of Olens 293
10.3 Conjugate Eliminations 293
10.3.1 1,6-Conjugate Eliminations 293
Contents xi
10.3.2 1,4-Conjugate Eliminations 295

10.4 AdditionElimination Reactions 296
10.4.1 AdditionElimination on Vinylogous Systems 296
10.4.1.1 Entry to Aminomethyleneoxazolones 296
10.4.1.2 Entry to Benzopyrones 297
10.4.1.3 2,3-Dihydro-4-pyridone Libraries 298
10.4.2 Cycloreversions 299
10.4.2.1 Pyrrole Libraries 299
10.4.2.2 Imidazole Libraries 300
10.4.2.3 Traceless Solid-phase Synthesis of Furans 300
10.4.2.4 1,2-Diazines 301
10.5 Summary 302
References 302
11 Addition to CC Multiple Bonds (Except for CC Bond Formation) 305

Adrian L. Smith
11.2 Addition to CbC Double Bonds 306
11.2.1 Epoxidation and Subsequent Epoxide Opening 306
11.2.2 Dihydroxylation 309
11.2.3 Oxidative Cleavage 311
11.2.4 Electrophilic Addition of AaX 313
11.2.5 Hydrogenation 315
11.2.6 Hydrometallation 316
11.2.7 1,4-Addition to a,b-Unsaturated Carbonyl Systems 317
11.3 Addition to CcC Triple Bonds 318
References 319
12 Addition to CarbonHetero Multiple Bonds 322

Philipp Grosche, Jorg Rademann, and Gunther Jung
12.2 Additions to CN Double Bonds in sp2 Systems 322
12.2.1 Attack by Hydride (Reductive Alkylation) 323
12.2.2 Addition of Carbon Nucleophiles 324
12.2.2.1 Imino Aldol Reaction 324
12.2.2.2 Reaction with Boronic Acids 326
12.2.2.3 Addition of Allylsilanes (Imino-Sakurai Reaction) 327
12.2.2.4 Reaction with Grignard Reagents, Lithium Organyles, and Zinc
Organyles 328
12.2.2.5 Addition of Copper Alkynes 329
12.2.2.6 Addition of Electron-rich Aromatic and Heteroaromatic Cycles 329
12.2.2.7 Radical Reactions 330
12.2.3 Addition of Nitrogen Nucleophiles 331
12.2.4 Addition of Phosphorus Nucleophiles 332
12.2.5 Reactions with Oxygen Nucleophiles 333
xii Contents
12.2.6 Addition of Sulfur Nucleophiles 333

12.3 Additions to CN Double Bonds in sp-Systems 334
12.3.1 Additions to Carbodiimides 335
12.3.2 Reaction of Isocyanates and Isothiocyanates 335
12.3.2.1 Addition of Carbon Nucleophiles 336
12.3.2.2 Addition of Nitrogen Nucleophiles 336
12.3.2.3 Addition of Oxygen Nucleophiles 337
12.3.3 Addition to CS Double Bonds in sp2 Systems 338
12.3.4 Reaction of CS Double Bonds in sp Systems 339
12.4 Additions to CN Triple Bonds (Cyanides, not Isocyanides) 339
12.4.1 Addition of Carbon Nucleophiles 339
12.4.2 Addition of Nitrogen Nucleophiles 340
12.4.3 Addition of Sulfur Nucleophiles 342
References 342
13 Chemistry of the Carbonyl Group 346

Tobias Wunberg
13.2 Chemistry of the Carbonyl Group and Combinatorial Chemistry 346
13.3 Chemistry of Carboxylic Acids 347
13.3.1 C(O)aX Bond-forming Reactions: General Remarks 347
13.3.1.1 Amides and Ureas 347
13.3.1.2 Esters and Urethanes 353
13.3.2 Transformation of Carboxylic Acids into Other Functional Groups 355
13.3.2.1 Formation of Ketones 355
13.3.2.2 Formation of Amines: Curtius Degradation 356
13.3.2.3 Tebbe Olenation 356
13.3.2.4 Formation of Thioamides 357
13.4 Reactions of Aldehydes and Ketones 357
13.4.1 Reactions of Carbonyl Groups with CaH Acidic Compounds 357
13.4.1.1 Wittig and HornerEmmons Olenations 357
13.4.2 Reductive Amination 360
13.4.2.1 General Aspects 360
13.4.2.2 Formation of Imines 360
13.4.2.3 Reduction of Imines/Enamines 361
13.4.2.4 Applications 362
References 365
14 Oxidation Except CC Double Bonds 369

Henning Steinhagen
14.2 Oxidation of Alcohols to Aldehydes and Ketones 369
14.2.1 Examples of the Oxidation of Polymer-bound Primary Alcohols to
Aldehydes 371
14.2.2 Examples of the Oxidation of Polymer-bound Secondary Alcohols to
Ketones 372
Contents xiii
14.2.3 Examples of the Oxidation of Alcohols by Polymer-bound

Reagents 373
14.3 Oxidation of Polymer-bound Aldehydes to Carboxylic Acids 375
14.4 Oxidation of Sulfur-containing Compounds 376
14.4.1 Examples of the Oxidation of Polymer-bound Suldes to Sulfoxides and
Sulfones 376
14.5 Oxidation of Selenium- and Phosphorus-containing Compounds 378
14.5.1 Examples of the Oxidation (Cleavage) of Selenides to Selenoxides on
Solid Support 378
14.6 Oxidative Formation of Heterocycles on Solid Support 379
14.7 Oxidative Coupling and Cleavage Reactions on Solid Support 380
14.7.1 Examples of Oxidative Coupling Reactions on Solid Support 381
14.7.2 Examples of Oxidative Cleavage Reactions on Solid Support 382
References 382
15 Reductions in Combinatorial Synthesis 387

Christopher P. Corrette and Conrad W. Hummel
15.2 Solid-phase Reductions 387
15.2.1 Aldehyde Reductions 387
15.2.2 Ketone Reductions 388
15.2.3 Ester Reductions 390
15.2.4 Mixed Anhydride Reductions 392
15.2.5 Thioester Reductions 393
15.2.6 Weinreb Amide Reductions 394
15.2.7 Sulfur Reductions 396
15.2.8 Selenium Reductions 397
15.2.9 Quinone Reductions 399
15.2.10 Amide Reductions 399
15.2.11 Carbamate Reductions 400
15.2.12 Reductive Amination 401
15.2.12.1 General Considerations 401
15.2.12.2 Imine Formation 402
15.2.12.3 Reducing Agents for Reductive Amination 403
15.2.12.4 Reductive Aminations as the Entry Point for Library Preparation 403
15.2.12.5 Recent Examples of Reductive Amination on Resin 405
15.2.13 Azide Reductions 406
15.2.13.2 Azide Reductions in Glycopeptide Preparations 406
15.2.13.3 Small Molecule Libraries Incorporating Azide Reduction 407
15.2.13.4 Recent Examples of Azide Reduction on Resin 408
15.2.14 Nitro Group Reductions 409
15.2.14.2 Tin-mediated Nitro Reductions 409
15.2.14.3 Nitro Reductions with Alternative Reagents 411
15.2.14.4 Recent Examples of Nitro Reduction on Resin 411
xiv Contents
15.2.15 Imine Reductions (not Reductive Amination) 411

15.2.16 Nitrile Reduction 413
15.2.17 NaN and NaO Bond Reductions 413
15.2.18 Miscellaneous Reductions 414
15.3 Solution-phase Reductions 414
15.3.1 Supported Reagents 414
15.3.1.1 Asymmetric Reagents 414
15.3.1.2 Non-asymmetric Reagents 415
15.3.2 Supported Catalysts 422
15.3.2.1 Asymmetric Catalysis 422
15.3.2.2 Non-asymmetric Catalysis 428
15.3.3 Unsupported Reagents Using Catch-and-release Purication 430
15.3.3.1 Reductive Amination 430
15.3.3.2 Amide Reductions 430
15.3.4 Fluorous Chemistry 430
15.4 Conclusions 431
References 431
16 Cycloadditions in Combinatorial and Solid-phase Synthesis 440

Markus Albers and Thorsten Meyer
16.2 4 2 Cycloadditions 441
16.2.1 DielsAlder Reaction with Resin-bound Dienes 441
16.2.2 DielsAlder Reaction with Resin-bound Dienophiles 445
16.2.3 Intramolecular DielsAlder Reaction on Solid Support 448
16.2.4 Hetero-DielsAlder Reaction on Solid Support 450
16.2.5 DielsAlder Reaction in Solution Phase 451
16.3.1 Formation of Isoxazoles, Isoxazolines, and Isoxazolidines 453
16.3.2 Formation of Pyrrolidines 458
16.3.3 Formation of Furans 460
16.3.4 Formation of Imidazoles, Pyrroles, Pyrazoles, and Other Nitrogen-
containing Heterocycles 461
16.5 6 3 Cycloadditions on Solid Support 464
16.6 Rearrangements 465
References 467
17 Main Group Organometallics 470

Christopher Kallus
17.2 Reactions of Metalated Aromatics 471
17.3 1,2-Additions to CbX Groups 474
17.3.1 Reactions with Aldehydes 474
17.3.2 Reaction with Ketones 477
17.3.3 Reaction with Imines 479
Contents xv
17.3.4 Reaction with Enolates 481

17.4 Conjugate Addition to a,b-Unsaturated Carbonyls and Related
Systems 482
17.5 Nucleophilic Substitutions 483
17.6 Reactions on Carboxylic Acid Derivatives and Related Systems 484
17.6.1 Reaction with Esters 484
17.6.2 Reactions with Weinreb Amides and Related Systems 485
17.7 Aminolysis of Esters 489
References 490
18 Enolates and Related Species in Combinatorial and Solid-phase

Synthesis 492
Jochen Kruger
18.2 Aldol Reactions 492
18.2.1 General Aspects 492
18.2.2 Li, Na, K, and Zn Enolates in Aldol Reactions 493
18.2.3 Boron Enolates in Aldol Reactions 495
18.2.4 The Mukaiyama Aldol Reaction 498
18.2.4.1 Solution-phase Protocols Using Polymer-bound Reagents 498
18.2.4.2 Solid-phase Protocols 502
18.3 1,4-Addition of Enolates to Michael Acceptors 503
18.4 Alkylation of Enolates 506
18.4.1 a-Alkylation of Carbonyl Compounds 506
18.4.2 a- and g-Alkylation of 1,3-Dicarbonyl Compounds 507
18.4.3 Stereoselective Alkylations of Enolates 510
18.4.4 Alkylation of Protected Glycines 513
18.5 Claisen-type Condensations 515
18.6 Dieckmann Condensations 516
18.7 Knoevenagel Condensations 518
18.8 Addition of Enolates to Imines 520
18.8.1 Synthesis of b-Amino Esters and Alcohols via Enolate Addition to
Imines 520
18.8.2 Solid-phase Synthesis of b-Lactams via Enolate Additions to
Imines 522
18.9 Nitro-aldol Reactions 522
18.10 The BaylisHillman Reaction 524
18.11 Miscellaneous 525
References 527
19 Solid-phase Palladium Catalysis for High-throughput Organic

Synthesis 531
Yasuhiro Uozumi and Tamio Hayashi
19.2 CarbonCarbon and CarbonNitrogen Bond-forming Reactions of Aryl
and Alkenyl Halides 531
xvi Contents
19.2.1 Cross-coupling Reactions 531

19.2.1.1 Reactions of Aryl and Alkenyl Halides with Organoboron
Reagents 532
19.2.1.2 Reactions of Aryl and Alkenyl Halides with Organotin Reagents 543
19.2.1.3 Reactions of Aryl Halides with Terminal Alkynes 544
19.2.1.4 Solid-phase Palladium-catalyzed Cross-coupling Using Aryl and
Benzylzinc Reagents 553
19.2.2 Palladium-catalyzed Arylation and Alkenylation of Olens 555
19.2.3 Amination of Aryl Halides 561
19.2.4 Miscellaneous Reactions 565
19.2.4.1 Heteroannulation 565
19.2.4.2 Insertion Cross-coupling Sequence (Dialkylation of Tropene) 566
19.2.4.3 Coupling Reactions on Various Solid Supports 567
19.3 Solid-phase Reactions by Way of p-Allylpalladium Intermediates 568
19.3.1 Cleavage of Allyl Ester Linkers 568
19.3.2 N-Allylation via p-Allylpalladium Intermediates 571
19.3.3 Insertionp-Allylic Substitution System 571
19.4 Palladium Catalysis with Solid-supported Complexes 573
19.4.1 Preparation of Solid-supported Palladium Complexes and Their Use in
Palladium Catalysis 574
19.4.2 Solid-supported Chiral Palladium Catalysts 579
References 581
20 Olefin Metathesis and Related Processes for CC Multiple Bond

Formation 585
Florencio Zaragoza
20.2 Olen Metathesis in Solution 588
20.2.1 Scope and Limitations of Olen Metathesis in Solution 588
20.2.2 Examples of Library Preparation by Cross-metathesis in Solution 589
20.2.3 Examples of Library Preparation by Ring-closing Metathesis in
Solution 592
20.2.4 Examples of Library Preparation by Ring-opening Metathesis
Polymerization in Solution 595
20.3 Olen Metathesis on Solid Phase 595
20.3.1 Cleavage from the Support by Olen Metathesis 597
20.3.1.1 Scope and Limitations 597
20.3.1.2 Examples of Cleavage from the Support by Olen Metathesis 599
20.3.2 Ring-closing Metathesis on Solid Phase 600
20.3.2.2 Examples of Ring-closing Metathesis on Solid Phase 601
20.3.3 Cross- and Self-metathesis on Solid Phase 603
20.3.3.2 Examples of Cross- and Self-metathesis on Solid Phase 603
20.4 Conclusion 606
References 606
Contents xvii
Volume 2
Part III Special Synthetic Topics 611
21 Solid-phase Synthesis of Natural Products and Natural Product-like

Libraries 613
K. C. Nicolaou and Jeffrey A. Pfefferkorn
21.2 Solid-phase Derivatization of Natural Product Scaolds
Combinatorial Semisynthesis 614
21.2.1 Solid-phase Semisynthesis of Rauwolfa Alkaloids 615
21.2.2 Solid-phase Synthesis of Purine Derivatives 617
21.2.3 Solid-phase Semisynthesis of a Taxoid Library 618
21.2.4 Solid-phase Semisynthesis of Sarcodictyns A and B and Libraries
Thereof 620
21.2.5 Solid-phase Semisynthesis of Vancomycin 623
21.3 Solid-phase Total Synthesis of Natural Products Combinatorial Total
Synthesis 626
21.3.1 Solid-phase Synthesis of Prostaglandins and Libraries Thereof 626
21.3.2 Solid-phase Synthesis of Epothilone A and Libraries Thereof 628
21.3.3 Solid-phase Synthesis of (S)-Zearalenone 630
21.3.4 Solid-phase Synthesis of (DL)-Muscone and Libraries Thereof 632
21.3.5 Solid-phase Synthesis of the Vitamin D3 System 633
21.3.6 Solid-phase Synthesis of Carpanone-like Molecules 634
21.4 Combinatorial Solid-phase Synthesis of Natural Product-like
Libraries 634
21.5 Conclusion 639
21.6 Addendum 639
References 640
22 Solid-phase Synthesis of Heterocyclic Systems (Heterocycles Containing One

Heteroatom) 643
Roland E. Dolle
xviii Contents

22.2 Solid-phase Synthesis of Heterocycles Containing One Nitrogen
Atom 643
22.2.1 Aziridines 643
22.2.2 b-Lactams 649
22.2.3 Pyrrolidines and Derivatives 651
22.2.4 Tetramic Acids 653
22.2.5 Pyrroles 655
22.2.6 Piperidine and Derivatives 655
22.2.7 Dihydropyridines 659
22.2.8 Pyridines 661
22.2.9 Azepanes, Benzazepines, and Derivatives 662
22.2.10 Indoles 665
22.2.11 Tetrahydroquinolines 668
22.2.12 Quinolinones 671
22.2.13 Quinolines 672
22.2.14 Tetrahydroisoquinolines 674
22.3 Solid-phase Synthesis of Heterocycles
Containing One Oxygen Atom 675
22.3.1 Tetrahydrofurans and g-Butyrolactams 675
22.3.2 Furans 676
22.3.3 Benzofurans 677
22.3.4 Pyrans, Benzopyrans, and Derivatives 678
22.4 Solid-phase Synthesis of Thiophenes 678
22.5 Summary 679
References 680
23 Multicomponent Reactions 685

Arounarith Tuch and Stefan Walle
23.2 Mannich Reaction 685
23.3 Hantzsch Reaction 689
23.4 BaylisHillman Reaction 690
23.5 Grieco Three-component Reaction 691
23.6 Biginelli Reaction 692
23.7 Multicomponent Reactions with Isocyanides 693
23.7.1 History of Isocyanides 693
23.7.2 Isocyanide Chemistry 694
23.7.3 Isocyanides on Solid Phase 695
23.7.4 Passerini Reaction 696
23.7.5 The Ugi Reaction 697
23.7.6 The Ugi Reaction on Solid Phase 699
23.7.7 Other Multicomponent Reactions with Isocyanides 701
References 703
Contents xix
24 Strategies for Creating the Diversity of Oligosaccharides 706

Pamela Sears and Chi-Huey Wong
24.2 Chemical Synthesis of Oligosaccharides 707
24.3 Enzymatic Synthesis of Oligosaccharides 711
24.4 Programmable One-pot Synthesis 717
24.5 Conclusions 720
References 721
Part IV Molecular Design and Combinatorial Compound Libraries 723
25 Design Criteria 725

Josef Pernerstorfer
25.2 Properties of Combinatorial Libraries for Drug Development 725
25.3 Dierentiation of Drug-like and Nondrug-like Compounds 728
25.4 Diversity in Combinatorial Chemistry for Drug Development 730
25.4.1 Introduction 730
25.4.2 Descriptors 731
25.4.3 Selection Algorithms 732
25.4.4 Diversity Assessment 734
25.5 Privileged Structures 735
25.5.2 Further Examples of Privileged Structural Motifs 736
25.5.3 Substructure Analysis of Drugs 738
25.6 Conclusion 740
References 740
26 Estimation of Physicochemical and ADME Parameters 743

Michael W. Harter, Jorg Keldenich, and Walter Schmitt
26.2 ADME/PK Considerations in Combinatorial Library Design 744
26.3 Estimation of ADME/PK from Physicochemical Parameters 745
26.3.1 Models for Permeation Through Membranes (Absorption) 746
26.3.2 Models for Distribution in the Body 749
26.3.3 Models for Clearance and Metabolism 752
26.4 Estimation of Physicochemical Parameters 753
26.4.1 Lipophilicity 754
26.4.2 Solubility Including pK a Eects 755
26.4.3 Plasma Protein Binding 758
References 758
27 Virtual Compound Libraries and Molecular Modeling 761

Roger M. Brunne, Gerhard Hessler, and Ingo Muegge
xx Contents

27.2 Lead-nding Libraries 762
27.2.1 Diversity Assessment of Library Compounds 762
27.2.2 Drug-likeness of Library Compounds 763
27.3 Focused Libraries 765
27.3.1 Targeting Protein Families 766
27.3.2 Privileged Structures 767
27.3.3 Similarity 770
27.3.4 Docking 772
27.4 Methods for Library Optimization 774
27.4.1 Genetic Algorithm 775
27.4.2 Fitness Function 775
27.4.2.1 Potency 775
27.4.2.2 Diversity 776
27.4.2.3 Physicochemical Properties 776
27.5 Conclusion 778
References 781
28 Erythropoietin Sensitizer A Case Study 784

Berthold Hinzen, Gabriele Braunlich, Christoph Gerdes, Thomas Kramer,
Klemens Lustig, Ulrich Nielsch, Michael Sperzel, Josef Pernerstorfer
28.2 Results 785
28.2.1 High-throughput Screening and Biological Evaluations 785
28.2.2 Concept for Chemical Optimization 787
28.2.3 4-Fluoro-3-nitroaniline as Central Core 787
28.2.4 Libraries Around Single Heterocycles 789
28.2.4.1 Hydantoins 789
28.2.4.2 Pyrazoles 790
28.2.5 The Candidate for Preclinical Development 801
28.3 Combinatorial Chemistry in Drug Discovery 802
Acknowledgements 802
References 803
29 Estimation of Stability and Shelf Life for Compounds, Libraries, and

Repositories in Combination with Systematic Discovery of New
Rearrangement Pathways 806
Ferenc Darvas, Gyorgy Dorman, Tamas Karancsi, Tamas Nagy, and Istvan Bagyi
29.1.1 Stability and Shelf Life Characterization: the Need 806
29.1.2 Stability Characterization: Empirical Studies 807
29.1.3 Stability and Shelf Life Estimation: Model-based Approaches 807
29.2 Methods and Tools for Combinatorial Stability Assessment 808
29.2.1 Modeling Intrinsic and Extrinsic Factors Inuencing the Stability of
Individual Compounds 808
Contents xxi
29.2.2 Modeling: from Compounds to Libraries 809

29.2.3 Modeling: from Libraries to Repositories 809
29.2.4 Realization of Shelf Life Estimation for Individual Compounds and
Combinatorial Libraries 810
29.2.5 Instrumentation 812
29.3 Validation Studies for Combinatorial Stability Assessment 812
29.3.1 General Experimental Conditions 812
29.3.2 Stability Study for an Indole Library 812
29.3.3 Combinatorial Stability Investigation for a Small Repository 815
29.4 Stability Investigations in Combinatorial Drug Discovery 816
29.4.1 Pilot Design Phase 816
29.4.2 Libraries 817
29.5 A Way Towards Systematic Discovery of New Rearrangement
Pathways 818
29.6 Summary 823
29.7 Appendix I: Stability Testing of Drug Substances 823
29.7.1 Stress Stability Testing 823
29.7.2 Accelerated Stability Testing 824
29.7.3 Long-term Stability Testing 824
29.8 Appendix II: The Arrhenius Model 824
29.9 Appendix III: Model Realization the Stabex TM System 825
References 827
Part V Novel Applications of Combinatorial Chemistry 829
30 Concepts of Combinatorial Chemistry in Process Development 831

Markus Eckert and Ulrich Notheis
30.1.1 General 831
30.1.2 Subject of this Chapter 831
30.1.3 Literature 832
30.2 Process Development 834
30.2.1 Overview and Denition 834
30.2.2 Combinatorial Chemistry in Process Development 835
30.2.3 Demands on Process Development 835
30.2.4 Process Development for Dierent Applications 837
30.3 Parallelization in Process Development 838
30.3.1 Number of Experiments Compared with Scale of Experiment 838
30.3.2 Requirements and Equipment for Parallelization in Dierent
Development Phases 840
30.3.2.1 Route Scouting 840
30.3.2.2 Process Screening 841
30.3.2.3 Process Optimization 847
30.3.2.4 Process Characterization and Validation 849
xxii Contents
30.3.3 Requirements for Analytical Instruments 850

30.4 Planning of Parallel Process Development 851
30.4.1 Screening Strategies 851
30.4.1.1 Experimental Design 852
30.4.2 Strategies for the Selection of the Equipment 853
30.4.2.1 Automation versus Manual Work? 853
30.4.2.2 What is the Right Distribution and Number of Pieces of Apparatus for
Dierent Stages? 855
30.4.2.3 Buying Commercially Available Systems or Carrying out In-house
Development? 856
30.5 Case Studies 857
30.6 Summary 861
References 861
31 High-throughput Screening Applied to Process Development 864

Oliver Brummer, Bernd Jandeleit, Tetsuo Uno, and W. Henry Weinberg
31.1.1 General 864
31.1.2 Automation and Experimental Design 865
31.1.3 High-throughput Process Development 866
31.2.1 High-throughput Combinatorial Process Discovery 867
31.2.2 Route Scouting, Screening, Optimization, and Validation 869
31.2.3 Miscellaneous 880
31.3 Summary and Outlook 882
Acknowledgments 883
References 883
32 Combinatorial Methods in Catalysis 885

Bill Archibald, Oliver Brummer, Martin Devenney, Sasha Gorer, Bernd Jandeleit,
Tetsuo Uno, W. Henry Weinberg, and Thomas Weskamp
32.1.1 Combinatorial Catalysis 885
32.1.2 Combinatorial Organic and Organometallic Catalysis 887
32.2 Metal-binding Ligands, Polymeric Enzyme Mimetics, and Metal
Complexes as Enzyme Mimetics 888
32.2.1 Combinatorial Approaches to Metal-binding Ligands 888
32.2.1.1 Combinatorial Functionalization of Metal-binding Core
Structures 888
32.2.1.2 Combinatorial Synthesis of Metal-binding Ligands from Building
Blocks with Metal-coordinating Functionalities 892
32.2.1.3 Miscellaneous 895
32.2.2 Combinatorial Libraries of Polymeric Catalysts as Enzyme
Mimetics 899
32.2.3 Combinatorial Synthesis Enzyme Mimetics 903
Contents xxiii
32.2.3.1 Hydrolytically Active Metal Complexes 903

32.2.3.2 Evolutionary Solid-phase Synthesis of Oxygenase Mimics 904
32.2.3.3 Libraries of Organic Acylation Catalysts 905
32.3 Combinatorial Catalysis in Asymmetric Synthesis 906
32.3.1 Combinatorial Catalyst Libraries in Enantioselective Additions of
Dialkyl Zinc Reagents 906
32.3.2 Ligands for the Lewis Acid-catalyzed Asymmetric Aza-DielsAlder
Reaction 908
32.3.3 Divergent Ligand Synthesis for Enantioselective Alkylations 909
32.3.4 Chiral Phosphine Ligands for Asymmetric Hydrogenation 912
32.3.5 Asymmetric Reactions Catalyzed by Schi Base-type Ligands the
Positional Scanning Approach 913
32.3.6 Identication of Novel Catalysts for the Asymmetric Epoxidations via
the Positional Scanning Approach 916
32.4 Multidimensional Combinatorial Screening 917
32.4.1 Catalyst Discovery and Optimization Using Catalyst Arrays 919
32.4.2 Parallel Array Screening for Catalyst Optimization Using Discovery and
Focused Ligand Libraries 925
32.5 One-pot, Multisubstrate Screening 927
32.6 Combinatorial Approaches to Olen Polymerization Catalysts 930
32.7 Combinatorial Inorganic Catalysis 936
32.7.1 Combinatorial Libraries of Homogeneous Polyoxometalate-based
Catalysts 936
32.7.2 Combinatorial Libraries and High-throughput Screening of
Heterogeneous Polyoxometalate Catalysts 938
32.8 Combinatorial Heterogeneous Catalysis 939
32.8.2 Case Studies 944
32.8.2.1 Oxidative Dehydrogenation of Ethane 944
32.8.2.2 Oxidative Dehydrogenation of Propane 945
32.8.2.3 Catalytic Oxidation of CO and the Reduction of NO 947
32.9 Combinatorial Electrocatalysis 947
32.9.1 Electrocatalysts for Fuel Cells 947
32.9.2 Combinatorial Electrosynthesis 951
32.10 Novel High-throughput Screening Tools 952
32.10.1 Infrared Screening Tools 953
32.10.1.1 Infrared Thermography 953
32.10.1.2 High-throughput Infrared Spectroscopy 956
32.10.2 Optical High-throughput Screening Techniques 957
32.10.2.1 Colorimetric Assays 958
32.10.2.2 Resonance-enhanced Multiphoton Ionization (REMPI) 963
32.10.2.3 Photothermal Deection 965
32.10.2.4 Enantiomeric Excess by Circular Dichroism 966
32.10.3 High-throughput Screening Using Mass Spectrometry 966
32.10.3.1 Scanning Mass Spectrometry 966
xxiv Contents
32.10.3.2 Mass Tags as Chirality Probes 968

32.10.4 Electronic High-throughput Methods 969
32.10.4.1 Electrochemical Analysis with Electrode Arrays 969
32.10.4.2 Solid-state Temperature Sensors 970
32.10.4.3 Solid-state Gas Sensors 971
32.10.5 Array Reactors 973
32.10.5.1 Array Microreactors 973
32.10.5.2 Micromachined Array Reactors 976
32.10.5.3 Catalysis on a Chip 977
32.10.6 Capillary Array Electrophoresis 977
References 979
33 Diversity-Based Identification of Efficient Homochiral Organometallic

Catalysts for Enantioselective Synthesis 991
Amir H. Hoveyda
33.2 Factors Critical to the Success of Diversity-based Reaction
Development 992
33.3 Peptidic Schi Bases as Chiral Ligands 994
33.3.1 Ti-Catalyzed Enantioselective Addition of Cyanide to Meso
Epoxides 995
33.3.2 Ti-Catalyzed Enantioselective Addition of Cyanide to Imines 1000
33.3.3 Zr-Catalyzed Enantioselective Addition of Dialkyl Zincs to
Imines 1004
33.3.4 Cu-Catalyzed Enantioselective Addition of Dialkyl Zincs to Allylic
Phosphates: Pyridyl Dipeptides as Chiral Ligands 1006
33.3.5 Cu-Catalyzed Enantioselective Conjugate Addition of Dialkyl Zincs to
Unsaturated Ketones: Peptidic Phosphines as Chiral Ligands 1009
33.4 Conclusions and Outlook 1012
Acknowledgments 1013
Endnotes and References 1013
34 Combinatorial Aspects of Materials Science 1017

Bill Archibald, Oliver Brummer, Martin Devenney, Daniel M. Giaquinta, Bernd
Jandeleit, W. Henry Weinberg, and Thomas Weskamp
Abstract 1017
34.2 Combinatorial Solid-state Materials Science 1020
34.2.1 Materials Library Synthesis 1022
34.2.2 Vapor Deposition Techniques 1022
34.2.3 Alternative Library Synthesis Techniques 1026
34.3 High-throughput Screening 1030
34.3.1 Optical Screening 1030
Contents xxv
34.3.2 X-Ray Characterization 1031

34.4 Applications 1032
34.4.1 Superconductivity 1032
34.4.2 Ferromagnetic Semiconductors 1033
34.4.3 Magnetoresistant Materials 1034
34.4.4 Dielectric and Ferroelectric Materials 1035
34.4.5 Luminescent Materials 1038
34.5.1 Materials Discovery 1041
34.5.2 Device Optimization 1042
34.6 Organic Materials and Polymers 1045
34.6.1 Schi Bases for Nonlinear Optical (NLO) Materials 1045
34.6.2 Articial Receptors for Small Organic Molecules 1046
34.6.3 New Materials for the Separation of Enantiomers 1046
34.6.4 Molecular Imprinting 1050
34.6.5 Polymers with Novel Topologies and Functionalization 1050
References 1057
35 Reprogramming Combinatorial Biology for Combinatorial Chemistry 1063

Sean V. Taylor
35.2 Combinatorial Biosynthesis: Creation of Novel Small-molecule Natural
Products 1064
35.2.1 Polyketide Combinatorial Biosynthesis 1066
35.2.1.1 Combinatorial Biosynthesis from Type II PKSs 1068
35.2.1.2 Combinatorial Biosynthesis from Type I Modular PKSs 1070
35.2.2 Combinatorial Biosynthesis of Nonribosomal Peptide Products 1074
35.2.3 Combinatorial Biosynthesis from Hybrid PKS/NRPS Systems 1075
35.2.4 Combinatorial Biosynthesis of Carbohydrates 1077
35.3 Other Combinatorial Aspects of Biology 1081
35.3.1 Combinatorial Libraries of Random DNA and RNA 1082
35.3.2 Peptide Combinatorial Libraries 1084
35.3.3 Protein Combinatorial Libraries 1085
35.4 Perspectives 1090
References 1092
Index 1099
xxvii
List of Authors
Markus Albers Stefan Brase

Bayer AG Kekule-Institut fur Organische Chemie und
Central Research Biochemie
D-51368 Leverkusen Universitat Bonn
Germany Gerhard-Domagk-Strae 1
D-53121 Bonn
Valery V. Antonenko
Germany
Aymax Research Institute
3410 Central Expressway Gabriele Braunlich
Santa Clara Bayer AG
CA 95051 Pharma BPA
USA Leverkusen
Germany
Bill Archibald
H3-Technologies Inc.
O. Brummer
1021 Grebe Street
Symyx Technologies Inc.
Foster City
3100 Central Expressway
CA 94404
Santa Clara
USA
CA 95051
Istvan Bagyi USA
ComGenex Inc.
Bem rkp. 33-34 Roger M. Brunne
Bayer AG
H-1024 Budapest
Hungary Pharma Research Centre
42096 Wuppertal
Carmen Baldino Germany
Department of Chemistry
ArQule Inc. David L. Coen
19 Presidential Way Discovery Partners International
Woburn San Diego
MA 01801 CA 92121
USA USA
Marcus Bauser Christopher P. Corrette

Bayer AG Array Biopharma Inc.
Pharma Research 1885 33rd Street
PH-R-CR VII Boulder
D-42096 Wuppertal CO 80301
Germany USA
xxviii List of Authors
Stefan Dahmen Christoph Gerdes

Kekule-Institut fur Organische Chemie und Bayer AG
Biochemie Pharma Research
Universitat Bonn Pharmacology
Gerhard-Domagk-Strae 1 42096 Wuppertal
D-53121 Bonn Germany
Germany
D. Giaquinta
Ferenc Darvas Symyx Technologies Inc.
ComGenex Inc. 3100 Central Expressway
Bem rkp. 33-34 Santa Clara
H-1024 Budapest CA 95051
Hungary USA
M. Devenney
Symyx Technologies Inc. S. Gorer
3100 Central Expressway Symyx Technologies Inc.
Santa Clara 3100 Central Expressway
CA 95051 Santa Clara
USA CA 95051
USA
Roland E. Dolle
Department of Chemistry Philipp Grosche
Adolor Corporation Institute for Organic Chemistry
371 Phoenixville Pike University of Tubingen
Malvern Auf der Morgenstelle 18
PA 19355 D-72076 Tubingen
USA Germany
Gyorgy Dorman
ComGenex Inc. Rainer Haag
Bem rkp. 33-34 Freiburger Materialforschungszentrum und
H-1024 Budapest Institut fur Makromolekulare Chemie
Hungary Albert-Ludwigs-Universitat Freiburg
Stefan-Meier-Strae 21
Markus Eckert D-79104 Freiburg
Bayer AG Germany
Chemicals Division
Business Unit Fine Chemicals R. Hanko
Research and Development Bayer AG
D-51368 Leverkusen Chemical Division
Germany Head of BUFine Chemicals
Demosthenes Fokas D-51368 Leverkusen
Department of Chemistry Germany
ArQule Inc.
19 Presidential Way Jan-Gerd Hansel
Woburn Bayer AG
MA 01801 Central Reseach
USA D-51368 Leverkusen
Germany
A. Ganesan
Department of Chemistry Michael W. Harter
University of Southampton Business Group Pharma
Higheld Building 470
Southampton SO17 1BJ D-42096 Wuppertal
UK Germany
List of Authors xxix
Wolfgang Hartwig Stephan Jordan

Bayer AG Bayer AG
Geschaftsbereich Pharma Central Reseach
Leiter Forschung International D-51368 Leverkusen
D-42096 Wuppertal Germany
Tamio Hayashi Gunther Jung

Department of Chemistry Institute for Organic Chemistry
Graduate School of Science University of Tubingen
Kyoto University Auf der Morgenstelle 18
Sakayo, Kyoto 606-8502 D-72076 Tubingen
Japan Germany
Andre Hebel Christopher Kallus

Freiburger Materialforschungszentrum und Bayer AG
Institut fur Makromolekulare Chemie Central Research
Albert-Ludwigs-Universitat Freiburg D-51368 Leverkusen
Stefan-Meier-Str. 21 Germany
D-79104 Freiburg
Tamas Karancsi
Germany
ComGenex Inc.
Gerhard Hessler Bem rkp. 33-34
Bayer AG H-1024 Budapest
Central Research Hungary
D-51368 Leverkusen Jorg Keldenich
Germany Business Group Pharma
Berthold Hinzen Building 470
Bayer AG D-42096 Wuppertal
Pharma Research Germany
Medicinal Chemistry Thomas Kramer
D-42096 Wuppertal Bayer AG
Germany Pharma Research
Medicinal Chemistry
Amir H. Hoveyda
D-42096 Wuppertal
Department of Chemistry
Germany
Merkert Chemistry Center
Boston College Jochen Kruger
2609 Beacon Street Bayer AG
Chestnut Hill Business Group Pharma
MA 02467 PH-R CR-MC III
USA D-42096 Wuppertal
Germany
Conrad Hummel
Array Biopharma Inc. Nicolay V. Kulikov
1885, 33rd Street Aymax Research Institut
Boulder 3410 Central Expressway
CO 80301 Santa Clara, CA 95091
USA USA
Bernd Jandeleit Joachim E. A. Luithle
XenoPort Inc. Bayer AG
2631 Hanover Street Business Group Pharma
Palo Alto Medicinal Chemistry
CA 94304 D-42096 Wuppertal
USA Germany
xxx List of Authors
Klemens Lustig Ulrich Notheis

Bayer AG Bayer AG
Pharma Research Chemicals Division
Pharmakokinetics Business Unit Fine Chemicals
42096 Wuppertal Research and Development
Germany D-51368 Leverkuten
Germany
Thorsten Meyer
Bayer AG Josef Pernerstorfer
Central Research Bayer AG
D-51368 Leverkusen Pharma Research
Germany Medicinal Chemistry
D-42096 Wuppertal
Reza Mortezaei Germany
Aymax Research Institut
3410 Central Expressway Jerey A. Pfeerkorn
Santa Clara, CA 95091 Pharmacia Corp.
USA Combinatorial and Medicinal Chemistry
7000 Portage Rd
Ingo Muegge Kalamazoo, MI 49001
Bayer Research Center USA
400 Morgan Lane
Jorg Rademann
West Haven
Institute for Organic Chemistry
CT 06516
University of Tubingen
USA
Auf der Morgenstelle 18
D-72076 Tubingen
Tamas Nagy
Germany
ComGenex Inc.
Bem rkp. 33-34 Walter Schmitt
H-1024 Budapest Business Group Pharma
Hungary Building 470
D-42096 Wuppertal
K. C. Nicolaou
Germany
Department of Chemistry and the Skaggs
Institute for Chemical Biology Pamela Sears
The Scripps Research Institute Department of Chemistry
10550 North Torrey Pines Road The Scripps Research Institute
La Jolla 10550 N. Torrey Pines Rd
CA 92037 La Jolla
USA CA 92037
and USA
Department of Chemistry and Biochemistry
University of California Mukund P. Sibi
San Diego Department of Chemistry
9500 Gilman Dr North Dakota State University
La Jolla, CA 92093 Fargo
USA ND 58105-5516
USA
Ulrich Nielsch
Bayer AG Adrian L. Smith
Pharma Research Amgen Inc.
Pharmacology One Amgen Center Drive
42096 Wuppertal Thousand Oaks, CA 91320
Germany USA
List of Authors xxxi
Hubertus Stakemeier Stefan Walle

Bayer AG Bayer AG
Central Research Central Research
ZF-LSc ZF-LSc-KC
D-51368 Leverkusen D-51368 Leverkusen
Germany Germany
Henning Steinhagen W. H. Weinberg
Bayer AG Symyx Technologies Inc.
Business Group Pharma 3100 Central Expressway
PH-R CR-MC II Santa Clara
D-42096 Wuppertal CA 95051
Germany USA
Jean-Francois Stumbe T. Weskamp
Freiburger Materialforschungszentrum und Symyx Technologies Inc.
Institut fur Makromolekulare Chemie 3100 Central Expressway
Albert-Ludwigs-Universitat Freiburg Santa Clara
Stefan-Meier-Str. 21 CA 95051
D-79104 Freiburg USA
Germany
Chi-Huey Wong
Sean V. Taylor Department of Chemistry and Skaggs
Laboratorium fur Organische Chemie Institute for Chemical Biology
ETH Honggerberg-HCI The Scripps Research Institute
CH-8093 Zurich 10550 N. Torrey Pines Rd
Switzerland La Jolla
CA 92037
Arounarith Tuch
USA
Bayer AG
Central Research Tobias Wunberg
ZF-LSc-KC Bayer AG
D-51368 Leverkusen Business Group Pharma
Germany PH-R CR-MC II
D-42096 Wuppertal
Tetsuo Uno
Germany
Genomics Institute of the Novartis Research
Foundation Florencio Zaragoza
3115 Merryeld Row Suite 200 Novo Nordisk A/S
San Diego Novo Nordisk Park
CA 92121 DK-2760 Malv
USA Denmark
Yasuhiro Uozumi
Laboratory of Complex Catalysis
Institute for Molecular Science
Nishigonaka 38
Myodaiji
Okazaki 444-8585
Japan
1
Part I
General Aspects
Handbook of Combinatorial Chemistry. Drugs, Catalysts, Materials. Vol. 1.

ISBN: 3-527-30509-2
3
1
Combinatorial Chemistry in Perspective
K. C. Nicolaou, R. Hanko, and W. Hartwig
1.1
Introduction
A fundamental aspect of organic chemistry is its ability to create new carbon-

containing substances. This endeavor, called organic synthesis, made huge con-
tributions to society by delivering a myriad of synthetic materials. Until recently
the science of organic synthesis and its branches, such as medicinal chemistry,
practiced the construction of organic molecules by targeting one molecule at a
time. During the last decade of the twentieth century, however, a new concept took
hold by which a collection of molecules is targeted, simultaneously producing a
library of compounds instead of a single product. This strategy of concurrently
synthesizing large numbers of compounds is called combinatorial chemistry or
combinatorial synthesis. Although the roots of combinatorial chemistry were al-
ready in place, this philosophy took on a special meaning and assumed high pri-
ority in the 1990s because of pressures within the pharmaceutical industry to
speed up the drug discovery process and because of the advent of high-throughput
screening.
Although combinatorial chemistry was initially met with resistance from some
medicinal and other chemists, it rapidly became mainstream, and its practice
today is widespread in academia and industry. It is utilized to synthesize libraries
of compounds either as mixtures or as single compounds. The latter approach is
preferred by most practitioners, and as new synthetic technologies, high-speed
purication techniques and characterization strategies are developed, combinato-
rial chemistry will assume an increasingly prominent position within the arma-
mentarium of the synthetic chemist. Combinatorial chemistry is currently being
applied, in addition to natural product synthesis and drug discovery, to agricultural
chemistry, chemical biology, catalyst discovery and material science.
Combinatorial synthesis may be performed either in solution or on solid sup-
port. Each having their own advantages and disadvantages, both methods have
been widely used in the construction of various compound libraries. Although
solid-phase chemistry is currently not as well developed as solution-phase chem-
istry, particularly with regard to small organic molecules, the former method has

Copyright 8 2002 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
ISBN: 3-527-30509-2
4 1 Combinatorial Chemistry in Perspective
distinct advantages over the latter. First, in solid-phase synthesis, large excesses of
reagents can be used to accelerate reactions and to drive them to completion; these
reagents can then conveniently be removed at the end by ltration and washing.
Furthermore, and because of easy separation, solid-phase chemistry can be auto-
mated through robotics to a higher degree than solution chemistry can. Most im-
portantly, solid-phase chemistry can be applied to the elegant and powerful split-
and-pool synthesis strategy for combinatorial chemistry. Despite its dramatic
contribution to increasing eciency over traditional methods, high-throughput
parallel synthesis remains a laborious task. Thus, combinatorial chemists quickly
recognized the benets of automation as a crucial component of combinatorial
chemistry. Besides the synthetic sequence, purication and characterization of
compounds are also important aspects of combinatorial chemistry. The develop-
ment of high-throughput chromatography methods to support automated parallel
synthesis and of high-performance liquid chromatographymass spectrometry
(HPLC/MS) systems to direct the collection of the desired products are only the
beginning of such high-throughput methods. Progress in this area is moving
quickly and will be indispensable to any serious combinatorial chemistry eort.
1.2
Brief History of Combinatorial Chemistry
While combinatorial synthesis is a relatively new eld of chemistry, Nature has

been utilizing the same principles since the beginning. Although biologists had
previously recognized the power of combinatorial chemistry, its application to
problems relating to chemistry did not emerge until recently. Chemists condence
in rational design has previously kept them away from systematic explorations in
chemical synthesis.
The rather dramatic developments in molecular biology and high-throughput
screening increased the demand for large numbers of small organic molecules
to be screened against the ever-increasing biological targets. A solution to these
challenges came from the peptide and oligonucleotide chemists, who could con-
veniently implement combinatorial chemistry strategies given the ease with which
the amide and phosphate bonds could be constructed from the readily available
building block libraries of amino acids and nucleotides respectively.
Solid-phase chemistry was pioneered by Merrield [1] and applied to the peptide
and oligonucleotide elds quite eectively. In the early 1970s developments had
already occurred in solid-phase synthesis of nonpeptide and nonoligonucleotide
molecules. For example, the groups of Lezno [2], Frechet [3], Camps [4], Patch-
ornik [5] and Rapoport [6] all reported early results on solid-phase synthesis.
Camps et al. even applied solid-phase synthesis to the pharmaceutically relevant
benzodiazepine system [7].
In Germany in the 1980s Frank and coworkers synthesized collections of oligo-
nucleotides and, later, peptides on circles of cellulose paper [8]. Geysen et al. in
1.2 Brief History of Combinatorial Chemistry 5
Australia prepared a library of peptides [9] on functionalized polypropylene pins by

immersing them sequentially into various solutions of activated amino acids held
in the wells of a microtiter plate. Houghten at The Scripps Research Institute in La
Jolla synthesized a library of 260 peptides [10] in polypropylene mesh containers
encapsulating polystyrene resin, a process that came to be known as the tea-bag
strategy. Both the pin and the tea-bag techniques went on to gain wide popularity
and led to new generations of improved technologies for combinatorial chemistry.
Researchers at Aymax reported very large spatially addressable libraries on glass
chips using photolithographic techniques in conjunction with photolabile protect-
ing group chemistry [11]. In parallel with the chemical approaches to peptide di-
versity, phages were being exploited to display very large libraries of peptides [12].
In 1992, Bunin and Ellman reported another synthesis of a benzodiazepine
library [13] using the multi-pin technology pioneered by Geysen. At about the
same time, a group of scientists at ParkeDavis reported the construction of hy-
dantoins and benzodiazepines using a semiautomated robotic synthesizer [14]. In
addition, a Chiron group reported the synthesis of a library of peptoids [oligo(N-
substituted glycine)] and a robotic synthesizer of such compounds [15].
In the meantime, an elegant and ingenious strategy for combinatorial synthesis
was proposed and demonstrated. This strategy called split synthesis or split and
pool was introduced by Furka and coworkers at two European symposia in 1988;
this work was published in 1991 [16]. The groups of Lam [17] and Houghten
[18] independently developed the same technique and also published their results
in 1991. These strategies led to the concept of one beadone compound and
promised the delivery of millions of compounds synthesized simultaneously on
beads and with unprecedented rapidity. As elegant as it is, this method left much
to be desired in terms of structure deconvolution and quantity of material pro-
duced. To solve the rst problem, a number of encoding strategies were developed
based on technologies ranging from DNA sequences to polychlorinated aromatics
as well as nonchemical encoding methods such as radiofrequency tagging and
two-dimensional (2D) bar-coding (for further discussion of library encoding, see
Chapter 5).
From the early 1990s onwards, the chemical literature exploded with reports ad-
dressing all aspects of combinatorial synthesis, including solid-phase chemistry,
encoding strategies and molecular diversity.
In the late 1990s alternative strategies were investigated, and an interesting
compromise between solid-phase and solution-phase chemistry was found with
polymers which are soluble in certain solvents but can be precipitated eciently in
others [19]. Thus the reactions on such polymers are carried out in homogeneous
solution while the convenience of purication via a simple ltration is maintained.
In a highly ecient extension of this principle, Curran and coworkers [20] have
developed a number of uorous tags which allow extraction of tagged compounds
into a three-phase separation system (aqueous, organic, and uorinated).
Today, many well-known solution-phase reactions have been demonstrated to
perform equally well on solid phase [21] and a plethora of reagents have been im-
mobilized on solid supports [22]. Such techniques lead to high-speed purication

procedures and often to higher yields of targeted products, which in turn lead to
an increase in eciency and productivity.
While the peptide and oligonucleotide chemists may have opened the eld of
combinatorial chemistry, it was left to those chemists concerned with small or-
ganic molecules to make the methods widely applicable to more lead-like and
drug-like structures. Of particular interest were new solid-phase synthetic strat-
egies, new linkers for solid-phase chemistry [23], and new polymer-bound reagents
[24].
1.3
Applications of Combinatorial Chemistry
With the advent of combinatorial chemistry, the traditional one molecule at a time
approach to drug discovery was severely shaken. The initial euphoria of the early
1990s, however, was based to a considerable extent, on faulty grounds. The idea of
synthesizing a myriad of compounds randomly, often as mixtures, sounded like a
dream to many chemists of biotechnology and pharmaceutical companies. Soon
thereafter, however, the principles of combinatorial chemistry for small organic
molecules crystallized on a more pragmatic platform. The prevailing approach
today is that based on both solution-phase and solid-phase chemistry applied in
parallel or split-and-pool formats and directed at discrete and high-purity com-
pounds [25, 26]. Initial-phase combinatorial chemistry is applied to discover lead
compounds rapidly which are then subjected to lead optimization to produce drug
candidates. The last part of the process is the domain of the medicinal chemists,
who may also practice combinatorial strategies to achieve their goals. Thus,
smaller focused libraries are carefully designed and synthesized, either in parallel
or by the split-and-pool strategy using solution- or solid-phase chemistry. Combi-
natorial chemistry has, therefore, penetrated the laboratories of medicinal chem-
ists who recognized its power in delivering the targeted compounds in a much
faster way, and in acceptable quantities and purities. In similar ways, academic
laboratories have adopted and rened combinatorial techniques in their quest for
libraries of compounds needed for chemical biology studies [27].
The capability of combinatorial chemistry to produce large numbers of com-
pounds rapidly is a powerful tool not only for chemical biology and drug discovery
but also for a host of other research endeavors. Indeed, this philosophy and these
combinatorial processes have been successfully applied to reaction optimization,
the discovery of new materials [28] and the development of new catalysts [29].
In pioneering work, Fuchs and coworkers [30] reported in 1984 the use of auto-
mation to optimize reaction conditions with multiple variables. Reddington and
Sapienza [31] reported in 1998 results from a highly parallel, optical screening
method to discover novel electrocatalysts. Such practices are currently gaining
wide popularity in industry for the optimization of process chemistry. The rst
1.4 Outline of the Book 7
report of a combinatorial approach to new high-technology materials came from

Schultz and coworkers [32], who prepared a spatially addressable array of potential
superconducting materials. Similar techniques were then applied to a number of
studies including ferroelectric materials [33] and phosphorescent materials [34].
Combinatorial techniques have also been applied to the development of chiral
separation methods [35, 36] and optimization of protein catalysts through DNA-
shuing techniques [37]. Most signicantly, combinatorial chemistry has proven
itself to be useful in the discovery of new catalytic systems. Early examples include
Liu and Ellmans synthesis of 2-pyrrolidinemethanol ligands intended for enantio-
selective additions [38], Burgess and coworkers diazo-compound library for a CaH
insertion [39], Hoveyda and coworkers library of dipeptide Schi base ligands for
enantioselective addition of trimethylsilylcyanide to epoxides [40], and Sigman and
Jacobsens Schi base catalysts for the Strecker reaction [41].
The payo of combinatorial chemistry to drug discovery is already becoming
obvious to the industry in terms of a signicant increase in the number of drug
candidates and of decreases in time from target identication to drug candidates
and manpower employed per drug candidate. Similar benets are beginning to
emerge in process chemistry, catalyst discovery and material science, where com-
binatorial chemistry techniques have also been implemented.
1.4
Outline of the Book
The following chapters in this series will address the various aspects of combina-
torial chemistry in order to facilitate further advances in the eld as well as to aid
the reader in his or her practice of combinatorial chemistry.
The book is divided into three parts. The rst chapters (15) serve as the in-
troductory part and build the foundation on which the next chapters are based.
The following part (Chapters 520) deals with basic reaction mechanisms. The
aim is to describe thoroughly the repertoire of combinatorial chemistry in solution
and on solid support and to provide the reader with a critical overview of the best
methods and conditions found so far. As an introduction, each chapter briey dis-
cusses the applicability of the reactions dealt with for library synthesis in general
and for solution-phase or solid-phase chemistry in particular. This entry is fol-
lowed by the detailed reection of each reaction type including the most recent
developments/achievements. Based on mechanistic considerations, emphasis is
put on the suitability of a given reaction for library synthesis using either solid-
phase or solution-phase chemistry.
Generally, synthetic examples from all techniques are presented (solution-phase
parallel synthesis, solid-phase chemistry, solid-supported reagents). In most cases
examples originate from syntheses of large libraries.
The last part of the book (Chapters 2135) describes special topics such as ap-
plications, design and instrumentation as well as aspects beyond pure synthetic
organic chemistry. In addition, since combinatorial chemistry is a tool aiming at

specic applications, for example medicinal chemistry, material research and ca-
talysis, selected examples of breakthroughs in these applications are discussed.
Acknowledgments
This book would not have been possible without the dedicated work of the editing
team, especially Berthold Hinzen and Tobias Wunberg. We would also like to
thank P. Golitz and his team for their conceptual contributions and their support
to ensure the ambitious scheduling of this book.
References
1 R. B. Merrield, J. Am. Chem. Soc. 12 J. K. Scott, G. P. Smith, Science

1963, 85, 21492154. 1990, 249, 386390.
2 a) C. C. Leznoff, J. Y. Wong, Can. J. 13 B. A. Bunin, J. A. Ellman, J. Am.
Chem. 1972, 50, 28922893; b) C. C. Chem. Soc. 1992, 114, 1099710998.
Leznoff, Acc. Chem. Res. 1978, 11, 14 S. H. DeWitt, J. S. Kiely, C. J.
327. Stankovic, M. C. Schroeder,
3 J. M. J. Frechet, Tetrahedron 1981, D. M. R. Cody, M. R. Pavia, Proc. Natl.
37, 663683. Acad. Sci. USA 1993, 90, 69096913.
4 F. Camps, J. Castells, M. J. 15 R. N. Zuckermann, J. M. Kerr, M.
Ferrando, J. Font, Tetrahedron Lett. A. Siani, S. C. Banville, Int. J. Pept.
1971, 20, 7131714. Protein Res. 1992, 40, 497506.
5 A. Patchornik, M. A. Kraus, J. Am. 16 A. Furka, F. Sebestyen, M.
Chem. Soc. 1970, 92, 75877589. Asgedom, G. Dibo, Highlights of
6 a) J. I. Crowley, H. Rapoport, J. Modern Biochemistry, Proceedings of
Am. Chem. Soc. 1970, 92, 63636365; the 14th International Congress of
b) J. I. Crowley, H. Rapoport, Acc. Biochemistry, Prague, Czechoslovakia,
Chem. Res. 1976, 9, 135144. 1988, VSP, Ultrecht, The Netherlands,
7 F. Camps, J. Castells, J. Pi, An. Quim. 1988, 13, 47; b) A. Furka, F.
1974, 70, 848849. Sebestyen, M. Asgedom, G. Dibo,
8 R. Frank, W. Heikens, G. Int. J. Peptide Prot. Res. 1991, 37, 487
Heisterberg-Moutsis, H. Blocker, 493.
Nucl. Acids Res. 1983, 11, 43654377. 17 K. S. Lam, S. E. Salmon, E. M.
9 H. M. Geysen, R. H. Meloen, S. J. Hersh, V. J. Hruby, W. M.
Barteling, Proc. Natl. Acad. Sci. USA Kazmierski, R. J. Knapp, Nature
1984, 81, 39984002. 1991, 354, 8284.
10 R. A. Houghten, Proc. Natl. Acad. 18 R. A. Houghten, C. Pinilla, S. E.
Sci. USA 1985, 82, 51315135. Blondelle, J. R. Appel, C. T. Dooley,
11 a) S. P. A. Fodor, R. J. Leighton, J. H. Cuervo, Nature 1991, 354, 84
M. C. Pirrung, L. Stryer, A. T. Lu, 86.
D. Solas, Science 1991, 251, 767 19 D. J. Gravert, K. D. Janda, Chem.
773;b) C. Y. Cho, E. J. Moran, Rev. 1997, 97, 489510.
S. R. Cherry, J. C. Stephans, 20 A. Studer, S. Hadida, R. Ferritto,
S. P. A. Fodor, C. L. Adams, A. S.-Y. Kim, P. Jeger, P. Wipf, D.
Sundaram, J. W. Jacobs, P. G. Curran, Science 1997, 275, 823826.
Schultz, Science 1993, 261, 1303 21 a) P. H. H. Hermkens, H. C. J.
1305. Ottenheijm, D. Rees, Tetrahedron
References 9
1996, 52, 45274554; b) P. H. H. 29 For recent reviews, see: a) K. D.

Hermkens, H. C. J. Ottenheijm, Shimizu, M. L. Snapper, A. H.
D. Rees, Tetrahedron 1997, 53, 5643 Hoveyda, Chem. Eur. J. 1998, 4,
5678. 18851889; b) T. Bein, Angew. Chem.
22 S. V. Ley, J. Chem. Soc. Perkin Trans 1, Int. Ed. 1999, 38, 323326.
2000, 1235. 30 A. R. Fisbee, M. H. Nantz, G. W.
23 For a review of linkers, see: I. W. Kramer, P. L. Fuchs, J. Am. Chem.
James, Tetrahedron 1999, 55, 4855 Soc. 1984, 106, 71437145.
4946 31 E. Reddington, A. Sapienza, Science
24 For a recent review, see: S. 1998, 280, 1735.
Bhattacharyya, Comb. Chem. High 32 X.-D. Xiang, X.-D. Sun, G. Briceno,
Throughput Screening 2000, 3, 6592. Y. Lou, K. A. Wang, H. Chang, W.
25 H. N. Weller, M. G. Young, S. J. G. Wallace-Freedman, S.-W. Chen,
Michalczyk, G. H. Reitnauer, R. S. P. G. Schultz, Science 1995, 268,
Cooley, P. C. Rahn, D. J. Loyd, D. 17381740.
Fiore, S. J. Fishman, Mol Diversity 33 H. Chang, C. Gao, I. Takeuchi, Y.
1997, 3, 6170 Yoo, J. Wang, P. G. Schultz, X.-D.
26 L. Zeng, L. Burton, K. Yung, B. Xiang, R. P. Sharma, M. Downes, T.
Shushan, D. B. Kassel, J. Chromat. A Venkatesan, Appl. Phys. Lett. 1998,
1998, 794, 313. 72, 21852187.
27 For examples, see: a) S. Feng, J. K. 34 E. Danielson, J. H. Golden, E. W.
Chen, H. Yu, J. A. Simon, S. L. McFarland, C. M. Reaves, W. H.
Schreiber, Science 1994, 266, 1241 Weinberg, X. D. Wu, Nature 1997,
1247; b) K. C. Nicolaou, N. 389, 944948.
Winssinger, J. Pastor, S. Ninkovic, 35 K. Sada, K. Yoshikawa, M. Miyata,
F. Sarabia, Y. He, D. Vourloumis, Z. Chem. Commun. 1998, 17631764.
Yang, T. Li, P. Giannakakou, E. 36 P. Murer, K. Lewandoski, F. Svec, J.
Hamel, Nature 1997, 387, 268272; c) M. J. Frechet, Chem. Commun. 1998,
N. S. Gray, L. Wodicka, A.-M. W. H. 25592560.
Thunnissen, T. C. Norman, S. 37 W. P. C. Stemmer, Nature 1994, 370,
Kwon, F. H. Espinoza, D. O. 389391.
Morgan, G. Barnes, S. LeClerc, L. 38 G. C. Liu, J. A. Ellman, J. Org. Chem.
Meijer, S.-H. Kim, D. J. Lockhart, 1995, 60, 77127713.
P. G. Schultz, Science 1998, 281, 39 K. Burgess, H.-J. Lim, A. M. Porte,
533538. G. A. Sulikowski, Angew. Chem. Int.
28 a) B. Jandeleit, D. J. Schaefer, T. S. Ed. Engl. 1996, 35, 220222.
Powers, H. W. Turner, W. H. 40 B. M. Cole, K. D. Shimizu, C. A.
Weinberg, Angew. Chem. Int. Ed. Krueger, J. P. A. Harrity, M. L.
1998, 38, 24942532; b) P. G. Snapper, A. H. Hoveyda, Angew. Chem.
Schultz, X.-D. Xiang, Curr. Opin. Int. Ed. Engl. 1996, 35, 16681671.
Solid State Mater. Sci. 1998, 3, 153 41 M. S. Sigman, E. N. Jacobsen, J. Am.
158. Chem. Soc. 1998, 120, 49014902.
10
2
Introduction to Combinatorial Chemistry
David L. Coen and Joachim E. A. Luithle
2.1
Combinatorial Chemistry in Drug Discovery a Perspective
The categorical imperatives of modern drug discovery are to produce better clinical
candidates that are less prone to failure at a late-stage, and to do this more rapidly
than the industry performance standards of the past two decades would predict
and at a cost that is responsive to social and political pressures on drug prices.
Combinatorial chemistry is nothing less than a cornerstone technology in the re-
alization of these imperatives. Its function is basically that of a high-output engine,
providing very large numbers of well-designed, well-made, high-quality com-
pounds for high-throughput evaluation as potential drug candidates. In fact, this
ability to leverage productivity has prompted researchers in other elds, such as
catalysis and material science, to adopt and adapt this engine to their needs as
well.
The purpose of this chapter is to provide an overview of the basic principles of
combinatorial chemistry and to outline the operating principles associated with its
most widely practiced forms. Subsequent chapters provide more detailed accounts
of how the various types of synthetic chemistry are utilized, of specic combinato-
rial chemistry technologies, and of specic applications.
By way of background one can compare how a typical medicinal chemist of 1975
would set about making a compound for testing with the way that the same
chemist would approach the task today. First of all, each decision about what com-
pound to make was typically embedded in the program category in which the
chemist was a participant. The program description frequently included a struc-
tural component, such as muscarinic cholinergics, cephalosporin antibiotics,
benzodiazepine anxiolytics, or tricyclics, and the chemist would have had con-
siderable expertise in the synthetic aspects, structureactivity relationships, the lit-
erature and patents, and, to some extent at least, the pharmacology of the particu-
lar compound class. Each new hypothesis was based on a blend of past experience,
recent papers and/or patents in the eld, and on the latest biological testing re-
sults, and was then refracted through knowledge of how to make the compounds
of interest and what was available to make them from. If the synthesis worked, a

ISBN: 3-527-30509-2
2.2 Key Issues 11
15-g sample (huge by todays standards) would be made and rigorously puried
by column chromatography or recrystallization. Meticulous analyses using, as a
minimum, thin-layer chromatography (TLC), mass spectrometry (MS), infrared
(IR), nuclear magnetic resonance (NMR), ultraviolet (UV), and combustion analy-
sis determined if the sample was suitable for registration and biological testing.
A compound data sheet that included analytical results, melting point, solubility
data, and other information would typically be prepared, reviewed, approved, and
led before a sample could be sent for testing. Using this process, a chemist with
one or two assistants was deemed productive if 50200 new compounds a year
were forthcoming, depending on the complexity of the structural class.
In contrast, the drug designer of year 2000 is most likely a hybrid medicinal,
combinatorial, computational, and analytical chemist with a working knowledge
of molecular and cellular biology. He or she spends little time in the library, lots of
time at a computer, and much of the remaining time meeting with the project
team to review results and plan activities. Also, in comparison with the handful
of laboratory appliances considered essential 25 years ago, todays chemistry labo-
ratory is replete with complex (and expensive) productivity-enhancing equipment,
making it possible for the 200 compounds of yesteryear to be made in an auto-
mated synthesizer during the hour spent in a meeting.
The decision as to which compound to make next has been replaced by a design
process regarding which set (or library) of compounds to make next. Routine syn-
thesis of single compounds now occurs mainly in the later stages of lead opti-
mization. The design process ows not from a compound class associated with
a particular drug discovery program, but from the biomolecular targets associated
with the program. This fact underlies the critical relationship between modern
medicinal chemistry and structural biology/computational chemistry. As an illus-
tration, a 1970s program on inuenza drugs might be centered on aminoadaman-
tane derivatives (antiviral compound class), whereas a modern program might be
focused on inhibitors of neuraminidase (viral protein target). The discovery phase
of the program is driven by the target and by knowledge of its structure and natu-
ral ligand in the case of a receptor or by its mechanism of catalysis and natural
substrate in the case of an enzyme.
Overall, it can be stated that the integration of biomolecular target-driven com-
putational design methods, combinatorial techniques for compound production,
and high-throughput biological screening technologies has, in principle, resulted
in a huge increase in productivity in medicinal chemistry. The role of combinato-
rial chemistry in modern pharmaceutical research and development (R&D) is per-
haps best shown in Figs. 2.1 and 2.2, which depict as triads the major components
of both the overall R&D process and its discovery phase.
2.2
Key Issues
The basic principles of combinatorial chemistry are often tied to, and sometimes
confused with, the origins of combinatorial chemistry. The founding (but awed)
12 2 Introduction to Combinatorial Chemistry
Fig. 2.1. The essential elements of modern pharmaceutical research and development.
principle was that, given a suciently large and diverse set of compounds to test,
the discovery of an ideal drug for any given disease state would be statistically un-
avoidable. This principle was frequently popularized in metaphorical terms, such
as the likelihood that any lock could be opened if a suciently large number of
keys are tried, or that the pharmacological richness of natural products could be
easily accessed and expanded through the laboratory equivalent of a rain forest.
The anticipated surge in overall pharmaceutical R&D productivity has not ma-
terialized and this optimistic view of combinatorial chemistry has largely been
abandoned. The contemporary view is more pragmatic and generally conforms to
the principles outlined below.
1 The synthesis of many compounds simultaneously is more ecient than the synthesis
of a single compound. In terms of simple time utilization, this principle was
Fig. 2.2. The essential elements of the discovery phase.

2.2 Key Issues 13
intuitive to generations of chemists who set up two or more reactions in a hood

each night. In the combinatorial context it has far greater signicance as the
number of compounds made from combinations of reagent sets increases geo-
metrically with the number of reagents in these sets.
2 Any synthesis scheme can be executed in a manner that aords multiple products
if individual reagents are replaced by complementary reagent sets used in dierent
combinations. This perception is eponymous with combinatorial chemistry and
lies at its heart. It can be readily illustrated with a DielsAlder reaction (Fig.
2.3).
Fig. 2.3. Combinatorial chemistry illustrated with a DielsAlder reaction.
A chemist could easily execute this synthesis in a single workday. How-

ever within this same day, that chemist could weigh and prepare stock solu-
tions of ten dienes and ten dienophiles. Then by making equimolar com-
binations of each diene with each of the ten dienophiles and running the
corresponding DielsAlder reactions, a total of 100 DielsAlder adducts could
be synthesized, thus achieving a 100-fold productivity gain. When a synthesis
scheme provides for three reagent sets (incorporated into the products), the use
of ten members in each set aords 1000 products. Similarly the use of four sets
of ten reagents distributed over one (e.g. Ugi reaction) or several stages of a
synthesis aords 10,000 possible combinations. The number of products in-
creases geometrically (A B C) whereas the number of reagents increases
arithmetically (A B C) and in this simple reality lies the true power of
combinatorial chemistry.
3 Rigorous design of products and synthesis is critical and large numbers cannot
compensate for poor design. Combinatorial chemistry, often viewed and applied
solely as a tool to leverage serendipity, frequently fails to meet expectations.
However when used to leverage the output of sound experimental designs
based on synthetic and medicinal chemistry knowledge, the outcome is gener-
ally more satisfactory. There is probably a more fundamental principle behind
this empirically derived view and it relates to the fact that the pharmacological
eects of bioactive small molecules are derived from their ability to bind to and
modulate the function of macromolecular targets, usually proteins. Proteins
are built from a bounded set of amino acids. Their biological and biochemical
functions have structural determinants derived from a bounded set of second-
ary structure motifs and these are usually associated with small molecule
binding. Thus the number and types of small molecules that are likely to ex-
hibit biological activity also represent bounded sets and combinatorial chem-
istry applied within this domain is far more likely to succeed than a totally
random approach.
4 While synthetic organic chemistry evolved primarily in terms of serial processing, its
productivity can be greatly enhanced by introducing parallel processing. Strong em-
phasis needs to be put on the importance of parallel processing as an explicit
component of experimental design. The synthesis plan must comprehend the
fact that hundreds or thousands of compounds are being synthesized simulta-
neously using hundreds or thousands of reagent combinations in each syn-
thetic step. Each unit operation and each operating parameter such as solvent
used, temperature, and level of agitation should encompass the conditions
needed to bring each reagent combination to complete reaction while mini-
mizing side-reactions and product decomposition. Sample tracking and in-
process control data must also be managed at very high volume.
5 Laboratory automation, robotics, and mechanical devices enabling the simultaneous
performance of multiple tasks are essential to combinatorial chemistry. The range of
enabling tools goes from simple devices such as multichannel hand pipettes to
high-performance, fully integrated systems such as the Irori NanoKan system.
This issue will be revisited, but the basic principle is that the successful prac-
tice of combinatorial chemistry requires some level of commitment to and in-
vestment in laboratory automation.
6 Robust process chemistry is required to assure the desired outcome. In the pharma-
ceutical world, the importance of process chemistry lies at the two extremes.
For single compound synthesis in a medicinal chemistry laboratory, a good
process may be on the nice to have list, but as long as the synthesis scheme
aords some of the desired compounds, intermediate and endstage puri-
cations will overcome deciencies in the process. For bulk pharmaceutical
production, the process is everything: it must be extremely ecient, fully vali-
dated, and conform to regulated manufacturing practices. The importance of
process chemistry in combinatorial synthesis is closer to the bulk production
context.
For large compound libraries, the opportunity for product purication is
very limited (although technologies for doing this are evolving nicely). Library
members with poor-quality or outright failures are highly undesirable as they
waste time and resources in biological testing laboratories. The best resolution
of this dilemma is to develop the synthesis scheme to be used for production of
a library into a robust, well-dened process. This requires careful optimization
of reaction conditions, validating the individual members of the reagent sets,
developing reliable analytical methods, and dening the process in something
equivalent to a standard operating procedure.
7 Electronic tracking and control systems are critical components of combinatorial
chemistry. Every chemist has been exposed to the tedium of labeling samples by
hand, lling out analytical request forms, and completing compound data
sheets. Preserving the identity of samples and information about them by
linkage to laboratory notebook pages is a cumbersome system that works when
a few hundred samples per year are involved but it cannot function when indi-
vidual experiments are producing thousands of individual compounds. The
data management aspect of combinatorial chemistry requires access to elec-
tronic tracking and control systems for sorting and labeling samples (e.g. with
machine-readable barcodes), for generating structure lists (SD les) that link
sample codes to compound structures, and for collecting and processing ana-
lytical data and linking these data to sample codes and structure les. In addi-
tion to these sample and data management applications, electronic control sys-
tems embedded in the operating software of automated synthesis systems are
necessary to ensure that each in-process material is in the right place at the right
time for each step in order to ensure that the library plan is faithfully executed.
8 Analysis and quality control procedures are just as important in combinatorial
chemistry as in other forms of synthetic chemistry. The shortcomings of early ex-
pressions of the combinatorial concept included the misperception that quality
was not important. In fact many libraries were deliberately prepared as com-
pound mixtures. It was taken for granted that biologically active samples could
be separated, deconvoluted, or in some way dealt with after hits were detected.
Two things resulted. The fact that synthesis without analysis is a prescription
for poor science was rearmed and condence in combinatorial chemistry as
a productive discovery tool developed rather slowly. At its current state of
development and acceptance, combinatorial chemistry is expected to provide
samples of individual compounds with a purity level [by high-performance
liquid chromatography (HPLC)] of at least 80%. The identity of compounds is
routinely veried by mass spectrometry, using electronic comparison of proba-
ble molecular ion peaks with calculated molecular weights. Combined liquid
chromatography/mass spectrometry (LC/MS) is preferable as it will conrm or
deny that the major peak in an HPLC trace corresponds to the design intent for
that particular library member. An aspect of quality control which needs fur-
ther development is the application of in-process control procedures (IPCs)
which are basic and routine in multistep synthesis of single compounds.
9 Since the purpose of combinatorial chemistry is to facilitate the discovery of useful
compounds, combinatorial syntheses must be reproducible and scalable. This is not
to say that the reaction sequence and mode of synthesis (solid or solution
phase) must eventually serve to provide multikilogram supplies, but the com-
pounds in a library have little value if interesting compounds cannot be con-
veniently resynthesized in small amounts for closer examination.
10 As a nal basic principle it should be understood that combinatorial chemistry is a
productivity-enhancing tool for chemists engaged in pharmaceutical research,
agrochemicals, catalysis, and materials science any eld where the prepara-
tion and testing of new compositions of matter are the essential elements of
discovery. However it does not displace or supplant established elds of syn-
thetic chemistry such as medicinal chemistry its best use is to leverage the
productivity of existing elds.
2.3
Combinatorial Synthesis
As mentioned before libraries of mixtures and of single compounds are accessible

by combinatorial chemistry. Furthermore the syntheses can either be performed in
solution or on solid support. In the following, both methods will be discussed in

detail and the underlying principles will be described. To be able to compare the
advantages and disadvantages of these technologies the following aspects will be
emphasized: reaction conditions, equipment, and possible degree of automation.
2.3.1
Solid-phase Combinatorial Synthesis
Solid-phase combinatorial chemistry relies on the fact that the molecule under
construction is attached via a linker to a polymeric carrier (bead) (Fig. 2.4). This
immobilization allows a simple separation of intermediates and nally of the
product from reagents and soluble byproducts. To guarantee the ecacy of this
principle, the bead and linker have to be stable under the reaction conditions. Fur-
thermore, the bond between the target product and the linker has to be cleaved
selectively under mild conditions without destroying the product. Thus, after
simple ltration, nothing but the liberated pure product AB is obtained.
Fig. 2.4. Solid-phase chemistry. After reaction the product is liberated and ltered o.
2.3.1.1 Reagents and Conditions

A key feature of solid-phase synthesis is the possibility of driving reactions to
completion with excess reagent. In normal solution-phase chemistry such forcing
conditions would have devastating eects on product quality, whereas in solid-
phase chemistry the excess reagents are simply removed by ltration. Another im-
portant eect is the pseudo dilution caused by spatial separation of reactive sites.
Difunctional compounds such as diamines or diacids react selectively in a mono-
functional manner with only one of the two groups resulting in a highly eective
desymmetrization. The spatial separation of the functional groups also renders
the macrocyclization reaction a comparatively eective processe. Solution-phase
chemistry, on the other hand, often aords statistical mixtures of products under
these conditions.
The positive features mentioned before are opposed by some drawbacks: adapt-
ing a standard solution-phase reaction to solid phase frequently entails problems
associated with nding suitable, robust and versatile linkers points of attach-
ment in the starting material. These inherent features limit the choice of possible
reaction conditions. Furthermore, the selection of usable solvents can be quite re-
stricted. While crosslinked polystyrene resin beads may be insoluble, polyethylene
or polypropylene used in containers, pins, etc. will deform or dissolve in many
solvents at elevated temperatures. Another restriction stems from the swelling/
shrinking characteristics of crosslinked polystyrene beads. Dichloromethane, tetra-
hydrofuran (THF), dimethylformamide (DMF), toluene, and (marginally) dimethyl
sulfoxide (DMSO) are all suitable in this respect, but ether, methanol, ethyl acetate,
acetonitrile, and water are not. Tentagel resins are compatible with more solvents
but introduce several more restrictions. Also the temperature that can be applied is
restricted: 100 C is generally at or beyond the upper limit for most solid-phase
systems room temperature to 80 C being the comfort zone. It should be noted,
however, that very low temperature operations involving, for example, reactive
enolates generated at 78 C are more easily handled in a directed split-and-pool
solid-phase mode (fewer batches). Chemistry involving heterogeneous catalysts
such as palladium on charcoal or solid reagents such as manganese dioxide are
intrinsically incompatible with solid-phase synthesis methods. Furthermore, the
solid-phase chemistry literature is still limited, and only a relatively small propor-
tion of the synthetic solution-phase repertoire has been adapted to solid phase.
Therefore the development of a suitable methodology for the synthesis of large
libraries can be time-consuming (several months). Another drawback is the di-
culty to analyze the outcome of a given reaction. On-bead analysis is still not sat-
isfying, although NMR and IR as well as MS techniques have been improved. In
most cases, reaction products have to be cleaved from the support and are ana-
lyzed by normal methods (HPLC, NMR).
2.3.1.2 Automation
As pointed out before, the ltration of the reaction mixture, e.g. the separation of
solid-supported products from starting materials and reagents, is the key process
in solid-phase chemistry. Because of its simplicity, this process can easily be auto-
mated and run in parallel. Thus, the rst robotic synthesizers were those for solid-
phase chemistry: many reactions were set up in parallel by automated dispensing
stations and the normally very tedious work-up procedure was reduced to simple
ltrations. This worked ne as long as the library size was not too large (<1000
compounds). Larger libraries are dicult to prepare by this process. A much more
ecient way to prepare large libraries is the so-called split-and-combine protocol.
2.3.1.3 Split and Combine

As depicted in Fig. 2.5, a polymer support is reacted with three dierent sub-
stances A, B, and C in separate reaction vessels. Subsequently, the beads are
combined and again split into three portions. Each of them is submitted to a re-
action with one of the substances D, E, or F. This process can be repeated, and
with each iteration the number of compounds produced is multiplied by a factor
of 3. It has to be emphasized that every bead bears only one compound. This is
especially true because reactions can be driven to completeness by excess reagent,
which is nally washed away together with impurities. After a sequence of two
iterations nine compounds, and after three iterations 27 compounds, are produced.
However, to prepare single compounds and not mixtures, several encoding tech-
nologies had to be developed.
Structure elucidation is possible employing chemical encoding technologies. In
addition to the reagent, a small quantity (e.g. 1%) of a chemical tag is reacted with
the bead, which makes the tracking of the history of a bead, and thus the identi-
cation of the product, unambiguously possible. The tagging process should neither
interfere with the reaction nor consume too much of the bead capacity. After the
Fig. 2.5. The split-and-combine protocol.
reaction the product is selectively cleaved from the bead. The identity of the prod-
uct can subsequently be determined by conventional analytical methods analyzing
the tagged bead. W. Clark Still invented in 1993 the rst binary encoding using
haloaromatic reagents for tagging (see Chapter 5). Several more possibilities, such
as tagging with oligonucleotides or peptides, can be used for the chemical encod-
ing of single beads.
When encapsulated in porous containers, aliquots of beads traverse the split-
and-pool protocol with the same outcome as a single bead all the beads in each
container carry the same compound at every stage. Today radiofrequency tagging
is the most prominent encoding technology. This method is based on a small radio
transponder, which is attached to the synthetic platform (e.g. a polypropylene re-
actor). Upon activation this device emits a given radiofrequency, thus making the
identication possible. Development of chemically passive tagging systems for
solid-phase synthesis vastly enhanced the utility of the split-and-pool protocol. The
enormous gain-in-function oered by split and pool can now be used to produce
huge libraries of pure, single compounds in multimilligram quantities with min-
imal synthetic eort. For example, the production of a 160,000-compound library
can be achieved in just 80 discrete synthetic operations if the library design em-
braces four sets of building blocks with 20 members in each set. Automated sort-
ing and washing stations have been built, but handling became so easy that small
libraries can be prepared with minimal automation.
2.3.1.4 Cost
Modest capital investments are required for tag-reading/sorting devices, apparatus
for cleavage and delivery of compounds to plates, and centrifugal evaporation. The
instrumentation requirements for product quality control (QC) are, of course, the
same as in solution-phase chemistry. Solid-phase methods foster proigate use of
reagents to drive reactions to completion, as mentioned before. Added to these
considerations is the fact that speciality resins, hi-tech linkers, and single-use
resin containers can add substantial material costs to library production.
2.3.1.5 The Products from Solid-phase Chemistry

Each compound in a library produced by solid-phase methods will generally have a
structural feature, usually a functional group, associated with its covalent linkage
to a resin bead. This feature becomes an obligatory part of every compound in the
library they will all be amines, phenols, acids, etc. depending on the type of
linker used. Such features are not always desirable, and considerable eort is
being invested in the development of traceless linkers often silicon based (see
Chapter 4). Another approach utilizes intramolecular displacement cleavage strat-
egies in which a (desirable) new ring is formed at the cleavage stage.
2.3.2
Solution-phase Combinatorial Synthesis
When combinatorial chemistry rst emerged solution-phase reactions were not

considered to be suitable for preparation of larger libraries (> 1000 compounds).
Only a few reactions lead to quantitative conversion using equimolar amounts of
reagents. Solution-phase methods encourage parsimony in the use of reagents as
any excess can become a product impurity. The use of excess reagents in solution
phase can only be contemplated when facile removal of the excess is possible.
However, purication and isolation procedures were tremendously improved in
the last year, allowing the purication of hundreds of compounds per day by prep-
arative HPLC methods. Furthermore, more recently, a number of technologies
have emerged making combinatorial chemistry in solution phase competitive to
solid-phase reactions.
2.3.2.1 Reagents and Conditions

In principle, any chemistry and any reaction can be employed in solution-phase
methods, including complex organometallic reagents, biocatalysis, etc. Few, if any,
of the reactions and procedures documented in compendia of organic syntheses
and organic reactions could not be adapted to solution-phase combinatorial chem-
istry if suitable time and eort were applied. Adapting viable reactions to solution-
phase combinatorial chemistry entails a set of problems which can be routinely
solved in a month or two. The problems are fairly standard and address aspects
such as control of stoichiometry, capturing a broad range of reactivity within a

single set of reaction conditions, and product quality assurance.
Complex molecule synthesis relies heavily on protecting groups. However their
use in solution-phase library synthesis is restricted to situations where their re-
moval gives volatile byproducts, e.g. Boc or Cbz groups. Certain synthetic trans-
formations that produce nonvolatile coproducts are also a problem in solution. For
example, Mitsunobu reactions, which produce phosphine oxide and hydrazide
coproducts, work very well in solid phase but require major adaptation of proce-
dures for use in solution. Multistep synthesis conducted in normal solution-phase
parallel synthesis leads to rapid deterioration of product quality because of incom-
plete reactions and accumulating byproducts.
Compatibility with automated solution-handling devices is the only solvent and
reagent restriction for solution-phase methods. Problems that may exist, such as
loss of accuracy in dispensing small volumes of highly volatile solutions in ether
or dichloromethane, can usually be overcome with less volatile alternatives such as
dioxane or tetrachloroethylene.
Solution-phase systems equipped to prevent condensation of water vapor (or
icing up) at the low end, or equipped to condense/reux solvent vapor at the high
end, can easily operate in the 20 C to 150 C range.
2.3.2.2 Scavenger Resins, Polymer-supported Reagents and Fluorous Tags

Solution-phase combinatorial chemistry suers from one main disadvantage. To
drive reactions to completion, more than one equivalent of reagent is frequently
necessary, but the use of excess reagents is often prohibitive because their removal
causes in most cases severe problems. Two new techniques were established to
overcome these diculties: polymer-supported reagents and scavenger resins. The
latter are functional group-specic, reactive resins, e.g. polystyrene-bound iso-
cyanates which react selectively with primary and secondary amines. Thus excess
reagents are rst used to drive reactions to completion. Subsequently, scavenger
resins are added to the reaction mixture. After selective coupling of the resin to the
excess starting material the insoluble material is removed by ltration and the
product remains in pure form (Fig. 2.6).
Also the second approach to simplify solution-phase chemistry relies on the
separation of insoluble material from the reaction mixture and combines the ben-
ets of solid- and solution-phase chemistry (Fig. 2.7): instead of immobilizing the
starting material on the support, only the employed reagents are polymer sup-
ported. Again, the work-up and purication are reduced to a simple ltration.
Furthermore, dierent polymer-supported reagents do not interfere with each
other, making one-pot reactions possible that would not work in classic solution
Fig. 2.6. Excess reagents can easily be removed using scavengers.

Fig. 2.7. The principle of polymer-supported reagents.
Fig. 2.8. The total synthesis of (G)-oxomaritidine and (G)-epimaritidine.
chemistry (Fig. 2.8). The versatility of this approach has been proved by Ley
et al. in the total synthesis of two natural products, (G)-oxomaritidine and (G)-
epimaritidine.
Another possibility to deal with the problem of excess reagents in solution-phase
combinatorial chemistry is the use of uorous tagging and extraction with uori-
nated solvents (Fig. 2.9). Substrate A is attached to a moiety which is polyuo-
rinated. Because of the uorous tag the product of the reaction is exclusively so-
luble in the uorous solvents. After reaction with excess quantities of reagent B
an extraction with a polyuorinated solvent is performed. Reagent B is more solu-
Fig. 2.9. Fluorous tagging a powerful tool for solution-phase chemistry.

ble in the organic phase and can be separated from the product. Finally the uo-
rous tag is cleaved o, removed by another extraction and the pure product can be
isolated.
2.3.2.3 Equipment and Costs

Automation in solution-phase chemistry is more dicult than in solid-phase
chemistry. Especially the purication of products requires large systems for prepa-
ratory HPLC. For highly automated solution-phase parallel synthesis on the scale of
>100,000 compounds per year, an investment of several million dollars may be
required to build and equip a suitable facility.
2.4
Conclusion
Solid-phase chemistry has made tremendous progress during recent years, and
today highly complex natural products can be prepared on solid supports (see
Chapter 3). Nevertheless, method development is slow and often fails to produce
the compounds needed, e.g. in medicinal chemistry optimization programs. Thus,
careful validation of the possible outcome of solid-phase chemistry has to be given
the highest priority before the development of methodology is started. However,
for the preparation of large libraries with only minor time constraints, solid-phase
chemistry remains the method of choice. On the other hand, solution-phase
chemistry is much more exible and quicker. However, the production of large
libraries is very tedious owing to the dicult purication of the products.
Polymer-supported reagents and scavengers represent a versatile addition to
solid-phase organic synthesis and parallel solution-phase chemistry. The combina-
tion of these reagents oers exciting possibilities. The methods described in this
chapter are interesting and fascinating but, so far, they do not enable the chemist
to exploit all the synthetic routes that he or she might think of. Thus, there is a
need for more solid-supported reagents, linkers, scavengers, and, especially, solid-
phase methodology.
Bibliography
1 J. N. Abelson, Combinatorial 4 A. W. Czarnik, S. H. DeWitt, A

Chemistry, Academic Press, San Practical Guide to Combinatorial
Diego, 1996. Chemistry, American Chemical
2 G. Jung, Combinatorial Peptide and Society, Washington, DC, 1997.
Nonpeptide Libraries: A Handbook, 5 G. B. Fields, Solid-Phase Peptide
VCH, Weinheim, 1996. Synthesis, Academic Press, San Diego,
3 I. M. Chaiken, K. D. Janada, 1997.
Molecular Diversity and Combinatorial 6 B. A. Bunin, The Combinatorial Index,
Chemistry: Libraries and Drug Academic Press, San Diego, 1998.
Discovery, ACS, Washington, DC, 7 E. M. Gordon, J. F. Kerwin, Combi-
1996. natorial Chemistry and Molecular
Bibliography 23
Diversity in Drug Discovery, John Wiley Gordon, J. Med. Chem. 1994, 37,
& Sons, New York, 1998. 12331251.
8 K. Burgess, Solid-Phase Organic 16 E. M. Gordon, R. W. Barrett, W. J.
Synthesis, John Wiley & Sons, New Dower, S. P. A. Fodor, M. A. Gallop,
York, 2000. J. Med. Chem. 1994, 37, 13851401.
9 D. Obrecht, Solid-Supported 17 G. Lowe, Chem. Soc. Rev. 1995, 24,
Combinatorial and Parallel Synthesis 309382.
of Small-Molecular-Weight Com- 18 Dedicated issue, Account. Chem. Res.
pound, Pergamon Press, Oxford, 1996, 29, 111170.
1998. 19 F. Balkenhohl, C. von dem
10 W. Bannwarth, E. Felder, Combi- Bussche-Hunnefeld, A. Lansky, C.
natorial Chemistry. A Practical Zechel, Angew. Chem. Int. Ed. Engl.
Approach, Wiley-VCH, Weinheim, 1996, 35, 22882337.
New York, 2000. 20 P. H. H. Hermkens, H. C. J.
11 M. R. Pavia, T. K. Sawyer, W. H. Ottenheijm, D. Rees, Tetrahedron
Moos, Bioorg. Med. Chem. Lett. 1993, 1996, 52, 45274554.
3, 387396. 21 R. E. Dolle, Mol. Diversity 1997, 2,
12 W. H. Moos, G. D. Green, M. R. 223236.
Pavia, Annu. Rep. Med. Chem. 1993, 22 P. H. H. Hermkens, H. C. J.
28, 315324. Ottenheijm, D. Rees, Tetrahedron
13 K. S. Lam, M. Lebl, Methods: A 1997, 53, 56435678.
Companion to Methods in Enzymology 23 R. E. Dolle, Mol. Diversity 1998, 3,
1994, 6, 372380. 199233.
14 K. D. Janda, Proc. Natl. Acad. Sci. 24 D. P. Curran, Angew. Chem. Int. Ed.
USA 1994, 91, 1077910785. 1998, 37, 11751196.
15 M. A. Gallop, R. W. Barrett, W. J. 25 R. E. Dolle, K. H. Nelson, Jr,
Dower, S. P. A. Fodor, E. M. J. Comb. Chem. 1999, 1, 235282.
Valuable Internet Links
http://www.5z.com/divinfo/
http://www.combinatorial.com/
24
3
Solid Phase and Soluble Polymers for
Combinatorial Synthesis
Rainer Haag, Andre Hebel, and Jean-Francois Stumbe
3.1
Introduction
Polymeric supports have revolutionized organic synthesis in the past decade and
have become a major driving force for laboratory automation and combinatorial
chemistry in general. While polystyrene (PS)-based ion exchange resins have been
known since the 1950s, the rst solid-phase peptide synthesis on modied PS
microbeads was reported by Merrield in 1963 [1]. Until the late 1980s, when the
rst nonpeptidic molecule libraries were reported [2], polymeric supports were
mainly used for special applications, such as peptide and oligonucleotide synthe-
sis. In these cases the polymeric support had to be stable only toward two repeti-
tive reaction conditions (coupling and deprotection). Therefore, some of these
original supports are of limited use for parallel multistep synthesis of small or-
ganic molecules, generally known as combinatorial chemistry. In the last decade a
rapidly increasing number of new polymeric supports, crosslinked (insoluble) [3
5] and noncrosslinked (soluble) polymers [610], have been described and used for
combinatorial synthesis. Although solid-phase synthesis on PS-based resins ex-
hibits a number of problems due to the heterogeneous nature of reactions and the
low concentration of functional groups (typically a1.5 mmol substrate/g polymer)
[11], no other polymeric support has yet found the same broad application for
combinatorial synthesis [12]. However, the reader should be aware of the fact that
there is no polymeric support for general application in organic synthesis. Every
polymer has its drawbacks (e.g. chemical stability, polarity) and hence is stable
only within a certain range of reaction conditions.
In this chapter, we will describe the structure and the properties of polymeric
supports as well as the eects of dierent spacers (Fig. 3.1). Spacer molecules,
compared with linker molecules, are used to provide more accessible linker func-
tionalities and to modify the properties of the polymer backbone (e.g. polarity,
swelling characteristics). Linker functionalities, which also inuence the materials
properties, will be the subject of the next chapter. In the following sections the two
major classes of polymeric supports solid and soluble polymers will be further
classied by their chemical structures and the polymer topologies. A special focus

ISBN: 3-527-30509-2
Fig. 3.1. General structure of a polymeric support.
will be put on the polymer properties, such as stability, swelling property, reactive
site distribution, loading capacity and the range of applications in organic synthe-
sis.
3.2
Solid-phase Supports
3.2.1
Polystyrene-based Resins
Functionalized polystyrenes are available as linear noncrosslinked and as cross-

linked polymers. The latter, generally referred to as PS resins, are among the most
commonly used solid supports for solid-phase organic synthesis (SPOS), solid-
phase-supported peptide (SPPS) synthesis and nucleotide synthesis. Nowadays,
numerous types of polystyrene resins are commercially available and a nonex-
haustive list of the most frequently used resins is given in Table 3.1. They are
available in dierent sizes, with dierent loading capacities (amount of functional-
ization) and degrees of crosslinking.
Macroporous and microporous polystyrene resins are typically prepared by sus-
pension polymerization. The basis of this process is the dispersion of an organic
phase (consisting of a monomer, a radical initiator, a crosslinking agent and po-
tentially a comonomer) into an aqueous phase [13, 14]. The size of the initial
droplets is adjusted by emulsifying the organic phase under stirring in the pres-
ence of a polymeric surfactant, which governs the nal size and the nal size dis-
tribution of the beads after polymerization. The dierent bead sizes are then sepa-
rated by a multiple sieving process. This is why the size of the beads is usually
given in mesh (number of sieve holes per inch); however, for most chemists the
mm size of the nal bead is more relevant for handling (Fig. 3.2). Resin beads used
for combinatorial synthesis are spherical particles typically in the range 50500
mm which can be easily handled (weighting, ltering and drying).
3.2.1.1 General Aspects
Crosslinkers In order to obtain insoluble resins, given amounts of crosslinking

agent have to be used for the synthesis of the beads by suspension polymerization
(see also Sect. 3.2.1.2 and Sect. 3.2.1.3). A crosslinking agent is generally a bi- or
multifunctional molecule that can be incorporated into two or more growing
26 3 Solid Phase and Soluble Polymers for Combinatorial Synthesis
Tab. 3.1. Features and applications of frequently used solid-phase resins.
Type Common features Representatives Applications a Loading

[mmol gC1 ]
Gel (microporous) High capacity 1% or 2% A, B, D, E 0.25.0

crosslinked PS
(Merrield resin)
Dierent solvent
swelling
Reagent access by PEGA, A, F 0.4
diusion PAP 0.7
Uniform sites POEPOP A 0.40.7
SPOCC 0.41.2
POEPS-3 0.20.3
Many unsuitable for CLEAR A, F 0.20.3
continuous ow
synthesis
Hybrid High capacity ROMP D 3.0
Dierent solvent Rasta silanes D 1.63.8
swelling (but less
than microporous
gels)
Encapsulated gel Suitable for PolyHIPE F 1.05.0
continuous ow (acrylamide resin
synthesis encapsulated in
PS shell)
Unstable to agitation Pepsyn-K (similar A, F
resin encapsulated
in inorganic
scaold)
Graft copolymers Lower capacity PEG-PS D, E 1.22.9
More uniform Tentagel9 A, B, D 0.250.6
swelling
Pressure stable Argogel9 A, B, D 0.40.5
Suitable for NovaGel9 A, B, D 0.50.7
continuous ow
synthesis
Rigid Capacity and Highly crosslinked E, F <1.0
macrorporous eciency depend PS
supports on specic surface
area, mean pore
volume, pore
distribution, and
mean pore size
Silica A, E, F 0.0060.06
CPG A, B, E, F 0.1
a Applications: A, peptide synthesis; B, oligonucleotide synthesis;
C, oligosaccharide synthesis; D, synthesis of small organic mole-
cules; E, polymer supported reagents; F, continuous ow
synthesis.
Fig. 3.2. Relation between mesh size and bead diameter in micrometers.
chains during the polymerization process, leading to interconnected chains. The

most popular crosslinking agent, used in the presence of styrenic monomers, is
divinylbenzene (DVB).
Crosslinked polystyrene resins can be further modied in many ways, such as
FriedelCrafts acylations [15, 16], electrophilic substitutions [17, 18], lithiations
and so forth. The resulting beads can be used in further reactions to produce
resins with various linker functionalities. However, for the synthesis of standard
Merrield resins, the functional group (e.g. chloromethyl styrene) is typically in-
corporated as a comonomer during the polymerization process.
Structure, morphology, and reactive sites distribution of crosslinked polymer beads

For chemists working with polymeric supports, it is of great importance to have a
good knowledge of the internal structure and morphology of the microbeads be-
cause they strongly inuence the physical properties and, as a consequence, the
reactivity of the functional sites. For example, if active sites are located in highly
crosslinked microdomains, as can be the case in macroporous resins, they will
remain inaccessible for reactions and the eective loading will be lower than the
theoretical one [11].
Even in microporous resins, one can expect some heterogeneity due to the
dierent reactivities of the monomers and crosslinking mixtures involved in the
suspension polymerization process [19, 20]. For example, if styrene is copoly-
merized with DVB and chloromethylstyrene, the reaction mixture consists of at
least six monomer entities: styrene, chloromethylstyrene, m-DVB (1), p-DVB (2),
and m; p-ethylvinylbenzenes (3).
For a better understanding of the polymer properties, several groups have
studied the structure, morphology and reactive site distribution of Merrield resin
and its derivatives in more detail. The analytical techniques include autoradiog-
raphy [21], confocal uorescence spectroscopy (CFS) [22], confocal raman spec-
troscopy [23], and scanning secondary ion mass spectrometry [24]. For Merrield
resin, an inhomogeneous site distribution and reactivity have recently been dis-
cussed in the literature on the basis of whole-bead CFS [22]. However, the unex-
pected results described in this work were recently revised by further studies using
confocal raman spectroscopy [23] and confocal uorescence spectroscopy of thin
slices in order to avoid uorescence quenching [25]. It is now obvious that the
distribution of active sites is essentially uniform throughout polystyrene resins, as
shown already by Merrield [21]. However, for large beads, diusion processes can
certainly play an important role and lead to an unequal reactivity of functional
groups located closer to the core and the shell of the individual bead. Based on geo-
metrical considerations, one should also be aware of the fact that, in microbeads
with a diameter of 100 mm, 50% of the active sites are within the rst 10 mm of the
outer shell [23].
3.2.1.2 Macroporous Resins

Macroporous resins are generally highly (>5%) crosslinked polystyrene micro-
beads [12]. The term macroporous refers to their inner skeleton, which is made
up of a permanent porous structure even in the dry state (see Scheme 3.1c). His-
torically, functionalized macroporous resins have mainly been used for ion exchange.
Nowadays, many new applications, especially in the eld of polymer-supported re-
agents [26, 27], have been developed (see also Section end).
Macroporous resins are prepared by suspension polymerization of monomers
such as styrene, vinyl pyridine, acrylamide, or glycidyl methacrylate with a porogen
agent (Scheme 3.1) [28, 29]. Thus, a mixture of monomer with potentially a como-
nomer and a crosslinking agent are copolymerized after dispersion in an aqueous
medium in the presence of the porogen, which, remains within the beads during
the polymerization and acts as a template for the formation of the permanent in-
ternal porous structure of the nal resin. Porogen agents can be of dierent na-
tures (e.g. solvents, noncrosslinked polymers). After completion of the polymer-
ization the porogens are removed by processes dependent on their characteristics
and a hard opaque bead with a rough surface remains. The opacity of the macro-
porous resins, compared with the glassy appearance of the microporous beads, is
due to their heterogeneous structure, which is made up of highly crosslinked
polymeric microdomains and pores that are devoid of polymer [20, 30].
Scheme 3.1. Synthesis and structure of interconnected pores. (1) Porogen and network
macroporous resins: (a) polymer network start to phase separate; (2) porogen phase
forming; (b) porogen phase acts as pore removed to yield pores (hatched area,
template; (c) dry macroporous resin with large crosslinked polymer; dots, porogen phase).
As mentioned above the generation of pores can take place in two ways: non-
crosslinked polymers as well as organic solvents [28, 31]. For instance, if linear
Fig. 3.3. Dierent chemical species present in the technical grade DVB mixture.
and noncrosslinked macromolecules are dissolved in the starting organic phase,

they can be removed from the nal polymerized beads by Soxhlet extraction. In
this process, these linear soluble macromolecules act as templates by creating per-
manent pores after their removal [32, 33]. The size and the distribution of the
pores can be controlled by the characteristics of the linear polymer (i.e. molecular
weight, concentration) [29]. Another possibility is suspension polymerization in
the presence of an organic solvent that is a poor solvent, or even a nonsolvent, of
the nal polymer. Phase separation that occurs within the beads during the poly-
merization process leads to the formation of globular entities that are free of poly-
mer with characteristics that depend on the nature and on the concentration of the
porogen [20]. The amount of crosslinking agent plays a major role in the forma-
tion of the macroporous structure and has to be carefully considered. For example,
during polymerization conducted with relatively large amounts of crosslinkers
(up to 2025 mol% compared to the monomer), the formation of highly DVB-
crosslinked microdomains ensures a rapid phase separation [20, 32]. The most
commonly used crosslinking agents for the preparation of macroporous resins are
divinylbenzenes (DVB) (1, 2). The technical grade DVB typically used is a mix-
ture of three chemical species: 27% m-DVB (1), 53% p-DVB (2), and 20% ethyl-
vinylbenzenes (3) (Fig. 3.3).
Other frequently used crosslinkers for macroporous resins include ethyl-
eneglycol dimethacrylate (EGDMA) (4) and methylene bisacrylamide (6) (Fig. 3.4).
They are selected depending on the nature and reactivity of the monomer engaged
in the polymerization.
Structure and physical properties of macroporous resins As a consequence of their

mode of preparation, macroporous microbeads consist, on one side, of a perma-
nent macroporous internal structure and, on the other side, of highly crosslinked
areas (Scheme 3.1c). The porous areas are made up of numerous interconnected
cavities of dierent sizes leading to a large internal surface available for function-
alization, whereas, the crosslinked areas provide the rigidity for such structures
[20, 28]. This high internal surface area typically ranging from 50 to 1000 m 2 g1
(determined by N2 BET-isotherm) is accessible even in the dry state [20].
In general macroporous resins show very low swelling in organic solvents be-
cause of the very highly crosslinked areas. For this reason, macroporous beads re-
main unaected by changes in the direct environment, even in the presence of
good solvents. Another consequence is that the pores can accommodate a large
variety of solvents, including polar solvents such as water and low-molecular-
Fig. 3.4. Dierent crosslinking agents for PS beads.
weight alcohols. The pore size and the presence of channels interconnecting these
cavities allow solvents to diuse quickly in and out of these pores.
One drawback of these heterogeneous structures is the very low accessibility of
the solvents and reagents to the highly crosslinked areas, leading to limited load-
ing capacities with a typical range of 0.81.0 mmol g1 [34, 35]. However, some
commercial ion exchange resins, also used for organic reagents, have loading ca-
pacities up to 4.5 mmol g1 [26]. Generally, macroporous resins display lower
reactivities than microporous swollen beads. In contrast to microporous resins,
they show high resistance toward osmotic shock (see Fig. 3.5b) [20], but they can
be brittle when not manipulated carefully [13].
Applications of macroporous resins The most extensively used macroporous

resins are polystyrene-based ionic exchange resins. They are made of poly(styrene-
co-divinylbenzene) copolymers and are subsequently modied to arylsulfonic
acids, quarternary ammonium salts or other derivatives mainly located on the in-
ternal surface of the pores [28, 36]. This renders them accessible to numerous or-
ganic solvents, including water and alcohols. Recently, these ion exchange resins
have had a revival for the immobilization of ionic reagents in automated synthesis
[26, 27]. Macroporous beads have also been used for the immobilization of cata-
Fig. 3.5. ESEM pictures demonstrating the of a swollen resin (24 h, 300 rpm, 20 C,
mechanical stability of 2% crosslinked DMF); (d) after mechanical shaking of a
Merrield resins under dierent conditions: (a) swollen bead (7 days, 60 rpm, 20 C, DMF).
after swelling in THF and drying; (b) after The ESEM pictures were taken by Dr. Rudiger
osmotic shock (swelling in THF, washing with Landers, Materials Research Center, University
MeOH and drying); (c) after magnetic stirring of Freiburg, Germany.
lysts [28] and as adsorbents [37]. Other interesting applications involve their use as
chromatographic materials and for continuous ow synthesis in columns [28, 38,
39].
3.2.1.3 Microporous Resins

Microporous beads are weakly crosslinked resins obtained by suspension polymer-
ization of undissolved styrene and divinylbenzene in the absence of any porogen
agent. This process leads to the formation of a homogeneous network evidenced
by a glassy and transparent appearance. The size of the beads is controlled by the
stirring conditions and by the nature and the amount of the stabilizing agent, e.g.
a partially hydrolyzed polyvinylalcohol (PVA) (8587%) [40]. The most commonly

used supports for solid-phase organic synthesis are styrenedivinylbenzene co-
polymers crosslinked with 12% DVB. Numerous derivatives of these copolymers
are commercially available. Three synthetic routes are used for the preparation of
functionalized polystyrene microbead derivatives (i.e. Merrield resins):
1 chemical transformation of the unfunctionalized poly(styrene-co-divinylbenzene)

[1, 41, 42];
2 copolymerization of a mixture of styrene, divinylbenzene with 4-(chloromethyl)-
styrene [43, 44];
3 copolymerization of the mixture styrene, divinylbenzene with a-methylstyrene
and its consecutive transformation by chlorination [45, 46].
The loading capacity is controlled by the yield of the electrophilic aromatic sub-
stitution in method 1 or by the amount of 4-(chloromethyl)-styrene incorporated
in the starting organic phase for copolymerization in method 2. Typical loading
values are between 0.2 and 4.0 mmol g1 , and a loading capacity of 1.5 mmol g1
(for the most commonly used Merrield resins) corresponds approximately to 20%
substituted aromatic groups. Higher loading Merrield resins (4 mmol g1 ) have
also been used in organic synthesis [47]; however, the highest possible loading
6.55 mmol g1 , which corresponds to 100% chloromethylstyrene, would not be
useful in practice [12].
For microporous resins the exact degree of crosslinking and the nature of the
crosslinker are even more important than for macroporous resins, owing to the
severe eect on the swelling properties. The most common microporous resins are
12% crosslinked, but resins with less crosslinkage have also been studied [48].
They are mechanically weak and consequently easily subject to damage. However,
increased reaction rates have been observed for these more exible polymer net-
works. It is important to keep in mind that the DVB used for crosslinking is usu-
ally a technical grade product with a composition that can vary from one batch
to another (see Fig. 3.3), which inuences the properties of the beads. The con-
sequences are that varying amounts of crosslinking agents are incorporated in
resins depending on the dierent polymerization batches, which generally leads to
relatively high error values (G0.5%) in the degree of crosslinking indicated in the
catalogues of many suppliers.
Other crosslinkers are ethyleneglycol dimethacrylate (EGDMA) (4), N,N-
methylene bisacrylamide (6) (MBA), trimethylolpropane trimethacrylate (8)
(TRIM), and, more recently, novel crosslinkers have been introduced such as 1,4-
bis(vinylphenoxy)-butane (5) [49], and bis(vinylphenoxy)-polyethylene glycol (PEG)
(7) [50, 51] which present the advantage of having a strong inuence on the swell-
ing properties due to the increased exibility between the two crosslinking units
(Fig. 3.4).
In addition, styryl-terminated dendrimers have been introduced as novel poly-
mer crosslinkers (9). They consist of 816 peripheral styryl units attached to aryl end
branches of dendritic TADDOL or BINAP ligands and these were copolymerized
with styrene by suspension polymerization [52]. However, it is not yet clear

whether such highly functional crosslinkers are of any advantage for practical use.
Physical properties of microporous resins In contrast to macroporous resins, mi-

croporous beads have a low internal surface area in the dry state of less than 10
m 2 g1 (determined by N2 BET-isotherm) [20], owing to their more homogeneous
structure that does not allow the diusion of gases or bad solvents into the
polymeric network. As polystyrene is hydrophobic and nonpolar, swelling of
microporous polystyrene resins will occur in nonprotic solvents such as dioxane,
dichoromethane, dimethylformamide (DMF), tetrahydrofuran (THF), or toluene,
but not in polar protic solvents (e.g. water, alcohols) and apolar aprotic solvents
(e.g. alkanes) [53].
However, the swelling of a resin depends not only on the nature of the solvent
but also on the degree of crosslinking and the spacer molecules [48, 54]. It is in-
deed obvious that the percentage of swelling is inversely proportional to the cross-
linkermonomer ratio. Thus, 1% DVB polystyrene swells 46 times its volume in
dichloromethane, whereas in contrast 2% DVB polystyrene swells 24 times its
volume in dichloromethane. The transformation of Merrield microbeads by the
conversion of the chloromethyl groups or the grafting of spacer groups can lead to
dramatic changes in the swelling properties, as illustrated in Table 3.2. In order to
anticipate the swelling properties of a modied resin, the chemist can compare the
Hildebrand solubility parameters of solvents and of the polymer [55]. Thus, the
calculation of the solubility parameter for crosslinked polystyrene gives values of
9.1 (Cal mL1 ) 0:5 and this value can then be compared with the solubility param-
eters of dierent solvents [49]. It is generally accepted that polymers and solvents
are miscible when the dierence of solubility parameters is not higher than 1. For
example, the comparison of the values for the solubility parameter of polystyrene
and of dierent solvents allow for the selection of good solvents for swelling the
resin beads such as chloroform, DMF, dioxane, toluene, or THF, which was con-
rmed experimentally (Table 3.2) [49].
Mechanical and chemical stability of microporous resins Care has to be taken when
working with microporous resins in dierent solvents. Osmotic shock can occur
when a preswollen bead (in a good solvent) is introduced into a bad solvent.
The beads start to shrink rapidly under expulsion of the good solvent and are
subjected to stress. This leads to mechanical damage or at least to non-negligible
modications of the structure, as shown in Fig. 3.5b (compare with the surface of
the original Merrield resin in Fig. 3.5a).
Another problem that has to be encountered when conducting a reaction on
swollen microporous resins is that they can break if agitation conditions are too
vigorous. Figure 3.5c shows an example of beads after a solid-phase reaction con-
ducted with a magnetic stirrer. The scanning electron microscope (SEM) picture
reveals that most of the beads are broken compared with the beads collected after
a reaction conducted on a mechanical shaker (Fig. 3.5d). The consequence for
broken resin beads is the clogging of the lters used during their purication.
34
Tab. 3.2. Swelling of selected solid phase resins (mL g1 ).
Solvent Merrield Tentagel S ROMP PS denrimers PAP CLEAR POEPOP SPOCC POEPS-3
resins (1% spheres
crosslinked) Polyamide Arylether Mn (PEG)F1500 g mol C1
dendrimer dendrimer
CF3 CH2 OH 14.1 12.0

Water 3.6 3.2 3.5 10.5 8.0 14.0 10.5 8.0
MeOH 1.6 3.6 1.0 3.3 9.5 7.0
EtOH 1.7 2.9 4.0 8.1
2-Propanol 7.3
DMF 5.6 4.7 1.8 4.0 5.8 6.4 8.0 15.5 11.0 9.5
DMSO 1.3 5.4
MeCN 3.2 4.2 1.5 6.5 12.0 7.9 6.0
EtOAc 1.9 5.0
THF 8.8 5.0 2.2 3.2 4.7 6.5 12.5 8.1 7.0
Dioxane 7.8 5.4 2.8
Acetone 1.5
CH2 Cl2 8.3 6.3 2.2 3.7 4.6 6.4 10.0 22.8 15.5 12.0
3 Solid Phase and Soluble Polymers for Combinatorial Synthesis
CHCl3 4.0 6.8

Et2 O 4.0 1.9 1.5
Toluene 8.5 4.8 3.0 5.0
Hexane 2.4 3.0
Concerning the chemical stability of Merrield resins and their derivatives, it

has been shown that they are relatively stable toward weak oxidants, strong bases,
and acids. In fact, reactions that are known to proceed on alkyl substituted aro-
matic compounds, especially electrophilic substitutions, will also occur on cross-
linked polystyrene [12]. Strong oxidants at elevated temperatures and electrophilic
reagents should therefore be avoided [12, 13].
3.2.2
Polystyrene Hybrid Supports
3.2.2.1 PEGylated Resins

Merrield resins and their derivatives are still the most commonly used resins for
the synthesis of small molecules, but one of their limitations is the poor swelling
in polar protic solvents. For instance, Merrield resins cannot be applied for syn-
thesis of polar compounds in water or alcohols. This problem, however, can be
overcome by designing amphiphilic resins made of a 1% crosslinked polystyrene
matrix onto which polyethylene oxide chains are grafted [56, 57]. These resins
are commercially available as TentaGel9 (Fig. 3.6). Typically, their composition is
70 wt% of polyethylene glycol (PEG) grafts (average molecular weight of 3000
g mol1 ) and 30 wt% of PS. These resins can be prepared by two dierent path-
ways:
1 grafting of PEG chains onto Merrield resins [58, 59];

2 anionic ring opening polymerization of oxiranes initiated from the active sites of
a hydroxy-terminated polystyrene resin [56, 57, 60].
Fig. 3.6. Picture of Tentagel9 resin and chemical structures of

TentaGel9, ArgoGel9 and NovaGel9 resins.
The main drawback of the rst technique is the possibility of additional cross-
linking due to the fact that PEG macromolecules are bifunctional and conse-
quently that the two end chains can both react with the resin [56]. This, however,
can be overcome if monoprotected PEGs are used.
PEGylated supports are far more polar than Merrield resins and hence they
swell in a broad range of solvents from apolar aprotic to polar protic solvents
(Table 3.2) [53]. However, the loading of TentaGel9 resins is relatively low (loading
values range from 0.15 to 0.40 mmol g1 for PEG35 chains) compared with the
higher loading capacities that can be reached for Merrield resins. A similar type
of PEGylated resin known as ArgoGel9 has slightly higher loading capacities (up
to 0.5 mmol g1 for PEG35 chains) because it has two PEG chains that are grafted
onto every active site [61, 62].
PSPEG hybrid resins opened many new possibilities in combinatorial syn-
thesis by allowing the use of protic solvents. Even on bead, screening is possible
with these resins. However, the user should be aware of some drawbacks, such as
bleeding, which is dened as the loss and the release of PEG grafts when treated,
for example, with strong acids [63, 64]. It has been reported for instance that tri-
uoroacetic acid (TFA), which is commonly used for cleavage of protecting groups,
can also cleave the benzylicCH2 OPEG bond [65]. This problem can be overcome
by using a TentaGel9 resin with the PEG spacer attached to the polystyrene back-
bone via an alkyl linkage. This hybrid resin is not sensitive to acids or bases [34,
57, 62, 64]. Other drawbacks of such PSPEG hybrid resins originate from the
nature of the PEG polymer, which is hygroscopic. Hence, the presence of large
amounts of PEG (up to 70%) render the beads more sticky and more dicult to
manipulate in some cases than regular Merrield resins [20].
In order to overcome the decrease of loading capacity due to bleeding of the
PEG spacers, a similar type of resin has been designed (e.g. NovaGel9) with active
sites located on the PS backbone [64] rather than at the end of the PEG-grafted
chains as in TentaGel9 and ArgoGel9 resins. This results not only in a good
swelling behavior in both apolar and polar solvents due to the PEG chains (PEG
content @ 50%) but also in a slightly higher loading capacity (0.7 mmol g1 ). In
addition, eventual bleeding of the PEG grafts does not decrease the loading capac-
ity and only a slight modication of the swelling properties will occur. However,
the advantage of improved kinetics and better on-bead analytics (e.g. nuclear mag-
netic resonance) due to the highly exible polyether spacers are lost in this ap-
proach. It should be pointed out again that all PEGylated resins are sensitive to-
ward oxidation and hence bleeding will occur if not properly handled.
3.2.2.2 High-loading PS Hybrid Supports

A general problem in solid-phase combinatorial chemistry is low loading capacity
of the commonly used resins. Often, large quantities of resin are required in order
to obtain substantial amounts of products.
Ring-opening-metathesis-polymer hybrids: ROMP spheres A recent approach to-

ward high-loading solid-phase supports uses cross metathesis between vinyl poly-
styrene beads and norbornene derivatives [66]. In a rst step the immobilization of
the ruthenium catalyst (Grubbs catalyst) on vinyl polystyrene (11) can be achieved
via insertion of ruthenium into the styryl double bond (Scheme 3.2). The PS-
supported ruthenium alkylidene (12) shows good stability under normal atmo-
spheric conditions when dried. In the presence of solvents (e.g. dichloromethane),
however, the catalyst becomes inactive within a period of 5 h. Treatment of the PS-
supported catalyst (12) with an excess of a norbornene derivative (13) yields a
ROMP-based polymer (14), so-called ROMP spheres (Scheme 3.2).
Scheme 3.2. Cross metathesis of the supported Grubbs

catalyst and a norbornene derivate to yield ROMP spheres (14).
This resin shows high loading capacities (up to 3.0 mmol g1 ), but the swelling
properties are lower than for conventional resins, good solvents include THF
and DCM (see Table 3.2). The utility of these high-loading supports was exempli-
ed by a palladium-catalyzed coupling reaction between a resin-bound bromo-
benzoate and aryl zincates in a THF/MeOH (4:1) mixture. Also, crosslinked
ROMP-based polymers have been used as supports for catalysts [67] and high-
loading amine scavengers [68].
Rasta silanes Silyl linkers (see Chapter 4.3.5) oer a broad range of mild
and chemospecic cleavage conditions and are frequently used in SPOS. A high-
loading silyl-functionalized PS hybrid resin, so-called Rasta silane, has recently
been introduced for solid-phase chemistry [69]. The required silyl substituted
styrene monomer (16) can be prepared by lithiumhalogen exchange of p-
bromostyrene (15) and subsequent quenching with the appropriate dialkylchlo-
rosilane. A living free radical polymerization initiated by heating TEMPO-methyl
resin (17) with the silyl styrene (16) under solvent-free conditions at 130 C leads
to the formation of Rasta silanes (18) (Scheme 3.3).
Scheme 3.3. Formation of high-loading Rasta silane resins (18)

by living free radical polymerization.
Rasta resins are characterized by high loading levels between 1.6 and 3.8
mmol g1 with regard to the silicon linker. These values are signicantly higher
than for conventional silicon-linker resins, which show loading capacities between
0.5 and 1.6 mmol g1 . Easy conversion of the silyl units to reactive silyl chloride or
triate by standard synthetic methods allow the immobilization of alcohols and
phenols for solid-phase synthesis. It has been shown that these Rasta silanes allow
fast diusion of reagents throughout the resin beads [70].
Polystyrene dendrimer hybrids Another approach to high-loading resins are poly-

styrene dendrimer hybrids [71]. Dendrimers are highly branched macromolecules
built by a stepwise approach from a central core. The dendritic spacer molecules
provide a rapid and ecient method of increasing the loading capacity. For exam-
ple, the naturally occurring amino acid lysine has been used as a building block in
creating an inert dendrimeric scaold [72]. The tris-Boc-protected amino acid (20)
can be attached to a preswollen aminomethylated PS resin (19) (Scheme 3.4) and
thus creates the rst generation of this dendrimer (21).
Scheme 3.4. Synthesis of dendritic polyamide the DIPCDI-HOAt-mediated amide coupling

PS hybrid resins by stepwise attachment of a leads to the rst generation [G1] resin (22)
tris-Boc amino acid (20) to an amino- (Fmoc loading capacity 0.9 mmol g1 ) and
methylated PS resin (19) (0.8 mmol g1 ) via [G2] 23 (Fmoc loading capacity 1.2 mmol g1 ).
After coupling of a Rink amide linker [73] onto resin (21), the derivatized PS
dendrimer resin (22) with a loading capacity of 0.9 mmol g1 , with regard to the
Fmoc (9-uorenylmethoxycarbonyl) amino groups, is obtained. Repeating this
procedure yields the second generation [G2] (23). This exhibits a slightly higher
loading capacity of 1.17 mmol g1 . It is important to mention that the loading per
gram of resin does not increase substantially because of the mass of the attached
linker. However, the loading per bead increases geometrically from one generation
Fig. 3.7. [G2] of a triple branched symmetrical PS dendrimer

resin (24) (loading capacity 0.8 mmol g1 , 30.6 nmol per
bead).
to the next. These PS dendrimer resins have successfully been tested in the syn-
thesis of small peptides [72].
The synthesis of symmetrical tri-branching dendrimers on aminomethyl poly-
styrene macrobeads has also been described [74]. These [G2] dendritic resins (Fig.
3.7) oer loadings of 30.6 nmol per macrobead (0.8 mmol g1 ). A split-and-mix
synthesis (e.g. SPPS, Suzuki-coupling) on a gram of these resin beads (@ 27,000
beads g1 ) provides the number of compounds and the amounts necessary for a
single bead screening approach (including 1 H-NMR!). The obtained beads, espe-
cially the PS[G2] dendrons (24), show higher swelling values in polar solvents
such as methanol (MeOH) and dimethyl sulfoxide (DMSO) than the originally
used aminomethyl resin (see Table 3.2).
Some aryl ether dendrimers can be synthesized directly on hydroxymethyl poly-
styrene (25). Mitsunobu reaction with 3,5-bis(acetoxymethyl)-phenol (26) gives the
branched precursor (27) (Scheme 3.5) [75]. After deprotection and repetition of the
sequence a [G3] dendrimer resin was obtained with a loading capacity of 2.85
mmol g1 (3 nmol per bead). In unpolar solvents such as DCM and THF the den-
drimer resin (28) swells better than in MeOH or water.
The development of high-loading immobilized catalysts is another interesting
application for PS dendrimer resins. An example is given by the rhodium complex
Scheme 3.5. Synthesis of PSarylether dendrimer hybrid (28)

(loading capacity 2.85 mmol g1 ).
Fig. 3.8. PS[G2] dendrimer hybrid (29) supporting a

tetravalent catalyst for heterogeneous hydroformylation
reactions.
with dendritic phosphine ligands that are anchored onto a PS resin (Fig. 3.8) [76].
Dierent dendrimer generations have been prepared and tested as catalysts for the
hydroformylation reaction of several olens. The PS[G2] dendrimer (29) shows
higher reactivities than the rst generation and does not decrease for up to ve
cycles. The origin of this increased reactivity might be due to the higher density of
ligands on the outer core and cooperative eects.
High internal phase emulsion polymers: PolyHIPE PolyHIPE structures are formed
by polymerization of a high internal phase emulsion with styrene and divinylben-
zene [77]. The resulting material consists of an extremely porous and rigid matrix,
which provides a scaold onto which functional polymers (e.g. polyacrylamide
gels) can be chemically bound (Scheme 3.6). The polyacrylamide gel is prepared
Scheme 3.6. Preparation of highly porous PolyHIPE

PSacrylamide composite resins.
from N,N 0 -dimethylacrylamide (31), acryloylsarcosine methyl ester (32), a cross-

linker and a radical initiator that is grafted onto the highly porous support (30).
The polymer matrix (30) can be obtained from aminomethylated PS and acrylic
chloride. Although these polyacrylamide grafts are of limited use for SPOS, very
high loading capacities (up to 5 mmol g1 ) can be achieved by this approach [78].
The high internal surface area and the limited swelling allow the usage of these
materials in column reactors for automated synthesis. Applications in low-pressure
continuous-ow solid-phase peptide synthesis have already been described [78]. In
principle these highly porous PS structures (see Scheme 3.6) should also be suit-
able as supports for reagents or catalysts in SPOS.
3.2.3
Other Crosslinked Polymeric Supports
3.2.3.1 Crosslinked Acrylamides

Solid-phase crosslinked acrylic amides possess a more polar character than the
frequently used polystyrene supports. Thus, they are rather compatible in respect
to solvation properties with a growing peptide chain. A wide range of polar and
protic solvents can freely permeate and swell these materials. This class of resins,
however, has been specically developed for peptide and oligonucleotide synthesis.
The limited chemical stability of the amide bonds causes these resins to be less
suitable for broad application in SPOS with only some limited specic applications.
Pepsyn-K resins Crosslinked and functionalized polydimethylacrylamide gels

which are kept inside the pores of an inert, rigid and macroporous matrix are well
suited for continuous ow applications. Compared with PolyHIPE materials, in
which crosslinked polystyrene is used as matrix material, Pepsyn-K resins contain
a highly porous kieselguhr matrix as the scaold [79]. A mixture of dimethylacry-
lamide (31), ethylene bisacrylamide (33), acryloylsarcosine methyl ester (32) in
DMF and water is soaked into kieselguhr particles and then polymerized at room
temperature (Scheme 3.7). This support is a hybrid between an inorganic and an
organic support. So far it has been used only for peptide synthesis.
Scheme 3.7. Synthesis of Pepsyn-K resins from

dimethylacrylamide (31), ethylene bisacrylamide (33), and
acryloylsarcosine methyl ester (32) on a highly porous
kieselguhr matrix.
Poly(ethylene glycol)-copoly(N,N 0 -dimethylacrylamide) (PEGA) Another ow-stable,

highly polar solid support is poly(ethylene glycol)-copoly(N,N 0 -dimethylacrylamide)
(PEGA). This resin is accessible by an inverse suspension copolymerization of
N,N 0 -dimethyl acrylamide (31), acryloylsarcosine ethyl ester (34) and bis-2-acryl-
amidoprop-1-yl-PEG1900 (35) in silicon oil as a dispersing medium (Scheme 3.8)
[80, 81].
Scheme 3.8. Synthesis and structure of the high-capacity PEGA

resin (36), suitable for continuous ow synthesis.
The obtained PEGA resin (36) is characterized by good mechanical stability as

well as by high swelling properties in both organic solvents and aqueous buers.
The loading capacity is 0.4 mmol g1 . Furthermore, it has been shown that larger
peptides and other macromolecules can easily diuse through the PEGA polymer
matrix [82]. It is, therefore, suitable for solid-phase synthesis using both the batch
method and the continuous ow synthesis [83]. In addition, it was demonstrated
that biological screening is possible on the resin-bound substrate without further
cleavage [84].
Poly(N-acrylylpyrrolidine) (PAP) It has been reported that acrylamide polymers

swell very well in polar solvents such as water, DMF, and certain alcohols but
less well with CH2 Cl2 and CHCl3 [85]. Development of poly(N-acrylylpyrrolidine)
(PAP) allows peptide-coupling reactions in organic media of high and low polarity
as well as in aqueous solution. The synthesis of PAP (39) can be achieved by in-
verse suspension polymerization. An aqueous solution made up of the monomer
N-acrylpyrrolidine (37), the functionalization agent N-acryl-1,6-diaminohexane hy-
drochloride (38) and the crosslinker N,N 0 -bis(acrylyl)-1,2-diaminoethane (33) is
dispersed in a mixture of hexane and carbon tetrachloride. The polymerization is
then initiated with a redox initiator system consisting of ammonium peroxydisulf-
ate and N,N,N 0,N 0 -tetramethyl-1,2-diaminoethane (Scheme 3.9) [86].
Scheme 3.9. Preparation and structure of poly(N-acrylyl-

pyrrolidine) (PAP) resins (39).
The obtained PAP resin (39) has a loading capacity of 0.7 mmol g1 (amino
groups), which can be used for SPPS. In either its protonated or acylated form,
this resin exhibits high swelling values in water, methanol, CH2 Cl2 and CHCl3 .
Several applications of PEGA resins have been reported for SPPS [87].
Crosslinked-ethoxylate acrylate resins (CLEAR) Another class of highly crosslinked

polymeric supports for SPPS are crosslinked ethoxylate acrylate resins (CLEARs)
[88]. The CLEAR supports are prepared from branched crosslinker (8, 40) that is
used in high molar ratios for copolymerization with dierent monomers (4144)
(Fig. 3.9). The resulting polymers show a polyethylene glycol-like character, al-
though individual chains are quite short compared with chains of already known
PEG-containing resins such as PEGA or TentaGel9.
Both the oxyethylene chains and the ester functionalities are responsible for the
hydrophilic character of this class of resins. In contrast to many other resins,
amino groups can be introduced directly onto the resin. It does not require addi-
tional transformations of other functional groups or deprotection of a protected
amino polymer. CLEAR supports have good swelling properties, in both hydro-
philic and hydrophobic solvents (see Table 3.2). This magnies the range of
chemistry that could be carried out using these resins. The loading capacities are
typically between 0.20 and 0.29 mmol NH2 g1 , which is signicantly lower than
those of PAP (39), POEPOP (51), and SPOCC (52) (see below). CLEAR supports
have been successfully tested in batchwise and continuous-ow peptide synthesis
Fig. 3.9. CLEAR supports consist of these monomers which

can be combined in dierent ways, yielding resins that are
suitable for batchwise and continuous-ow modes.
but they should also be suitable for limited application in SPOS, especially when
protic solvents are required.
3.2.3.2 Crosslinked PEGs

This class of PEG-based supports is chemically more stable than the poly-
acrylamide-based supports. However, their applications in SPOS have not yet been
extensively demonstrated. Interesting features of these resins include the magni-
tude of swelling in all kinds of solvents and a relatively high loading capacity when
compared with regular PSPEG hybrid resins (see Sect. 3.2.2.1).
Polyoxyethylene-polyoxypropylene (POEPOP) Polyethylene glycol derivatives [e.g.

polyethylene glycol polyacrylamide (PEGA 36)], as a result of their inert character,
oer a wide range of applications in polymer chemistry and biomedical sciences.
Endgroup-modied PEGs (see Section 3.2.2.1) are often used as polymeric sup-
ports in peptide and combinatorial synthesis [89]. In the case of PEGA, a limiting
factor is its amide backbone. An exchange of the amide linker in PEGA for
the more stable ether linkages oers a larger diversity for application in organic
reactions. These properties are represented in polyoxyethylene-polyoxypropylene
(POEPOP 51), which can be obtained by anionic polymerization between end-
modied PEG macromonomers (46, 47) and epichlorhydrin (48) (Scheme 3.10)
[90]. The resulting POEPOP (51) shows an optimized balance between hydrophilic
and hydrophobic properties and has a high mechanical and chemical stability [91].
However, due to the physical properties of the PEG chains these beads might be
sticky in some cases [20].
One prerequisite for a successful polymeric support is that good swelling prop-
erties are available both in organic solvents and in enzyme buers. The POEPOP
resins swell best in CH2 Cl2 , less in DMF and water, and much less in THF and
MeOH (see Table 3.2) [90]. However, swelling is strongly inuenced by the length
of the PEG chains. The longer the chain the higher the swelling, but at the same
Scheme 3.10. Preparation of PEG macromonomers and

polymerization to provide the hydrophilic POEPOP (51),
SPOCC (52) and POEPS-3 (53) resins.
time the loading capacity drops. Typical loading capacities for POEPOP resins
are between 0.4 and 0.7 mmol g1 . In comparison with typical polystyrene-based
TentaGel9 resins (see Table 3.1), this is still a relatively high value [90]. POEPOP
supports have been successfully employed for a solid-phase synthesis of peptide
isoesters by nucleophilic reactions [91].
Polyoxyethylene-polyoxethane (SPOCC) As a result of the secondary ether bonds

that are formed during the polymerization reaction, POEPOP (51) is unstable under
extremely strong acidic or basic conditions. Cationic polymerization of end-modied
PEG macromonomers (46, 47) with 3-methyl-oxetan-3-yl-4-methyl toluenesulfonate
(49) leads to polyoxyethylene-polyoxetanes (SPOCC 52; Scheme 3.10) [89]. It con-
tains only primary ethers and alcohols and exhibits, therefore, an excellent chemi-
cal stability. No changes in the SPOCC structure were observed by treatment with
37% HCl or neat anhydrous hydrogen uoride. In addition, heating with a large
excess of thionyl chloride in toluene did not change the resin structure. The same
conditions, however, dissolve POEPOP within a few minutes. Loading capacities of
SPOCC are typically in the range 0.41.2 mmol g1 . The swelling behavior is
similar to that of POEPOP in the same solvents, but SPOCC resins swell slightly
more than POEPOP resins with equal PEG chain length [90]. Easy conversion of
the primary alcohols into amine or thiol functionalities is possible and therefore
allows dierent types of chemistry. Solid-phase glycosylation of peptides as well as
enzymatic reactions have been performed on this resin [89].
Polyoxyethylene-polystyrene (POEPS-3) Another class of crosslinked polyethylene

glycols are polyoxyethylene-polystyrene resins (POEPS-3 53). These supports can
be obtained via radical polymerization of an end-modied PEG macromonomer

(46, 47) with chloro-propyl-styrene (50) (Scheme 3.10). In order to obtain beads
this reaction is performed by inverse suspension polymerization [90]. Loading ca-
pacities are similar to TentaGelSOH and are in the range 0.20.3 mmol g1 .
POEPS-3 (53) shows similar swelling properties to POEPOP and SPOCC. With re-
gard to the chemical stability of these compounds, POEPS-3 is less stable than
SPOCC but more stable than PEGA due to its polyether backbone. As shown by
uorescence quenching diusion experiments in DMF, diusion processes are
slower than in TentaGel and ArgoGel. In water, however, all three crosslinked
PEG-based resins show faster diusion rates than the PSPEG hybrid resins [90].
So far POEPS-3 resins have been used exclusively for SPPS [92].
3.2.4
Inorganic Supports
In the following section, we give a short overview of some inorganic supports that
are suitable for SPOS. A good summary was published recently [4, 26]. Dierent
forms of silica gel are very often used for SPOS. They oer a number of advan-
tages and are now commercially available in various derivatized forms. These sup-
ports are rigid and do not swell or contract in the solvents employed in synthetic
cycles. Reagents and products can easily diuse into and out of the pores. Typical
pore sizes are between 2 and 10 nm, and the surface area is between 200 and 800
m 2 g1 . Although higher coupling rates in peptide synthesis were obtained on
silica than on polystyrene [93], silica gel did not become an established support
for solid-phase organic synthesis. In the meantime, silica gel has been partially
replaced by controlled pore glass (CPG) as an inorganic support [38, 9498]. The
main advantages of CPG, compared with silica gel, are its more regular particle
size and shape, and greater mechanical stability. Functionalization with long-chain
alkylamine groups leads to exceptional properties: rigid, nonswelling, mechanical
stability within a series of polar solvents, and chemical stability over the whole pH
range. Furthermore, CPG is unreactive to a broad variety of nucleophiles and elec-
trophilic reagents. Its stability during heating and its excellent solvation and ow
properties make it the support of choice for automated solid-phase synthesis. Typ-
ical loading capacities, however, are rather low (0.1 mmol g1 ).
3.3
Soluble Polymeric Supports
In contrast to solid supports, soluble noncrosslinked polymers give rise to homo-

geneous reaction conditions [68, 10]. Many of the problems of crosslinked poly-
mers arising from heterogeneous reaction conditions, such as nonlinear kinetic
behavior, reactive site distribution and solvation problems, can be overcome by us-
ing soluble polymeric supports. Unlike solid-phase supports, soluble supports en-
able the use of insoluble reagents or catalysts and also allow for the characteriza-
tion of intermediates by standard analytical techniques (e.g. NMR, UV), in the

homogeneous phase. On the other hand, the isolation and separation of these sol-
uble materials is not as straightforward as for solid-phase resins. Although soluble
polymeric supports have been used in organic synthesis since the 1970s, it is only
recently that several groups have started to investigate automated separation tech-
niques that enable the use of these soluble supports for parallel synthesis.
Soluble polymeric supports can be classied according to their topology, which
strongly inuences the physical properties of these materials. Linear polymers
with one or two functional endgroups, polyfunctional linear structures with many
functional groups along the chain and highly branched dendritic polymers will be
discussed in the following sections.
3.3.1
Separation Techniques for Soluble Polymeric Supports
It is generally believed that soluble polymeric supports, neglecting their advan-

tages, are dicult to separate from the reaction mixture. For many years the tech-
nique of precipitation and subsequent ltration seemed to be the most promising
method for separating soluble polymers from low-molecular-weight species. How-
ever, for automation several other separation techniques appear to be more prom-
ising [10]. Especially in the eld of homogeneous catalysis, membrane ltration
techniques have found application and show great potential for industrial use [99].
Therefore it seems appropriate to summarize briey the multiple commercially
available techniques for the separation of soluble polymers from the reaction mix-
ture, i.e. low-molecular-weight compounds (Table 3.3). There are several methods
which have been used for the separation of macromolecules by size, i.e. dialysis
[100, 101], membrane ltration [102], preparative size exclusion chromatography
(SEC) [103] and ltration through a silica cartridge [68]. All of them are suitable
for automation. However, little eort has been undertaken to develop multiparallel
automation in this area compared with the progress achieved in solid-phase syn-
thesis. For ecient and fast separations by size, soluble polymeric supports should
have medium molecular weights (500010,000) and narrow molecular weight dis-
tributions (< 1.5). In addition, macromolecules with a more globular branched
structure are preferable to a linear polymer structure.
Other separation techniques for soluble polymers, such as precipitation/
ltration and liquidliquid phase separation rely on polymer properties rather
than on their hydrodynamic volume. Precipitation is frequently used in polymer
chemistry to purify the respective polymer from low-molecular-weight impurities.
This method works especially well when the polymer is crystalline and the Tg is
above ambient temperature. It has also been used in the separation of functional-
ized PEG supports [68, 10]. Precipitation, however, is unsuitable for multistep
syntheses because impurities often remain trapped in the polymer. In addition,
large solvent volumes are required to perform quantitative precipitations and
hence automation of the process is dicult. Another relatively simple separation
technique, which is suitable for the separation of organic molecules from water-
48
Tab. 3.3. Separation techniques for soluble polymeric supports.
Parameter Dialysis Ultraltration SEC Filtration through Precipitation/ Liquidliquid phase

a silica cartridge ltration separation
Separation by Hydrodynamic Hydrodynamic Hydrodynamic Hydrodynamic Solubility Phase distribution

volume volume volume volume, polarity coecients
Minimum MW >1000 g mol1 >1000 g mol1 >3000 g mol1
of polymer
Typical sample 10 mL to 1 L 1100 mL <1 mL 0.110 mL 1100 mL 10 mL to 1 L
volume
Commercially Yes Yes Yes Yes Yes
available
Suitable for Yes Yes Yes Yes No Yes
automation
Suitable for high No Yes Yes Yes No No
throughput
3 Solid Phase and Soluble Polymers for Combinatorial Synthesis
Limitations Unsuitable for Suitable only for Unsuitable for Dierent solubilities
nal cleavage nal cleavage multistep required
step step or removal syntheses
of polymeric
reagents
soluble polymers, is based on liquidliquid phase separation between an organic

phase which contains the cleaved organic product and an aqueous phase which
contains the water-soluble polymer [104]. This separation technique, however, is
limited to systems with dierent distribution coecients of the components in the
two phases. Yet another separation technique that is used for soluble polymeric
reagents is ltration through a silica cartridge [68]. This technique has already
been established for automated synthesis in many laboratories and does not re-
quire additional equipment. However, it can only serve for purication of the prod-
uct after the nal cleavage step or the removal of a polymeric reagent.
3.3.2
Terminal Functionalized Linear Polymeric Supports
Linear polymers that carry functionalities only on their chain ends (e.g. PEGs),
have been frequently used as soluble polymeric supports and are listed in Table 3.4
(Entries 1 and 2) [610]. Because of the limited number of functional groups (one
or two per chain) these materials have rather poor loading capacities (typically
<0.5 mmol g1 ) and products coupled to the polymeric support are more dicult
to analyze (e.g. by NMR) than higher loading supports. On the other hand, these
soluble polymers do not dramatically change their physical properties upon func-
tionalization. This is extremely important if precipitation is used for separation.
The most widely used soluble polymeric support in organic synthesis is mono-
methylated polyethylene glycol (typically MPEG 5000), which is soluble in many
organic solvents and easily precipitated in nonpolar solvents (e.g. diethyl ether) [7,
105]. It was introduced by Bayer and Mutter in the 1970s for peptide synthesis and
was rediscovered by Janda and others as a soluble support for organic synthesis in
the 1990s [6, 8, 9]. Owing to the linear topology of this polyether, it contains only
one reactive functionality and hence exhibits a rather poor loading capacity (0.2
mmol g1 ). In order to increase the loading capacity, bifunctional PEGs endcapped
with benzylether dendrons have been prepared and used for the synthesis of
b-lactams [106, 107]. Another approach is the coupling of PEG arms onto a multi-
functional core to give a PEG-star polymer. Such multiarm PEG-star polymers
have been recently introduced as supports for organic synthesis based on pentae-
rythritol [108], hyperbranched polyglycerol (see Section 3.3.4) [109] and cyclo-
triphosphazene [110]. The advantages of these polyethers are their high chemical
stability and the good reactivity of the functional groups in homogeneous phase.
The achieved loading capacities of these multifunctional PEG polymers (a 1.0
mmol g1 ), however, are only marginal better than the commercially available
mono- and bifunctional PEG derivatives (0.2 and 0.4 mmol g1 respectively).
3.3.3
Polyfunctional Linear Polymeric Supports
Polyfunctional linear polymeric supports that carry reactive side-groups on every

monomer unit are summarized in Table 3.4 (Entries 310). These high-loading
Tab. 3.4. Selected linear soluble polymeric supports for organic synthesis.
Entry Structure Name Loading a Applications b
1 Polethylene glycol (PEG) 0.20.5 A, B, C, D, E

(MPEG)
2 Polypropylene oxide (PPO) 0.20.4 A
3 Polystyrene non-crosslinked (PS) (6.6) A, B, C
4 Polyacrylic acid (13.9) A
5 Polyacrylamide (14.1) C
6 Polyvinylalcohol 10.0 A, B, C, D
(22.7)
7 Polynorbornene ROMP gel 3.35.8 E

(9.4)
8 Cellulose (18.5) B
9 Poly(vinyl alcohol-b-1-vinyl-2- (6.5) A, B

pyrrolidone)
10 Poly(styrene-b-vinyl-alcohol) (6.8) D
a Loading capacity: experimental (theoretical) [mmol g1 ].

b Applications: A, petide synthesis; B, oligonucleotide synthesis;
C, oligosaccharide synthesis; D, synthesis of small organic mole-
cules; E, polymer-supported reagents.
polymers have been used for various organic synthesis applications as well as for
polymer-supported reagents. However, the physical properties (i.e. solubility) of
these materials change dramatically upon functionalization and can be problem-
atic in some cases for broad application in combinatorial synthesis.
The most frequently used examples are polyvinylalcohol, polyacrylamide, non-

crosslinked polystyrene and more recently ROMP-based polymers. For example,
commercially available polyvinylalcohol (PVA) (Table 3.4) has been used as a solu-
ble support for oligonucleotide synthesis, and a loading of up to 10 mmol g1 of
mononucleotide has been reported [111113]. However, polymeric supports with a
lower loading capacity and better solubility in polar organic solvents were recom-
mended by the authors. Another plausible reason for the limited use of PVA as a
soluble polymeric support is its poor solubility in organic solvents and the need for
harsh reaction conditions for functionalization [10]. Therefore block copolymers of
PVA with other monomers, such as styrene, have also been used as multifunc-
tional polymeric supports with improved solubilities [114].
Another high-loading linear polymeric support is polyacrylamide [115, 116].
This very polar resin has better solubilities than PVA and allows the copolymeri-
zation of functional monomers. Several applications, for example synthesis of oli-
gonucleotides, have been reported for this soluble support [6, 7]. A limiting factor
for the general use of polyamide supports, however, is their reduced chemical sta-
bility compared with polystyrene or polyether supports, especially for reactions
with organometallic reagents and strong bases. A soluble form of Merrield resin
(non-crosslinked PS/chloromethyl-PS copolymer) has recently been used for com-
binatorial solution-phase synthesis [9]. Even though this resin has been used for
peptide chemistry before, this was the rst application in the synthesis of natural
products (e.g. prostaglandins). In this application the support was isolated by pre-
cipitation.
More recently high-loading ROMP-based polymers (Table 3.4) have been intro-
duced as polymer-supported reagents. As these ROMPgels have so far been used
only as polymeric reagents, in this case the limited chemical stability of the poly-
norbornene backbone is of minor concern. For example, ROMPgels have been
used for HornerEmmons olenations, as acylation reagents and for the synthesis
of oxadiazoles [117119]. These polymers have a gel-like behavior when solvated in
organic solvents and can be removed from the reaction mixture by ltration
through a silica cartridge. An advantage in the preparation of ROMP-based re-
agents is the great tolerance of the ruthenium (Grubbs) catalyst toward many
functional groups.
3.3.4
Dendritic Polymeric Supports
The disadvantages of linear polymers, such as limited solubility in many organic

solvents, gel formation and problematic thermal behavior (high melting points
and Tg values) in some cases, can be overcome by the use of dendritic polymer ar-
chitectures. An extreme in terms of tree-like branching are the perfectly branched
dendrimers [120]. These well-dened macromolecules are soluble in many organic
solvents (depending on their end functionalities) and possess a maximum capacity
of functional groups in their periphery. However, the relatively high price and
limited chemical stability of the commercially available polyamidoamine or poly-
amine dendrimers might well be the reasons for their limited use as supports in
organic synthesis. Despite these problems, polyamidoamine dendrimers have been

successfully used as high-loading supports in the synthesis of indoles [121]. In this
case, the separation of the macromolecules from low-molecular-weight species
was performed by size exclusion chromatography. More recently, polysilane den-
drimers have been used as high-loading soluble polymeric supports in organic
synthesis [122].
A very promising class of high-loading polymeric supports are dendritic ali-
phatic polyethers as highly branched analogues of PEG [123, 124]. They are chemi-
cally stable, soluble in many organic solvents, show good accessibility and reactiv-
ity of the functional groups, and possess a high concentration of OH groups (up to
14 mmol g1 ). However, the general drawback of any dendrimer is the tedious
multistep preparation of higher generations (molecular weight exceeding 1500
g mol1 ), which is the lower limit for dialysis and ultraltration procedures (see
Table 3.3). Yet another problem of high-generation dendrimers appears to be steric
hindrance and sitesite interaction at the outer functional shell. This problem
might be overcome by using randomly branched polymer structures as supports
[125]. Nevertheless, in some cases the high degree of catalytically active sites on a
dendrimer surface can result in cooperative eects and enhanced reactivities [126].
In contrast to perfect dendrimers, hyperbranched polymers are easily available
in one reaction step. They contain dendritic, linear and terminal units in their
skeleton and hence can be considered as intermediates between linear polymers
[degree of branching (DB) 0%] and dendrimers (DB 100%) with an approxi-
mate DB of between 50% and 75% [127]. The high potential loading capacities
of these hyperbranched polymers are similar to those for dendrimers (514
mmol g1 ) and some hyperbranched polymers are commercially available [128].
The use of these commercial materials as supports for organic synthesis, however,
is limited because of the chemical stability of the respective polymer backbone (e.g.
polyamines, polyesters) and the relatively broad molecular weight distributions
(typically >2).
Hyperbranched polymers (Fig. 3.10) have recently been introduced as soluble
supports in organic synthesis [103, 104]. A commercial polyester support (Boltorn
54) containing 1,3-diols as terminal units was used for the synthesis of di-
saccharides (Scheme 3.6) [103]. Theoretically, these polyesters have a relatively high
loading capacity (8.8 mmol OH g1 ), but the experimentally achieved loading with
monosaccharides attached to a photo-labile linker was 0.8 mmol g1 , additionally
reduced by the weight of the linker functionality. The general use of this hyper-
branched polymer (54) as a soluble polymeric support, however, is limited as a
result of the chemical sensitivity and the low molecular weights of the polyester
backbone [129]. This is especially problematic for the separation by dialysis or ul-
traltration with a minimum molecular weight cut-o (MWCO) of 1000 g mol1
(see Table 3.3).
Recently, the controlled synthesis of well-dened hyperbranched polyglycerols
(55) (R H) has been achieved, by using both racemic and enantiomerically pure
glycidol monomers [130, 131]. These polyether polyols are conveniently prepared
in a one-step synthesis on a kilogram scale [132], and possess molecular weights
(Mn ) up to 30.000 g mol1 with molecular weight distributions typically below 1.5.
Fig. 3.10. Dendritic polyester (54) and polyether (55) (R H,

alkyl, glyceryl) as high-loading soluble polymeric supports.
The dendrimer-like structure of the hyperbranched polyglycerol (55) is charac-

terized by exactly one core unit with multiple hydroxyl groups randomly incorpo-
rated as linear (OH groups) and terminal groups (1,2-diols). The total density of
functional groups in polymer 55 (R H) is 13.5 mmol OH g1 polymer, of which
approximately 60% (8.2 mmol OH g1 ) are terminal 1,2-diols. These terminal diols
can be used directly as linker functionalities for many applications in organic syn-
thesis [10].
The complete derivatization of the terminal diols in polyglycerol (55) (R H),
with, for example, acetals, leaves about 40% of the OH groups unaected (see
Scheme 3.3). These remaining OH groups might limit the scope of this new poly-
meric support for some synthetic applications. For the preparation of a chemically
inert polyether support (55) (R alkyl) these residual OH groups can be selec-
tively alkylated by using phase transfer conditions to obtain dendritic polymers
with exclusively diol linkers [133]. This approach also permits the introduction of a
second type of functional group and tunes the solubility of the polymer in various
organic solvents. In order to increase the loading capacity of the dendritic poly-
glycerol support further, the linear glycerol units can also be converted into termi-
nal 1,2-diols [124]. This strategy increases the capacity of the terminal 1,2-diol
units from 4.1 mmol g1 for the hyperbranched polymer (55) (R H) to 7.1
mmol g1 for the dendritic structure (55) (R glyceryl) and preserves all advan-
tages of the polyether scaold.
For a more general application of polyglycerol (55) in organic synthesis and
in order to increase the scope of possible reactions on this support, the conversion
of the hydroxyl groups into various other linker functionalities by postsynthetic
transformations has been explored [134]. In one or two synthetic steps after the
polymerization several reactive linker functionalities, such as aldehydes, alkenes,
amines, carbonic acids and esters, are accessible in good yields and with high
loading [135]. Dendritic polyglycerols (55) are readily soluble in many organic sol-
vents and can easily be separated from low-molecular-weight compounds by dialy-
sis or ultraltration with a typical MWCO of 1000 g mol1 . Because of the high
exibility of the branches, the terminal 1,2-diol groups show excellent accessibility
and can be used directly as linker groups for various applications in organic syn-
thesis [104]. In addition the characterization of these dendritic polyethers by stan-
dard analytical techniques (e.g. NMR) is much more rapid than the monofunc-
tionalized PEG derivatives owing to the high loading capacity of functional groups
[104].
3.3.5
Microgels
Recently, Wul et al. introduced microgels as a new type of polymeric supports

for use in parallel synthesis [136]. Microgels are intramolecularly crosslinked
polymer molecules that build stable solutions in suitable solvents [137]. Oxazabor-
olidine functionalized PS-microgels have been prepared and used as catalysts in
enantioselective reduction of prochiral ketones [136]. In contrast to gel-type poly-
mer supports (see Section 3.2.1.3), microgels oer the advantage of higher loading
capacities and homogeneous reaction conditions. Like dendritic polymeric sup-
ports (see Section 3.3.4), they have a very low solution viscosity, which simplies
the handling of the reaction mixture. Also, separation can be performed by ultra-
ltration and the process can be performed in an automated or continuous mode.
3.4
Conclusions
After more than 10 years of intensive research on the preparation and the applica-
tion of new polymeric supports in combinatorial chemistry many new polymeric
materials have been developed and evaluated. However, there is still no polymeric
support for general application in combinatorial chemistry. Every polymer has its
drawbacks (e.g. chemical stability, polarity, loading capacity). Therefore, a poly-
meric support has to be carefully selected for the synthetic problem that needs to
be solved. In solid-phase organic synthesis several new supports with better swell-
ing properties in a wider range of organic solvents and higher loading capacities
have been introduced. Among these are several new PS hybrid resins as well as a
new family of crosslinked PEGs. In terms of material stability, inorganic supports,
i.e. controlled pore glass, cannot be beaten. However, the width of synthetic appli-
cations is very limited so far and will depend on the chemical stability of the
spacer and linker molecules used. In addition, these supports suer a heterogenic
nature and rather low loading capacities.
Soluble polymeric supports, like solid supports, have had a similar revival over
the past decade. In terms of stability, aliphatic polyethers and noncrosslinked poly-
styrene are among the most promising candidates. Dendritic and linear polyfunc-
tional soluble polymers have by far the highest loading capacities and show great
potential as supports for reagents and catalysts in combinatorial synthesis because
of their homogeneous reaction conditions. The use of these soluble polymers for
References 55
SPOS, however, requires further progress in automation of solution-phase separa-

tion techniques. Nevertheless, the current trend in the pharmaceutical industry to
move back to combinatorial solution-phase chemistry renders these high-loading
soluble polymers as potential homogeneous supports for solution-phase synthesis.
References
1 R. B. Merrield, J. Am. Chem. Soc. 21 V. K. Sarin, S. B. H. Kent, R. B.

1963, 85, 21492154. Merrield, J. Am. Chem. Soc. 1980,
2 S. R. Wilson, A. W. Czarnik, 102, 54635970.
Combinatorial Chemistry, Wiley, New 22 S. R. McAlpine, S. L. Schreiber,
York, 1997. Chem. Eur. J. 1999, 5, 35283532.
3 D. Hudson, J. Comb. Chem. 1999, 1, 23 J. Kress, A. Rose, J. G. Frey, W. S.
333360. Brocklesby, M. Ladlow, G. W.
4 D. Hudson, J. Comb. Chem. 1999, 1, Mellor, M. Bradley, Chem. Eur. J.
403457. 2001, 7, 380383.
5 J. W. Labadie, Curr. Opin. Chem. Biol. 24 S. B. Roscoe, J. M. J. Frechet, J. F.
1998, 2, 346352. Walzer, A. J. Dias, Science 1998, 280,
6 D. J. Gravert, K. D. Janda, Chem. 270273.
Rev. 1997, 97, 489509. 25 J. Rademann, M. Barth, R. Brock,
7 K. E. Geckeler, Adv. Polymer Sci., G. Jung, H.-J. Egelhaaf, 2001, to be
1995, 121, 3179. published.
8 P. Wentworth, K. D. Janda, 26 S. V. Ley, I. R. Baxendale, R. N.
Chem. Commun. 1999, 1917 Bream, P. S. Jackson, A. G. Leach,
1924. D. A. Longbottom, M. Nesi, J. S.
9 P. H. Toy, K. D. Janda, Acc. Chem. Scott, R. I. Storer, S. J. Taylor, J.
Res. 2000, 33, 546554. Chem. Soc. Perkin I 2000, 38154195.
10 R. Haag, Chem. Eur. J. 2001, 7, 327 27 A. Kirschning, H. Monenschein,
335. R. Wittenberg, Angew. Chem., Int.
11 P. Hodge, Chem. Soc. Rev. 1997, 26, Ed. Engl. 2001, 4, 650679.
417424. 28 F. Svec, J. M. J. Frechet, Science
12 F. Zaragosa-Dorwald, Organic 1996, 273, 205211.
Synthesis on Solid Phase, Wiley-VCH, 29 J. Seidl, J. Malinsky, K. Dusek, W.
Weinheim, 2000. Heitz, Adv. Polym. Sci. 1967, 5, 113
13 A. Akelah, A. Moet, Functionalized 213.
Polymers and their Applications, 30 R. Kunin, E. Meitzner, N.
London, 1990. Bortnick, J. Am. Chem. Soc. 1962,
14 X. Hohenstein, US Patent No. 84, 305306.
2524627, 1950. 31 J. R. Millar, D. G. Smith, W. E.
15 T. Mizaguchi, Chem. Pharm. Bull. Marr, T. R. E. Kresman, J. Chem.
1970, 18, 14651474. Soc. 1963, 218224.
16 R. B. Scarr, M. A. Findeis, Pept. Res. 32 I. M. Abrams, J. R. Millar, React.
1990, 3, 238241. Funct. Polym. 1997, 35, 722.
17 M. J. Farrall, J. M. J. Frechet, J. 33 A. Guyot, Synthesis and Separations
Org. Chem. 1976, 41, 38773882. Using Functional Polymers, Chap. 1,
18 H. Seliger, Makromol. Chem. 1973, Wiley, Chichester, UK, 1988.
169, 8393. 34 J. W. Labadie, Curr. Opin. Chem. Biol.
19 R. H. Wiley, Pure Appl. Chem. 1975, 1998, 2, 346352.
43, 5775. 35 M. Hori, D. J. Gravert, P.
20 D. C. Sherrington, Chem. Commun. Wentworth, K. D. Janda, Bioorg.
1998, 22752286. Med. Chem. Lett. 1998, 8, 23632368.
36 A. Guyot, Pure Appl. Chem. 1988, 60, Makromol. Chem. 1983, 184, 2603
365376. 2617.
37 J. M. J. Frechet, Makromol. Chem., 59 S. A. Kates, B. F. McGuiness, C.
Macromol. Symp. 1993, 289, 7071. Blackburn, G. W. Griffin, N. A.
38 H. Koster, F. Cramer, Liebigs Ann. Sole, G. Barany, F. Albericio,
Chem. 1974, 946958. Biopolymers 1998, 47, 365380.
39 C. McCollum, A. Andrus, Tetra- 60 P. Wright, D. Lloyd, W. Rapp, A.
hedron Lett. 1991, 32, 40694072. Andrus, Tetrahedron Lett. 1993, 34,
40 T. Balakrishnan, W. T. Ford, J. Appl. 33733376.
Polym. Sci. 1982, 27, 133138. 61 O. W. Gooding, S. Baudart, T. L.
41 K. W. Pepper, H. M. Paisley, M. A. Deegan, K. Heisler, J. W. Labadie,
Young, J. Chem. Soc. 1953, 40974105. W. S. Newcomb, J. A. Porco Jr, P. V.
42 R. P. Pinnel, G. D. Khune, N. A. Eikeren, J. Comb. Chem. 1999, 1,
Khatri, S. L. Manatt, Tetrahedron 113122.
Lett. 1984, 25, 35113514. 62 J. A. Porco, T. Deegan, W.
43 R. Arshasy, G. W. Kenner, A. Devonport, O. W. Gooding, K.
Ledwith, Makromol. Chem. 1976, 177, Heisler, J. W. Labadie, B. Newcomb,
29112918. C. Nguyen, P. V. Eikeren, J. Wong,
44 W. T. Ford, S. A. Yacoub, J. Org. P. Wright, Mol. Diversity 1997, 2,
Chem. 1981, 46, 819821. 197206.
45 S. Mohanraj, W. T. Ford, Macro- 63 V. Smali, N. J. Wells, G. J. Langley,
molecules 1986, 19, 24702472. M. Bradley, J. Org. Chem. 1997, 62,
46 Q. Sheng, H. D. H. Stover, 49024903.
Macromolecules 1997, 30, 67126714. 64 J. H. Adams, R. H. Cook, D.
47 S. P. Raillard, G. Ji, A. D. Mann, Hudson, V. Jammalamadaka, M. H.
T. A. Baer, Org. Process Res. Dev. 1999, Lyttle, M. F. Songster, J. Org. Chem.
3, 177183. 1998, 63, 37063716.
48 S. Rana, P. White, M. Bradley, J. 65 E. Bayer, W. Rapp in: Poly(ethylene
Comb. Chem. 2001, 3, 915. glycol) chemistry: Biotechnical and
49 A. R. Vairo, K. D. Janda, J. Comb. Biomedical Applications, Harris, M.
Chem. 2000, 2, 579596. (ed.), Plenum Press, New York, 1992,
50 S. Itsuno, I. Moue, K. Ito, Polym. p. 325.
Bull. 1989, 21, 365370. 66 A. G. M. Barrett, S. M. Cramp, R. S.
51 M. Renil, M. Meldal, Tetrahedron Roberts, Org. Lett. 1999, 1, 1083
Lett. 1996, 37, 61856188. 1086.
52 P. B. Rheiner, H. Sellner, D. 67 M. R. Buchmeiser, K. Wurst, J. Am.
Seebach, Chem. Eur. J. 2000, 6, 3692 Chem. Soc. 1999, 121, 1110111107.
3705. 68 T. Arnauld, A. G. M. Barrett, S. M.
53 R. Santini, M. C. Griffith, M. Qi, Cramp, R. S. Roberts, F. J. Zecri,
Tetrahedron Lett. 1998, 39, 8951 Org. Lett. 2000, 2, 26632666.
8954. 69 C. W. Lindsley, J. C. Hodges, G. F.
54 S. Pickup, F. D. Blum, W. T. Ford, Filzen, B. M. Watson, A. G. Geyer,
M. Periyasami, J. Am. Chem. Soc. J. Comb. Chem. 2000, 2, 550559.
1986, 108, 39873990. 70 S. R. McAlpine, C. W. Lindsley, J. C.
55 D. W. V. Krevelen, Properties of Hodges, D. M. Leonard, G. F.
Polymers, 3rd edn, Elsevier, New York, Filzen, J. Comb. Chem. 2001, 3, 15.
1990. 71 V. Swali, N. J. Wells, G. J. Langley,
56 E. Bayer, Angew. Chem., Int. Ed. Engl. M. Bradley, J. Org. Chem. 1997, 62,
1991, 30, 113128. 49024903.
57 B. D. Park, H. I. Lee, S. J. Ryoo, Y. S. 72 A. Mahajan, S. R. Chabra, W. C.
Lee, Tetrahedron Lett. 1997, 38, 591 Chan, Tetrahedron Lett. 1999, 40,
594. 49094912.
58 H. Hellermann, H. W. Lucas, J. 73 H. Rink, Tetrahedron Lett. 1987, 28,
Maul, V. N. R. Pillai, M. Mutter, 37873790.
References 57
74 C. Fromont, M. Bradley, Chem. 96 P. K. Ghosh, P. Kumar, K. C. Gupta,

Commun. 2000, 283284. J. Indian Chem. Soc. 1998, 75, 206218.
75 A. Basso, B. Evans, N. Pegg, M. 97 K. K. Ogilvie, M. J. Nemer, Tetra-
Bradley, Chem. Commun. 2001, 697 hedron Lett. 1980, 21, 41594162.
698. 98 H. Koster, J. Biernat, J. McManus,
76 A. Arya, N. V. Rao, J. Singkhonrat, A. Wolter, A. Stumpe, C. K.
J. Org. Chem. 2000, 65, 18811885. Narang, N. D. Sinha, Tetrahedron
77 N. R. Cameron, D. C. Sherrington, Lett. 1984, 40, 103112.
Adv. Pol. Sci. 1996, 126, 163214. 99 For a recent example, see: K. D. Smet,
78 P. W. Small, D. C. Sherrington, S. Aerts, E. Ceulemans, I. F. J.
Chem. Commun. 1989, 21, 15891591. Vanklecom, P. A. Jacobs, Chem.
79 E. Atherton, E. Brown, R. C. Comm. 2001, 597598.
Sheppard, Chem. Commun. 1981, 100 H. Koster, Tetrahedron Lett. 1972,
11511152. 15351538.
80 M. Meldal, Tetrahedron Lett. 1992, 33, 101 D. Paul, Chem. i. u. Zeit 1998, 32,
30773080. 197205.
81 M. Renil, M. Meldal, Tetrahedron 102 H. Determann, K. Lampert, Mitt.
Lett. 1995, 36, 46474650. Dtsch. Pharmaz. Ges. 1970, 40, 117
82 M. Meldal, F. I. Auzanneau, O. 134.
Hindsgaul, M. M. Palcic, Chem. 103 A. B. Kantchev, J. R. Parquette,
Commun. 1994, 18491850. Tetrahedron Lett. 1999, 40, 80498053.
83 M. Meldal, F. I. Auzanneau, O. 104 R. Haag, A. Sunder, A. Hebel,
Hindsgaul, M. M. Palcic, Chem. S. Roller, J. Combinational Chem.,
Commun. 1994, 194919850. 2001, in press.
84 P. M. S. Hilaire, M. Meldal, Angew. 105 M. Mutter, E. Bayer, Angew. Chem.
Chem. 2000, 112, 12101228. 1974, 86, 101102.
85 E. Atherton, D. L. J. Clive, R. C. 106 M. Benaglia, R. Annunziata, M.
Sheppard, J. Am. Chem. Soc. 1975, Cinquini, F. Cozzi, S. Ressel, J. Org.
97, 65846585. Chem. 1998, 63, 86288629.
86 G. L. Stahl, R. Walter, C. W. Smith, 107 R. Annunziata, M. Benaglia, M.
J. Am. Chem. Soc. 1979, 101, 5383 Cinquini, F. Cozzi, Chem. Eur. J.
5394. 2000, 6, 133138.
87 C. W. Smith, G. L. Stahl, R. Walter, 108 J. Chang, O. Oyelaran, C. K. Esser,
Pept. Prot. Res. 1979, 13, 109112. G. S. Kath, G. W. King, B. G.
88 M. Kempe, G. Barany, J. Am. Chem. Uhrig, Z. Konteatis, R. M. Kim, K.
Soc. 1996, 118, 70837093. T. Chapman, Tetrahedron Lett. 1999,
89 J. Rademann, M. Grtli, M. Meldal, 40, 44774480.
K. Bock, J. Am. Chem. Soc. 1999, 121, 109 R. Knischka, P. Lutz, A. Sunder, R.
54595466. Mulhaupt, H. Frey, Macromolecules
90 M. Grtli, C. H. Gotfredsen, J. 2000, 33, 315320.
Rademann, J. Buchardt, A. J. 110 N. N. Reed, K. D. Janda, Org. Lett.
Clark, J. . Duus, M. Meldal, J. 2000, 2, 13111313.
Comb. Chem. 2000, 2, 108119. 111 H. Schott, F. Brandstetter, E.
91 J. Rademann, M. Meldanl, K. Bock, Bayer, Makromol. Chem. 1973, 173,
Chem. Eur. J. 1999, 5, 12181225. 247251.
92 M. Renil, M. Meldal, Tetrahedron 112 H. Schott, Angew. Chem. 1973, 85,
Lett. 1996, 37, 61856188. 263264.
93 E. Bayer, G. Jung, I. Halasz, I. 113 H. Schott, F. Brandstetter, E.
Sebastian, Tetrahedron Lett. 1970, Bayer, Makromol. Chem. 1975, 176,
45034505. 21632175.
94 R. T. Pon, K. K. Ogilvie, Tetrahedron 114 J. J. V. Eynde, D. Rutot, Tetrahedron
Lett. 1984, 25, 713716. 1999, 55, 26872694.
95 J. W. Engels, W. Uhlmann, Angew. 115 D. A. Wellings, A. Williams,
Chem. Int. Ed. 1989, 28, 716734. Reactive Polymers 1987, 6, 143157.
116 E. Ranucci, G. Spagnoli, L. 126 R. Breinbauer, E. N. Jacobsen,

Sartore, P. Ferruti, P. Caliceti, O. Angew. Chem. 2000, 112, 3750
Schiavon, F. Veronese, Makromol. 3753.
Chem. Phys. 1994, 195, 34693479. 127 A. Sunder, J. Heinemann, H. Frey,
117 A. G. M. Barrett, S. M. Cramp, R. S. Chem. Eur. J. 2000, 6, 24992505.
Roberts, F. J. Zecri, Org. Lett. 1999, 128 H. Frey, R. Haag, in Encyclopedia of
1, 579582. Materials, Science and Technology.
118 A. G. M. Barrett, S. M. Cramp, R. S. Mulhaupt, R., Kramer, E. (eds),
Roberts, F. J. Zecri, Org. Lett. 2000, Elsevier, New York, 2001.
2, 261264. 129 A. Burgath, A. Sunder, H. Frey,
119 A. G. M. Barrett, S. M. Cramp, R. S. Macromol. Chem. Phys. 2000, 201,
Roberts, F. J. Zecri, Comb. Chem. 782791.
High Throughput Screening 2000, 3, 130 A. Sunder, R. Hanselmann, H.
131133. Frey, R. Mulhaupt, Macromolecules
120 G. R. Newkome, C. N. Mooreeld, 1999, 32, 42404246.
F. Vogtle, Dendrimers and Dendrons: 131 A. Sunder, R. Mulhaupt, R. Haag,
Concepts, Syntheses, Perspectives, Wiley- H. Frey, Macromolecules 2000, 33,
VCH, Weinheim, 2001. 253254.
121 R. M. Kim, M. Manna, S. M. 132 For further information, see:
Hutchins, P. R. Griffin, N. A. www.hyperpolymers.com.
Yates, A. M. Bernick, K. T. 133 R. Haag, J. F. Stumbe, A. Sunder,
Chapman, Proc. Natl. Acad. Sci. USA H. Frey, A. Hebel, Macromolecules
1996, 93, 1001210017. 2000, 33, 81588166.
122 N. J. Hovestad, A. Ford, J. T. B. H. 134 A. Sunder, H. Turk, R. Haag, H.
Jstrzebski, G. v. Koten, J. Org. Chem. Frey, Macromolecules 2000, 33, 7682
2000, 65, 63386344. 7692.
123 S. M. Grayson, M. Jayaraman, J. M. 135 A. Sunder, R. Mulhaupt, R. Haag,
Frechet, Chem. Commun. 1999, H. Frey, Adv. Mater. 2000, 12, 235
13291330. 239.
124 R. Haag, A. Sunder, J.-F. Stumbe, J. 136 C. Schunicht, A. Biffis, G. Wulff,
Am. Chem. Soc. 2000, 122, 29542955. Tetrahedron 2000, 56, 16931699.
125 C. Schlenk, A. W. Kleij, H. Frey, G. 137 For a review see: M. Antonietti,
v. Koten, Angew. Chem. 2000, 112, Angew. Chem. Int. Ed. Engl. 1988, 27,
35873589. 17431747.
59
4
Linkers for Solid-phase Synthesis
Stefan Brase and Stefan Dahmen
4.1
Introduction
Solid-phase organic chemistry is one of the key tools in combinatorial chem-

istry [16] used to synthesize large compound libraries of potential new drugs and
other biologically active compounds, especially in automated synthesis. With the
aid of linkers that are capable of attaching building blocks or intermediates onto
solid support as well as facilitating their ultimate release into solution, the syn-
thetic gap between solid and liquid phase is diminished [710].
Linkers and their associated synthesis strategies, therefore, play a pivotal role in
the successful implementation of solid-phase organic synthesis and its application
to combinatorial chemistry [11].
9 Linker: bifunctional chemical moiety attaching a compound

to a solid support or soluble support which can be cleaved to
release compounds from the support. A careful choice of the
linker allows cleavage to be performed under appropriate
conditions compatible with the stability of the compound and
assay method [12].
In solid-phase synthesis, a starting material is attached reversibly to a linker,

which is bound again directly or over a spacer (Sect. 4.2.2, for example a polyeth-
ylene glycol chain such as that shown in Fig. 4.1) to the actual resin (usually with
divinylbenzene crosslinked polystyrene, see Chapter 3). Anchoring groups for the
use of soluble polymers [MeO-polyethylene glycol (PEG)] are in principle the same
as for the use of insoluble polymers. Therefore, throughout this chapter they will
not be distinguished.
While the group attached to the solid support is in general unchanged upon
cleavage, the anchoring bond to the compound is sensitive to certain conditions,
which then lead to bond breakage and release of the nal compounds. Tradition-
ally, linkers were designed to release one functional group and hence acted more
or less as bulky protecting groups (see Sect. 4.3). Therefore, the release of carbox-

ISBN: 3-527-30509-2
60 4 Linkers for Solid-phase Synthesis
Fig. 4.1. Linker construct.
ylic acids and amines, which are essential for peptide synthesis, has been studied
extensively. However, the synthesis of nonoligomeric compound libraries requires
more versatile linkers (see Sect. 4.5) [13].
A particular linker should resist the entire synthesis sequence without bias to
the diversity or structure of the target compound library and without limiting the
chemical methodology. None of the reaction conditions used for the construction
of the building blocks should lead to a premature cleavage (orthogonality principle;
Sect. 4.3.8). Beyond that, the linker must be cleavable o the resin as mildly as
possible to insure that the product will not be aected.
In this chapter, linker types classied according to their structures, and cleavage
strategies are presented. In general, linkers for all kinds of building blocks (pep-
tides, oligosaccharides, nucleic acids and small molecules) are covered.
4.2
General Linker Structures
4.2.1
Immobilization of Molecules
In general, the anchoring of molecules to a resin can be realized by two dierent

strategies. Direct loading is clearly the most straightforward technique for the
set-up of a solid-phase organic synthesis. A molecule with a reactive or potentially
reactive functional group is coupled directly to the preformed linker. This strategy
is useful if the linker and the building block can be coupled eciently. Coupling
rates greater than 90% are essential at this point. Successful examples are, for in-
stance, the formation of an amide bond, reductive aminations, alkylation reactions
(including Mitsunobu reactions), and olen metathesis. Since the building blocks
can be used without any additional purication step, this method is especially
suitable for the anchoring of libraries of starting materials and/or automated syn-
thesis. The attachment of molecules to a particular resin is strongly dependent on
the nature of the linker and will be discussed for each linker separately. While in
4.2 General Linker Structures 61
Fig. 4.2. The unloaded Knorr linker (2) as a handle.
some cases a simple and rapid mixing of reagents is sucient to drive the attach-
ment to completion, in other cases tedious monitoring is necessary. Additionally,
in some cases the attachment proceeds under similar conditions as the detach-
ment, for example the formation of ketals, where excess reagents are required to
drive the reaction to completion.
In a second general method for attachment, the building block can be coupled
to give the preformed linker in solution. The fragment thus formed, which is
called the handle (see for example Fig. 4.2), can then be activated for attachment
onto the resin using the coupling strategies outlined above. This method requires
an additional step in solution, which can be advantageously used for an increase of
purity. Especially in cases where the activated linker tends to decompose (e.g. silyl
chlorides) or can be formed only in moderate yields and purities, this handle ap-
proach can be favorable. However, in automated synthesis, the required solution-
phase step is clearly a drawback.
4.2.2
Spacers
The linker either can be attached directly to the resin or can be located further
from the polymeric backbone using spacers. These bifunctional constructs either
can be built sequentially or can be attached via a handle approach. The spacer acts
as a connection to give the building block more mobility and hence the kinetics for
a given reaction are superior to the corresponding resin without spacers [14]. Fur-
thermore, larger spacers considerably change the physical properties, such as
swelling behaviors. This has been demonstrated with Tentagel resin [15]. However,
one must take into account both that the use of spacers requires an additional
synthetic step usually connected with a decrease of loading capacity and that the
spacer has to be as robust as the linker toward the reaction conditions performed
on the bead; Tentagel resin, in particular, leads to bleeding.
For the characterization of compounds attached to a polymeric support by nu-
clear magnetic resonance (NMR) spectroscopy, however, long spacers are an ad-
vantage, because they increase the mobility of the substrate and reduce the line
broadening usually observed in NMR spectra of polymers.
In most cases, a clear distinction between linker and spacer is not easy. The
linker is the minimal part of the resin required for the functional cleavage (for the
silyl linkers this is the silyl group, for the trityl linkers this is the triphenylmethyl
moiety, for the triazene linker this is the 1-aryltriazenyl group, and so on).
The spacer therefore is the part between the linker and the resin as depicted in
Fig. 4.1 and described in Chapter 3 of this book.
4.2.3
Functionalized Linkers as Analytical Constructs
Functionalized spacers or linkers can play an important role for the determination
of loading and reaction conversion. The NMR-active uorinated linkers are espe-
cially suitable in this regard [16].
4.3
Linker Families
Usually, linkers are categorized according to the kind of functional group or sub-
strate class they are able to selectively immobilize (linkers for carboxylic acids,
alcohols, amines, and so on). As there are various types of linkers available for
solid-phase synthesis, many of them belong to certain well-established classes of
protecting groups (Table 4.1) and therefore can be grouped into families. The
members of each family have certain reactivity patterns in common.
While a linker presents the chemical structure essential for the loading and
cleavage of a particular functional group, a linker system provides the whole pro-
tocol for the attachment to and cleavage from the resin.
However, because of an increased demand for the exible anchoring of mole-
cules, other families of linkers such as sulfur linkers, triazenes linkers, among
others, have emerged. Nevertheless, the largest number of linkers developed so far
are based on benzylic-type groups.
Tab. 4.1. Common protecting groups and the analogous linker families.
Protecting group in Functional group Linkers or linker families

liquid phase protected
Benzyl Alcohols, esters Benzyl-type linkers: Sect. 4.3.1,

Table 4.2
Allyl Amines Allyl-type linkers: Sect. 4.3.2
Cbz (Z) Amines Carbamate-based linkers: Sect.
4.3.4 [17]
Alloc Amines Allyl-type linkers: Sect. 4.3.2
Boc Alcohols Boc-type linker [18]
Silyl ether Alcohols Silyl-type linkers: Table 4.6. [19,
20]
Alkyl ester Carboxylic esters Sect. 4.3.4
SEM (trimethylsilylethoxymethyl) Alcohols SEM linker (99) [21]
4.3.1
Benzyl-type Linkers Including Trityl and Benzhydryl Linkers
Benzyl-type linkers are the most common anchoring groups for various kinds of
functionalities. In particular, esters, amides, amines, alcohols, and thiols can be
immobilized by this linker family.
As the pioneering works of Merrield [22] and Wang [23] are based on this
linker type, they represent the starting point of modern linker development. Ben-
zylic linkers are typically cleaved by strong acids (e.g. triuoroacetic acid, TFA),
which causes a protonation and subsequent elimination. A nucleophilic scavenger
usually quenches the resonance-stabilized cation thus formed. An increase of acid
lability can thus be achieved by stabilization of this intermediate by, for example, o-
and p-substitution of methoxy groups onto the ring [24]. This has been demon-
strated in the development of the SASRIN resin (11; super acid-sensitive resin: 1%
TFA cleavable) [25, 26] with one additional alkoxy group related to the Wang resin
and the HAL linker (13; hypersensitive acid labile: 0.1% TFA cleavable) [27] having
two additional alkoxy groups. In addition, benzyl-type linkers might be cleaved by
ammonolysis [28], light (Sect. 4.4.3; see Table 4.15), metal salts [29] (see Scheme
4.8), and oxidation reagents (e.g. Wang resin with H2 O2 [30] or dichlorodicyano-
benzoquinone (DDQ) [31]). The introduction of nitro groups onto benzyl-type
linkers leads to photolabile systems (see Sect. 4.4.3).
The prototype of a functional group with an appropriate breakable bond is the
Wang resin (6), which contains a 4-hydroxybenzyl alcohol linker moiety. The ben-
zyl alcohol hydroxyl group can be functionalized using either electrophilic or nu-
cleophilic substrates (Scheme 4.1) to give a benzylic linkage. It is very stable in a
whole set of reactions, but can be cleaved by acids such as triuoroacetic acid or
HF. Acids, alcohols, esters, and amides can be obtained as products after cleavage.
Scheme 4.1. Loading of the Wang resin (6). DEAD, diethyl

azodicarboxylate. DMAP, 4-dimethylaminopyridine.
The Rink resin is particularly useful for the attachment of various functionalities
such as primary amines (see for example [82]; Scheme 4.2) and is commercially
available from various sources. The loading can be achieved via the Rink chloride
(29) or triate (30) (Table 4.2).
A linker that is particularly suitable for peptide amides and cyclopeptides is the
PAL linker and the backbone amide linker (BAL) concept [83] (Scheme 4.3).
Scheme 4.2. The Rink resin as a linker for primary amines according to Garigipati [82].
Scheme 4.3. Backbone amide linkage using the PAL linker by

Barany and coworkers [83]. Pg, Protecting Group.
Trityl resins (3843) (Table 4.2) are especially suitable for the immobilization of
nucleophilic substrates such as acids, alcohols, thiols, and amines. They are quite
acid sensitive and can be cleaved with acetic acid, for example; this feature is use-
ful in cases where acid-labile protecting groups are used. The stability of trityl
resin can be tailored using substituted arene rings, as demonstrated with the
chlorotrityl resin, which furnishes a more stable linker than the trityl resin itself.
Furthermore, the steric hindrance prohibits the formation of diketopiperazines
during the synthesis of peptides. The orthogonality towards allyl-based protective
groups was demonstrated in the reverse solid-phase peptide synthesis of oligopep-
tides [84] (Scheme 4.4).
Scheme 4.4. Reverse (N ! C) directed solid-phase peptide

synthesis with the 2-chlorotrityl resin according to Thieriet et al.
[84].
Tab. 4.2. Structures and properties of benzyl-type linkers including trityl and benzhydryl linkers (excluding
photolabile linkers: see Sect. 4.4.3, Table 4.15).
Generic name of the resin Structure Cleavage Comments
Merrield resin (X Cl: 3) HF Standard resin

[22]; AM PS (Aminomethyl
polystyrene) (X NH2 : 4);
hydroxymethyl polystyrene
(X OH: 5)
Wang linker (X OH: 6) [23], Cleavage for thiols: Standard resin;
Boba resin (X NH2 : 7) [32] HF [33]; for esters: very robust; for
CF3 SO3 H [34]; 95% Boc strategy
TFA [23]; H2 O2 [30]
PAM (8) ( phenylacetamido- Cleavage for esters: Very robust
methyl) [3537] 90% HF, anisole
[35]; stable in 50%
TFA, CH2 Cl2 [35]
HMPA (9) (hydroxymethyl- Cleavage for esters:
phenoxyacetic acid) [38] 95% TFA [28, 39];
20% TFA, CH2 Cl2
(incomplete) [40]
HMPP (10) (hydroxymethyl- Cleavage for esters:
phenoxypropionic acid) [40] 20% TFA, CH2 Cl2
[40]
SASRIN (11) (super acid- Cleavage for esters: Very sensitive

sensitive resin) [25] 1% TFA, CH2 Cl2 ,
20 C, 5 min [25]
R Me: AMEBA (12) (acid- Precursor of the
sensitive methoxy- SASRIN linker
benzaldehyde) [41, 42]; (R Me)
MALDRE (a-methoxybenz-
aldehyde resin) [43]; [44];
R H: AHB linker [45]
HAL (13) (hypersensitive Cleavage for esters: Very sensitive
acid labile) [27] 0.1% TFA (CH2 Cl2 ),
25 C, 1 h
PAL (peptide amide linker) Cleavage for amides:

(14) [46, 47] TFA [48]; TFA or HF
[49] (quinoxalinone)
BAL (backbone amide linker) Cleavage for esters:

(15) [50] [14]
Tab. 4.2. (continued)
Extended HAL linker (16) [51] Cleavage for amides:

25% TFA, CH2 Cl2
[51]
Ramage linker (17) [52, 53] Cleavage for esters:

nBu 4 NF
HMB (18) (Sheppard) [28] Cleavage for amides:

NH3 [28]
19 [54] Cleavage for amides:

20% TFA, CH2 Cl2
[54]
SAL linker (20) [55] Cleavage for amides:

(silyl amide linker) 90% TFA, scavenger
[55]
SAC linker (21) [56] Cleavage for acids:

(silyl acid linker) TBAF [56]
BHA (22) [57] (benzylhydryl Starting resin for

amin) various linkers
MBHA (23) (methylbenzyl- Cleavage for amides:

hydryl amin) [58] HF; CF3 SO3 H [58],
HF/PhOMe (sec.
amide) [59]
MAMP linker (24) (Merrield, Cleavage for amides:

a-methoxybenzyl) [60, 61] TFA/CH2 Cl2 /H2 O
(9:90:1) [60]
p-Acyloxy BHA (25) [62] Cleavage for amides:

HF, cresol (9:1) [62,
63]
SCAL (26) (safety-catch acid- Cleavage for amides:

sensitive linker) (Sect. 4.5.1) TFA/(EtO)2 (PS)SH
[64] (cf. [65]) [64]; Me3 SiBr/
PhSMe/TFA [64]
Rink acid (X OH: 27); Rink Cleavage for esters: Widely used
amide (X NH2 : 28) [66, 67]; 10% AcOH, CH2 Cl2 , anchor for
Rink chloride (X Cl: 29); 20 C, 1.5 h; 1% TFA amines
Rink triate (X OTf: 30) [66]; cleavage for
amides: TFA [66];
20% TFA, CH2 Cl2
[68]
Rink amide AM (31) (RAM) Similar to the
(rink amide aminomethyl) Rink resin above
32 [69, 67] Cleavage for esters:

TBAF or Cs2 CO3 [69]
Sieber XAN (33) [7072] Cleavage for amides:

[70]
2-XAL (34), 3-XAL (35) (xanthyl Cleavage for amides:

acid-labile linker) TFA [71]
CHA (36), CHE (37) Cleavage for amides: More sensitive

(dibenzo[a,d]cyclohepta(e)ne) 10% TFA, CH2 Cl2 than Rink or
[73] [73] PAL [73]
Trityl (38) [74, 75] Cleavage for esters: 1% Quite unstable

TFA/AcOH [76, 77] for esters
2-Chlorotrityl (39) Cleavage for esters: Increased stability

(CF3 )2 CHOH (HFIP) compared to trityl
(20%), CH2 Cl2 [48]; linker
AcOH/CF3 CH2 OH/
CH2 Cl2
4-Methyltrityl (40) Cleavage for esters: Increased stability

AcOH/CF3 CH2 OH/ compared to
CH2 Cl2 (1:1:8) 2-chlorotrityl
linker
4-Methoxytrityl (41) Cleavage for esters: Increased stability

AcOH/CF3 CH2 OH/ compared to
CH2 Cl2 [78] 4-methyltrityl
linker
4-Fluoro(chloro)-tritylcarboxyl Cleavage for esters:

linker (42) 0.1% TFA [79],
AcOH/CF3 CH2 OH/
CH2 Cl2 (1:1:8)
4-Cyanotrityl (43) Cleavage for esters: [80]
(44) [81] Cleavage for esters: TFA

[81]
Besides benzyl-type linkers, other arylmethyl moieties can serve as linkers. Re-
cently, a new backbone amide linker has also been devised using indole chemistry
[85] (Scheme 4.5).
Scheme 4.5. The indole linker according to Estep et al. [85].
4.3.2
Allyl-based Linkers
A second, to the benzyl linkers related class is the family of the allyl-based linkers
(Table 4.3). They have been used for the attachment of carboxylic acids, which can
Tab. 4.3. Overview of allylic linkers.
Structure Reference
[86]
[86]
[90, 91, 98]
[93]
[94]
be detached using metal catalysis. The advantages of linker cleavage under palla-
dium catalysis are the mild reaction conditions and the orthogonality (Sect. 4.3.8)
to various protecting groups. Kunz et al. [86, 87] developed the rst and simplest
linker to use the p-allyl detachment strategy. Starting from 2-bromocrotonic acid,
attachment to an amino group on a resin and further reaction with the cesium salt
of an appropriate protected amino acid or peptidic structure yields the HYCRAM
(hydroxycrotonylamide) resin [88]. The allylic cleavage proceeds with Pd(PPh3 )4
and morpholine or hydroxybenzotriazole [89]. The readily available (hydroxycrotyl-
oligoethyleneglycol-n-alkanoyl) HYCRON linker [9092] is based on a similar con-
cept; however, in this case, a handle comprising an amino acid and a preformed
linker has been used to minimize the risk of racemization upon cleavage. A higher
stability towards unwanted nucleophilic cleavage was achieved than that observed
with the HYCRAM linker. The incorporation of b-alanine facilitates easier moni-
toring of the reaction. Several other similar constructs have been used for compa-
rable purposes [9396]. Recently, the semisynthesis of vancomycin on solid sup-
port was accomplished using an allylic linker [97].
An example for the use of the allyl linkers has been provided in the synthesis of
peptide nucleic acids (PNAs) [91] (Scheme 4.6).
Scheme 4.6. Synthesis of PNAs using the HYCRON linker according to Seitz [91].
4.3.3
Ketal/acetal-based Linkers
Ketals and their corresponding sulfur analogs are well-established protecting

groups in solution-phase synthesis. However, only a few constructs have been used
in solid-phase organic synthesis (SPOS) as linkers (Table 4.4).
The most versatile ketal linker is the tetrahydropyranyl THP linker developed by
Thompson and Ellman [99]. This linker allows the attachment of alcohols, phe-
nols, and nitrogen functionalities in the presence of pyridinium toluene sulfonate.
Both the loading and the detachment proceed under acidic conditions. Similarly,
other acetal linkers have also been used for the attachment of alcohols [100, 106].
All these linkers are stable toward bases and organometallic reagents. However, a
drawback is certainly the formation of diastereomers as a result of the chirality of
these linkers.
Tab. 4.4. Overview of acetal/ketal-based linkers.
Structure Reference Comments
THP resin [99] Most common linker for alcohols
[100] New linker for alcohols
[101104] Common linker for ketones and aldehydes
[105] Linker for sterically hindered ketones

An example of the synthesis of complex molecules using THP-type linkers was

provided by Chen and Janda [107] in their synthesis of prostaglandins on non-
crosslinked polystyrene (Scheme 4.7). Further successful examples demonstrate
the generality of the THP ketal-type linkers [108114].
Scheme 4.7. Prostaglandin synthesis on solid phase according

to Chen and Janda [107]. TBS, tert-butyldimethylsilyl.
Another class of linkers incorporating a ketal moiety are the Lezno diol-linked
aldehydes [101, 102] and ketones [103, 104]. A similar linker using dithianes is
also suitable for ketones [105] (Sect. 4.3.7.1).
4.3.4
Ester-, Amide-, and Carbamate-based Linkers
Ester and amide moieties are, apart from being used in the benzyl and allyl linker
types, also suitable for attachment. Various examples have demonstrated the use-
ful applications of these functional groups (Table 4.5). Basically, two dierent
strategies can be used (Fig. 4.3). For example, May et al. [115] recently introduced
thioesters as linkers for alcohols, ketones, and lactones.
Fig. 4.3. Ester linkers: general structures.

Tab. 4.5. Overview of some ester- and amide-based linkers (see also Table 4.16).
Structure Reference Possible structures achievable
e.g. [116] Esters: cleavage with methoxide;

alcohols: cleavage by Grignard
reagents [117]
Alcohols: cleavage with methoxide
[118] Alcohols: cleavage with enzymes
[115] Ketones, amides: cleavage with

reducing reagents
[17] Amines: cleavage with Pd(OAc)2 ,

H2 (45 psi), DMF, rt, 16 h
[119] Amides, esters: cleavage with

Cu(II) salts
[120] Methyl arenes: cleavage under

photolytic conditions
Benzyl carbamates are also useful linkers for the synthesis of amines since they
are readily cleavable by palladium salts [17] (Scheme 4.8).
Carboxylic esters have been released by the action of alkoxides on ester resins. In
most cases, the cleavage has been performed using methoxide in methanol (e.g.
[116]; Scheme 4.9). Drawbacks to this method are the need to remove excess metal
salts and/or the aqueous work-up. Alternatively, after cleavage from solid support,
postsynthesis of methyl esters with diazomethane is also possible [121] (Scheme
4.10).
Scheme 4.8. Detachment of peptides from polymeric benzyl-type protecting groups [17].
Scheme 4.9. The use of esters as linkers for benzoic acid derivative by Kondo et al. [116].
Scheme 4.10. Synthesis of macrocycles by Soucy et al. [121].
Arylhydrazides can serve as safety-catch linkers for C-terminal carboxylic

acid, amide, or ester functionalities. The cleavage proceeds via an oxidation with
copper(II) and subsequent cleavage of the diazenyl moiety by means of a nucleo-
phile (Scheme 4.11) [119].
Scheme 4.11. Detachment of peptides from hydrazide resins by Millington et al. [119].
4.3.5
Silyl Linkers
The electronic and steric properties of silicon compounds have been used in many
applications for the design and use of new linker types (Table 4.6).
The dierent applications can be divided as follows:
1 Direct attachment of building blocks on silylated resins: linker for alcohols [19,
20], traceless linkers for arenes (Sect. 4.5.5).
2 Use of the b-silicon eect for elimination reactions: e.g. the SEM (2-trimethylsi-
lylethoxymethyl) linker [21].
3 Silylated benzhydryl linkers: [69, 122].
Tab. 4.6. Overview of silyl linkers.
[123] Alcohols; cleavage with

(Tetrabutylammonium
uoride) TBAF
[21] Alcohols
[124] Traceless linking of arenes

(Scheme 4.60)
[127129] Traceless linking of arenes;

cleavage with uoride
[55] Amides; cleavage with 90% TFA,

scavenger
[56] Acids; cleavage by TBAF [56]
[122] Carboxylic acids; cleavage with

TBAF
[52, 53] Carboxylic acids; cleavage with

TBAF
[21] Alcohols; cleavage with TBAF
[67, 69] Estes; cleavage with TBAF or

Cs2 CO3 [69]
The robustness of silicon linkers against basic and organometallic reagents

makes them especially suitable for solid-phase organic synthesis. Cleavage can be
aected by electrophiles such as protons (triuoroacetic acid; TFA). A special fea-
ture of silyl linkers is their sensitivity to uoride ions, which makes them ideally
orthogonal (Sect. 4.3.8) to various other functionalities present in the molecule.
The ne-tuning of electronic and steric properties is possible by using dierent
substituents on the silicon atom (trimethylsilyl vs. tert-butyldimethylsilyl).
The rst traceless linkers (Sect. 4.5.5) for arenes were described independently
by Ellman and coworkers [125, 130] and Chenera et al. [124] (see Scheme 4.60) in
the 1990s using silyl linkers. This linker type was used in Ellmans synthesis of a
benzodiazepine library, which is a milestone in the solid-phase synthesis of small
organic molecules (Scheme 4.12). The synthesis of the linker involves a lithium
halogen exchange and, after chlorosilane attachment, coupling with an aryl halide.
As the silyl arene might be cleaved in the unwanted direction to give silylated
arenes, further improvement led to the development of a germanium linker [131],
which gives rise to the formation of pure material (Sect. 4.5.5, see Scheme 4.61).
In addition, cleavage of these linkers can be accomplished by electrophiles other
than protons to yield halogenated residues, thus rendering this linker into a mul-
tiple cleavage linker system [see 379] (Sect. 4.5.6). The range of electrophiles is
limited, since only small, reactive electrophiles (e.g. iodine, bromine, and chlorine)
react to give the desired products.
Scheme 4.12. Synthesis of a benzodiazepine library using silyl linker [131].
The silicon-based linkers, which are commercially available [132], were devel-
oped further by several groups [133] and have been used in the synthesis of vari-
ous systems for the traceless detachment of various arenes and heteroarenes [126
128, 133143]. They are also suitable as traceless linkers for allyl silanes to give
alkenes [144] (Sect. 4.5.5).
A recent traceless application was demonstrated in the synthesis of chrome-
nones (104) [145]. In this case, a mild cyclization method was used to circumvent
a premature cleavage for the support (Scheme 4.13). Similarly, heteroarenes are
also accessible [128] (Scheme 4.14).
Other linkers having silyl fragments are the silyl acid linker (SAC linker 21)
[56], the silyl amide linker (SAL linker 20) [55], the Pbs linker (silico Wang
linker) (98) [122], the Ramage silyl linker (15) [52], the SEM linker (99) [21], and
silylated benzhydryl linkers (32) [69].
Scheme 4.13. Silicon linker for the synthesis of chromenones

104 by Harikrishnan and Showalter [145].
Scheme 4.14. Synthesis of oligo 3-arylthiophenes 107 by Briehn et al. [128].
4.3.6
Boronate Linkers
Boronates have been used in various linker types either as linkers for diols [146] or
as precursors for metal-mediated cleavage (Table 4.7).
A boronic acid ester, which contains an aryl iodide moiety attached by an ap-
propriate tether, can act as an intramolecular arylation agent. Thus, Li and Bur-
gess [148] developed a polymer-bound precursor, the ensuing cleavage of which
furnished a macrocyclic constrained b-turn peptide mimic via biaryl coupling
(Scheme 4.15).
Tab. 4.7. Overview of boronate linkers.
[147] Arenes; cleavage by Ag
[148] Biaryls by Suzuki crosscoupling
[146] Diols
Scheme 4.15. Intramolecular cleavage Suzuki coupling by Li and Burgess [148].
Immobilized aryl boronic esters (113) can be cleaved to the corresponding

hydrogen-substituted products (115) (traceless cleavage, Sect. 4.5.5) using aqueous
silver nitrate solution [147] (Scheme 4.16).
Scheme 4.16. Traceless cleavage of boronic acid derivatives according to Pourbaix et al. [147].
4.3.7
Sulfur, Stannane- and Selenium-based Linkers
A set of modern linkers (Table 4.8) based on sulfur, stannane, and selenium chem-
istry can be found in the literature. Their popularity obviously stems from the fact
that these elements can favorably be tailored for use as fragile points of attach-
ment.
4.3.7.1 Sulfur-based Linkers

Sulfur has been used in linkers as thioethers, sulfoxides, sulfones, sulfonic acids,
and their corresponding derivatives. The relatively weak carbonsulfur bond can
be cleaved under reductive conditions (see Scheme 4.62) [155, 156], photolytic
conditions, or in the presence of strong bases [160]. Since thiols can be oxidized to
the corresponding sulfoxides and/or sulfones, various safety-catch linkers [155,
156] (Sect. 4.5.1) have beneted from this fact.
Tab. 4.8. Overview of sulfur, stannane and selenium linkers.
[149] (Scheme 4.42) Amides
[150] (Scheme 4.43) Carboxylic acids
[151] (Scheme 4.20) Amines
[115] Ketones, amides; cleavage with

reducing reagents
[105] Linker for sterically hindered

ketones
[152, 153] a) R Aryl: Arenes (Scheme

4.17); cleavage with
palladium/formate; b)
R a-carbonylalkyl:
heterocycles
[154] Diaryl methanes (Scheme
4.18); cleavage with
alkylation/Suzuki coupling
[155159] Alkanes (Scheme 4.62);

cleavage with Na/Hg
[160] Benzofurans (Scheme 4.56);

cleavage with bases
[161] Methylarenes; photolytic

cleavage
[162] Methylarenes; cleavage under

photolysis
[120] Methylarenes; photolytic

cleavage
[163] Alkenes (Scheme 4.35,

Scheme 4.36); cleavage with
oxidants
[164, 165] Alkanes, alkenes
Aryl sulfonates can be used as linkers for arenes, as shown by Jin et al. [152].
These can be cleaved under reducing conditions to give the corresponding hydro-
carbons (130). In addition, this linker might be suitable as a multifunctional an-
chor, as proposed in a patent [166] (Scheme 4.17).
Scheme 4.17. Cleavage-hydrogenation reaction with a sulfonate

linker (129) according to Jin et al. [152].
Arylmethyl(homobenzyl)ethylsulfonium salts are also appropriate substrates for

Suzuki-type coupling reactions. In this reaction performed on a polymer-bound
sulfonium tetrauoroborate, the benzyl fragment on the sulfur is transferred to
the boronic acid residue. The sulfonium salt was prepared from an alkylthiol resin
by alkylation with a substituted benzyl halide to give thioether (131) and subse-
quent alkylation with triethyloxonium tetrauoroborate. Reaction with a boronic
acid derivative yielded a diaryl methane (132) [154] (Scheme 4.18).
The cleavage of sulfonamides on substituted thiophenes deposited on platinum
electrodes can be conducted by an electrochemical cleaving step [167] (Scheme
4.19).
Scheme 4.18. Cleavage Suzuki coupling approach using sulfonium salts by Vanier et al. [154].
Scheme 4.19. The use of an electrocleavable anchoring by Marchand et al. [167].
Photolabile sulfur linkers are based either on the relatively weak carbonsulfur
bond in thioethers [161] or on the photolytic decarboxylation of thiohydroxamic
acids to give methylindoles [120]. Also, a safety-catch linker (Sect. 4.5.1) for amines
is based on 2-(thiobenzyl)ethylcarbamates [151, 168]. The linkage is performed
with preformed handles containing ethenyloxycarbonyl-protected amines (138).
Attachment to thiomethylated polystyrene (139) was performed under conditions
involving radicals. The cleavage was carried out with an oxidizing agent, which
forms the retro-Michael substrate [151] (Scheme 4.20).
The utility of a thioacetal-based anchor (68) as a chemically robust linker for
the immobilization of ketones employed the commercially available (G)-alpha-
lipoic acid. The products were easily cleaved from solid support by treatment with
[bis(triuoroacetoxy)iodo]-benzene [105] (Table 4.4).
Recently, Nicolaou et al. [153] have shown that the reaction of alkenes in the
presence of dimethyldioxirane could be used for loading onto polystyrene sulfonic
acid resin. Subsequent cleavage with nucleophiles proceeded smoothly to give a
vast array of heterocycles.
Scheme 4.20. Thiobenzylethylcarbamates as linkers for amines

according to Timar and Gallagher [151]. AIBN, Azobis-
isobutyronitrile.
4.3.7.2 Stannane-based Linkers

Stannanes have become prominent members in the area of multifunctional an-
choring groups. A polymer-bound tin hydride (142) has been used to hydrostanny-
late alkynes under palladium catalysis to give polymer-bound alkenylstannanes
(143). Alternatively, the latter can be prepared from a polymer-bound tin chloride
and an alkenyl lithium or magnesium halide reagent [163] (Scheme 4.21). These
alkenyl stannanes were employed in intermolecular [169] as well intramolecular
Stille reactions. Alkenylstannanes can also undergo protonation to give alkenes
(145) in a traceless fashion (Sect. 4.5.5). Therefore, this linker is able to operate in
a multifunctional mode (see Fig. 4.5) (Sect. 4.5.6).
Scheme 4.21. The stannane linker for Stille reactions according to Nicolaou et al. [163].
4.3.7.3 Selenium-based Linkers

The seleniumcarbon bond is, because of its weakness (E 217 kJ mol1 ), prone
to undergo homolytic cleavage, thus producing radicals. This fact was rst recog-
nized and used for solid-phase synthesis by Michels et al. in 1976 [170]. More re-
cently, Nicolaou et al. [164] and Ruhland et al. [165] independently developed
more ecient methods for the preparation of selenium-containing supports in

their development of traceless linkers (Sect. 4.5.5). Starting from polystyrene, vari-
ous steps including selenation with selenium powder or MeSeSeMe give rise to
the formation of selenium resins, which can then be alkylated to give selenoethers
(148). The traceless cleavage that yields alkanes (149) can be conducted by reduc-
tion with tributyltin hydride, while the formation of alkenes (150) can be observed
after mild oxidation (Scheme 4.22). This linker holds promise for numerous ap-
plicability since the starting materials (alkenes, alkyl halides) are readily available,
although the toxicity of the reagents and starting materials has to be considered.
Scheme 4.22. The selenium linker for alkanes and alkenes

according to Nicolaou et al. [164]. TBDPS, tert-butyldiphenyl-
silyl.
Based on a similar concept, a selenium linker has been described that is loaded
via a preformed handle [171]. Oxidation and thermal elimination give rise to the
formation of alkenes (153) (Scheme 4.23). Interestingly, the selenoxides (152) de-
compose at room temperature, whereby the corresponding sulfoxides fragment at
100 C.
Scheme 4.23. The selenium linker according to Russell et al. [171].
The selenium bromide linker (154) (Scheme 4.24) is also the starting point for a
library of natural products and analogs of the benzopyran type through reaction of
prenylphenols [172174] (Scheme 4.24). Furthermore, this linker enables the syn-
thesis of medicinally interesting molecules [175].
Besides phenols, allyl anilines can be used in this sequence to produce indo-
lines. Depending on the substitution pattern, either traceless (! 162) (Sect. 4.5.5)
Scheme 4.24. The selenium linker in chromene synthesis according to Nicolaou et al. [172].
or cyclative (! 160) cleavage can be realized [176] (Scheme 4.25). The seleno
linker has also been used in the synthesis of 2-deoxy glycosides, orthoesters, and
allyl orthoesters [177]. Finally, the SEM linker for the attachment and detachment
of alcohols takes advantage of the substitution of phenylselenyl groups at seleno
acetal resins [21].
Scheme 4.25. The selenium linker in the indoline synthesis by Nicolaou et al. [176].
4.3.8
Triazene-based Linkers
Inspired by the use of triazenes in the total synthesis of vancomycin [178] and the
pioneering work of Moore and coworkers [179, 180] and Tour and coworkers [181]
in the synthesis of triazenes on a solid support and the nal detachment to give
iodoarenes (180-I), a whole set of triazene-based linkers (Table 4.9) has been de-
veloped [182].
The chemistry of diazonium salts provides tremendous opportunities for the
construction of a wide range of aromatic compounds. Triazenes, which have been
used as traceless linkers for arenes as shown in Sect. 4.5.5, provide both interest-
ing new possibilities for activation of the ortho-position of the arenes and are ideal
synthons for diazonium salts. Triazenes are stable toward light, moisture, and
bases; however, they are cleaved by Brnsted acids and certain Lewis acids to give
diazonium salts and amines.
Tab. 4.9. Overview of triazene linkers.
Structure Possible structures achievable
Iodoarenes [179]
T1 resin: traceless linker [182185]; synthesis

of phenols [186], biaryls, alkyl arenes [187,
188], azides [189], aromatic hydrazines, halides
[190, cf. 180, 181], ester, azo compounds,
cinnolines [191], benzotriazoles [192]
As above
T2 resin: synthesis of substituted amines [193],

amides (peptides) [194], (thio)ureas [194, 195],
hydrazines, alcohols, esters [183, 196, 197],
guanidines [195], alkyl halides [183, 196, 197],
sulfoximines
T2 resin: as above [198]; scavenger for amines
and phenols
Two linkers based on triazene chemistry have been developed. While the T1
linker system consists of 3,3-dialkyl-1-aryl triazene bound to a support via the alkyl
chain (Scheme 4.26), the T2 linker family is based on immobilized aryl diazonium
salts.
Scheme 4.26. Concept of the T1 linker [183].

The triazene T1 linker has been successfully used as a linker for arenes (see
also Sect. 4.5.5). Until now, approximately 100 dierent anilines (168) have been
immobilized. Functionalization on the bead has been demonstrated extensively.
These immobilized diazonium derivatives are stable towards various reaction con-
ditions, such as alkyl lithium reagents, reducing agents, and oxidizing reagents.
However, acids cleave the triazenes to give the amine resin (170) and the modied
aryl diazonium salts (173).
The latter can be transformed into various dierent products giving modied
arenes in high yields and purities [purities > 9095% according to gas chroma-
tography (GC), NMR, and high-performance liquid chromatography (HPLC)] di-
rectly at the cleavage step [183] (Scheme 4.27).
Scheme 4.27. Possibilities of the T1 triazene linker [183].
The diazonium salts, for example, can be reduced to the hydrocarbon (180-H) in
THF with the aid of ultrasound [182]. The latter facilitates this reduction due to a
radical pathway. A new reagent for this reduction was found to be trichlorosilane
[184]. This is not only a source of traces of hydrochloric acid, which cleaves the
triazene moiety, but, as a hydride donor, it is also able to reduce diazonium ions
cleanly (Scheme 4.27 and see Scheme 4.64).
As already shown by Moore and coworkers [180] and Tour and coworkers [181],
addition of methyl iodide to a triazene resin at elevated temperature (110 C) gives
rise to aryliodides (180-I) (Nu I) in excellent yields. Furthermore, aryl halides
(180-X) (X Cl, Br, I) are readily available by the action of lithium halides in the
presence of an acidic ion exchange resin or with the corresponding trimethylsilyl
halide at room temperature [190]. A mixture of acetic anhydride and acetic acid
produces phenol acetates (180-OAc) [186]. Although quite exible in the range of
possible electrophiles that may be employed, the most striking feature was the de-
velopment of a cleavage cross-coupling strategy [187]. Starting from modied tri-
azene resins, a one-pot cleavage cross-coupling reaction was conducted with two
equivalents of triuoroacetic acid in MeOH at 0 C to give a diazonium ion. In situ
coupling with various alkenes (182) in the presence of catalytic amounts (5 mol%)
palladium(II) acetate furnished the corresponding products (183) in excellent yield
and purities. Using palladium on charcoal as the catalyst has the advantage of de-
creasing palladium contamination, as well as providing a subsequent hydrogena-
tion option [187]. Multicomponent Heck reactions (domino Heck DielsAlder re-
action) are possible in this context and lead to further diversication [187]. In the
examples above, the diazonium group, upon cleavage from the resin, is lost as
dinitrogen. However, a suitable nucleophilic ortho-substituent favors cyclization
to give heterocyclic structures. Benzotriazoles, for example, are accessible from
o-aminoaryl-substituted triazenes [192]. Other heterocyclic systems such as cin-
nolines (178) are available by a cleavage Richter reaction strategy, which starts from
o-alkynylaryl triazenes. Cleavage was conducted with aqueous hydrogen chloride
or hydrogen bromide in acetone or dioxane at room temperature to produce vari-
ous cinnolines (178) in a library format with up to 95% yield and with a range of
purities between 60% and 95% [191]. In addition to these methods, reduction
of diazonium salts gives rise to the formation of hydrazines (177) [199], which are
important building blocks for the synthesis of other heterocyclic compounds.
Whereas the T1 linker involves the immobilization of a diazonium salt on an
amine resin, the T2 linker represents the reverse of this concept. Thus, an immo-
bilized diazonium salt (190) was prepared from Merrield resin (3) in two steps,
and subsequent additions of primary and secondary amines generated triazenes
(191). In addition, attachment of hydroxylamines, hydrazines, sulfoximines, and
phenols (to give azo coupling products) proceeds equally well (Scheme 4.28).
Secondary amines can be cleaved directly [193] or after modication from the
resin. Primary amines can be derivatized on the free NaH functionality and can
therefore be modied to an array of products [194, 195, 198]. Thus, ureas (198)
[194], thioureas (197) [195], guanidines (196) [195], and carboxamides (199) [194]
were prepared in excellent yields (Scheme 4.29).
While the cleavage of trisubstituted triazenes gives rise to the formation of sec-
ondary amines in excellent yields [193], the cleavage of disubstituted triazene (194)
gives rise to aliphatic diazonium salts [183, 196, 197]. The diazonium ion thus
formed undergoes substitution with the nucleophile present in the reaction mix-
Scheme 4.28. Synthesis of the T2 linker [193].
Scheme 4.29. Possibilities with the T2 linker [183].
ture. Therefore, alkyl halides (202), alcohols (201-OH), and alkyl esters (201-
OCOR) can be formed by cleavage with trimethylsilyl halides (X I, Br, Cl) or
carboxylic acids (X for example OAc, OTfa) [200] [183, 196, 197]. The regio-
selectivity of the cleavage can be explained by the presence of one tautomer of the
triazene in which the hydrogen atom is next to the arene ring. Overall, this reac-
tion sequence provides a substitution of an amino group with oxygen or a halogen
(Cl, Br, I).
Various immobilized diazonium salts have been prepared [201], thermo-analyti-
cally characterized [202], and used for the linkage of nucleophiles. The structure of
the salts clearly inuences the stability of the diazonium moiety. The thermally
Tab. 4.10. Orthogonality of linker families.a
Cleavage reagents Benzyl- Ketal/ Esters/ Silyl Triazene Selenium/

type acetal amide linkers linkers sulfur/
linkers linkers linkers stannyl
linkers
Electrophiles
Nucleophiles 0 0 0 0 0
Fluoride 0 0 0 0 0
hn () 0 0 0 0
Oxidative conditions 0 0 0 0 0/
Reductive conditions 0 0 0 0/
a (): specially designed linker; : cleavage; : partial cleavage;
0: no cleavage.
stable diazonium ion (194a) (Z Cl, Y CH2 O) [t1=2 (25 C) > 100 days] is also
capable of scavenging various nucleophiles (amines, phenols, and anilines) [198].
4.3.9
Orthogonality Between Linkers
The orthogonality of linkers is important for the design and execution of both
simple and complex reaction sequences performed on a solid support. Recently, an
entire set of innovative linkers and cleavage strategies has been disclosed, which
enables the full set of orthogonality to be produced.
As discussed above, each linker family is sensitive toward a certain spectrum of
cleavage conditions and is therefore stable to dissimilar conditions. Since most of
the linkers are based on well-established protecting groups, Table 4.10 can be used
for the determination of orthogonality. For example, benzyl-type linkers, which are
mostly cleaved by electrophiles and are stable toward nucleophiles, can be com-
bined with ester-based protective groups.
4.4
Cleavage
In this section, various methods and reagents for the cleavage of linkers are pre-
sented. In most cases, cleavage of linkers is conducted with protons. However,
other electrophiles, photones, oxidizing and reducing reagents, and nucleophiles
can be used in many cases.
4.4.1
Electrophilic and Nucleophilic Cleavage
Cleavage of linkers can be conducted with various kinds of electrophiles and nu-
cleophiles (Tables 4.11 and 4.12). The most popular cleaving reagent is triuoro-
4.4 Cleavage 89
Tab. 4.11. Typical electrophiles and Lewis acids used for detachment.
Electrophiles Solvent Additive Example for a Product

(concentration) suitable linker
HF [203205]
HF Wang linker [33] Thiols
HF Anisole PAM resin [35] Carboxylic acids
HF Cresol p-Acyloxy BHA Amides
resin [62]
CF3 SO3 H [206]
TFA (0.1% to neat) CH2 Cl2 Various linkers
TFA p-Cresol [205, 207, 208]
TFA p-Cresol, Me2 S [205]
TFA Anisole (PhOMe)
TFA (25%) Et3 SiH [209]
TFA Ethanedithiol [210]
(EDT)
TFA iPr3 SiH [211]
TFA Et3 SiH [212, 213]
TFA PhSMe [214]
HCl Dioxane Ketals [103] Ketones
CF3 SO2 OSiMe3 [215]
HBr/Ac2 O [216, 217]
AcOH CH2 Cl2 [66]
AlCl3 CH2 Cl2 /MeNO2 [218]
Et2 AlCl [219]
Me3 SiCl [194]
Tab. 4.12. Typical nucleophiles used for detachment.
Nucleophile Solvent Additive Suitable linker Products(s)

(concentration)
RMgX Carboxyl linker

Ketones, alcohols
RMgX THF Thioester Alcohols [115]
R2 CuLi THF Thioester Ketones [115]
NaOH Carboxyl linker
Carboxylic acids
KOH THF/H2 O Reissert complex
Isoquinolines [351]
NaOMe Carboxyl linker
Esters
F Silyl linkers
Hydrocarbons, alcohols
(Sect. 4.3.5)
HSCH2 CH2 OH DMF NMM, AcOH Dinitroaryl linker Thiols [229]
(2-mercaptoethanol)
nPrNH2 (10%) DMF Dde [228] Primary amines
N2 H4 DMF Dde [226] Primary amines
NH3 (vapor) [230]
Fig. 4.4. The REM and the Dde linker.
acetic acid in various solvents and concentrations. Because of its low boiling point,
removal is readily achieved. Besides this reagent, various other acids have been
used. Anhydrous HF, quite a toxic reagent, or triic acid are required for more
stable linkers. A mild reagent is trimethylsilyl chloride, which solvolyzes slowly to
HCl and hexamethyldisiloxane.
Typical nucleophilically cleavable linkers are the REM (regenerated Michael ac-
ceptor) linker (203) [220225] and Dde (Dimethyldioxocyclohexylidene)ethyl group
(204) (ADCC anchor) [226228], which are linkers for tertiary and primary amines,
respectively (Fig. 4.4).
4.4.2
Oxidative/Reductive Methods
Besides electrophiles and nucleophiles, several linkers are designed to be cleaved

by oxidative or reductive methods (Tables 4.13 and 4.14). Besides the feature of
Tab. 4.13. Some reducing agents used for detachment.
Reducing agent Solvent Suitable linker Product
nBu3 SnH Toluene Selenium linker Hydrocarbons (Scheme 4.25) [176]

NaBH4 THF/H2 O Amide Alcohols [231]
LiBH4 THF Thioester Alcohols [115]
Na/Hg MeOH Sulfon linker Alkanes [155] (Scheme 4.62)
Phosphines Disulde linker Thiols [232235]
Tab. 4.14. Some oxidizing agents used for detachment.
Oxidant Solvent Suitable linker Product
mCPBA CH2 Cl2 Thiol-based safety-catch Secondary amines [151]

linkers
mCPBA CH2 Cl2 Selenium linkers Alkenes [177]
[Bis(triuoroacetoxy)iodo] Thioketal-based linker Ketones [105] (Sect. 4.3.7.1)
benzene
DDQ Wang resin Alcohols [31]
H2 O2 Wang resin Carboxylic acids [30]
Cu(OAc)2 Pyr, MeCN Hydrazide linker Amides (Scheme 4.48) [236]
Cu(OAc)2 Hydrazide linker Arenes [237]
4.4 Cleavage 91
orthogonality with other cleaving methods, a drawback for the use of oxidative or
reductive reagents is the necessity to remove excess reagents or byproducts.
4.4.3
Photocleavable Linkers
Light-induced cleavage oers new possibilities for orthogonal use of linkers (Sect.
4.3.8) and acid- or base-labile protecting groups (Table 4.15).
The rst photolabile linker (215), which was based on the o-nitrobenzyl protect-
ing group, was developed by Rich and Gurwara [238, 247] for the synthesis of pro-
tected peptides (Scheme 4.30). This linker was developed further because in the
synthesis of the original linker, a nitration of Merrield resin was involved, thus
leading to nitration of excess phenyl rings. Therefore, mostly preformed handles
have been used. In all cases, upon ultraviolet (UV) photolysis the photo byproduct,
a nitrosobenzaldehyde, is also photoactive and causes a reduction in cleavage yield
from the support. To circumvent this problem, an additional methyl group was
introduced to give linkers, which lead to the photoreactive nitrosoactophenone
system [248]. Moreover, introduction of methoxy groups para to the nitro groups
(vanilline-type linker) [249] improves cleavage properties and the compounds are
typically released within 3 h in >90% yield and >95% purity under neutral con-
ditions [241, 250, 251]. Therefore, these linkers are biocompatible and are suitable
for Fmoc solid-phase peptide synthesis (Fmoc-SPPS) (however, see [252]). Various
modications and improvements [239, 241, 248, 253258] and applications [259]
of this linker type have been reported [260263].
Scheme 4.30. The prototype of a photolabile linker according to Rich and Gurwara [238].
Benzoins [264] and related b-keto systems (phenacyl esters) [245, 246, 265]
have been used as linkers for over 25 years now. A novel safety-catch linker (217)
(Sect. 4.5.1) based on the benzoin-protecting group has been utilized to anchor
carboxylic acids. The use of a dithiane-protected 3-alkoxy-benzoin allows for elabo-
ration of molecules, linked as esters to the secondary hydroxy function of the ben-
zoin, prior to deprotection of the dithiane and photolytic cleavage [244, 266]
(Scheme 4.31).
A new photolabile linker (126) based on a thiohydroxamic acid has been shown
to be an ecient traceless linker yielding an aliphatic CH bond upon photolysis
Tab. 4.15. Overview of photolabile linkers.
[238] Carboxylic acids
[240] Amines
[241] Amines
[243] Alcohols
[161] Methylarenes
4.4 Cleavage 93
[162] Methylarenes
[120] Methylarenes
[245, 246] Carboxylic acids
Scheme 4.31. A benzoin safety-catch photolabile linker

according to Balasubramanian and coworkers [244, 266].
at 350 nm [120]. Alternatively, the Methoxynitrophenyldithiooxopropylphenyl-

acetamide NPSSMPact handle is suitable for the detachment of benzyl-type struc-
tures (124, 125) for the traceless synthesis of methylarenes [161, 162] (see Scheme
4.59).
Besides these structures, various other linkers, such as those (209, 210) intro-
duced by Giese and coworkers [242, 243] that are cleavable by CaC fragmentation
reaction, and other systems have been developed [267272].
4.4.4
Metal-assisted Cleavage
Cleavage mediated or catalyzed by (transition) metals is particularly interesting for

several reasons. First, this type of cleavage is in most cases orthogonal (Sect. 4.3.8)
to other procedures, thus enabling various types of transformations. Second, reac-
tive intermediate organometallics can be suitable for further transformations.
In particular, the cleavage of substrates from a solid support using palladium-
promoted or -catalyzed reactions has some advantages over other cleavage meth-
ods. Since most protecting groups and functionalities are resistant towards palla-
dium complexes, a selective surgical removal is frequently possible. In addition,
intermediate p-allyl and s-arylpalladium complexes can in principle be used for
further derivatization with the use of appropriate linker types.
Boronates can be reduced to the corresponding hydrocarbons using silver salts,
making this linker as a traceless linker (Sect. 4.5.5) for arenes [147]. Similarly, aryl
sulfonates are reduced by the action of palladium or a reducing medium [166].
4.4.4.1 Cleavage with Ensuing Allylic Substitution or Cross-coupling Reactions

The detachment of molecules with a concomitant cross-coupling or allylic substi-
tution is an elegant method for the increase of diversity upon cleavage (see also
Chapter 19). A common drawback of most methods is the contamination with
transition metal catalysts and organometallic byproducts. However, various meth-
ods are available for the sequestering of transition metals from the products. The
same holds true the removal of other byproducts.
Allylic substitution reactions The cleavage of polymer-bound allyl esters with pal-
ladium catalysts provides a general access to p-allyl complexes, which can react
with various nucleophiles. This approach has been used in the development of p-
allyl-based linkers (Sect. 4.3.2).
Schurer and Blechert [273] reported on an eneyne cross metathesis (see also
Sect. 4.4.4.2) and a subsequent cleavage in the presence of various nucleophiles to
yield the corresponding functionalized dienes (224) (Scheme 4.32).
Scheme 4.32. Cleavage via formation of p-allyl intermediates

according to Sch
urer and Blechert [273].
Similarly, polymer-bound 1-alkenylcyclobutylsulfones (225) can be reacted with

suitable nucleophiles (226) and palladium catalysts to give the corresponding
cyclobutylidene derivatives (227) [274] (Scheme 4.33). The latter linker employed in
an allylic substitution reaction can be regarded as a multifunctional linker (Sect.
4.32).
4.4 Cleavage 95
Scheme 4.33. Cleavage of allylsulfones according to Cheng et al. [274].
Heck reactions Cleavage by an ensuing Heck reaction was developed utilizing the
T1 triazene linker [187]. Upon cleavage with triuoroacetic acid, a diazonium ion
is formed which can couple to an alkene under palladium catalysis (Scheme 4.34).
The coupling proceeds well with simple terminal alkenes, styrenes, as well as di-
and even trisubstituted alkenes. The coupling with 1,3-cyclohexadiene eventually
yields a biaryl, apparently by a facile dehydrogenation of the primary coupling
product. The advantage of this process is clearly the possibility of using volatile al-
kenes (and alkynes) without contamination of any salt or other less volatile by-
products, particularly with the use of palladium on charcoal as the catalyst. In this
case, a subsequent hydrogenation is also possible [187].
Scheme 4.34. Cleavage with ensuing Heck coupling using the

triazene linker by Brase and Schroen [187].
Stille couplings The intermolecular Stille reaction of aryl halides with immobi-
lized stannanes (Scheme 4.21) provide coupling products in good yields, as dem-
onstrated by Kuhn and Neumann [169]. In addition, the stannylated resin pro-
duced in the cleavage coupling can be recycled. Although the products obtained
were not contaminated by any stannane, they were separated from an excess of the
reactive electrophiles that had to be applied in the cleavage-coupling step. The in-
tramolecular variant, which was used by Nicolaou et al. [163] to produce macro-
cyclic ring systems such as the natural product (S)-zearalenone (231), does not
have this drawback (Schemes 4.35 and 4.36).
Suzuki couplings Suzuki couplings following a cleavage reaction are potentially

applicable in a multifunctional sense (Sect. 4.5.6). However, owing to the tendency
Scheme 4.35. A cleavage Stille strategy using a stannane linker

for the synthesis of zearalenone (231) by Nicolaou et al. [163].
Mem, methoxyethoxymethyl.
Scheme 4.36. Schematic reaction for the Stille cleavage reaction.
of the boronic acid derivative to give homocoupling products, the need to apply
additional ligands, and the low volatility of the boronic acid derivative, a more or
less tedious work-up is required after these types of transformations. A few studies
have proven that certain functionalities, when generated during cleavage, may act
as leaving groups for a subsequent Suzuki reaction. One of these is the diazonium
group, which can be generated by cleavage of the triazene T1 linker. While the
Heck-type coupling with alkenes gives good yields of the desired products [187]
(Scheme 4.34), the analogous reaction with phenylboronic acid appears to be di-
cult because of work-up problems [187] (Scheme 4.37).
Arylmethyl(homobenzyl)ethylsulfonium salts [154] and aryl boronates [148]
have been used as precursors for a cleavage/Suzuki approach (Schemes 4.15 and
4.20).
Scheme 4.37. Cleavage with subsequent Suzuki coupling according to Br

ase and Schroen [187].
4.4 Cleavage 97
Sonogashira-type couplings The coupling of alkynes with diazonium salts has

been reported in the context of the T1 linker. Here, the product (240) was isolated
in moderate yields, and it had to be separated by chromatography from alkyne
homodi- and trimers [187] (Scheme 4.38).
Scheme 4.38. Sonogashira coupling associated with the

cleavage according to Brase and Schroen [187].
4.4.4.2 Cleavage via Alkene Metathesis

The cleavage via alkene metathesis is particularly useful since a clean and selective
scissoring of molecules is possible (see also Chapter 20). The cleavage by meta-
thesis (Scheme 4.39) can be performed by cyclization during cleavage [275281]
(ring-closing metathesis, RCM), by intermolecular metathesis [144, 281] (cross-
metathesis) (Sect. 4.5.6), or by intramolecular metathesis [275]. Successful exam-
ples for this cleavage/cyclization method are the synthesis of epothilone A [277]
and medium-sized heterocycles [278282].
Scheme 4.39. The concept of metathetic cleavage by Blechert

and coworkers [275, 276], Nicolaou et al. [277], Piscopio et al.
[278280], and Van Maarseveen et al. [281].
The intermolecular cross-metathesis of alkenes and alkynes provides a general

access to 1,3-dienes [273] (see also Sect. 4.4.4, Scheme 4.32). A new anchoring
group for the solid-phase synthesis of oligosaccharides has been described by
Melean et al. [283]. Alkenyl units are not suitable for glycosidation reactions in the
presence of strong electrophilic activators. However, using the 4,5-dibromooctane

(DBOD) anchor, an iodide-mediated elimination reaction provides the active linker,
which can be cleaved under metathesis conditions [283] (Scheme 4.40).
Scheme 4.40. Oligosaccharide synthesis on solid support

using a linker cleavable by metathesis according to Melean
et al. [283].
4.4.5
Unusual Cleavage Methods
While most linkers are cleavable with electrophilic or nucleophilic reagents, or

under photolytic conditions, some more or less unusual cleaving conditions have
occasionally been used.
An enzyme-labile safety-catch linker (Sect. 4.5.1) was reported by Grether and
Waldmann [118] (Scheme 4.41). They used an acyl-protected amine, which was
deprotected by an acylase that triggered the release of the ester-bound substrate. A
number of other enzyme-labile linkers have also been reported [284, 285].
4.5
Linker and Cleavage Strategies
Apart from simple monofunctional cleavage, various dierent linker strategies

have been developed in recent years. In particular, new concepts based on safety-
Scheme 4.41. An enzyme-labile linker by Grether and Waldmann [118].
catch linkers (Sect. 4.5.1), cyclative cleavage strategies, and fragmentation reactions
have been presented.
Cleavage of linkers might be monofunctional or with functionalization of the
linking site, whatever is required (Fig. 4.5). In the latter case, which is also known
as the multifunctional cleavage strategy (see Sect. 4.5.6), the membership of library
compounds is multiplied by the number of building blocks or functional groups
that can be incorporated into the cleavage step. Hence, an anchoring group capa-
ble of functionalization and traceless linking is a versatile tool for enhancing di-
versity in a given system.
4.5.1
Safety-catch Linkers
9 Safety-catch linker: a linker which is cleaved by performing

two dierent reactions instead of the normal single step, thus
providing greater control over the timing of compound release
[12].
The safety-catch consists of a linker that, during synthesis, is inert towards the
cleavage conditions and has to be activated (Table 4.16). Ellman and coworkers
[286288] have used this strategy in various applications, such as in the sulfona-
mide linker proposed by Kenner et al. [289]. Since safety-catch means the activa-
Fig. 4.5. Linker types for solid-phase synthesis [197].
tion of the linker before cleavage, such a system can be applied to monodirectional
linkers, such as traceless linkers (Sect. 4.5.5) or to multifunctional linkers (Sect.
4.5.6), as well as to cleavage-cyclization strategies.
Recent applications of the Kenner linker have been shown in the synthesis of
vinylsulfones [149] (Scheme 4.42) or in the synthesis of amides [294, 295].
The oxidation of suldes to sulfones [150] or the reduction in the opposite di-
rection [64, 65] are popular methods for the design of a safety-catch protocol.
A resin-bound thioether can be activated by oxidation to insure the nucleophilic
cleavage of a phenoxide moiety [150] (Scheme 4.43).
A safety-catch p-allyl-cleavable linker was developed for the synthesis of DNA on
solid support. Starting from a resin carrying an Alloc-protected amino group frag-
ment, conventional phosphoramidite chemistry was carried out to build up the
desired nucleotide (267). Removal of the Allyloxycarbonyl (Alloc) group under palla-
Tab. 4.16. Overview of safety-catch linkers.
[289] Amides, carboxylic acids,

hydrazides
[149] (Scheme 4.42) Amides
[290] Amides
[150] (Scheme 4.43) Carboxylic acids
[151] (Scheme 4.20) Amines
[64] (cf. [65]) Amines; cleavage with TFA/

(EtO)2 (PS)SH [64];
Me3 SiBr/PhS Me/TFA
[64]
[65] Esters
[296] Nucleic acids

[291, 292] Amides
[118] Alcohols; cleavage with

enzymes
[293] Amides
[236] Diketopiperazines
[160] Benzofurans (Scheme 4.56);

cleavage with bases
dium catalysis and neutral conditions produces a polymer-bound intermediate

(268) with a free amino group that can intramolecularly attack the activated phos-
phonates and liberate the nucleotide (269) from the solid support [296] (Scheme
4.44).
Other safety-catch linkers have been developed using the selenium (Scheme
4.22), amide [293] and ester linkers [297], the Phenyloxycarbonyl (Phoc) linker [291,
292], intramolecular catalysis by an imidazole residue [298], hydrazide linkers
[236], sulfone linkers [156], and other structures [290, 299303].
Scheme 4.42. The Kenner safety-catch linker according to Overkleeft et al. [149].
Scheme 4.43. Sulde safety-catch linker by Marshall and Liener [150].
Scheme 4.44. A safety-catch palladium activated linker by Lyttle et al. [296]. Nuc nucleotide.
4.5.2
Cyclative Cleavage (Cyclorelease Strategy)
9 Cyclative cleavage: cleavage resulting from intramolecular

reaction at the linker which results in a cyclized product. The
cleavage may also act as a purication if resin-bound side-
products are incapable of cyclizing, and thus remain attached
to the solid support on release of the desired material [12].
The cyclization-cleavage strategy (cyclative cleavage or cyclorelease strategy) is a

typical example of the reaction for the synthesis of cyclic structures on solid sup-
port. It uses the characteristics of quasi-high-dilution kinetics on solid support and
thus oers advantages that are not found in solution-phase chemistry.
In general, the starting material for cyclative cleavage is anchored to the resin
via a leaving group (Scheme 4.45). An internal nucleophile provides the ring clo-
sure by displacement of this leaving group either directly or after activation. Apart
from nucleophilic attack, cyclative cleavage can be achieved, for example, by Stille
(Scheme 4.35) or WittigHorner reactions [304, 305].
Scheme 4.45. General scheme for the cyclative cleavage.
Since the intramolecular reaction is by far faster than any intermolecular step,
this strategy provides an additional purication step since only the cyclized struc-
tures are detached from the bead. Incomplete building blocks will remain on the
solid support.
Cyclative cleavage has to be distinguished from cases in which the cyclization
occurs in solution after cleavage because unsuccessful cyclization precursors re-
main in the liquid phase (Sect. 4.5.3).
In most cases, the precursor for the cyclization cleavage is linked via an ester
bond to solid support whereby the nucleophile is based on an amine functionality.
The product thus formed is therefore a cyclic amide or analog. Indeed, one of
the rst examples of this type was the pioneering benzodiazepine synthesis by
Camps and Castells in 1974 [306]. In this case, the benzodiazepine ring formation
proceeded by simultaneous cleavage from the bead. A vast list of examples has ap-
peared since that suggests various kinds of heterocyclic systems. Examples are lac-
tams, hydantoins [307319], thiohydantoins [315], oxazolidinones [320, 321]
(Scheme 4.46), diketopiperazines [322331], benzodiazepines and benzodiazepi-
nones [306, 318, 332334], pyrazolones [335, 336], diketomorpholines [323], tetra-
mic acids [337340], quinazolinediones [341], dihydropyrimidine-2,4-diones [342],
quinolinones [343], tetrahydrocarbolines [326], thiazoles [317], perhydrodiazepin-
ones [327], sulfahydantoins [344], and benzimidazoles [345].
Scheme 4.46. Synthesis of oxazolidines (276) by cyclative

cleavage according to Buchstaller [320].
In addition to nitrogen functionalities, oxygen nucleophiles can also act eec-

tively. This concept was demonstrated by an approach to 3,5-disubstituted 1,3-
oxazolidinones (276) via a ring-opening cyclization-cleavage step [320] (Scheme
4.46). Lactones are also accessible in a similar way [346].
The intramolecular Wittig reaction provides elegant access to cyclic alkenes.
Here, an intermediate ylide is formed which interacts with an internal carbonyl
functionality. Release from the bead is achieved via nal elimination or cyclorever-
sion. Thus, starting from the appropriate substituted phosphonium salts that have
regional amide functionality, treatment with a base provides indoles when this re-
action is performed under anhydrous conditions [364] (Scheme 4.47). Even phos-
phonates can undergo cyclative cleavage, as shown by Nicolaou et al. [304] in their
synthesis of a; b-unsaturated macrolactones using the HornerWadsworth alkene
synthesis.
Scheme 4.47. The phosphonium linker for the synthesis of indoles by Hughes [363].
A new safety-catch linker (Sect. 4.5.1), which is based on the lability of the dia-
zenyl carbonyl derivative, was developed for the synthesis of monoketopiperazines
(285) (piperazinones). After elaboration of the anchoring system, the dimethylben-
zyl group was removed by TFA and the hydrazide thus formed was oxidized by
copper(II) acetate furnishing a diazenyl group. This motif was attacked intra-
molecularly by the primary amine functionality, which resulted in cleavage of the
product from the resin [236] (Scheme 4.48). The potential of this linker class for
the synthesis of heterocyclic amidic structures is discussed in Chapter 22.
A cyclative approach for the synthesis of thiazoles (288) begins with the acylated
Rink amide resin (286) which has been transformed into the thioamide using Law-
esson reagent. The S-alkylation with a-bromo ketones (287) proceeds with con-
comitant cleavage from the resin [347] (Scheme 4.49).
The intramolecular Stille reaction proceeds similarly under cyclorelease con-
ditions (see above; see also Schemes 4.35 and 4.36).
4.5.3
Cleavage-cyclization Cases
The cleavage-cyclization reaction has to be distinguished from cases where a cycli-

zation proceeds after cleavage (and not at the same time). This is true for most
acidic cleavage conditions. In these cases, larger quantities of non-cyclized bypro-
Scheme 4.48. A safety-catch linker for the cyclative cleavage by

Murray and coworkers [236]. TBAD, tert-butyl azodicarboxylate.
DiPEA, diisopropylethylamine.
Scheme 4.49. Cyclorelease strategy for the synthesis of

thiazoles by Brookeld and coworkers [347].
ducts can be obtained, e.g. the synthesis of benzofurans. The alkylidenylation of

esters with thioacetals (290) and titanium complexes by the Takeda process pro-
ceeds without any problems [348]. The resulting enol ethers can be cleaved from
the solid support, resulting in the formation of benzofurans (291) (Scheme 4.50).
Scheme 4.50. Alkylidenylation and subsequent cleavage-

cyclization reaction for the synthesis of benzofurans (291) by
Hartley and coworkers [348].
Another example is the synthesis of imidazoquinoxalinones (293) (Scheme 4.51)

[209, 349]. Likewise, diketopiperazines are formed using the T2 linker and immo-
bilized glycinamide (294) [350] (Scheme 4.52). Finally, the synthesis of certain
heterocycles belongs to this strategy (Chapter 22; Sect. 4.6.1.11).
Scheme 4.51. Cleavage and subsequent cyclization in the

synthesis of heteroanellated benzimidazoles (293) by Mazurov
[209].
Scheme 4.52. Cleavage of diketopiperazines (295) from

triazene T2 resin by Brase and Lazny [350].
4.5.4
Fragmentation Strategies
The fragmentation strategy is related to the traceless anchoring groups (dened in

Sect. 4.5.5) and also contains strategies which can be considered as retro-cyclo-
addition cleavage, cycloelimination, or cyclofragmentation reactions. Here, a double
or triple bond results from 1,n-elimination processes. Occasionally, a retro-cyclo-

addition should also be considered as a fragmentation cleavage.
The only example so far of an attachment of heteroarenes via an addition/elimi-
nation strategy has been described by Kurth and coworkers [351, 352]. While
arenes are more or less resistant toward addition, heteroaromatic systems such as
isoquinolines (296) are prone to the addition of nucleophiles. Subsequent reactions
with the addition of electrophiles results in the so-called Reissert compounds
(298). These are stable compounds, which for example can be alkylated. In the
case of solid-phase synthesis, the electrophile chosen was a polymer-based acid
chloride. The detachment can be carried out by simple addition of hydroxide ions
(Scheme 4.53).
Scheme 4.53. The Reissert complex strategy used by Kurth and coworkers [351].
Recently, Gibson et al. demonstrated that arenes can be attached to a solid sup-
port using chromium arene complexes (301) [353; cf. 354] (Scheme 4.54). This
method even allows, at least from a theoretical point of view, the complete varia-
tion of the arene backbone; however, modication of the arene ring system might
be limited to a certain extent. It has already been shown that various other metals
or unsaturated molecules (e.g. alkynes with dicobaltoctacarbonyl fragments) can
lead to interesting examples for the design of new linkers [355]. Linkers based on
arene complexes have been patented [356, 357].
Scheme 4.54. The p-complexation for the linkage of arenes by Gibson et al. [353].
The fragmentation-cleavage strategy has been used for the synthesis of pyrazoles
(308) [358]. An a-silylated N-nitrosamide (304) has been rearranged via a thermal
silyl shift to an azomethine ylide (306), which then reacted with the dipolarophile
(305); subsequent fragmentation yielded the target pyrazoles (308) (Scheme 4.55).
Scheme 4.55. The synthesis of pyrazole (308) according to Komatsu and coworkers [358].
A recent synthesis of benzofurans was based on cyclofragmentation. An appro-

priately substituted sulfone was used as a nucleophile in an intramolecular ring
opening of an epoxide, wherein the resulting molecule lost a sulnate and formal-
dehyde. By immobilization of the sulfone precursor to a resin, this sequence can
be used for the cleavage of benzofurans from solid support, as demonstrated by
Nicolaou et al. [160] (Scheme 4.56).
Scheme 4.56. Benzofuran synthesis according to Nicolaou et al. [160].

Further examples of the fragmentation strategy have also been published [359
362]. The semisynthesis of vancomycin clearly demonstrates the advantage of this
kind of linker strategy [97].
4.5.5
Traceless Linkers
9 Traceless linker: type of linker which leaves no residue on the

compound after cleavage, i.e. replaced by hydrogen [12].
The term traceless linker has led to ambiguous interpretations in the past. Many
authors have claimed their linkers to be traceless because the term has, in the
past, been quite fashionable even when the reported linker was used to immobi-
lize and release amines (which upon cleavage carry a hydrogen).
Traceless linking is nowadays considered to be leaving no functionality,
meaning for arenes and alkanes that only a CaH bond remains at the original po-
sition of attachment (Scheme 4.57). A broadening of this denition to OH or NH
groups is not useful, because otherwise every linker derived from polymeric pro-
tecting groups would have to be regarded a traceless linker.
Scheme 4.57. Principle of a traceless linker.
When designing a traceless linker, one has to start from a heteroatomcarbon

bond, which is labile toward protogenolytic, hydrogenolytic, or hydridolytic cleav-
age. Since most heteroatomcarbon single bonds are less stable than a carbon
carbon bond, traceless linkers can be synthesized based on nearly all heteroatoms.
However, the enthalpies of CaX bonds are only relevant for homolytic bond scis-
sion. Many linkers are cleaved heterolytically, and the kinetic stability toward het-
erolytic bond cleavage is decisive in these cases.
The rst traceless linker was developed by Kamogawa and coworkers as early as
1983 [367]. Starting from a polymer-bound sulfonylhydrazine, formation of a sul-
fonylhydrazone resin (325) was achieved by reaction with ketones or aldehydes.
The cleavage step was conducted either by reduction with borohydride or alanate
to yield alkanes (326), or by treatment with a base to give the corresponding al-
kenes (327) (BamfordStevens reaction) (Scheme 4.58).
In addition, one of the rst papers dealing with traceless linkers was published
in 1994 by Sucholeiki [161] and describes the use of thioethers (328) that are
attached via an aromatic core that enhances the photolytic cleavage (Sect. 4.4.3).
Irradiation at 350 nm gives rise to the formation of hydrocarbon 329 [161, 162]
Scheme 4.58. The rst traceless linker by Kamogawa et al. [367].
(Scheme 4.59). So far, this linker has not been fully explored and is limited in its
range of functionalized arenes, since a phenyl substitution instead of biphenyl re-
sults in the formation of disuldes.
Scheme 4.59. Photolabile traceless linkage by Sucholeiki [161].
However, the most prominent anchors for traceless linkage for arenes (Table
4.17) are based on silyl linkers [124, 125, 369, 370] (Scheme 4.60) (Sect. 4.3.5). The
generation of a diverse benzodiazepine library by Plunkett and Ellman [131] has
shown clearly the advantages of this type of detachment since no additional func-
tionalities were retained in the nal molecules, which might bias the library.
Starting from an immobilized stannane, palladium-catalyzed coupling with acid
chlorides, deprotection of the aniline protecting group, acylation of the aniline
with a series of Fmoc amino acids, Fmoc deprotection, and cyclization aorded
resin-bound benzodiazepines, which were cleaved from the support using triuo-
roacetic acid. Improvements in the chemoselectivity of the cleavage step the silyl
linker produces a substantial amount of the silyl arene upon cleavage were ac-
complished using a germanium linker, which is more labile towards acids [131,
Scheme 4.60. The traceless silicon linker according to Veber and coworkers [124].
Tab. 4.17. Overview of traceless linkers for arenes.
Structure Reference Cleavage
[124] Scheme 4.60; cleavage with

uoride
[125] Cleavage with TFA
[126]
[127, 128] Cleavage with TBAF
[131, 363] Scheme 4.61
[152] Scheme 4.17; cleavage with

palladium/formate
[182185] T1 resin: cleavage with HCl/THF

or HSiCl3
[182] T1 resin: cleavage with HCl/THF

or HSiCl3
[237] Scheme 4.65
[147] Arenes; cleavage by Ag

(Scheme 4.16)
363] (Scheme 4.61). For example, the synthesis of the silyl linker has been opti-
mized using preloaded handles to assist the coupling of the product to the resin.
Other arylsilyl linkers have also been used (Table 4.6) to facilitate loading, synthe-
sis, and/or detachment from the support [126128, 130, 134136].
Scheme 4.61. Synthesis of a benzodiazepine library with the

aid of a germanium linker by Plunkett and Ellman [131].
Furthermore, silicon linkers can be used for the attachment for allylsilanes,
which can be cleaved to alkenes in a traceless fashion [144].
The use of sulfones as suitable anchoring groups for alkanes in soluble polymer
chemistry has been reported previously [155, 156] (Table 4.18). After oxidation of a
sulde to a sulfone (338), treatment of the latter with sodium/mercury gives rise to
the formation of the parent hydrocarbon (339) in high yields. However, aqueous
work-up is necessary to provide the pure product (339) [155] (Scheme 4.62).
Another traceless linker type was independently developed by the groups of
Nicolaou et al. [164] and Ruhland et al. [165]. Starting from lithiated selenium
polystyrene (146), readily available from metallated polystyrene and selenium re-
agents, reaction with iodoalkanes led to the smooth formation of alkylated com-
pounds. The cleavage can be conducted in such a way as to give alkenes (150)
Tab. 4.18. Overview of traceless linkers for alkenes and alkanes.
[161] Methylarenes; photolytic cleavage
[120] Methylarenes; photolytic cleavage
[364, 365] Scheme 4.63
[366] Scheme 4.67
[156, 155] Alkanes; cleavage with Na/Hg
[164, 165] Alkanes
[163] Alkenes
[367] Alkenes and alkanes; cleavage by

reducing media or bases
(Scheme 4.58)
[368] Ketones
Scheme 4.62. The sulfone traceless linker for alkanes according to Janda and coworkers [156].
upon treatment with hydrogen peroxide. Alternatively, tin hydride reduction leads
to the generation of alkanes (149) (Scheme 4.22).
Electron-poor aryl sulfonates are suitable candidates for oxidative palladium
insertion. Hence, immobilized phenol sulfonates (129) have been employed in a
palladium-catalyzed reductive cleavage using formic acid to yield arenes (130) with
overall traceless cleavage [152] (Scheme 4.17). It might be anticipated that this type
of linker is also suitable for functionalization (see below).
The phosphoruscarbon bond in phosphonium salts is readily cleavable by the
aid of a base in the absence of an aldehyde. Hence, the polymer-bound phospho-
nium salt (340) gives direct access to methylarenes (341). An interesting feature of
this linker is the fact that carbonyl compounds can be olenated, which leads to a
cleavage-olenation linker system [364, 365] (Scheme 4.63).
Scheme 4.63. The phosphonium linker for methylarenes according to Hughes [364].
Tin hydride reagents are versatile tools for the functionalization of alkenes
and alkynes. Based on this concept, Nicolaou and coworkers [163] developed a
polymer-bound tin hydride (142), which reacts in a hydrostannylation reaction
with alkynes to give alkenylstannanes (143). After further transformation, the lat-
ter undergo proteolytic traceless cleavage to yield unsubstituted alkenes (145) [163]
(Scheme 4.21).
The decarboxylation of appropriately substituted arenes [371] and alkanes [343,
368, 372375] has been used to generate the parent hydrocarbons. Since the neigh-
boring group eect is essential, limitation to special substrates is required.
One possible method for converting functionalized arenes into the correspond-
ing hydrocarbons is the reduction of diazonium compounds [182]. Hence, the syn-
thetic utility of the triazene linker as a traceless anchor for arenes has been dem-
onstrated by Brase et al. [182] using short reaction sequences. Thus, cinnamic
esters were synthesized in a sequence starting from the iodoarene resin (343).
Heck coupling with acrylates using palladium catalysis aords an immobilized
cinnamate. This can be detached either directly or by a sequence of transforma-
tions yielding to an allyl amine in a traceless fashion either using trichlorosilane
[184] or a HCl/THF mixture [182], to give the products 342 and 344, respectively,
in high yields and without further purication or aqueous work-up (Scheme 4.64).
Acyl aryl diazenes are known to fragment upon treatment with nucleophiles, a
strategy which was used for a linker for carboxylic acid derivatives [119] (Scheme
4.11). Waldmann and coworkers recently developed a traceless linker for arenes
based on this methodology [237]. Starting from a hydrazide resin (345), which
Scheme 4.64. The T1 linker for traceless cleavage [182, 184].
is converted into an activated species by oxidation, detachment of the molecule

is carried out by the addition of nucleophiles (Scheme 4.65). This safety-catch
principle the activated linker is generated before cleavage (Sect. 4.5.1) shows
promising stability in palladium-catalyzed reactions. Furthermore, arylboronic
acids can be used for the traceless synthesis of arenes [147] (Scheme 4.16).
Scheme 4.65. The hydrazide linker according to Waldmann and coworkers [237].
A new traceless photolabile linker has been published using a hydroxamic acid
derivative (83) [120].
The cleavage of specially designed polymeric benzyl-type protecting groups has
been achieved using heterogeneous palladium black. In these cases, the catalytic
hydrogenation furnishes methyl-substituted arenes as side products or targets. An
early example takes advantage of the properties of the MeO-PEG-type support for
the synthesis of di- and higher oligosaccharides (Scheme 4.66). It is interesting to
note that the DOX linker enables the cleavage of the PEG structure, leaving the p-
methylbenzyl group attached under certain conditions [376] (but see [29]) (Scheme
4.66).
Similarly, cleavage from polystyrene resins was achieved using homogeneous
palladium catalysis (palladium acetate) either with formate reduction [366]
(Scheme 4.67) or under an atmosphere of hydrogen [377] to yield methyl arenes.
The chemistry of traceless linkers is a fast-emerging eld in the intensively in-
vestigated area of solid-phase organic synthesis [ for reviews, see 183, 197, 378].
Although some confusion about the denition or classication has been related to
Scheme 4.66. Syntheses of methylarenes on polymeric support [376].
Scheme 4.67. Syntheses of methylarenes (351) on solid support [366].
this linker type, and therefore a careful designation has to be made, it is now clear
that this anchoring mode will play an important role in the design and syntheses
of drug-like molecules.
4.5.6
Multifunctional Cleavage
Traceless cleavage (Sect. 4.5.5) provides an ecient access to hydrocarbon-like

molecules. However, monofunctional linkers (Table 4.19) provide only one type of
compound in a library. The so-called multifunctional cleavage [379] oers an im-
portant opportunity to incorporate additional diversity upon cleavage (Scheme
4.68). Hence, the number of new functionalities (Fig. 4.5) can multiply the num-
ber of produced compounds. If the linker is amenable to various types of building
blocks (e.g. nucleophile [A] and electrophiles [B]) incorporated during cleavage, a
substantial library of novel molecules can be prepared from one immobilized
compound [380].
However, when considering using a multifunctional linker, one must take into
account the nature of the cleavage reagent and the cleavage step. A cleavage con-
sisting of, for example, addition of a Grignard reagent to an ester with a huge ex-
cess of the organometallic component requires an aqueous work-up and hence
potential annihilation of valuable material. Thus, the excess reagents need to be
easily removable (volatile, low or very high solubility in certain solvents, easy to
Tab. 4.19. Overview of multifunctional linkers.
[273] Scheme 4.32
[364] Alkenes by Wittig reaction
[163] Alkanes by crosscoupling (Scheme

4.35)
T1 resin: traceless linker [182

184]; synthesis of phenols [186],
biaryls, alkyl arenes [187, 188],
azides, aromatic hydrazines,
halides [190, cf. 181, 180], ester,
azo compounds; cinnolines
[191], benzotriazoles [192]
T2 resin: synthesis of alcohols,
esters [196, 197, 183], alkyl
halides [196, 197, 183]
T2 -resin: as above [198]
[381] (Scheme 4.69) Amines, thiols [381], halides [382],

azides [382], acetates [382] by
nucleophilic displacement
[274] (Scheme 4.32) Alkenes by palladium-catalyzed

cleavage
[154] (Scheme 4.18) Diaryl methanes by activation and

subsequent palladium-catalyzed
cleavage
[153] Heterocycles by cleavage with

nucleophiles
[277, 154] (Scheme 4.70) Alkenes by cleavage through

metathesis
Scheme 4.68. Traceless vs. multifunctional cleavage.
eliminate or to be removed by for example scavenger resins, etc.) and should not
interfere with the functionalities of the library compounds.
The addition of nucleophiles such as amines, alkoxides, thiolates, and carbon
nucleophiles to carbonyl groups leading to modied carbonyl moieties has been
used widely for multifunctional cleavage. Hence, anchoring a Weinreb amide to
the resin and cleaving with Grignard reagents leads to the formation of ketones
[383]. Alternatively, thioesters provide access to amides or ketones, whereas sulfo-
nate esters such as 359 provide access to amines and thiols (360) [381] (Scheme
4.69), halides [382], azides [382], or acetates [382].
Scheme 4.69. Synthesis of tertiary amines, thioethers or

imidazoles using a nucleophilic substitution cleavage [381].
Aromatic sulfones, synthesized by oxidation of thiopyrimidines (safety-catch

linker, Sect. 4.5.1), have been used for the synthesis of aminopyrimidines by dis-
placement with amines [384]. Silyl linker 96, described previously [126], may be
used for a smooth multifunctional cleavage. Hard electrophiles such as chlorine,
bromine, iodine, or nitrosyl replace the silicon at the ipso-position of the silyl
arene, leading to a variety of arenes upon cleavage. The same strategy has been
demonstrated with the germanium linker.
Cleavage by metathesis has been used by various groups to accomplish either
detachment by cyclization (ring-closing metathesis, RCM) [281], intermolecular
metathesis (cross-metathesis) [385] (Scheme 4.70), or intramolecular metathesis
[275] (see also Sect. 4.4.4.2). One advantage of cleavage by metathesis is the possi-
bility of introducing fragments with additional functionalities. The successful ex-
amples include the total synthesis of epothilone by this cleavage strategy [277].
The nucleophilic substitution of allylic fragments provides a general access
by multifunctional anchoring. Staring from dienes, prepared by en-yne cross-
Scheme 4.70. The concept of cleavage by cross-metathesis.
metathesis, nucleophilic substitution catalyzed by palladium via p-allyl complexes

provides access to functionalized dienes [273] (Scheme 4.33). Similarly, 1-alkenyl-
cyclobutylsulfones can be used to yield cyclobutylidene derivatives [274] (Scheme
4.32).
Besides the possibility of conducting traceless cleavage (Sect. 4.5.5) from tri-
azene linkers, a cleavage cross-coupling can be achieved using palladium catalysis
[187, 188] (Scheme 4.34). In addition, functionalization of triazene resins upon
cleavage leads to the formation of aryl halides (180-Nu, Nu halogen) [191], phe-
nols, and aryl ethers (180-Nu, Nu OAc), azo compounds (176), biaryls (185) by a
GombergBachmann reaction, Meerwein alkylation products (187), benzotriazoles
(177) [192], and Richter products such as cinnolines (178) [191] (Scheme 4.27).
Disubstituted triazenes (194) prepared on the T2 resin undergo cleavage to yield
aliphatic diazonium ions, which in turn solvolyze in the presence of nucleophiles
to give alkyl halides (202), alcohols (201-OH) and alkyl esters (201-OCOR) [see
200] [183, 196, 197] (Scheme 4.29). It is possible, but not fully established, that
silyl linkers can be cleared in a multifunctional fashion to enable the synthesis of
arenes and aryl halides (see Scheme 4.61).
A exible tool for the synthesis of heterocycles is the cleavage of a-sulfonylated
ketones attached to a solid support [153]. Since the loading proceeds smoothly
from alkenes or epoxides onto polystyrene sulfonic acid resin, this method pro-
vides ample possibilities for the functionalization of simple compounds.
4.5.7
Linkers for Asymmetric Synthesis
The use of enantiomerically pure drugs has increased within the pharmaceutical
industry over recent years. It is assumed that the market was well over US$120
billion in the year 2000 [386, 387], and approximately 60% of all marketed drugs
are enantiomerically pure. Chiral building blocks have been used extensively in
solid-phase synthesis (Fig. 4.6) and have been incorporated into modern small-
molecule compound libraries.
However, asymmetric synthesis based on linking strategies, with either diaster-
eoselective or enantioselective methods, has been more or less neglected. The ob-
vious advantage of a linker, which induces stereoselectivity, is the ease with which
the auxiliary can be removed and recycled [388].
Pioneering work on asymmetric synthesis on an insoluble support was de-
scribed in 1972 when Kawana and Emoto [389, 390] reported the synthesis of an
atrolactic acid on a polymer containing the sugar 1,2-o-cyclohexylidene-a-d-xylofur-
anose (365). Shortly after this, Lezno and coworkers [391, 392] demonstrated the
synthesis of a-chiral cyclohexanone derivatives using polymer-bound imines (366).
Fig. 4.6. Overview of chiral auxiliaries on solid support.
These early examples have demonstrated that polymer-bound chiral auxiliaries are
suitable both for anchoring of organic molecules and for the induction of asym-
metry. Furthermore, the recycling of chiral auxiliaries can be conrmed.
In recent years, a series of auxiliaries has been immobilized on solid support,
including oxazolidinones (372) according to Evans [231, 393398], oxazoles (367)
[399], mono- (368) [400] and bisalkoxymethylpyrrolidines (369) [401], as well as
SMP/SAMP auxiliaries (370, 371) by Enders and coworkers [402, 403]. Alter-
natively, polymer-bound chiral sulnamides [404], sulfoximines by Hachtel and
Gais [405], imines [406], and amines (as galactosylamine) (Scheme 4.71) have
been used.
Scheme 4.71. Stereoselective Ugi-3CC according to Kunz and coworkers [407].

A recent example is the diastereoselective Ugi reaction for the synthesis of a-

amino acids by Kunz et al. [407]. Starting from a galactosylamine (374), a three-
component reaction of aldehydes and isocyanides produced amides (375) in good
diasteroselectivities (Scheme 4.71) after removal of the auxiliary.
4.6
Linkers for Functional Groups
The requirement for diverse compound libraries by means of solid-phase synthesis

has led to the development of linkers for most functional groups found in organic
synthesis. The number of linkers developed for a specic group also reects the
distribution of pharmacophoric groups (Fig. 4.7) present in natural products and
other bioactive compounds. In this section, linkers for functional groups are high-
lighted. In all cases, the functional group that is attached to the solid support,
whether it remains unchanged upon cleavage or is formed during cleavage, acts as
the guide through this section. For example, a benzodiazepine attached via the ar-
omatic core would be found in the section for the linking of arenes (Sect. 4.6.7.2),
whereas attachment via the nitrogen atom (amide functionality) will be described
in Sect. 4.6.2.4.
Fig. 4.7. Distribution of pharmacophoric groups of com-

pounds in three dierent databases according to Henkel et al.
[408]. DNP, Dictionary of Natural Products; drugs, internal
database of the Bayer company; synthetika, screening pool of
the Bayer company.
4.6.1
Linkers for Nitrogen Functionalities
Nitrogen-containing structures are mandatory structural units in biologically active

compounds. Therefore, it is not surprising that a vast number of linkers for vari-
ous nitrogen functionalities has been developed.
4.6.1.1 Linkers for Amines

The solid-phase synthesis of primary amines is of great importance to various
elds of organic and medicinal chemistry, since these compounds are both valu-
able synthetic intermediates and often interesting target molecules. The genera-
tion of libraries of commercially unavailable amines has received considerable in-
terest within combinatorial chemistry as a large number of primary amines show
biological activity and the primary amine moiety is incorporated into various mol-
ecules encountered in medicinal chemistry. Moreover, these amines can serve as
building blocks in the preparation of further libraries. Consequently, linkers for
amines have been used excessively. Among these are the Rink linker, carbamate
linkers [301], and Rink carbamates [409].
4.6.1.2 Linkers for Primary Amines

For the solid-phase synthesis of primary amines miscellaneous linker types have
been developed [85, 94, 316, 410425] which are resistant to various reaction con-
ditions. The standard linker family suitable for the detachment of amines is the
benzyl-type linkers (Sect. 4.3.1) [32, 82, 426438], such as the Rink linker [82]
(Scheme 4.72), the trityl linkers [76], the indole linker [85], the BAL linker [14],
and others [226, 439]. Carbamates are suitable linkers for primary amines, which
can be released by diluted TFA [94, 268, 440446].
Scheme 4.72. The Rink resin as a linker for primary amines [82].
Alternatively, benzyl carbamates can be attached to the solid support, and hy-
drogenolytic cleavage can be used to detach the molecules, which are then usually
left with a nitrogen functionality (cleavage of CaO bond) [29, 447]. The polymers
in these cases are formally immobilized Benzyloxycarbonyl Cbz (Z) groups. Inter-
estingly, TentaGel and polystyrene give the products in similar yields under iden-
tical conditions [17] (Scheme 4.73). Benzylic linkers can also be used advant-
ageously in the presence of other benzylic protecting groups, since they can be
removed in the same step [29].
Scheme 4.73. Detachment of peptides from polymeric benzyl-type protecting groups [17].
Fig. 4.8. Overview of amine linkers.
An anchor for primary amines, which is cleavable under basic conditions (Table
4.12), is the dimedone-based Dde group (204) [226, 228, 425] (Fig. 4.8).
Anilines are released from the PAL linker, the Rink linker [82], the PhFl linkers
[437, 448], the p-benzyloxybenzylamine (BOBA) resin [32], and carbamate linkers.
The latter type has also been used as a safety-catch version [168] (Sect. 4.5.1).
A novel dialkylhydrazine linker (381), which is stable toward organometallic re-
agents, has recently been reported. A series of a-branched primary amines was
synthesized by attachment of various aldehydes, the resulting hydrazones (384)
were modied via 1,2-addition of organolithium reagents furnishing trisubstituted
hydrazines (385) which in turn were cleaved from the solid support to yield acy-
lated a-branched primary amines [449] (Scheme 4.74).
Scheme 4.74. Use of a hydrazine linker (381) according to

Enders and coworkers [449] for the synthesis of primary
amines.
The cleavage of primary sulfonamides to give primary amines can be performed

with electrochemical cleavage, when carried out on a conducting polymer [167]
(Scheme 4.19).
4.6.1.3 Linkers for Secondary Amines

Secondary amines have been detached from solid support using the trityl, chloro-
trityl, and other linkers [69, 193, 340, 416, 418, 450] (Fig. 4.9). Secondary amines
can be detached from benzyl-type resins if they are activated to the corresponding
a-chlorocarbamates 376 [417].
Fig. 4.9. Overview of linkers for secondary amines.
Carbamates are suitable linkers for secondary amines, which can be released by
diluted TFA [17, 345, 451, 452], as demonstrated in a Hantzsch dihydropyridine
synthesis by Breitenbucher and Figliozzi [409] (Scheme 4.75).
Scheme 4.75. Carbamates as linkers for amines by Breitenbucher et al. [409].

The triazene T2 linker is capable of clean detachment of secondary amines.

Since disubstituted triazenes can be alkylated with electrophiles in the presence of
a strong base, this method provides a clean procedure for the conversion of pri-
mary to secondary amines [198] (Sect. 4.3.8) (Scheme 4.76).
Scheme 4.76. The T2 linker for the synthesis of secondary amines on solid support [198].
Other linkers for secondary amines are the thiobenzylethylcarbamate linker

[151] (Scheme 4.20), PAL-type linkers [453] (dihydropyridines) [453] (Scheme
4.51) [454], and other systems [455457].
4.6.1.4 Linkers for Tertiary Amines

The cleavage of tertiary amines from solid support is somehow dierent from the
analogous primary and secondary amines, since no apparent linking site is avail-
able. However, the ease of formation of the tetravalent nitrogen moiety can be
favorably used for the linking of tertiary amines (Fig. 4.10).
The prototype is the REM resin, which is based on a Michael addition/alkylation
and elimination sequence on an immobilized acrylate [220225] (Scheme 4.77).
Besides acrylates, vinyl sulfones might serve the same purpose [458].
The cleavage of dialkylaryl triazenes with methyl iodide was investigated by
Moore and coworkers [180] and Tour and coworkers [181] during their synthesis of
aryl iodides on solid support (Sect. 4.14.3.8). Using the piperazine resin (394),
cleavage with methyl iodide in dichloromethane yielded the tertiary amines with
good purities. A quarternization of the nitrogen was not detected [459] (Scheme
4.78).
Similarly, the hydroxylamine linker (396) can be used for the synthesis of
tertiary amines [460], as demonstrated in the synthesis of the analgetic (G)-
Tramadol9 (401) on solid support [461] (Scheme 4.79).
Carbamates can be cleaved by means of lithium aluminum hydride in THF
to give N-methylalkylamines with high purities [446, 462, 463]. While the latter
Fig. 4.10. Overview of linkers for tertiary amines.
Scheme 4.77. The REM linker for the synthesis of tertiary amines [223].
Scheme 4.78. Alkylative cleavage of triazenes [459].
linker provides methylamines, the reaction of secondary amines with electrophiles

consisting of polymer-bound leaving groups enables the synthesis of higher sub-
stituted amines. However, the removal of the excess of secondary amine can be a
drawback to this method [153, 381] (Scheme 4.80).
Besides aliphatic electrophiles, certain heteroaromatic structures can also be
Scheme 4.79. Tramadol9 synthesis according to Grigg and coworkers [461].
Scheme 4.80. Synthesis of tertiary amines using a sulfonate linker [464].
used [384]. Furthermore, various other linkers are suitable for tertiary amines
[224, 225, 465].
4.6.1.5 Linkers for Hydrazines, Hydrazones and Hydroxylamines

While hydrazines can be released from trityl linkers, the detachment of disub-
stituted hydrazones (418) is possible with the triazene linker [466] (Scheme 4.81).
The hydrazones (417) are readily available from polymer-bound hydrazines and
subsequent condensation with aldehydes.
4.6.1.6 Linkers for Diazonium Salts

The triazene T1 linker is a suitable anchoring group for the detachment of diazo-
nium salts. Upon cleavage with dilute acids, the diazonium salts can be obtained
Scheme 4.81. Synthesis of hydrazones [466].

in high yields. However, owing to their instability, the diazonium ion is mostly
transformed in situ to a new functional group [467] (Scheme 4.82) (see also
Scheme 4.27).
Scheme 4.82. In situ cleavage of triazenes for the synthesis of diazonium salts [467].
4.6.1.7 Linkers for Azides

Aromatic and aliphatic azides are interesting targets and intermediates in solid-
phase organic synthesis. Aryl diazonium salts react with azide ions without a cata-
lyst to give aryl azides. In contrast to the classical Sandmeyer reaction, this trans-
formation proceeds without cleavage of the carbonnitrogen bond. This reaction
can be used for the synthesis of libraries of aryl azides. Starting from the triazene
T1 resin, cleavage with triuoroacetic acid in the presence of trimethylsilyl azide
furnished, after simple removal of the solvent, the aryl azides in good yields and
excellent purities [189] (Scheme 4.27). This synthesis can also be applied to the
synthesis of heterocycles such as benzofuroxanes [189]. Aliphatic azides have been
released from solid support using a sulfonate linker [382, 465, 468].
4.6.1.8 Linkers for Nitro Compounds

The reaction of arenes attached to silyl-type linkers with nitronium ions might lead
to the formation of nitroarenes, as proposed in [128].
4.6.1.9 Linkers for Azo Compounds

Although important structures for the synthesis of dyes, the synthesis of azo com-
pounds on solid support has scarcely being described. The transfer of diazonium
salts to nucleophiles such as phenols can be used for the synthesis of azo com-
pounds. This approach has been demonstrated either with diazonium salts immo-
bilized on an ion exchange resin [469] (Scheme 4.83) or starting from triazene T1
resins [199] (Scheme 4.84).
4.6.1.10 Linkers for Nitriles

Polymeric sulfonylhydrazines react readily with aldehydes and ketones to form
hydrazones, which can release the corresponding nitriles [367].
4.6.1.11 Linkers for N-Heterocycles

Various heterocyclic nitrogen compounds can be detached from solid support (for
a review, see [470]). Basically, two options are conceivable. The removal of hetero-
cycles bound via the nitrogen atom to solid support provides a general entry to this
Scheme 4.83. Azo coupling through immobilized diazonium salts according to Das et al. [469].
Scheme 4.84. Cleavage of a triazene with concomitant azo coupling [199].
class of compounds. Otherwise, a cleavage-cyclization technique can be considered

to build up the nitrogen heterocycle as the very last step. Both strategies have been
used extensively.
Tetrazoles, for example, can be attached to a THP linker. Cleavage is best
achieved either with 3% HCl or with TFA [112] (Scheme 4.85).
Scheme 4.85. Cleavage of tetrazoles from a THP-type linker [112].
The THP (Table 4.4) [99] and other acetal linkers [100] are also suitable for the
attachment of indoles. Alternatively, heterocyclic amines with a free NaH func-
tionality can be linked via an acetal, which can be cleaved rst under acidic and
then under basic conditions [456] (Scheme 4.86).
Scheme 4.86. Synthesis of indoles (434) using a diol linker by Gmeiner and coworkers [456].
Indole synthesis can be realized on solid support via a sulfone linker. Advanta-
geously, the heterocyclic core was installed in this case via a palladium-catalyzed
process [302] (Scheme 4.87). Similarly, benzimidazoles can be released via a retro-
Michael addition from sulfonate resins [471] (Scheme 4.88).
Scheme 4.87. Cleavage of indoles from sulfonate resins [302].
Scheme 4.88. Cleavage of benzimidazoles [471].
Other examples for the synthesis of aromatic nitrogen heterocycles include the
synthesis of pyridines and tetrahydropyridines [452], benzimidazoles [471], isox-
azolines [472], isoquinolines via Reissert complexes (Scheme 4.53) [351, 352],
quinoxalinones [49], benzisoxazoles [473], and imidazoles on trityl linkers [78].
The second strategy is dedicated to cleavage conditions, which result in the in-
stallation of the heterocyclic core; this strategy obviously belongs to the cleavage-
cyclization technique (Sect. 4.5.3). An example of this detachment uses diazonium

salts, which can be cyclized when a nucleophilic ortho-substituent is present
(Scheme 4.89). This reaction yields cinnolines [191] (Scheme 4.90), benzotriazoles
(Scheme 4.91) [192], benzothiadiazoles, indazoles, benzo[c]cinnolines, and other
structures. Suitable precursors are the triazene T1 resins (Sect. 4.14.3.8), which are
cleavable by mild acids. Azides are also precursors for a similar cyclization. This
process has been demonstrated in a synthesis of benzofuroxanes on solid support
[189] (Scheme 4.92). Finally, certain arylsulfonyl hydrazones cyclized to the corre-
sponding thiadiazoles (453) when treated with thionyl chloride [474] (Scheme 4.93).
Scheme 4.89. General synthesis of heterocycles via cyclization

of diazonium salts generated from the T1 linker [191].
Scheme 4.90. Synthesis of cinnolines (445) [191].
Scheme 4.91. Synthesis of benzotriazoles (448) [192].
Scheme 4.92. Synthesis of benzofuroxanes (438) [189].

Scheme 4.93. Synthesis of thiadiazoles [474].
4.6.2
Linkers for Carbonyl Functionalities
4.6.2.1 Linkers for Carboxylic Acids

The prominent number of linkers is certainly dedicated to the anchoring and
detachment of carboxylic acid. This is due to the widespread application of solid-
phase peptide synthesis. However, a large number of pharmacologically active, low-
molecular-weight compounds contain the carboxylic acid functionality and there-
fore new and innovative linkers have been developed [475]. In general, most syn-
theses rely on the Wang resin [476] or related benzyl, trityl, and benzhydryl systems,
which are cleavable by triuoroacetic acid [23, 34, 48, 66, 77] (see Table 4.2) or HF/
anisole [35]. Other examples include acetal resins, sulfones [477], b-thioethylesters
[168], uoride-labile linkers [52, 69, 122], Kaiser oxime resin [478], p-allyl linkers,
photo linkers [238, 241, 244, 245, 260, 266, 479], the safety-catch ketal linker [293],
and other linkers [18, 442, 443, 480, 481].
A new anchoring group based on phenanthridines has been developed [482],
which can be acylated by conventional methods. It shows stability toward acidic,
basic, and reductive conditions; however, in the presence of a suitable oxidant, de-
tachment of the carboxylate takes place (Scheme 4.94).
Scheme 4.94. Anchoring and detachment of carboxylic acids by Li et al. [482].
The well-optimized and established BMPSE (b-dimethylphenylsilylethyl) proto-

col for esters has been adapted by Kurth and coworkers [483] for the immobiliza-
tion of carboxylates, which can be cleaved under mild conditions (Scheme 4.95).
Scheme 4.95. The solid-phase BMPSE group by Kurth and coworkers [483].
Other reports describe the use of arylhydrazides as linkers [119, 484] and also
other linkers [372, 373, 485489].
4.6.2.2 Linkers for Carboxylic Esters, Anhydrides and Lactones

Carboxylic esters have been released mostly by the action of alkoxides onto ester
resins. In most cases, the cleavage has been performed using methoxide in meth-
anol (Scheme 4.96). A drawback is certainly the necessity to remove excess metal
salts.
Scheme 4.96. The use of esters as linkers for benzoic acid derivative by Kondo et al. [116].
A new safety-catch linker based on the activation of an amide bond by cycliza-

tion to an indolyl carboxamide is suitable for the release of methyl esters [293].
Similarly, the tert-butoxy group of polymer-bound 2-(tert-butoxy)phenyl carboxylates
may be removed with triuoroacetic acid, and subsequently the ester cleaved by
primary or secondary amines [121]. Alternatively, postsynthesis with diazomethane
is also possible [121] (Scheme 4.97).
Polymer-bound arylhydrazides have been used in the synthesis of peptide car-
boxylic esters in a safety-catch strategy (Sect. 4.5.1) [119, 484].
A direct synthesis of carboxylic esters based on the cleavage of triazene T1 resins
in the presence of a palladium catalyst under carbon monoxide atmosphere (1 bar)
to yield methyl benzoate (466) in 87% yield (92% purity) [187] (Scheme 4.98).
Arylalkyl triazenes with a free NH moiety can also be used for the synthesis of
carboxylic esters. Starting from amines attached to the T2 linker [183, 196, 197] or
the analogous para-substituted resin [200], cleavage with dierent carboxylic acids
proceeds smoothly to give esters (Scheme 4.99).
Scheme 4.97. Synthesis of macrocycles by Deslongchamps and coworkers [121].
Scheme 4.98. Cleavage and carbonylation of the triazene T1 resin (465) [187].
Scheme 4.99. Synthesis of carboxylic esters via triazene T2 resins [183, 196, 197].
Lactones are accessible via thioesters [115], esters [346, 400], or amides [490]
with a suitably positioned internal nucleophile or electrophile. In addition, alkyl
acetates are also accessible from sulfonates upon cleavage with sodium acetate
[382].
4.6.2.3 Linkers for Thiocarboxylic Acids and Esters

A benzhydryl linker has been used to attach thioesters, while the cleavage can be
conducted with HF [491]. Alternatively, treatment of an oxime linker with bistri-
ethylthioether results in the ssion of the product to give the thio carboxylic acid
[478, 492].
Fig. 4.11. Strategies for amide linkers.
4.6.2.4 Linkers for Carboxamides and Related Structures

The solid-phase synthesis of amide-containing structures is important to vari-
ous elds of organic and bioorganic chemistry. The solid-phase peptide synthesis
(SPPS) has provided the chemical community with various solutions toward link-
ing, reaction, and detachment of amide structures. In general, these protocols in-
volve the attachment of amine derivatives by their carbon backbone or, in case of
amino acids, by their carboxy functionality. The coupling with carboxyl derivatives
proceeds via the free amine, usually using Fmoc-protected amino acids.
Basically, two strategies have been used for the synthesis on solid support (Fig.
4.11). In most cases, an amine has been attached to solid support and then acy-
lated on the bead to give secondary amides (470). The latter can be cleaved under
acidic conditions. Alternatively, carboxyl functionalities (471) can be cleaved with
ammonia or with primary or secondary amines. A synthesis of secondary and
tertiary amides is based on Lewis acid-mediated cleavage of the ester resin [493].
Safety-catch approaches (Sect. 4.5.1) in the synthesis of peptide carboxamides
use polymer-bound arylhydrazides [119, 236, 484] (see Scheme 4.48) or indolyl
carboxamides [293].
Linkers for primary amides Primary amides can be synthesized on solid support
using, for example, the Rink resin [68, 494]. This support is suitable for various
reaction conditions, as outlined in Schemes 4.100 and 4.101.
Scheme 4.100. Detachment of primary amides from a Rink resin by Wang et al. [494].
Scheme 4.101. Synthesis of Nenitzescu products according to Wilson and coworkers [495].
Linkers for secondary amides Linking by the NaH of a secondary amide bond has
been developed, hence leading to so-called backbone amide linkers (BAL). Origi-
nally designed for the NaH protection of amide bonds to circumvent b-turns and
other problems during peptide synthesis, the Hydroxymethylbenzoic acid Hmb
group [496, 497] or the Silylmethylmethoxyhydroxybenzyl SiMB group [498] can
also serve as linkers for SPPS.
Although important in the synthesis of cyclopeptides, they also play an impor-
tant role in the synthesis of small molecule libraries containing amide moieties.
Barany and coworkers have described an application of a backbone amide linker
for the synthesis of oligopeptides [40, 83, 424, 499, 500] (Scheme 4.102), glycopep-
Scheme 4.102. Backbone amide linkage using the PAL linker by Barany and coworkers [83].
tides, and peptide aldehydes [501] based on the peptide amide linker (PAL) con-
cept. Attachment of amines furnishes alkylated products (482), which in turn can
be acylated under peptide-coupling reaction conditions to give amidic structures
(484). The latter can be cleaved from the resin using acidic media to give amides
(485). This concept was used for the synthesis of benzodiazepine libraries by Ell-
man and coworkers [47] (Scheme 4.103), hapalosin mimetics [502], and further
rened to yield an alternative, TFA-stable benzylamine linker [503]. Benzylamine-
based linkers have encountered some problems during cleavage which also caused
the fragmentation of the whole linker. Furthermore, the reactivity is decreased be-
cause of steric hindrance [14, 241].
Scheme 4.103. Synthesis of benzodiazepines according to Ellman and coworkers [47].
Recently, it has been shown that the BAL linker is also suitable as a safety-catch
linker (Sect. 4.5.1) for the synthesis oligosaccharides [454] (Scheme 4.104). Start-
ing from an aldehyde, reductive amination of a protected glucosamine and subse-
Scheme 4.104. Oligosaccharide synthesis via the BAL structure

according to Jensen and coworkers [454].
quent glycosidation with a glucopyranosyltrichloroacetimidate yielded the corre-

sponding disaccharide (492). The cleavage was performed after acylation of the
amine functionality, which is required to suppress premature decomposition.
In addition, the p-benzyloxybenzylamine (BOBA) resin (7) developed by Kobaya-
shi and Aoki [32, 504] shows interesting possibilities, such as reductive amination
and acylation. Furthermore, it can be cleaved under oxidative conditions to yield
the amidic structures.
Recently, a new backbone amide linker has been devised using indole chem-
istry [85] (Scheme 4.105). In addition, various other related benzyl-type linkers
[503, 505, 506] have been used for the synthesis of secondary amides. The Rink
linker (28) [507], the Merrield a-methoxybenzyl (MAMP) linker (24) [61], methyl-
benzylhydryl amine (MBHA) resin (23) (cleavable with HF/anisole) [59], or AHB
(4-alkoxy-2-hydroxybenzaldehyde) linker (12) (R H) [45], a reductively aminated
acetophenone linker [54], and SASRIN-related systems [44, 51] are also suitable.
Scheme 4.105. The indole linker according to Estep et al. [85].
The T2 linker has recently been shown to be a versatile backbone amide anchor
[194]. Immobilized disubstituted triazenes were acylated with carboxylic acid an-
hydrides or chlorides to give amidic structures (482) [194] (Scheme 4.106).
Scheme 4.106. Synthesis of amides using the triazene T2 linker [194].
A new backbone linker for b-lactams and secondary amides was presented using
a benzyloxyaniline linker, which is cleavable by ceric ammonium nitrate [508].
Secondary amides and ureas can be synthesized using supported hydroxyl-
amine, which can be cleaved by samarium(II) iodide [509].
Linkers for tertiary amides Linkers for tertiary amides are the ester anchors cleav-
able with secondary amines. In addition, the triazene T2 linker is also a precursor
for amides when cleaved by acid chlorides [193, 510].
Linkers for carbamates Both the SASRIN and the indole linker are suitable for the
synthesis of carbamates, however the SASRIN linker can be cleaved with 5% TFA
in dichloromethane [41], whereas 50% TFA in dichloromethane is required for the
indole linker [85].
Linkers for ureas Urea derivatives, which are important biologically active com-
pounds and building blocks for organic syntheses, have been synthesized on solid
support using various strategies.
A useful linker for ureas is the phoxime resin (498) (phosgenated oxime resin)
[511, 512], which is cleavable at elevated temperature with amines to yield ureas
(Scheme 4.107). Other linkers for ureas are the SASRIN linker [41, 44] and other
systems [422, 513].
Scheme 4.107. The phoxime resin for the synthesis of urea derivatives [511].
The T2 linker has also being used for the attachment and modication of pri-
mary amines, yielding urea derivatives after mild cleavage (Scheme 4.108).
Aminosulfonylureas have been released from carbamate linkers using primary
and secondary amines (multifunctional: Sect. 4.5.6) [420]. The samarium(II)
iodide-promoted cleavage of acylated polymer-bound hydroxylamines gives general
access to urea derivatives [509].
Linkers for thioureas Thioureas have been synthesized using the T2 linker [194]
(Scheme 4.109).
Linkers for isothioureas Isothioureas have been detached from solid support
using the T2 linker under mild conditions [514] (Scheme 4.110).
Linkers for guanidines Guanidines are basic molecules with the capacity of form-
ing H-bonding interactions. They are therefore a promising class of potentially use-
Scheme 4.108. The backbone amide-anchoring mode of the T2 linker [194].
Scheme 4.109. Synthesis of thioureas using the T2 linker [194].
Scheme 4.110. Synthesis of isothioureas using the T2 linker [514].
ful pharmacologically active compounds and the synthesis of guanidines in liquid

phase has found widespread application in organic chemistry [515].
The T2 linker [193, 194] and the improved T2*-linker [183, 198] oer a unique
possibility to immobilize and modify amine derivatives on solid support. Starting
from immobilized amines, a three-step sequence based on coupling with isothio-
cyanates, conversion to guanidines with amines, and subsequent cleavage presents
an approach to the formation of guanidines in which all three substituents can be
varied to a wide extent (Scheme 4.111) [195]. In addition, various other linkers for
guanidines are available [85, 427, 516524].
Scheme 4.111. Synthesis of functionalized guanidines [195].
Linkers for amidines Several techniques enable the synthesis of amidines on solid
support. In most cases, benzyl-type linkers such as the indole linker [85], the
Wang linker [525], or a carbamate system on the Wang linker [525] have been
used.
Linkers for hydroxamic acids Hydroxamic acids are important building blocks in
metalloproteinase inhibitors. Therefore, various linkers have been developed to sat-
isfy these requirements.
The Wang linker is, for example, suitable for the detachment of hydroxamic
acids as demonstrated in a cascade carbopalladation reaction [526] (Scheme
4.112).
Scheme 4.112. Carbonylation cascade on solid support toward

hydroxamic acids according to Grigg et al. [526].
Alternatively, the THP, the Wang resin [527, 528], the Rink linker [529], trityl
resin [530], PAL resin [528, 531], oxime resins [532], and others [285, 437, 533
537] are suitable linkers for hydroxamic acids.
4.6.2.5 Linkers for Hydrazides and Semicarbazones

Only a few linkers have been used for the synthesis of hydrazides and semicarba-
zones, including a phthalamide linker cleavable with hydrazines [538] and the
T2 linker (Sect. 4.14.3.8) [466] (Scheme 4.113). Hydrazides can be cleaved from
solid support using the trityl linkers, for example.
Scheme 4.113. Cleavage of semicarbazones from triazene resins [466].
4.6.2.6 Linkers for Cyclic Amides and Related Structures

Cyclic amide structures have found widespread application in the synthesis of bio-
logically active compounds. Most of the linkers mentioned above for tertiary and
secondary amide structures, ureas, and so forth, are suitable for the synthesis of
cyclic amidic moieties; however, the most widespread applications are dedicated to
the cyclative cleavage from the bead (Sect. 4.5.2).
Linkers for lactams The synthesis of b-lactams has been achieved using the hy-
droxyaniline linker [508] (Scheme 4.114).
Scheme 4.114. Linker for b-lactams and secondary amides [508].
Linkers for other heterocycle-containing amidic structures Various techniques have

been used for the synthesis of hydantoins [307, 308313, 319], thiohydantoins
[315], oxazolidinones [320, 321], diketopiperazines, frequently the byproducts of
peptide synthesis [322331], benzodiazepines and benzodiazepinones [306, 318,
332, 333], pyrazolones [335, 336], diketomorpholines [323], tetramic acids [337
340], quinazolinediones [341], dihydropyrimidine-2,4-diones [342], quinolinones
[343], tetrahydrocarbolines [326], thiazoles [317], and perhydrodiazepinones [327].
Sulfahydantoins (1,2,5-thiadiazolidin-3-one 1,1-dioxides) were prepared from ester-
bound amino acids, which were rst reductively alkylated, then reacted with sulfa-
moyl chloride, and nally cleaved from the resin using 1,8-diazabicyclo[5.4.0]-
undecene-7 (DBU) [344].
4.6.3
Linkers for Ketones and Aldehydes
The anchoring of carbonyl compounds is generally based on established protecting

groups. For example, alkyl hydrazones (Scheme 4.74) [449], sulfonyl hydrazones
[539], and semicarbazones [540] can be used as linkers for aldehydes and ketones.
Cleavage is conducted with acids, preferably in the presence of formaldehyde. In
addition, aldehydes and ketones can be synthesized using photo-labile linkers, re-
duction of or nucleophilic additions to Weinreb amides [541543], nucleophilic
addition to thioesters [115, 544], oxidative cleavage (ozonolysis) of alkenes [545,
546], hydrolysis of enamines [419], and using various other methods [547].
Since their introduction some 20 years ago by Lezno and coworkers [101, 102],
acetal linkers have been used in the solid-phase synthesis of ketones and aldehydes
[104, 548] (Scheme 4.115). Recently, it was demonstrated that even sterically hin-
dered ketones could be attached to this support using scandium triate and trime-
thylorthoformate by acetal exchange reaction [104]. Similarly, thioketal structures
are also suitable linkers for ketones [105] (Sect. 4.3.7.1).
Scheme 4.115. Cleavage of an acetal resin by Snieckus and coworkers [548].
4.6.4
Linkers for Alcohols, Phenols, Ethers, and Ketals
4.6.4.1 Linkers for Alcohols

Various linkers are suitable for the anchoring and release of alcohols; in particular,
silyl ethers have been frequently used [20]. An early example of this type was pro-
vided by Farrall and Frechet [549]. Furthermore, these linkers are suitable for gly-
copeptides [550], oligosaccharides [20], and prostaglandins (511) [123] (Scheme
4.116).
A direct loading of alcohols onto a silyl resin is possible using a hydridosilane
[133], which might be better than the procedure described using silyl chloride
[135]. A SEM (2-trimethylsilylethoxymethyl) linker is also suitable for the attach-
ment and detachment of sterically encumbered alcohols. In this case, cleavage is
conducted by tetrabutylammonium uoride [21]. In addition to the silyl linkers,
various ketal-based methods have been reported recently [23, 49, 69, 543, 551553]
(for a review, see [554]).
The method of choice for various applications are the THP-type linkers [99,
Scheme 4.116. Synthesis of prostaglandin by Ellman and coworkers [123].
108114] (Sect. 4.3.3), as demonstrated in the synthesis of indolactams on solid

support [555] (Scheme 4.117). However, other acetal linkers [100, 106] (Sect. 4.3.3)
(Scheme 4.118) have also been used in this context. In addition, alcohols can be
attached to a Wang or trityl resin, and can be cleaved in turn by the action of mild
acids [533].
Alternatively, the benzyl group can be attached to the solid support, and hy-
drogenolytic cleavage has been used to detach the molecules which are then usu-
Scheme 4.117. Synthesis of indolactam analogs according to Waldmann and coworkers [555].
Scheme 4.118. Synthesis of benzyl alcohols on solid support [100].

ally left with an oxygen or nitrogen functionality (cleavage of CaO Bn and CaN
bond respectively) [29, 447]. The polymers in these cases are formally immobilized
Z or Cbz groups. Interestingly, TentaGel and polystyrene give similar yields under
identical conditions. Benzylic linkers can also be used advantageously in the pres-
ence of other benzylic protecting groups, since they can be removed in the same
step [29] (Scheme 4.119).
Scheme 4.119. Detachment of saccharides from polymeric benzyl-type protecting groups [29].
Finally, alcohols can be released from ester [117, 556], thioester [115], and amide
resins using reductive methods (Sect. 4.4.2, Table 4.13). Furthermore, the reaction
of Grignard reagents with thioesters has been reported to give tertiary alcohols
[115]. Other anchoring groups are enzyme-labile linkers [285] and uoride-
sensitive linkers [557]. Cyclic ethers (tetrahydrofurans) are accessible via an iodo-
lactonization approach [558, 559].
4.6.4.2 Linkers for Phenols

Similar to alcohols, phenols have been linked to anchors such as Wang [560],
Rink [82], trityl [561], 2-chlorotrityl [562], and modied trityl [563] linkers. How-
ever, since these linkers are more acid stable, simple hydroxymethyl polystyrene
can serve as a linker when cleaved by triic acid [549, 557, 564, 565] (Scheme
4.120).
A direct method for the synthesis of phenol acetates has been demonstrated
with the triazene T1 linker. An in situ cleavage and acylation proceeds with good
yields when cleaved by acetic acid/acetic anhydride (Scheme 4.121) [186].
4.6.5
Linkers for Sulfur Compounds
4.6.5.1 Linkers for Thiols and Thioethers

Thiols can be synthesized using disuldes as remarkably stable linkers. The de-
tachment proceeds in the presence of certain phosphines [232235] or by exchange
Scheme 4.120. Synthesis of quinolones from avilylium salts according to Sato et al. [564].
Scheme 4.121. Synthesis of phenol acetates (541) [186].
with thiols [566]. However, other suitable linkers are the Wang linker, cleavable by
HF [33], Rink-type linkers [82, 567], thiocarbamates, cleavable by bases [568], dini-
troaryl linker, cleavable by nucleophiles [229]; and others [569, 570]. Because thiols
are prone to oxidation to give symmetrical disuldes, the latter were frequently
found during cleavage if oxygen had not been strictly excluded.
4.6.5.2 Linkers for Sulfonamides

The synthesis of sulfonamides is similar to the strategies used for carboxamides.
Therefore, primary sulfonamides were synthesized using, for example, the Rink
resin (Scheme 4.122) [67].
The indole resin [85], the SASRIN linker [41, 44], and a reductively aminated
acetophenone linker [54] are also suitable for the detachment for sulfonamides
[24, 41, 67, 415, 571574].
4.6.5.3 Linkers for Sulfonic Acids

Aryl and alkyl sulfonic acids have been detached from both Wang resin and
SASRIN-type resins under mild conditions (20% TFA in CH2 Cl2 ) after being at-
Scheme 4.122. Detachment of sulfonamides from the Rink resin [67].
tached to a solid support using the corresponding benzyl alcohol resins and sul-
fonyl chlorides [575].
4.6.5.4 Linkers for Sulfones and Sulfoxides

Only one example has been presented so far for the synthesis of sulfones [405].
Starting from Merrield resin, attachment of enantiopure sulfoximines and sub-
sequent aldol-type coupling gives access to highly substituted sulfoximines. Cleav-
age proceeds under oxidative conditions using meta-chloroperbenzoic acid (mCPBA)
to give sulfones (Scheme 4.123) [405].
Scheme 4.123. A linker for sulfones according to Gais and Hachtel [405].
4.6.5.5 Linkers for Sulfoximines

A linker for sulfoximines is the triazene T2 linker. The cleavage can be con-
ducted under mild condition using 10% trimethylchlorosilane solution in dichloro-
methane with retention of conguration [466].
4.6.6
Linkers for Hydrocarbons
Linkers for hydrocarbons are important tools in combinatorial chemistry for the
synthesis of the lipophilic compounds required for modern drug research. As de-
scribed above, access to hydrocarbons can proceed via the formation of either a
CaC bond or a CaH bond. The latter strategy has been discussed in detail in
Sect. 4.5.5 (traceless linkers), since the introduction of a hydrogen atom clearly is
the prototype for this kind of linker.
4.6.6.1 Linkers for Alkanes

Alkanes have been synthesized on solid support, mostly by reduction of a CaX
bond to a CaH functionality. This concept has been demonstrated using the sele-
nium [165], sulfur [120], and stannane linkers. The formation of CaC bonds for
the synthesis of alkanes has been described by Schiemann and Showalter [576].
Beginning with an aryl fragment attached to an immobilized benzotriazole, cleav-
age and subsequent CaC bond formation are achieved using organomagnesium
compounds.
4.6.6.2 Linkers for Arenes and Heteroarenes

Alternatively, Caaryl bonds were formed using various cross-coupling methods,
including stannanes [163, 169, 577], triazenes [187, 188] (Scheme 4.34), and boro-
nates [148] as precursors.
Naphthalene derivatives are accessible via an electrocyclic ring opening of ben-
zocyclobutane derivatives and a subsequent DielsAlder reaction with dienophiles
[578]. Hydrogenolytic removal of substrates from the solid support is important
as it cleaves the substrate to form a CH bond at the former binding site of the
polymer. These types of linkers are also called traceless linkers (Sect. 4.5.5) [183].
The detachment of substituted arylsulfonates in the presence of a reducing
agent such as formic acid provides a traceless cleavage. In this case, it is important
that the arene core is substituted with electron-withdrawing substituents to en-
hance the yields [152]. This approach has been described previously (without ex-
perimental details) quite early in a patent and includes the possible derivatization
of the intermediate s-aryl palladium aryl complex [579].
4.6.6.3 Linkers for Alkenes

Most of the linkers for alkenes are traceless linkers, such as those described in
Sect. 4.5.5. Besides these, classical double-bond-forming reactions, such as the
WittigHornerEmmons [304, 305] or the Wittig reaction, can be used for the for-
mation of CbC bonds [364]. Syntheses via metathesis (Sect. 4.4.4.2), for example
the ring-closing metathesis of olens [277, 580], have been used for the prepara-
tion of alkenes on solid support. In addition, multifunctional cleavage (Sect. 4.5.6)
can be achieved using cross-metathesis.
Allylic groups can be attached to solid support via a sulfone, which is prepared
by lithiation of polystyrene and subsequent treatment with sulfur dioxides and an
allylbromide. After modication on the bead, cleavage proceeds with the action of
a Grignard reagent in the presence of copper iodide. This overall SN 2 0 alkylation
provides a route to substituted alkenes [581] (Scheme 4.124).
The b-elimination generating alkenes has been used in the chemistry of the
sulfone and selenium linkers [164, 582, 583] (Scheme 4.22). Similarly, polymer-
bound 1-alkenylcyclobutylsulfones [274] (Scheme 4.33) or pentadienol carboxylates
[273] (Scheme 4.32) were cleaved from a resin in the presence of suitable nucleo-
philes and palladium catalysts to give substituted cyclobutylidene derivatives or di-
enes, respectively.
Scheme 4.124. Nucleophilic substitution of an allylic sulfone [581].
4.6.6.4 Linkers for Alkynes

Two linkers have been used for the detachment of alkynes from solid support.
Gibson and coworkers [355] have described the immobilization of alkynes onto
polymer-bound triphenyl phosphine via a dicobaltoctacarbonyl arm. The detach-
ment was conducted using air as the nal oxidant.
Alkynes were obtained by the cleavage cross-coupling strategy of the T1 triazene
resin (Scheme 4.26). In contrast to the Heck cleavage, these cleavage conditions
give rise to di- and trimerization, thus making a chromatographic separation nec-
essary [187] (Scheme 4.38).
4.6.7
Linkers for Aryl and Alkyl Halides
Aryl iodides have been synthesized by Moore et al. [179], starting from triazene
resin by the action of methyl iodide (Sect. 4.14.3.8) (Scheme 4.125). Aryl iodides,
bromides, and chlorides are also accessible from the triazene T1 linker using the
corresponding trimethylsilyl halide (Scheme 4.126) [190].
Scheme 4.125. The use of triazene anchoring groups in the

synthesis of iodo arenes by Moore and coworkers [179].
The cleavage of triazene T2-linked primary amines with trimethylsilyl chloride,

bromide, or iodide proceeds smoothly to give alkyl halides. This reaction proceeds
presumably via the aliphatic diazonium ion. In some cases, a rearrangement was
observed (Scheme 4.127).
Arylbromides and -iodides are accessible from silicon or germanium-linked
arene fragments (Sect. 4.3.5). The released can be conducted with either bromine/
pyridine [126, 131] or iodochloride [126, 138].
Scheme 4.126. Synthesis of aryl halides via the T1 triazene resin [190].
Scheme 4.127. Synthesis of alkyl halides via the triazene T2 linker [183, 196, 197].
The nucleophilic substitution of alkylsulfonates was used for the synthesis of

alkyl iodides. Starting from the corresponding alcohols, attachment to a sulfonyl
chloride and subsequent release from the bead was performed using sodium
iodide [382, 465]. Allyl bromides can be released from a trityl linker if cleaved with
hydrobromic acid in acetic acid [74]. Other methods start from with trityl linkers
[74, 163, 382, 559].
4.6.8
Linkers for Heterocycles
Various methods are applicable in the synthesis of heterocycles [361, 362, 384,
584]. The cyclofragmentation of a certain class of sulfones leads to 3-arylbenzo-
furans [160].
4.6.9
Linkers for Reactive Intermediates
Reactive intermediates cleaved from a solid support can be used for a subsequent
functionalization. Thus, radicals, carbanions, and carbocations might then react
with additional building blocks. This multifunctional cleavage mode (Sect. 4.14.5.6)
has, for example, been used with the stannane, selenium (Sect. 4.14.3.7), and tri-
azene linkers (Sect. 4.14.3.8).
4.6.10
Linkers for Other Functional Groups
4.6.10.1 Linkers for Phosphonates

Phosphonates can be released from the resin using trimethylsilyl iodide (Scheme
4.128) [585]. They have been attached to a solid support using the Wang linker
[586, 587, 588].
Scheme 4.128. Synthesis of phosphonates using

noncrosslinked polystyrene (NCPS) as support [585].
4.6.10.2 Linkers for Boronates

Diols are suitable anchors for boronic acids, as shown in the synthesis of hepatitis
C virus proteinases [589].
4.6.10.3 Linkers for Silanes and Silanols

Silanols are accessible from silyl ether linker [127]. The siliconoxygen bond can
be cleaved with TFA via a protio-ipsodesilylation.
4.7
Overview for Linkers for Functional Groups
Table 4.20 gives a short overview of the dierent linker families, as described in
Chapter X.
4.8
Conclusion, Summary and Outlook
In recent years, various new types of linkers have emerged. The design of a new
anchoring group can be essential for the success of a synthesis, especially for small
molecules on a solid support. Linker, cleavage conditions, and functional groups
are associated with each other. Therefore, the decision to use one specic linker
type has to be balanced with the requirements of the library to be synthesized.
Although the perfect or universal linker has not yet been developed, and
will prove unattainable, interesting new developments increase the exibility of
solid-phase synthesis by traceless (Sect. 4.5.5) and multifunctional cleavage (Sect.
References 153
Tab. 4.20. Short overview for various linker types.
Functional group Benzyl- Ketal/ Esters/ Silane Triazene Selenium/

type acetal amide linkers linkers sulfur/
linkers linkers linkers stannyl
linkers
p p p p p
R3 N
p p p p
ROH
p p p
R2 NCOR
p p p p p
RH (traceless) (Sect. 4.5.5)
p p
RCO2 H
p p p
Heterocycles
p p
BAL
p p
RX
p p p
Safety-catch option
p p p
Multifunctional cleavage
p
Photo cleavage
4.5.6). While traceless linkers provide access to unsubstituted compounds with

no memory of solid-phase synthesis, multifunctional cleavage allows the intro-
duction of various new functionalities during cleavage from the resin. Backbone
amide linkers present new opportunities for solid-phase synthesis of small amidic
structures, and cyclization-release strategies provide an opportunity to create novel
carbo- and heterocyclic structures upon cleavage.
An anchor for traceless linking can also be a safety-catch linker (Sect. 4.5.1), or it
can be suitable for multifunctional cleavage. Linker systems allow the introduction
of certain atoms or molecule fragments and will play an important role in the de-
velopment of diverse organic substance libraries. It is important to point out that
the nal diversication is achieved in the cleavage step and not in an additional
solution-phase reaction step after the cleavage. However, only a few linker systems
that are applicable to a wider range of substrates have been developed so far. As
these linker systems oer the widest possibilities for the nal diversication of a
synthesized library, they will be the subject of increasing attention in the future.
References
1 E. M. Gordon, R. W. Barrett, W. J. Keating, Acc. Chem. Res. 1996, 29,

Dower, S. P. A. Fodor, M. A. 123131.
Gallop, J. Med. Chem. 1994, 37, 4 F. Balkenhohl, C. von dem
13851401. Bussche-Hunnefeld, A. Lansky, C.
2 J. A. Ellman, Acc. Chem. Res. 1996, Zechel, Angew. Chem. Int. Ed. 1996,
29, 132143. 35, 22892337; Angew. Chem. 1996,
3 R. W. Armstrong, A. P. Combs, P. A. 108, 24362488.
Tempest, S. D. Brown, T. A. 5 J. S. Fruchtel, G. Jung in: Combi-
natorial Peptide and Nonpeptide 25 M. Mergler, R. Tanner, J. Gosteli,

Libraries: A Handbook. Jung, G. (ed.), P. Grogg, Tetrahedron Lett. 1988, 22,
VCH, Weinheim 1996, pp. 1978. 40054008.
6 P. H. H. Hermkens, H. C. J. 26 M. Mergler, J. Gosteli, P. Grogg,
Ottenheijm, D. Rees, Tetrahedron P. Nyfeler, R. Tanner, Chimia 1999,
1996, 52, 45274554. 53, 2934.
7 I. W. James, Tetrahedron 1999, 55, 27 F. Albericio, G. Barany, Tetrahedron
48554946. Lett. 1991, 32, 10151018.
8 F. Guillier, D. Orain, M. Bradley, 28 E. Atherton, C. J. Logan, R. C.
Chem. Rev. 2000, 100, 20912157. Sheppard, J. Chem. Soc., Perkin Trans.
9 A. C. Comely, S. E. Gibson, Angew. 1 1981, 538546.
Chem. Int. Ed. 2001, 40, 10121032; 29 S. Manabe, Y. Ito, T. Ogawa, Synlett
Angew. Chem. 2001, 113, 10431063. 1998, 628630.
10 F. Zaragoza Dorwald, Organic 30 G.-s. Lu, S. Mojsov, J. P. Tam, R. B.
Synthesis on Solid-phase: Supports, Merrield, J. Org. Chem. 1981, 46,
Linkers, Reactions, Wiley-VCH, 34333436.
Weinheim 2000. 31 T. L. Deegan, O. W. Gooding, S.
11 B. Carboni, F. Carreaux, J. F. Baudart, J. A. Porco, Abstr., Pap.
Pilard, Actual. Chimique 2000, Am. Chem Soc. 1997, 214, 238
913. ORGN.
12 D. Maclean, J. J. Baldwin, V. T. 32 S. Kobayashi, Y. Aoki, Tetrahedron
Ivanov, Y. Kato, A. Shaw, P. Lett. 1998, 39, 73457348.
Schneider, E. M. Gordon, Pure 33 D. R. Englebretsen, B. G.
Appl. Chem. 1999, 71, 23492365. Garnham, D. A. Bergman, P. F.
13 B. J. Backes, J. Ellman, Curr. Opin. Alewood, Tetrahedron Lett. 1995, 36,
Chem. Biol. 1997, 1, 8693. 88718874.
14 C. T. Bui, F. A. Rasoul, F. Ercole, Y. 34 G. Barany, R. B. Merrield in: The
Pham, N. J. Maeji, Tetrahedron Lett. Peptides. Gross, E., Meienhofer, J.
1998, 39, 92799282. (eds), Academic Press, New York
15 W. Rapp, in: Combinatorial Peptide 1979.
and Nonpeptide Libraries: A Hand- 35 A. R. Mitchell, B. W. Erickson, M.
book. Jung, G. (ed.), VCH, Weinheim N. Ryabtsev, R. S. Hidges, R. B.
1996, pp. 425464. Merrield, J. Am. Chem. Soc. 1976,
16 A. Svensson, T. Fex, J. Kihlberg, J. 98, 73577362.
Comb. Chem. 2000, 2, 736748. 36 D. Seebach, A. Thaler, D. Blaser, S.
17 J. R. Hauske, P. Dorff, Tetrahedron Ko, Helv. Chim. Acta 1991, 74, 1102
Lett. 1995, 36, 15891592. 1119.
18 K. Akaji, Y. Kiso, L. A. Carpino, J. 37 J. V. Aldrich, S. C. Story, Int. J.
Chem. Soc., Chem. Commun. 1990, Pept. Protein Res. 1992, 39, 8792.
584586. 38 R. C. Sheppard, B. Williams, Int. J.
19 T. H. Chan, W. Q. Huang, J. Chem. Pept. Protein Res. 1982, 20, 451454.
Soc., Chem. Commun. 1985, 909 39 R. M. Valerio, A. M. Bray, N. J.
911. Maeji, Int. J. Pept. Protein Res. 1994,
20 J. T. Randolph, K. F. McClure, S. J. 44, 158165.
Danishefsky, J. Am. Chem. Soc. 1995, 40 F. Albericio, G. Barany, Int. J. Pept.
117, 57125719. Protein Res. 1985, 26, 9297.
21 W. J. Koot, J. Comb. Chem. 1999, 1, 41 A. M. Fivush, T. M. Willson, Tetra-
467473. hedron Lett. 1997, 38, 71517154.
22 R. B. Merrield, J. Am. Chem. Soc. 42 X. Ouyang, N. Tamayo, A. S.
1963, 85, 21492154. Kiselyov, Tetrahedron 1999, 55, 2827
23 S.-S. Wang, J. Am. Chem. Soc. 1973, 2834.
95, 13281333. 43 D. Sarantakis, J. J. Bicksler, Tetra-
24 B. Yan, N. Nguyen, L. Liu, G. hedron Lett. 1997, 38, 73257328.
Holland, B. Raju, J. Comb. Chem. 44 E. E. Swayze, Tetrahedron Lett. 1997,
2000, 2, 6674. 38, 84658468.
References 155
45 T. Okayama, A. Burritt, V. J. Hruby, 64 M. Patek, M. Lebl, Tetrahedron Lett.

Org. Lett. 2000, 2, 17871790. 1991, 32, 38913894.
46 F. Albericio, N. Kneib-Cordonier, 65 Y. Kiso, T. Fukui, S. Tanaka, T.
S. Biancalana, L. Gera, R. I. Kimura, K. Akaj, Tetrahedron Lett.
Masada, D. Huson, G. Barany, J. 1994, 35, 35713574.
Org. Chem. 1990, 55, 37303743. 66 H. Rink, Tetrahedron Lett. 1987, 28,
47 C. G. Boojamra, K. M. Burow, J. A. 37873790.
Ellman, J. Org. Chem. 1995, 60, 67 K. A. Beaver, A. C. Siegmund, K. L.
57425743. Spear, Tetrahedron Lett. 1996, 37,
48 K. Barlos, O. Chatzi, D. Gratos, G. 11451148.
Stavropulos, Int. J. Pept. Protein Res. 68 A. L. Marzinzik, E. R. Felder,
1991, 37, 513520. Tetrahedron Lett. 1996, 37, 10031006.
49 V. Krchnak, L. Szabo, J. Vagner, 69 A. Routledge, H. T. Stock, S. L.
Tetrahedron Lett. 2000, 41, 28352848. Flitsch, N. J. Turner, Tetrahedron
50 K. J. Jensen, J. Alsina, M. F. Lett. 1997, 38, 82878290.
Songster, J. Vagner, F. Albericio, 70 P. Sieber, Tetrahedron Lett. 1987, 28,
G. Barany, J. Am. Chem. Soc. 1998, 21072110.
120, 54415452. 71 Y. X. Han, S. L. Bontems, P. Hegyes,
51 L. S. Harikrishnan, H. D. H. M. C. Munson, C. A. Minor, S. A.
Showalter, Synlett 2000, 13391341. Kates, F. Albericio, G. Barany, J.
52 R. Ramage, C. A. Barron, S. Org. Chem. 1996, 61, 63266339.
Bidecki, D. W. Thomas, Tetrahedron 72 W. C. Chan, S. L. Mellor, J. Chem.
Lett. 1987, 28, 41054108. Soc., Chem. Commun. 1995, 1475
53 R. Ramage, C. A. Barron, S. 1477.
Bielecki, R. Holden, D. W. Thomas, 73 M. Noda, M. Yamaguchi, E. Ando,
Tetrahedron 1992, 48, 499514. K. Takeda, K. Nokihara, J. Org.
54 C. T. Bui, A. M. Bray, F. Ercole, Y. Chem. 1994, 59, 79687975.
Pham, F. A. Rasoul, N. J. Maeji, 74 J. M. J. Frechet, L. Nuyens, Can. J.
Tetrahedron Lett. 1999, 40, 34713474. Chem. 1976, 54, 926934.
55 H. Chao, M. S. Bernatowicz, G. R. 75 T. M. Fyles, C. C. Leznoff, Can. J.
Matsueda, J. Org. Chem. 1993, 58, Chem. 1976, 54, 935942.
26402644. 76 K. Barlos, D. Gatos, J. Kallitsis, D.
56 H. G. Chao, M. S. Bernatowicz, Papaioannou, P. Sotiriu, Liebigs
P. D. Reiss, C. E. Klimas, G. R. Ann. Chem. 1988, 10791081.
Matsueda, J. Am. Chem. Soc. 1994, 77 K. Barlos, D. Gatos, J. Kallitsis, G.
116, 17461752. Papaphotiu, W. Yao, W. Schafer,
57 P. G. Pietta, G. R. Marshall, J. Tetrahedron Lett. 1989, 30, 39433946.
Chem. Soc. D 1970, 650651. 78 S. Eleftheriou, D. Gatos, A.
58 G. R. Matsueda, J. M. Stewart, Panagopoulos, S. Stathopoulos, K.
Peptides 1981, 22, 4550. Barlos, Tetrahedron Lett. 1999, 40,
59 M. E. Theoclitou, J. M. Ostresh, 28252828.
V. Hamashin, R. A. Houghten, 79 C. C. Zikos, N. G. Ferdierigos,
Tetrahedron Lett. 2000, 41, 2051 Tetrahedron Lett. 1994, 35, 1767
2054. 1768.
60 R. C. Orlowski, R. Walter, D. 80 L. Leondiadis, I. Vassiliadou, C.
Winkler, J. Org. Chem. 1976, 41, Zikos, N. Ferderigos, E. Livaniou,
37013705. D. S. Ithakissios, G. P. Evan-
61 D. S. Brown, J. M. Revill, R. E. gelatos, J. Chem. Soc., Perkin Trans
Shute, Tetrahedron Lett. 1998, 39, I 1996, 10, 971975.
85338536. 81 T. Wieland, C. Birr, P.
62 J. P. Tam, J. Org. Chem. 1985, 50, Fleckenstein, Liebigs Ann. Chem.
52915298. 1972, 756, 1419.
63 J. P. Tam, R. D. DiMarchi, R. B. 82 R. S. Garigipati, Tetrahedron Lett.
Merrield, Tetrahedron Lett. 1981, 1997, 38, 68076810.
22, 28512854. 83 J. Alsina, T. S. Yokum, F. Albericio,
G. Barany, J. Org. Chem. 1999, 64, Leznoff, Can. J. Chem. 1983, 61,
87618769. 14051409.
84 N. Thieriet, F. Guibe, F. Albericio, 104 R. Maltais, M. Berube, O. Marion,
Org. Lett. 2000, 2, 18151817. R. Labrecque, D. Poirier, Tetra-
85 K. G. Estep, C. E. Neipp, L. M. S. hedron Lett. 2000, 41, 16911694.
Stramiello, M. D. Adam, M. P. 105 C. M. Huwe, H. Kunzer, Tetrahedron
Allen, S. Robinson, E. J. Roskamp, Lett. 1999, 40, 683686.
J. Org. Chem. 1998, 63, 53005301. 106 G. T. Wang, S. Li, N. Wideburg, G.
86 H. Kunz, B. Dombo, Angew. Chem. A. Krafft, D. J. Kempf, J. Med. Chem.
Int. Ed. Engl. 1988, 12, 711712; 1995, 38, 29953002.
Angew. Chem. 1988, 100, 732734. 107 S. Q. Chen, K. D. Janda, Tetrahedron
87 H. Kunz, W. Kosch, J. Marz Lett. 1998, 39, 39433946.
(Orpegen GmbH), Patent No. 108 J. S. Koh, J. A. Ellman, J. Org. Chem.
US5214195, 1990. 1996, 61, 44944495.
88 C. Schumann, L. Seyfarth, G. 109 E. K. Kick, J. A. Ellman, J. Med.
Greiner, S. Reissmann, J. Pept. Res. Chem. 1995, 38, 14271430.
2000, 55, 428435. 110 G. Wess, K. Bock, H. Kleine, M.
89 T. Johnson, R. C. Sheppard, J. Kurz, W. Guba, H. Hemmerle, E.
Chem. Soc., Chem. Commun. 1991, Lopez-Calle, K. H. Baringhaus, H.
16531655. Glombik, A. Enhsen, W. Kramer,
90 O. Seitz, H. Kunz, J. Org. Chem. Angew. Chem. Int. Ed. 1996, 35, 2222
1997, 62, 813826. 2224; Angew. Chem. 1996, 108, 2363
91 O. Seitz, Tetrahedron Lett. 1999, 40, 2366.
41614164. 111 W. H. Pearson, R. B. Clark, Tetra-
92 O. Seitz, C. H. Wong, J. Am. Chem. hedron Lett. 1997, 38, 76697672.
Soc. 1997, 119, 87668776. 112 S. E. Yoo, J. S. Seo, K. Y. Yi, Y. D.
93 B. Blankemeyer-Menge, R. Frank, Gong, Tetrahedron Lett. 1997, 38,
Tetrahedron Lett. 1988, 29, 5871 12031206.
5874. 113 J. H. Ryu, J. H. Jeong, Arch. Pharm.
94 K. Kaljuste, A. Unden, Tetrahedron Res. 1999, 22, 585591.
Lett. 1996, 37, 30313034. 114 M. Ramaseshan, J. W. Ellingboe,
95 F. Guibe, O. Dangles, G. Balavoine, Y. L. Dory, P. Deslongchamps,
A. Loffet, Tetrahedron Lett. 1989, 30, Tetrahedron Lett. 2000, 41, 47434749.
26412644. 115 P. J. May, M. Bradley, D. C.
96 X. H. Zhang, R. A. Jones, Tetra- Harrowven, D. Pallin, Tetrahedron
hedron Lett. 1996, 37, 37893790. Lett. 2000, 41, 16271630.
97 K. C. Nicolaou, N. Winssinger, R. 116 Y. Kondo, T. Komine, M. Fujinami,
Hughes, C. Smethurst, S. Y. Cho, M. Uchiyama, T. Sakamoto, J. Comb.
Angew. Chem. Int. Ed. 2000, 39, 1084 Chem. 1999, 1, 123126.
1089; Angew. Chem. 2000, 112, 1126 117 L. F. Tietze, A. Steinmetz, Angew.
1130. Chem. Int. Ed. 1996, 35, 651652;
98 O. Seitz, H. Kunz, Angew. Chem. Int. Angew. Chem. 1996, 108, 682683.
Ed. 1995, 34, 803805; Angew. Chem. 118 U. Grether, H. Waldmann, Angew.
1995, 107, 901904. Chem. Int. Ed. 2000, 39, 16291632;
99 L. A. Thompson, J. A. Ellman, Tetra- Angew. Chem. 2000, 112, 1688
hedron Lett. 1994, 35, 93339336. 1691.
100 S.-e. Yoo, Y.-D. Gong, M.-Y. Choi, 119 C. R. Millington, R. Quarrel, G.
J.-s. Seo, K. Y. Yi, Tetrahedron Lett. Lowe, Tetrahedron Lett. 1998, 39,
2000, 41, 64156418. 72017204.
101 C. C. Leznoff, J. Y. Wong, Can. J. 120 J. R. Horton, L. M. Stamp, A.
Chem. 1973, 51, 37563764. Routledge, Tetrahedron Lett. 2000, 41,
102 C. C. Leznoff, S. Greenberg, Can. J. 91819184.
Chem. 1976, 54, 38243829. 121 P. Soucy, Y. L. Dory, P. Deslong-
103 Z. H. Xu, C. R. McArthur, C. C. champs, Synlett 2000, 11231126.
References 157
122 D. G. Mullen, G. Barany, J. Org. Curran, J. Org. Chem. 1997, 62,

Chem. 1988, 53, 52405248. 29172924.
123 L. A. Thompson, F. L. Moore, Y. C. 144 M. Schuster, N. Lucas, S. Blechert,
Moon, J. A. Ellman, J. Org. Chem. Chem. Commun. 1997, 823824.
1998, 63, 20662067. 145 L. S. Harikrishnan, H. D. H.
124 B. Chenera, J. A. Finkelstein, D. F. Showalter, Tetrahedron 2000, 56,
Veber, J. Am. Chem. Soc. 1995, 117, 515519.
1199912000. 146 J. M. J. Frechet, L. J. Nuyens, E.
125 M. J. Plunkett, J. A. Ellman, J. Org. Seymour, J. Am. Chem. Soc. 1979,
Chem. 1995, 60, 60066007. 101, 432436.
126 Y. Han, S. D. Walker, R. N. Young, 147 C. Pourbaix, F. Carreaux, B.
Tetrahedron Lett. 1996, 37, 2703 Carboni, H. Deleuze, Chem.
2706. Commun. 2000, 12751276.
127 T. L. Boehm, H. D. H. Showalter, J. 148 W. Li, K. Burgess, Tetrahedron Lett.
Org. Chem. 1996, 61, 64986499. 1999, 40, 65276530.
128 C. A. Briehn, T. Kirschbaum, P. 149 H. S. Overkleeft, P. R. Bos, B. G.
Bauerle, J. Org. Chem. 2000, 65, 352 Hekking, E. J. Gordon, H. L.
359. Ploegh, B. M. Kessler, Tetrahedron
129 T. Kirschbaum, C. A. Briehn, P. Lett. 2000, 41, 60056009.
Bauerle, Perkin 1 2000, 12111216. 150 D. L. Marshall, I. E. Liener, J. Org.
130 F. X. Woolard, J. Paetsch, J. A. Chem. 1970, 35, 867868.
Ellman, J. Org. Chem. 1997, 62, 151 Z. Timar, T. Gallagher, Tetrahedron
61026103. Lett. 2000, 41, 31733176.
131 M. J. Plunkett, J. A. Ellman, J. Org. 152 S. J. Jin, D. P. Holub, D. J.
Chem. 1997, 62, 28852893. Wustrow, Tetrahedron Lett. 1998, 39,
132 NovaBiochem, Catalog and Peptide 36513654.
Synthesis Handbook 2000. 153 K. C. Nicolaou, P. S. Baran, Y. L.
133 Y. Hu, J. J. A. Porco, Tetrahedron Lett. Zhong, J. Am. Chem. Soc. 2000, 122,
1998, 39, 27112714. 1024610248.
134 K. A. Newlander, B. Chenera, D. F. 154 C. Vanier, F. Lorge, A. Wagner, C.
Veber, N. C. F. Yim, M. L. Moore, J. Mioskowski, Angew. Chem. Int. Ed.
Org. Chem. 1997, 62, 67266732. 2000, 39, 16791683; Angew. Chem.
135 Y. H. Hu, J. A. Porco, J. W. Labadie, 2000, 112, 17451749.
O. W. Gooding, B. M. Trost, J. Org. 155 K. W. Jung, X. Y. Zhao, K. D. Janda,
Chem. 1998, 63, 45184521. Tetrahedron 1997, 53, 66456652.
136 N. D. Hone, S. G. Davies, N. J. 156 K. W. Jung, X. Y. Zhao, K. D. Janda,
Devereux, S. L. Taylor, A. D. Tetrahedron Lett. 1996, 37, 64916494.
Baxter, Tetrahedron Lett. 1998, 39, 157 X. Zhao, K. D. Janda, Bioorg. Med.
897900. Chem. Lett. 1998, 8, 24392442.
137 R. Maltais, M. R. Tremblay, D. 158 X. Y. Zhao, K. D. Janda, Tetrahedron
Poirier, J. Comb. Chem. 2000, 2, Lett. 1997, 38, 54375440.
604614. 159 H. C. Zhang, K. K. Brumeld, B. E.
138 S. D. Brown, R. W. Armstrong, J. Maryanoff, Tetrahedron Lett. 1997,
Org. Chem. 1997, 62, 70767077. 38, 24392442.
139 R. H. Crabtree, Chem. Commun. 160 K. C. Nicolaou, S. A. Snyder, A.
1999, 16111616. Bigot, J. A. Pfefferkorn, Angew.
140 Y. Lee, R. B. Silverman, J. Am. Chem. Chem. Int. Ed. 2000, 39, 10931096;
Soc. 1999, 121, 84078408. Angew. Chem. 2000, 112, 11351138.
141 S. Curtet, M. Langlois, Tetrahedron 161 I. Sucholeiki, Tetrahedron Lett. 1994,
Lett. 1999, 40, 85638566. 35, 73077310.
142 A. Studer, S. Hadida, R. Ferritto, 162 F. W. Forman, I. Sucholeiki, J. Org.
S. Y. Kim, P. Jeger, P. Wipf, D. P. Chem. 1995, 60, 523528.
Curran, Science 1997, 275, 823826. 163 K. C. Nicolaou, N. Winssinger, J.
143 A. Studer, P. Jeger, P. Wipf, D. P. Pastor, F. Murphy, Angew. Chem.
Int. Ed. 1998, 37, 25342537; Angew. Moore, J. Org. Chem. 1996, 61, 8160
Chem. 1998, 110, 26772680. 8168.
164 K. C. Nicolaou, J. Pastor, S. 180 J. K. Young, J. C. Nelson, J. S.
Barluenga, N. Winssinger, Chem. Moore, J. Am. Chem. Soc. 1994, 116,
Commun. 1998, 19471948. 1084110842.
165 T. Ruhland, K. Andersen, H. 181 L. Jones, J. S. Schumm, J. M. Tour,
Pedersen, J. Org. Chem. 1998, 63, J. Org. Chem. 1997, 62, 13881410.
92049211. 182 S. Brase, D. Enders, J. Kobberling,
166 B. Chenera (Smithkline Beecham F. Avemaria, Angew. Chem. Int. Ed.
Corporation), Patent No. WO PCT. 1998, 37, 34133415; Angew. Chem.
98/17695, 1995. 1998, 110, 36143616.
167 G. Marchand, J. F. Pilard, J. 183 S. Brase, S. Dahmen, Chem. Eur. J.
Simonet, Tetrahedron Lett. 2000, 41, 2000, 6, 18991905.
883885. 184 M. Lormann, S. Dahmen, S. Brase,
168 C. Garcia-Echeverria, Tetrahedron Tetrahedron Lett. 2000, 41, 3813
Lett. 1997, 38, 89338934. 3816.
169 H. Kuhn, W. P. Neumann, Synlett 185 S. Schunk, D. Enders, Org. Lett.
1994, 123124. 2000, 2, 907910.
170 R. Michels, M. Kato, W. Heitz, 186 M. Lormann, S. Brase, unpublished.
Makromol. Chem. 1976, 177, 2311 187 S. Brase, M. Schroen, Angew. Chem.
2320. Int. Ed. 1999, 38, 10711073; Angew.
171 H. E. Russell, R. W. A. Luke, M. Chem. 1999, 111, 11391142.
Bradley, Tetrahedron Lett. 2000, 41, 188 A. de Meijere, H. Nuske, M. Es-
52875290. Sayed, T. Labahn, M. Schroen, S.
172 K. C. Nicolaou, J. A. Pfefferkorn, Brase, Angew. Chem. Int. Ed. 1999, 38,
A. J. Roecker, G. Q. Cao, S. 36693672; Angew. Chem. 1999, 111,
Barluenga, H. J. Mitchell, J. Am. 38813884.
Chem. Soc. 2000, 122, 99399953. 189 F. Avemaria, V. Zimmermann, S.
173 K. C. Nicolaou, J. A. Pfefferkorn, Brase, Org. Lett. 2001, submitted.
H. J. Mitchell, A. J. Roecker, S. 190 S. Brase, M. Lormann, J. Heuts,
Barluenga, G. Q. Cao, R. L. Chem. Eur. J. 2001, in preparation.
Affleck, J. E. Lillig, J. Am. Chem. 191 S. Brase, S. Dahmen, J. Heuts,
Soc. 2000, 122, 99549967. Tetrahedron Lett. 1999, 40, 6201
174 K. C. Nicolaou, J. A. Pfefferkorn, 6203.
G. Q. Cao, Angew. Chem. Int. Ed. 192 M. E. P. Lormann, C. H. Walker, S.
2000, 39, 734739; Angew. Chem. Brase, Chem. Commun. 2001, sub-
2000, 112, 750755. mitted.
175 K. C. Nicolaou, G. Q. Cao, J. A. 193 S. Brase, J. Kobberling, D. Enders,
Pfefferkorn, Angew. Chem. Int. Ed. M. Wang, R. Lazny, S. Brandtner,
2000, 39, 739743; Angew. Chem. Tetrahedron Lett. 1999, 40, 2105
2000, 112, 755759. 2108.
176 K. C. Nicolaou, A. J. Roecker, J. A. 194 S. Brase, S. Dahmen, M. Pfeffer-
Pfefferkorn, G. Q. Cao, J. Am. korn, J. Comb. Chem. 2000, 2, 710
Chem. Soc. 2000, 122, 29662967. 717.
177 K. C. Nicolaou, H. J. Mitchell, K. 195 S. Dahmen, S. Brase, Org. Lett. 2000,
C. Fylaktakidou, H. Suzuki, R. M. 2, 35633565.
Rodrguez, Angew. Chem. Int. Ed. 196 a) C. Pilot, Matrise de Chimie
2000, 39, 10891093; Angew. Chem. 1999, RWTH Aachen/Universite
2000, 112, 11311135. Strasbourg. b) C. Pilot, S. Dahmen,
178 K. C. Nicolaou, C. N. C. Boddy, S. F. Lauterwasser, S. Brase, Tetra-
Brase, N. Winssinger, Angew. Chem. hedron Lett. 2001, 42, 91799181.
Int. Ed. 1999, 38, 20962152; Angew. 197 S. Brase, Chimica Oggi 2000, 18(9),
Chem. 1999, 111, 22302287. 1418.
179 J. C. Nelson, J. K. Young, J. S. 198 S. Dahmen, S. Brase, Angew. Chem.
References 159
Int. Ed. 2000, 39, 36813683; Angew. 220 M. J. Plater, A. M. Murdoch, J. R.

Chem. 2000, 112, 38273830. Morphy, Z. Rankovic, D. C. Rees, J.
199 J. Heuts, S. Brase, unpublished. Comb. Chem. 2000, 2, 508512.
200 J. Rademann, J. Smerdka, G. Jung, 221 J. R. Morphy, Z. Rankovic, D. C.
P. Grosche, D. Schmid, Angew. Rees, Tetrahedron Lett. 1996, 37, 3209
Chem. Int. Ed. 2001, 40, 381385. 3212.
201 S. Brase, S. Dahmen, M. Schroen, 222 P. H. Toy, T. S. Reger, K. D. Janda,
unpublished. J. Comb. Chem. 2000, 2, 22052207.
202 S. Brase, S. Dahmen, C. Popescu, M. 223 A. R. Brown, D. C. Rees, Z.
Schroen, F.-J. Wortmann, Polym. Rankovic, J. R. Morphy, J. Am.
Degr. Stab. in press. Chem. Soc. 1997, 119, 32883295.
203 W. D. F. Meutermans, P. F. 224 X. H. Ouyang, R. W. Armstrong, M.
Alewood, Tetrahedron Lett. 1995, 36, M. Murphy, J. Org. Chem. 1998, 63,
77097712. 10271032.
204 R. B. Merrield, L. D. Vizioli, H. 225 X. H. Ouyang, A. S. Kiselyov,
G. Boman, Biochemistry 1982, 21, Tetrahedron Lett. 1999, 40, 5827
50205031. 5830.
205 J. P. Tam, W. F. Heath, R. B. 226 W. Bannwarth, J. Huebscher, R.
Merrield, J. Am. Chem. Soc. 1983, Barner, Bioorg. Med. Chem. Lett.
105, 64426455. 1996, 6, 15251528.
206 H. Yaijima, N. Fujii, H. Ogawa, H. 227 S. R. Chhabra, H. Parekh, A. N.
Kawatani, J. Chem. Soc., Chem. Khan, B. W. Bycroft, B. Kellam,
207 A. R. Mitchell, S. B. H. Kent, M. 228 S. R. Chhabra, A. N. Khan, B. W.
Engelhard, R. B. Merrield, J. Bycroft, Tetrahedron Lett. 2000, 41,
Org. Chem. 1978, 43, 28452852. 10991102.
208 K. C. Nicolaou, N. Winssinger, J. 229 J. D. Glass, A. Talansky, Z. Gronka,
Pastor, F. DeRoose, J. Am. Chem. I. L. Schwartz, R. Walter, J. Am.
Soc. 1997, 119, 449450. Chem. Soc. 1974, 96, 64766480.
209 A. Mazurov, Tetrahedron Lett. 2000, 230 A. M. Bray, N. J. Maeji, A. G.
41, 710. Jhingran, R. M. Valerio,
210 D. R. Englebretsen, C. T. Choma, G. Tetrahedron Lett. 1991, 32, 61636166.
T. Robillard, Tetrahedron Lett. 1998, 231 G. Faita, A. Paio, P. Quadrelli, F.
39, 49294932. Rancati, P. Seneci, Tetrahedron Lett.
211 P. R. Hansen, C. E. Olsen, A. Holm, 2000, 41, 12651269.
Bioconj. Chem. 1998, 9, 126131. 232 A. J. Souers, A. A. Virgilio, S. S.
212 Y. X. Han, G. Barany, J. Org. Chem. Schurer, J. A. Ellman, T. P. Kogan,
1997, 62, 38413848. H. E. West, W. Ankener, P.
213 M. C. Munson, G. Barany, J. Am. Vanderslice, Bioorg. Med. Chem. Lett.
Chem. Soc. 1993, 115, 1020310210. 1998, 8, 22972302.
214 G. Mezo, N. Mihala, G. Koczan, F. 233 K. Kurokawa, H. Kumihara, H.
Hudecz, Tetrahedron 1998, 54, 6757 Kondo, Bioorg. Med. Chem. Lett. 2000,
6766. 10, 18271830.
215 D. Limal, J. P. Briand, P. Dalbon, 234 A. A. Virgilio, S. C. Schurer, J. A.
M. Jolivet, J. Pept. Res. 1998, 52, Ellman, Tetrahedron Lett. 1996, 37,
121129. 69616964.
216 B. Yan, H. Gstach, Tetrahedron Lett. 235 A. J. Souers, A. A. Virgilio, A.
1996, 37, 83258328. Rosenquist, W. Fenuik, J. A.
217 J. Blake, C. H. Li, J. Am. Chem. Soc. Ellman, J. Am. Chem. Soc. 1999, 121,
1968, 90, 58825884. 18171825.
218 E. G. Mata, Tetrahedron Lett. 1997, 38, 236 F. Berst, A. B. Holmes, M. Ladlow,
63356338. P. J. Murray, Tetrahedron Lett. 2000,
219 J. D. Winkler, W. McCoull, Tetra- 41, 66496653.
hedron Lett. 1998, 39, 49354936. 237 F. Stieber, U. Grether, H.
Waldmann, Angew. Chem. Int. Ed. 260 A. Ajayagosh, V. N. R. Pillai, J. Org.

1999, 38, 10731077; Angew. Chem. Chem. 1987, 52, 57145717.
1999, 111, 11421145. 261 P. Lloyd-Williams, M. Gairi, F.
238 D. H. Rich, S. K. Gurwara, J. Am. Albericio, E. Giralt, Tetrahedron
Chem. Soc. 1975, 97, 15751579. 1993, 49, 1006910078.
239 S. J. Teague, Tetrahedron Lett. 1996, 262 H. Venkatesan, M. M. Greenberg, J.
37, 57515754. Org. Chem. 1996, 61, 525529.
240 R. P. Hammer, F. Albericio, E. 263 P. Lloyd-Williams, M. Gairi, F.
Giralt, G. Barany, Int. J. Pept. Albericio, E. Giralt, Tetrahedron
Protein Res. 1990, 28, 3145. 1991, 49, 98679880.
241 C. P. Holmes, D. G. Jones, J. Org. 264 R. S. Rock, S. I. Chan, J. Org. Chem.
Chem. 1995, 60, 23182319. 1996, 61, 15261529.
242 S. Peukert, B. Giese, J. Org. Chem. 265 J. C. Sheehan, K. Umezawa, J. Org.
1998, 63, 90459051. Chem. 1973, 38, 37713774.
243 R. Glatthar, B. Giese, Org. Lett. 266 A. Routledge, C. Abell, S.
2000, 2, 23152317. Balasubramanian, Tetrahedron Lett.
244 H. B. Lee, S. Balasubramanian, J. 1997, 38, 12271230.
Org. Chem. 1999, 64, 34543460. 267 T. D. Ryba, P. G. Harran, Org. Lett.
245 S.-S. Wang, J. Org. Chem. 1976, 41, 2000, 2, 851853.
32583261. 268 S. C. McKeown, S. P. Watson, R. A.
246 J. P. Tam, R. D. Dimarchi, R. B. E. Carr, P. Marshall, Tetrahedron
Merrield, Int. J. Pept. Protein Res. Lett. 1999, 40, 24072410.
1980, 16, 412425. 269 E. B. Akerblom, Mol. Diversity 1999,
247 D. H. Rich, S. K. Gurwara, J. Chem. 4, 5369.
Soc., Chem. Commun. 1973, 610611. 270 C. Dellaquila, J. L. Imbach, B.
248 A. Aiyaghosh, V. N. R. Pillai, Rayner, Tetrahedron Lett. 1997, 38,
Tetrahedron 1988, 44, 66616666. 52895292.
249 U. Zehavi, A. Patchornik, J. Am. 271 E. B. Akerblom, A. S. Nygren, K. H.
Chem. Soc. 1973, 95, 56735677. Agback, Mol. Diversity 1998, 3, 137
250 D. L. Whitehouse, S. N. Savinov, D. 148.
J. Austin, Tetrahedron Lett. 1997, 38, 272 M. R. Tremblay, D. Poirier, Tetra-
78517852. hedron Lett. 1999, 40, 12771280.
251 D. J. Yoo, M. M. Greenberg, J. Org. 273 S. C. Schurer, S. Blechert, Synlett
Chem. 1995, 60, 33583364. 1998, 166168.
252 M. Rinnova, M. Novakova, V. 274 W. C. Cheng, C. Halm, J. B. Evarts,
Kasicka, J. Jiracek, J. Pept. Sci. 2000, M. M. Olmstead, M. J. Kurth, J.
6, 355365. Org. Chem. 1999, 64, 85578562.
253 A. Ajayagosh, V. N. R. Pillai, J. Org. 275 J. U. Peters, S. Blechert, Synlett
Chem. 1990, 55, 28262829. 1997, 348350.
254 C. P. Holmes, J. Org. Chem. 1997, 62, 276 J. Pernerstorfer, M. Schuster, S.
23702380. Blechert, Chem. Commun. 1997,
255 M. Smet, L. X. Liao, W. Dehaen, D. 19491950.
V. McGrath, Org. Lett. 2000, 2, 511 277 K. C. Nicolaou, N. Winssinger, J.
513. Pastor, S. Ninkovic, F. Sarabia, Y.
256 B. B. Brown, D. S. Wagner, H. M. He, D. Vourloumis, Z. Yang, T. Li,
Geysen, Mol. Diversity 1995, 1, 412. P. Glannakakou, E. Hamel, Nature
257 R. Rodebaugh, B. Fraser-Reid, H. 1997, 387, 268272.
M. Geysen, Tetrahedron Lett. 1997, 38, 278 A. D. Piscopio, J. F. Miller, K.
76537656. Koch, Tetrahedron Lett. 1997, 38,
258 S. M. Sternson, S. L. Schreiber, 71437146.
Tetrahedron Lett. 1998, 39, 74517454. 279 A. D. Piscopio, J. F. Miller, K.
259 J. J. Baldwin, J. J. Burbaum, I. Koch, Tetrahedron Lett. 1998, 39,
Henderson, M. H. J. Ohlmeyer, J. 26672670.
Am. Chem. Soc. 1995, 117, 55885589. 280 A. D. Piscopio, J. F. Miller, K.
References 161
Koch, Tetrahedron 1999, 55, 8189 P. S. Gilbert, B. G. Main, K. Ple, J.

8198. Org. Chem. 2001, 66, 22402245.
281 J. H. Van Maarseveen, J. A. J. den 298 S. Hoffmann, R. Frank, Tetrahedron
Hartog, V. Engelen, E. Finner, G. Lett. 1994, 35, 77637766.
Visser, C. G. Kruse, Tetrahedron Lett. 299 O. Lorthioir, S. C. McKeown, N. J.
1996, 37, 82498252. Parr, M. Washington, S. P.
282 J. J. N. Veerman, J. H. Van Watson, Tetrahedron Lett. 2000, 41,
Maarseveen, G. M. Visser, C. G. 86098613.
Kruse, H. E. Schoemaker, H. 300 T. Masquelin, N. Meunier, F.
Hiemstra, F. P. J. T. Rutjes, Eur. J. Gerber, G. Rosse, Hetrocycles 1998,
Org. Chem. 1998, 25832589. 48, 24892505.
283 L. G. Melean, W.-C. Haase, P. H. 301 L. Yang, Tetrahedron Lett. 2000, 41,
Seeberger, Tetrahedron Lett. 2000, 41, 69816984.
43294333. 302 H. Zhang, H. Ye, A. Moretto, K.
284 B. Sauerbrei, V. Jungmann, H. Brumeld, B. Maryanoff, Org. Lett.
Waldmann, Angew. Chem. Int. Ed. 2000, 2, 8992.
1998, 37, 11431146; Angew. Chem. 303 C. Atrash, M. Bradley, Chem.
1998, 110, 11871190. Commun. 1997, 13971398.
285 G. Bohm, J. Dowden, D. C. Rice, I. 304 K. C. Nicolaou, J. Pastor, N.
Burgess, J. F. Pilard, B. Guilbert, Winssinger, F. Murphy, J. Am.
A. Haxton, R. C. Hunter, N. J. Chem. Soc. 1998, 120, 51325133.
Turner, S. L. Flitsch, Tetrahedron 305 C. R. Johnson, B. R. Zhang,
Lett. 1998, 39, 38193822. Tetrahedron Lett. 1995, 36, 92539256.
286 B. J. Backes, J. A. Ellman, J. Am. 306 F. Camps, J. Castells, J. Pi, Ann.
Chem. Soc. 1994, 116, 1117111172. Quim. 1974, 70, 848849.
287 B. J. Backes, J. A. Ellman, J. Org. 307 Y. D. Gong, S. Najdi, M. M.
Chem. 1999, 64, 23222330. Olmstead, M. J. Kurth, J. Org.
288 B. J. Backes, A. A. Virgilio, J. A. Chem. 1998, 63, 30813086.
Ellman, J. Am. Chem. Soc. 1996, 118, 308 S. H. Lee, S. H. Chung, Y. S. Lee,
30553056. Tetrahedron Lett. 1998, 39, 94699472.
289 G. W. Kenner, J. R. McDermott, R. 309 K. H. Park, E. Abbate, S. Najdi, M.
C. Sheppard, J. Chem. Soc., Chem. M. Olmstead, M. J. Kurth, Chem.
Commun. 1971, 636637. Commun. 1998, 16791680.
290 C. Hulme, J. Peng, G. Morton, 310 K. H. Park, M. M. Olmstead, M. J.
J. M. Salvino, T. Herpin, R. Kurth, J. Org. Chem. 1998, 63, 6579
Labaudiniere, Tetrahedron Lett. 1998, 6585.
39, 72277230. 311 S. Hanessian, R. Y. Yang, Tetrahedron
291 R. Sola, R. Saguer, M. L. David, Lett. 1996, 37, 58355838.
R. Pascal, J. Chem. Soc., Chem. 312 L. J. Wilson, M. Li, D. E. Portlock,
Commun. 1995, 17861788. Tetrahedron Lett. 1998, 39, 5135
292 R. Sola, J. Mery, R. Pascal, Tetra- 5138.
hedron Lett. 1996, 37, 91959198. 313 S. W. Kim, J. S. Koh, E. J. Lee, S. Ro,
293 M. H. Todd, S. F. Oliver, C. Abell, Mol. Diversity 1998, 3, 129132.
Org. Lett. 1999, 1, 11491151. 314 S. W. Kim, S. Y. Ahn, J. S. Koh, J. H.
294 A. Link, S. Vancalenbergh, P. Lee, S. Ro, H. Y. Cho, Tetrahedron
Herdewijn, Tetrahedron Lett. 1998, Lett. 1997, 38, 46034606.
39, 51755176. 315 J. Matthews, R. A. Rivero, J. Org.
295 A. Golisade, J. C. Bressi, S. Van Chem. 1997, 62, 60906092.
Calenbergh, M. H. Gelb, A. Link, J. 316 B. A. Dressman, L. A. Spangle, S. W.
Comb. Chem. 2000, 2, 537544. Kaldor, Tetrahedron Lett. 1996, 37,
296 M. H. Lyttle, D. Hudson, R. M. 937940.
Cook, Nucl. Acids Res. 1996, 24, 2793 317 J. Stadlwieser, E. P. Ellmerer-
2798. Muller, A. Tako, N. Maslouh, W.
297 C. L. Beech, J. F. Coope, G. Fairley, Bannwarth, Angew. Chem. Int. Ed.
1998, 37, 14021404; Angew. Chem. Goodman, W. Kolbeck, Biopolymers

1998, 110, 14871489. 1996, 38, 295300.
318 S. H. DeWitt, J. K. Kiely, C. J. 335 L. F. Tietze, A. Steinmetz, Synlett
Stankovic, M. C. Schroeder, D. M. 1996, 667668.
R. Cody, M. R. Pavia, Proc. Natl. 336 L. F. Tietze, A. Steinmetz, F.
Acad. Sci. USA 1993, 90, 69096913. Balkenhohl, Bioorg. Med. Chem. Lett.
319 A. Boeijen, J. A. W. Kruijtzer, R. M. 1997, 7, 13031306.
J. Liskamp, Bioorg. Med. Chem. Lett. 337 T. T. Romoff, L. Ma, Y. W. Wang,
1998, 8, 23752380. D. A. Campbell, Synlett 1998, 1341
320 H. P. Buchstaller, Tetrahedron 1998, 1342.
54, 34653470. 338 L. Weber, P. Iaiza, G. Biringer, P.
321 P. ten Holte, L. Thijs, B. Zwanen- Barbier, Synlett 1998, 11561158.
burg, Tetrahedron Lett. 1998, 39, 339 J. Matthews, R. A. Rivero, J. Org.
74077410. Chem. 1998, 63, 48084810.
322 V. S. Goodfellow, C. P. Laudeman, 340 B. A. Kulkarni, A. Ganesan,
J. I. Gerrity, M. Burkard, E. Tetrahedron Lett. 1998, 39, 43694373.
Strobel, J. S. Zuzack, D. A. McLeod, 341 A. L. Smith, C. G. Thomson, P. D.
Mol. Diversity 1996, 2, 97102. Leeson, Bioorg. Med. Chem. Lett. 1996,
323 A. K. Szardenings, T. S. Burkoth, 6, 14831486.
H. H. Lu, D. W. Tien, D. A. 342 S. A. Kolodziej, B. C. Hamper,
Campbell, Tetrahedron 1997, 53, Tetrahedron Lett. 1996, 37, 52775280.
65736593. 343 M. M. Sim, C. L. Lee, A. Ganesan,
324 J. Kowalski, M. A. Lipton, Tetra- Tetrahedron Lett. 1998, 39, 63996402.
hedron Lett. 1996, 37, 58395840. 344 F. Albericio, J. Garcia, E. L.
325 A. Van Loevezijn, J. H. Van Michelotti, E. Nicolas, C. M. Tice,
Maarseveen, K. Stegman, G. M. Tetrahedron Lett. 2000, 41, 31613163.
Visser, G. J. Koomen, Tetrahedron 345 W. L. Huang, R. M. Scarborough,
Lett. 1998, 39, 47374740. Tetrahedron Lett. 1999, 40, 2665
326 P. P. Fantauzzi, K. M. Yager, 2668.
Tetrahedron Lett. 1998, 39, 12911294. 346 C. Le Hetet, M. David, F. Carreaux,
327 R. A. Smith, M. A. Bobko, W. Lee, B. Carboni, A. Sauleau, Tetrahedron
Bioorg. Med. Chem. Lett. 1998, 8, Lett. 1997, 38, 51535156.
23692374. 347 J. F. Pons, Q. Mishir, A. Nouvet, F.
328 W. R. Li, S. Z. Peng, Tetrahedron Lett. Brookeld, Tetrahedron Lett. 2000,
1998, 39, 73737376. 41, 49654968.
329 A. K. Szardenings, D. Harris, S. 348 E. J. Guthrie, J. Macritchie, R. C.
Lam, L. H. Shi, D. Tien, Y. W. Wang, Hartley, Tetrahedron Lett. 2000, 41,
D. V. Patel, M. Navre, D. A. 49874990.
Campbell, J. Med. Chem. 1998, 41, 349 A. Mazurov, Bioorg. Med. Chem. Lett.
21942200. 2000, 10, 6770.
330 B. O. Scott, A. C. Siegmund, C. K. 350 S. Brase, R. Lazny, unpublished.
Marlowe, Y. Pei, K. L. Spear, Mol. 351 B. K. Lorsbach, R. B. Miller, M. J.
Diversity 1996, 1, 125134. Kurth, J. Org. Chem. 1996, 61, 8716
331 A. Golebiowski, S. R. Klopfenstein, 8717.
J. J. Chen, X. Shao, Tetrahedron Lett. 352 B. A. Lorsbach, J. T. Bagdanoff,
2000, 41, 48414844. R. B. Miller, M. J. Kurth, J. Org.
332 D. A. Goff, R. N. Zuckermann, J. Chem. 1998, 63, 22442250.
Org. Chem. 1995, 60, 57445745. 353 S. E. Gibson, N. J. Hales, M. A.
333 J. P. Mayer, J. W. Zhang, K. Peplow, Tetrahedron Lett. 1999, 40,
Bjergarde, D. M. Lenz, J. J. 14171418.
Gaudino, Tetrahedron Lett. 1996, 37, 354 M. F. Semmelhack, G. Hilt, J. H.
80818084. Colley, Tetrahedron Lett. 1998, 39,
334 L. Moroder, J. Lutz, F. Grams, S. 76837686.
Rudolph-Bohner, G. Osapay, M. 355 A. C. Comely, S. E. Gibson, N. J.
References 163
Hales, Chem. Commun. 1999, 2075 374 A. Patchornik, M. A. Kraus, J. Am.

2076. Chem. Soc. 1970, 92, 72877289.
356 M. A. Gallop (Glaxo Wellcome Inc., 375 B. C. Hamper, K. Z. Gan, T. J. Owen,
USA), US Patent No. 6057465 A, Tetrahedron Lett. 1999, 40, 49734976.
2000. 376 S. P. Douglas, D. M. Whiteld, J. J.
357 A. C. Comely, S. E. Gibson, N. J. Krepinsky, J. Am. Chem. Soc. 1995,
Hales, M. A. Peplow, PCT Int. Appl. 117, 21162117.
WO 0007966, 2000. 377 M. R. Pavia, G. Whitesides, D. G.
358 K. I. Washizuka, K. Nagai, S. Hangauer, M. E. Hediger (Sphinx
Minakata, I. Ryu, M. Komatsu, Pharmaceuticals Corporation), Patent
Tetrahedron Lett. 2000, 41, 691695. No. WO PCT. 95/04277, 1995.
359 L. Blanco, R. Bloch, E. Bugnet, S. 378 A. B. Reitz, Curr. Opin. Drug. Disc.
Deloisy, Tetrahedron Lett. 2000, 41, Develop. 1999, 2, 358364.
78757878. 379 D. Obrecht, J. M. Villalgordo in:
360 D. L. Whitehouse, K. H. Nelson, Solid-Supported Combinatorial and
S. N. Savinov, R. S. Lowe, D. J. Parallel Synthesis of Small-Molecular-
Austin, Bioorg. Med. Chem. Lett. 1998, Weight Compound Libraries, Elsevier,
6, 12731282. Oxford, 1998, p. 98.
361 M. R. Gowravaram, M. A. Gallop, 380 F. Zaragoza, Angew. Chem. Int. Ed.
Tetrahedron Lett. 1997, 38, 69736976. 2000, 39, 20772079; Angew. Chem.
362 D. L. Whitehouse, K. H. J. Nelson, 2000, 112, 21582159.
S. N. Savinov, D. J. Austin, Tetra- 381 J. K. Rueter, S. O. Nortey, E. W.
hedron Lett. 1997, 38, 71397142. Baxter, G. C. Leo, A. B. Reitz,
363 A. C. Spivey, C. M. Diaper, H. Tetrahedron Lett. 1998, 39, 975978.
Adams, A. J. Rudge, J. Org. Chem. 382 J. A. Hunt, W. R. Roush, J. Am.
2000, 65, 52535263. Chem. Soc. 1996, 118, 99989999.
364 I. Hughes, Tetrahedron Lett. 1996, 37, 383 R. Mohan, Y.-L. Chou, M. M.
75957598. Morrissey, Tetrahedron Lett. 1996, 37,
365 R. M. Slade, M. A. Phillips, J. G. 39633966.
Berger, Mol. Diversity 1998, 4, 215 384 L. M. Gayo, M. J. Suto, Tetrahedron
219. Lett. 1997, 38, 211214.
366 I. Sucholeiki (Solid-phase Sciences 385 M. Schuster, J. Pernerstorfer, S.
Corporation), Patent No. US5684130, Blechert, Angew. Chem. Int. Ed.
1997. 1996, 35, 19791980; Angew. Chem.
367 H. Kamogawa, A. Kanzawa, M. 1996, 108, 21112112.
Kadoya, T. Naito, M. M. Nanasawa, 386 S. C. Stinson, Chem. Ind. News 1999,
Bull. Chem. Soc. Jpn. 1983, 56, 762 77(41), 101120.
765. 387 S. C. Stinson, Chem. Ind. News 1999,
368 P. Garibay, J. Nielsen, T. Hoeg- 78(43), 5578.
Jensen, Tetrahedron Lett. 1998, 39, 388 J. H. Kirchhoff, M. E. P. Lormann,
22072210. S. Brase, Chimica Oggi 2001, in
369 Commercially available from press.
CalBioChem-NovaBioChem (Swiss). 389 M. Kawana, S. Emoto, Tetrahedron
370 Commercially available from Lett. 1972, 13, 48554858.
Advanced Chem Tech. 390 M. Kawana, S. Emoto, Bull. Chem.
371 J. M. Cobb, M. T. Fiorini, C. R. Soc. Jpn. 1974, 47, 160165.
Goddard, M.-E. Theoclitou, C. 391 P. M. Worster, C. R. McArthur, C.
Abell, Tetrahedron Lett. 1999, 40, C. Leznoff, Angew. Chem. Int. Ed.
10451048. Engl. 1979, 18, 221; Angew. Chem.
372 M. M. Sim, C. L. Lee, A. Ganesan, 1979, 91, 255.
Tetrahedron Lett. 1998, 39, 2195 392 C. R. McArthur, P. M. Worster,
2198. J.-L. Jiang, C. C. Leznoff, Can. J.
373 F. Zaragoza, Tetrahedron Lett. 1997, Chem. 1982, 60, 18361841.
38, 72917294. 393 S. M. Allin, S. J. Shuttleworth,
Tetrahedron Lett. 1996, 37, 8023 Thompson, J. A. Ellman, J. Org.

8026. Chem. 1997, 62, 12401256.
394 C. W. Phoon, C. Abell, Tetrahedron 414 A. S. Hernandez, J. C. Hodges, J.
Lett. 1998, 39, 26552658. Org. Chem. 1997, 62, 48614864.
395 V. Purandare, S. Natarajan, Tetra- 415 K. Ngu, D. V. Patel, Tetrahedron Lett.
hedron Lett. 1997, 38, 87778780. 1997, 38, 973976.
396 K. Burgess, D. Lim, Chem. Commun. 416 P. S. Furth, M. S. Reitman, A. F.
1997, 785786. Cook, Tetrahedron Lett. 1997, 38,
397 S. P. Bew, S. D. Bull, S. G. Davies, 54035406.
Tetrahedron Lett. 2000, 41, 75777581. 417 P. Conti, D. Demont, J. Cals, H. C.
398 A. Volonterio, P. Bravo, N. J. Ottenheijm, D. Leysen,
Moussier, M. Zanda, Tetrahedron Tetrahedron Lett. 1997, 38, 29152918.
Lett. 2000, 41, 65176521. 418 C. Kay, P. J. Murray, L. Sandow, A.
399 A. R. Colwell, L. R. Duckwall, R. B. Holmes, Tetrahedron Lett. 1997, 38,
Brooks, S. P. McManus, J. Org. 69416944.
Chem. 1981, 46, 30973102. 419 N. W. Hird, K. Irie, K. Nagai,
400 H. S. Moon, N. E. Schore, M. J. Tetrahedron Lett. 1997, 38, 71117114.
Kurth, J. Org. Chem. 1992, 57, 6088 420 L. J. Fitzpatrick, R. A. Rivero,
401 H. S. Moon, N. E. Schore, M. J. 421 H.-P. Hsieh, Y.-T. Wu, S.-T. Chen,
Kurth, Tetrahedron Lett. 1994, 35, Chem. Commun. 1998, 649650.
89158918. 422 B. A. Dressmann, U. Singh, S. W.
402 J. H. Kirchhoff, J. Kobberling, Kaldor, Tetrahedron Lett. 1998, 39,
D. Enders, S. Brase, Deutsche 36313634.
Patentanmeldung 100 07 704.8, 2000. 423 J. G. Breitenbucher, C. R. Johnson,
403 D. Enders, J. H. Kirchhoff, J. M. Haight, J. C. Phelan, Tetrahedron
Kobberling, T. H. Peiffer, Org. Lett. Lett. 1998, 39, 12951298.
2001, 3, 12411244. 424 M. Del Fresno, J. Alsina, M. Royo,
404 B. J. Backes, D. R. Dragoli, J. A. G. Barany, F. Albericio, Tetrahedron
Ellman, J. Org. Chem. 1999, 64, Lett. 1998, 39, 26392642.
54725478. 425 S. R. Chhabra, A. N. Khan, B. W.
405 J. Hachtel, H. J. Gais, Eur. J. Org. Bycroft, Tetrahedron Lett. 1998, 39,
Chem. 2000, 14571465. 35853588.
406 S. Itsuno, A. A. El-Shehawy, M. Y. 426 A. Nefzi, M. A. Giulianotti, N. A.
Abdelaal, K. Ito, New J. Chem. 1998, Ong, R. A. Houghten, Org. Lett.
22, 775777. 2000, 2, 33493350.
407 K. Oertel, G. Zech, H. Kunz, Angew. 427 J. M. Ostresh, C. C. Schoner, V. T.
Chem. Int. Ed. 2000, 39, 14311433; Hamashin, A. Nefzi, J. P. Meyer,
Angew. Chem. 2000, 112, 14891491. R. A. Houghten, J. Org. Chem. 1998,
408 T. Henkel, R. M. Brunne, H. 63, 86228623.
Muller, F. Reichel, Angew. Chem. 428 R. A. Tommasi, P. G. Nantermet,
Int. Ed. 1999, 38, 643647. M. J. Shapiro, J. Chin, W. K. D.
409 J. G. Breitenbucher, G. Figliozzi, Brill, K. Ang, Tetrahedron Lett. 1998,
Tetrahedron Lett. 2000, 41, 4311 39, 54775480.
4315. 429 A. V. Purandare, M. A. Poss,
410 M. Meisenbach, W. Voelter, Chem. Tetrahedron Lett. 1998, 39, 935938.
Lett. 1997, 12651266. 430 L. Gauzy, Y. Le Merrer, J. C.
411 J. Alsina, F. Rabanal, E. Giralt, F. Depezay, F. Clerc, S. Mignani,
Albericio, Tetrahedron Lett. 1994, 35, Tetrahedron Lett. 1999, 40, 60056008.
96339636. 431 A. R. Katritzky, L. Xie, G. Zhang,
412 L. Gouilleux, J. A. Fehrentz, F. Tetrahedron Lett. 1997, 38, 70117014.
Winternitz, J. Martinez, Tetra- 432 E. A. Boyd, W. C. Chan, V. M. Loh,
hedron Lett. 1996, 37, 70317034. Tetrahedron Lett. 1996, 37, 1647
413 C. G. Boojamra, K. M. Burow, L. A. 1650.
References 165
433 M. A. Youngman, S. L. Dax, Munoz, Tetrahedron Lett. 1998, 39,

Tetrahedron Lett. 1997, 38, 63476350. 217220.
434 J. J. McNally, M. A. Youngman, 452 C. X. Chen, B. Munoz, Tetrahedron
S. L. Dax, Tetrahedron Lett. 1998, 39, Lett. 1998, 39, 34013404.
967970. 453 M. F. Gordeev, D. V. Patel, E. M.
435 W. J. Hoekstra, B. E. Maryanoff, Gordon, J. Org. Chem. 1996, 61, 924
P. Andrade-Gordon, J. H. Cohen, 928.
M. J. Costanzo, B. P. Damiano, B. J. 454 J. F. Tolborg, K. J. Jensen, Chem.
Haertlein, B. D. Harris, J. A. Commun. 2000, 147148.
Kauffman, P. M. Keane, D. F. 455 J. M. Smith, V. Krchnak, Tetrahedron
McComsey, F. J. Villani, S. C. Lett. 1999, 40, 76337636.
Yabut, Bioorg. Med. Chem. Lett. 1996, 456 J. Kraxner, M. Arlt, P. Gmeiner,
6, 23712376. Synlett 2000, 125127.
436 W. J. Hoekstra, M. N. Greco, S. C. 457 A. L. Smith, G. I. Stevenson, C. J.
Yabut, B. L. Hulshizer, B. E. Swain, J. L. Castro, Tetrahedron Lett.
Maryanoff, Tetrahedron Lett. 1997, 1998, 39, 83178320.
38, 26292632. 458 F. E. K. Kroll, R. Morphy, D. Rees,
437 K. H. Bleicher, J. R. Wareing, D. Gani, Tetrahedron Lett. 1997, 38,
Tetrahedron Lett. 1998, 39, 4591 85738576.
4594. 459 M. Wang, S. Brase, unpublished.
438 Y. Hidai, T. Kan, T. Fukuyama, 460 P. Blaney, R. Grigg, Z. Rankovic,
Tetrahedron Lett. 1999, 40, 47114714. M. Thoroughgood, Tetrahedron Lett.
439 K. Yamada, S. I. Nishimura, Tetra- 2000, 41, 66356638.
hedron Lett. 1995, 36, 94939496. 461 P. Blaney, R. Grigg, Z. Rankovic,
440 H. Stephensen, F. Zaragoza, J. Org. M. Thoroughgood, Tetrahedron Lett.
Chem. 1997, 62, 60966097. 2000, 41, 66396642.
441 J. F. W. Keana, M. Shimizu, K. K. 462 C. Y. Ho, M. J. Kukla, Tetrahedron
Jernsted, J. Org. Chem. 1986, 51, Lett. 1997, 38, 27992802.
16411644. 463 J. J. N. Veerman, F. P. J. T. Rutjes,
442 M. W. Wilson, A. S. Hernandez, J. H. van Maarseveen, H. Hiemstra,
A. P. Calvet, J. C. Hodges, Mol. Tetrahedron Lett. 1999, 40, 60796082.
Diversity 1998, 3, 95112. 464 E. W. Baxter, J. K. Rueter, S. O.
443 R. Leger, R. Yen, M. W. She, V. J. Nortey, A. B. Reitz, Tetrahedron Lett.
Lee, S. J. Hecker, Tetrahedron Lett. 1998, 39, 979982.
1998, 39, 41714174. 465 T. Takahashi, S. Tomida, H. Inoue,
444 D. L. McMinn, M. M. Greenberg, T. Doi, Synlett 1998, 12611263.
Tetrahedron 1996, 52, 38273840. 466 T. Dahmen, S. Brase, unpublished.
445 L. E. Canne, R. L. Winston, S. B. H. 467 M. Lormann, S. Brase, H. Vogt in:
Kent, Tetrahedron Lett. 1997, 38, Proceedings of ECSOC-4, The Third
33613364. International Electronic Conference
446 F. J. Wang, J. R. Hauske, Tetrahedron on Synthetic Organic Chemistry,
Lett. 1997, 38, 65296532. http://www.mdpi.org/ecsoc-4.htm,
447 M. F. Gordeev, G. W. Luehr, H. C. Scope and Limitation of a Tin
Hui, E. M. Gordon, D. V. Patel, Promoted Amidation on Solid-phase:
Tetrahedron 1998, 54, 1587915890. A New Monitoring for the T1
448 K. H. Bleicher, J. R. Wareing, Triazene Linker, September 130, 2000.
Tetrahedron Lett. 1998, 39, 45874590. 468 D. Obrecht, C. Abrecht, A.
449 J. H. Kirchhoff, S. Brase, D. Grieder, J. M. Villalgordo, Helv.
Enders, J. Comb. Chem. 2001, 3, 71 Chim. Acta 1997, 80, 6572.
77. 469 P. J. Das, S. Khound, J. Dutta,
450 P. S. Furth, M. S. Reitman, R. Indian J. Chem. Sect. B 1995, 34, 161
Gentles, A. F. Cook, Tetrahedron Lett. 163.
1997, 38, 66436646. 470 S. Brase, C. Gil, K. Knepper, Bioorg.
451 X. Chen, I. A. McDonald, B. Med. Chem. 2001, submitted.
471 D. Tumelty, K. Cao, C. P. Holmes, 492 M. A. Findeis, E. T. Kaiser, Tetra-

Org. Lett. 2001, 3, 8386. hedron Lett. 1993, 34, 12691270.
472 S. Kobayashi, R. Akiyama, Tetra- 493 D. R. Barn, M. J. R., D. C. Rees,
hedron Lett. 1998, 39, 92119214. Tetrahedron Lett. 1996, 37, 32133216.
473 S. D. Lepore, M. R. Wiley, J. Org. 494 Y. Wang, T.-N. Huang, Tetrahedron
Chem. 1999, 64, 45474550. Lett. 1999, 40, 58375840.
474 Y. H. Hu, S. Baudart, J. A. Porco, J. 495 D. M. Ketcha, L. J. Wilson, D. E.
Org. Chem. 1999, 64, 10491051. Portlock, Tetrahedron Lett. 2000, 41,
475 C. T. Bui, A. M. Bray, T. Nguyen, F. 62536257.
Ercole, F. Rasoul, W. Sampson, N. J. 496 E. Nicolas, M. Pujades, J. Bacardit,
Maeji, J. Pept. Sci. 2000, 6, 4956. E. Giralt, F. Albericio, Tetrahedron
476 S. R. Klopfenstein, J. J. Chen, A. Lett. 1997, 38, 23172320.
Golebiowski, M. Li, S. X. Peng, X. 497 J. D. Wade, M. N. Mathieu, M.
Shao, Tetrahedron Lett. 2000, 41, Macris, G. W. Tregear, Lett. Pept.
48354839. Sci. 2000, 7, 107112.
477 S. B. Katti, J. Chem. Soc., Chem. 498 J. Howe, M. Quibell, T. Johnson,
478 W. F. DeGrado, E. T. Kaiser, J. Org. 499 J. Alsina, K. J. Jensen, F. Albericio,
Chem. 1980, 45, 12951300. G. Barany, Chem. Eur. J. 1999, 5,
479 F. S. Tjoeng, G. A. Heavner, J. Org. 27872795.
Chem. 1983, 48, 355359. 500 J. Alsina, T. S. Yokum, F. Albericio,
480 F. Albericio, E. Giralt, R. Eritja, G. Barany, Tetrahedron Lett. 2000, 41,
481 C. Blackburn, A. Pingali, T. Kehoe, 501 F. Guillaumie, J. C. Kappel, N. M.
L. W. Herman, H. Q. Wang, S. A. Kelly, G. Barany, K. J. Jensen,
Kates, Bioorg. Med. Chem. Lett. 1997, Tetrahedron Lett. 2000, 41, 6131
7, 823826. 6135.
482 W. R. Li, N. M. Hsu, H. H. Chou, 502 J. A. Olsen, K. J. Jensen, J. Nielsen,
S. T. Lin, Y. S. Lin, Chem. Commun. J. Comb. Chem. 2000, 2, 143150.
2000, 401402. 503 G. T. Bourne, W. D. F. Meutermans,
483 C. Alonso, M. H. Nantz, M. J. M. L. Smythe, Tetrahedron Lett. 1999,
Kurth, Tetrahedron Lett. 2000, 41, 40, 72717274.
56175622. 504 Y. Aoki, S. Kobayashi, J. Comb.
484 A. N. Semenov, K. Y. Gordeev, Int. J. Chem. 1999, 1, 371372.
Pept. Protein Res. 1995, 45, 303304. 505 G. T. Bourne, W. D. F. Meutermans,
485 M. Rottlander, P. Knochel, Synlett P. F. Alewood, R. P. McGeary, M.
1997, 10841086. Scanlon, A. A. Watson, M. L.
486 R. F. W. Jackson, L. J. Oates, M. H. Smythe, J. Org. Chem. 1999, 64,
Block, Chem. Commun. 2000, 1401 30953101.
1402. 506 W. D. F. Meutermans, S. W.
487 Y. Han, A. Roy, A. Giroux, Tetra- Golding, G. T. Bourne, L. P.
hedron Lett. 2000, 41, 54475451. Miranda, M. J. Dooley, P. F.
488 F. Homsi, K. Nozaki, T. Hiyama, Alewood, M. L. Smythe, J. Am.
Tetrahedron Lett. 2000, 41, 5869 Chem. Soc. 1999, 121, 97909786.
5872. 507 E. G. Brown, J. M. Nuss, Tetrahedron
489 S. Ma, D. Duan, Z. Shi, Org. Lett. Lett. 1997, 38, 84578460.
2000, 2, 14191422. 508 K. H. Gordon, S. Balasubramanian,
490 D. H. Ko, D. J. Kim, C. S. Lyu, I. K. Org. Lett. 2001, 3, 5356.
Min, H. S. Moon, Tetrahedron Lett. 509 R. M. Myers, S. P. Langston, S. P.
1998, 39, 297300. Conway, C. Abell, Org. Lett. 2000, 2,
491 L. E. Canne, S. M. Walker, S. B. H. 13491352.
Kent, Tetrahedron Lett. 1995, 36, 510 J. Kobberling, Dissertation, RWTH
12171220. Aachen 2001.
References 167
511 M. A. Scialdone, Tetrahedron Lett. 531 K. Ngu, D. Patel, J. Org. Chem. 1997,
1996, 37, 81418144. 62, 70887089.
512 M. A. Scialdone, S. W. Shuey, P. 532 A. Golebiowski, S. Klopfenstein,
Soper, Y. Hamuro, D. M. Burns, J. Tetrahedron Lett. 1998, 39, 3397
Org. Chem. 1998, 63, 48024807. 3400.
513 E. E. Swayze, Tetrahedron Lett. 1997, 533 S. Hanessian, F. Xie, Tetrahedron
38, 86438646. Lett. 1998, 39, 737740.
514 S. Dahmen, S. Brase, unpublished. 534 U. Bauer, W. B. Ho, A. M. P.
515 K. Burgess, J. Chen in: Solid-Phase Koskinen, Tetrahedron Lett. 1997, 38,
Organic Synthesis. Burgess, K. (ed.), 72337236.
John Wiley & Sons, New York 2000, 535 G. E. Atkinson, P. M. Fischer, W. C.
S. 123. Chan, J. Org. Chem. 2000, 65, 5048
516 J. Chen, M. Pattarawarapan, A. J. 5056.
Zhang, K. Burgess, J. Comb. Chem. 536 M. F. Gordeev, H. C. Hui, E. M.
2000, 2, 276281. Gordon, D. V. Patel, Tetrahedron
517 D. S. Dodd, O. B. Wallace, Tetra- Lett. 1997, 38, 17291732.
hedron Lett. 1998, 39, 57015704. 537 S. M. Dankwardt, Synlett 1998, 761.
518 L. J. Wilson, S. R. Klopfenstein, M. 538 J. Nielsen, P. H. Rasmussen,
Li, Tetrahedron Lett. 1999, 40, 3999 Tetrahedron Lett. 1996, 37, 33513354.
4002. 539 D. W. Emerson, R. R. Emerson, S. C.
519 M. Patek, M. Smrcina, E. Nakani- Joshi, E. M. Sorensen, J. E. Turek,
shi, H. Izawa, J. Comb. Chem. 2000, J. Org. Chem. 1979, 44, 46344640.
2, 370377. 540 A. M. Murphy, R. Dagnino, Jr, P. L.
520 J. A. Josey, C. A. Tarlton, C. E. Vallar, A. J. Trippe, S. L. Sherman,
Payne, Tetrahedron Lett. 1998, 39, R. H. Lumpkin, S. Y. Tamura, T. R.
58995902. Webb, J. Am. Chem. Soc. 1992, 114,
521 M. Bonnat, M. Bradley, J. D. 31563157.
Kilburn, Tetrahedron Lett. 1996, 37, 541 T. Q. Dinh, R. W. Armstrong,
522 H. M. Zhong, M. N. Greco, B. E. 542 J. A. Fehrentz, M. Paris, A. Heitz,
Maryanoff, J. Org. Chem. 1997, 62, J. Velek, C. F. Liu, F. Winternitz, J.
93269330. Martinez, Tetrahedron Lett. 1995, 36,
523 L. Gomez, F. Gellibert, A. Wagner, 78717874.
C. Mioskowski, Chem. Eur. J. 2000, 6, 543 S. Kobayashi, I. Hachiya, M.
40164020. Yasuda, Tetrahedron Lett. 1996, 37,
524 D. P. Arya, T. C. Bruice, J. Am. 55695572.
Chem. Soc. 1998, 120, 66196620. 544 I. Vlattas, J. Dellurecio, R.
525 P. Roussel, M. Bradley, I. Dunn, I. I. Sytwu, J. Stanton,
Matthews, P. Kane, Tetrahedron Lett. Tetrahedron Lett. 1997, 38, 73217324.
1997, 38, 48614864. 545 B. J. Hall, J. D. Sutherland, Tetra-
526 R. Grigg, J. P. Major, F. M. Martin, hedron Lett. 1998, 39, 65936596.
M. Whittaker, Tetrahedron Lett. 1999, 546 C. Pothion, M. Paris, A. Heitz, L.
40, 77097711. Rocheblave, F. Rouch, J. A.
527 L. S. Richter, M. C. Desai, Tetra- Fehrentz, J. Martinez, Tetrahedron
hedron Lett. 1997, 38, 321322. Lett. 1997, 38, 77497752.
528 C. D. Floyd, C. N. Lewis, S. R. Patel, 547 D. R. Cody, S. H. DeWitt, J. C.
M. Whittaker, Tetrahedron Lett. 1996, Hodges, B. D. Roth, M. C.
37, 80458048. Schroeder, C. J. Stankovic, W. H.
529 S. L. Mellor, W. C. Chan, Chem. Moos, M. R. Pavia, J. S. Kiely
Commun. 1998, 20052006. (Warner-Lambert Co.), Patent Nos
530 S. L. M. C. Mellor, W. C. Chan, WO PCT 9408711; US 958,383; CAN
Tetrahedron Lett. 1997, 38, 3311 122:106536, 1994.
3314. 548 S. Chamoin, S. Houldsworth, C. G.
Kruse, W. I. Bakker, V. Snieckus, 567 W. K. D. Brill, E. Schmidt, R. A.

Tetrahedron Lett. 1998, 39, 41794182. Tommasi, Synlett 1998, 906908.
549 M. J. Farrall, J. M. J. Frechet, J. 568 G. L. Stahl, R. Walter, C. W. Smith,
Org. Chem. 1976, 41, 38773882. J. Am. Chem. Soc. 1979, 101, 5383
550 A. Ishii, H. Hojo, A. Kobayashi, K. 5394.
Nakamura, Y. Nakahara, Y. Ito, Y. 569 J. M. Campagne, J. Coste, P. Jouin,
Nakahara, Tetrahedron 2000, 56, Tetrahedron Lett. 1995, 36, 20792082.
62356243. 570 J. Mery, C. Granier, M. Juin, J.
551 J. Swistok, J. W. Tilley, W. Brugiduo, Int. J. Pept. Protein Res.
Danhoho, R. Wagner, K. 1995, 42, 4452.
Mulkerins, Tetrahedron Lett. 1989, 571 M. F. Gordeev, E. M. Gordon, D. V.
30, 50455048. Patel, J. Org. Chem. 1997, 62, 8177
552 W. Neugebauer, E. Escher, Helv. 8181.
Chim. Acta 1989, 72, 13191323. 572 S. M. Dankwardt, D. B. Smith, J. A.
553 J. W. Apsimon, D. M. Dixit, Synth. Porco, C. H. Nguyen, Synlett 1997,
Commun. 1982, 12, 113116. 854856.
554 J. M. J. Frechet, Tetrahedron 1981, 573 B. Raju, T. P. Kogan, Tetrahedron Lett.
663683. 1997, 38, 49654968.
555 B. Meseguer, D. Alonso-Diaz, N. 574 B. Raju, T. P. Kogan, Tetrahedron Lett.
Griebenow, T. Herget, H. 1997, 38, 33733376.
Waldmann, Angew. Chem. Int. Ed. 575 A. Hari, B. L. Miller, Org. Lett. 1999,
1999, 38, 29022906; Angew. Chem. 1, 21092111.
1999, 111, 30833087. 576 K. Schiemann, H. D. H. Showalter,
556 L. F. Tietze, T. Hippe, A. Steinmetz, J. Org. Chem. 1999, 64, 49724975.
Chem. Commun. 1998, 793794. 577 D. P. Curran, M. Hoshino, J. Org.
557 Y. L. Chou, M. M. Morrissey, R. Chem. 1996, 61, 64806481.
Mohan, Tetrahedron Lett. 1998, 39, 578 D. Craig, M. J. Robson, S. J. Shaw,
757760. Synlett 1998, 13811383.
558 X. Beebe, N. E. Schore, M. J. Kurth, 579 B. Chenera (Smithkline Beecham
J. Am. Chem. Soc. 1992, 114, 10061 Corporation), Patent No. WO PCT.
10062. 98/17695, 1995.
559 X. Beebe, N. E. Schore, M. J. Kurth, 580 K. C. Nicolaou, D. Vourloumis,
J. Org. Chem. 1995, 60, 41964203. T. H. Li, J. Pastor, N. Winssinger,
560 B. C. Hamper, D. R. Dukesherer, Y. He, S. Ninkovic, F. Sarabia,
M. S. South, Tetrahedron Lett. 1996, H. Vallberg, F. Roschangar,
37, 36713674. N. P. King, M. R. V. Finlay, P.
561 B. B. Shankar, D. Y. Yang, S. Giannakakou, P. Verdier-Pinard,
Girton, A. K. Ganguly, Tetrahedron E. Hamel, Angew. Chem. Int. Ed. 1997,
Lett. 1998, 39, 24472448. 36, 20972103.
562 K. J. Elgie, M. Scobie, R. W. Boyle, 581 C. E. J. Halm, M. J. Kurth, Tetra-
Tetrahedron Lett. 2000, 41, 27532757. hedron Lett. 1997, 38, 77097712.
563 T. Takahashi, S. Ebata, T. Doi, 582 M. Yamada, T. Miyajima, H.
Tetrahedron Lett. 1998, 39, 13691372. Horikawa, Tetrahedron Lett. 1998, 39,
564 S. Sato, Y. Kubota, H. Kumagai, T. 289292.
Kumazawa, S. Matsuba, J. Onodera, 583 A. Barco, S. Benetti, C. Derisi, P.
M. Suzuki, Heterocycles 2000, 53, Marchetti, G. P. Pollini, V.
15231532. Zanirato, Tetrahedron Lett. 1998, 39,
565 H. V. Meyers, G. J. Dilley, T. L. 75917594.
Durgin, T. S. Powers, N. A. 584 D. A. Nugiel, L. A. M. Cornelius, J.
Winssinger, H. Zhu, M. R. Pavia, W. Corbett, J. Org. Chem. 1997, 62,
Mol. Diversity 1995, 1, 1320. 201203.
566 T. R. Lee, D. S. Lawrence, J. Med. 585 G. Hum, J. Grzyb, S. D. Taylor, J.
Chem. 1999, 42, 784787. Comb. Chem. 2000, 2, 234242.
References 169
586 X. D. Cao, A. M. M. Mjalli, Tetra- Macek, T. J. Merry, S. G.

hedron Lett. 1996, 37, 60736076. Pradeepan, M. Uesugi, V. M.
587 C. Z. Zhang, A. M. M. Mjalli, Varkhedkar, D. A. Holt, Tetrahedron
Tetrahedron Lett. 1996, 37, 5457 Lett. 1998, 39, 34353438.
5460. 589 R. M. Dunsdon, J. R. Greening,
588 C. A. Metcalf, C. B. Vu, R. Sun- P. S. Jones, S. Jordan, F. X. Wilson,
daramoorthi, V. A. Jacobsen, E. A. Bioorg. Med. Chem. Lett. 2000, 10,
Laborde, J. Green, Y. Green, K. J. 15771579.
170
5
Encoding Technologies
Thomas Kramer, Valery V. Antonenko, Reza Mortezaei,
Nicolay V. Kulikov
5.1
Introduction
With the application of combinatorial chemistry methods large collections of indi-

vidual chemical entities (chemical libraries) have been synthesized that require
some sort of organization to be used and handled eciently. Conventional and
convenient tracking methods such as writing codes on reaction asks and vials
with waterproof pens were no longer appropriate. Assuming that the solid- and
solution-phase reactions used to synthesize a combinatorial library member are
successful, then knowledge of the specic reaction sequence is equivalent to know-
ing the members chemical identity. Because the determination of chemical iden-
tity is typically not automatable and requires a substantial amount of material,
schemes that encode a members reaction history onto the synthesis platform are
of value [1, 2].
One of the most obvious methods for the encoding of chemical compounds is
spatial (or positional) encoding. The structure of a compound or its chemical his-
tory is encoded by the position of the corresponding reaction vessel in a spatially
xed, two-dimensional matrix. However, there are a number of options for encod-
ing a chemical structure: graphical encoding methods; the use of chemical tags
consisting of peptides, oligonucleotides or aromatic compounds; spectrometric en-
coding; or radiofrequency encoding, which is the most advanced technique.
Encoding is a prerequisite for the ecient handling of compound libraries and
oers two major advantages: establishing a relational nomenclature and providing
automated compound and data handling (if the tags were machine-readable). Read-
ability of tags by technical devices is of major importance since manual handling
of a large number of chemical entities is either very tedious or simply not possible.
Post-synthesis encoding is successfully being applied in the compound re-
positories of major pharmaceutical companies where hundreds of thousands of
archived test samples are stored in bar-coded vials. In this case the bar code main-
tains the relation between the vial and the corresponding compound data [struc-
ture, molecular weight (MW), amount, etc.] and oers robotic vial handling. How-

ISBN: 3-527-30509-2
ever, for combinatorial library syntheses before or during synthesis encoding (i.e.
encoding compound libraries at the time of their synthesis, rather than afterwards)
is far more ecient. Again, it is the synthetic history of a compound that is en-
coded rather than its chemical identity.
Furthermore, a major requirement of encoding during synthesis is that the tag
must invariably be connected to the compound itself (like a protecting group) or to
the polymer on which the compound is being synthesized. Consequently, the tags
need to be chemically inert under the reaction conditions used to synthesize the
library compounds, i.e. tag chemistry and library chemistry have to be orthogonal.
Since some compounds are screened for biological activity in an on-bead screening
assay (with the tag still attached), the tags should also not interfere with the bio-
logical properties of the library compound. Therefore, it is essential that tags have
to be chemically and biologically inert.
In the following sections a review of the existing methods for encoding combi-
natorial libraries will be given that divide encoding strategies into two categories:
chemical encoding and non-chemical (physical) encoding.
5.2
Chemical Encoding Methods
One of the solutions to the structure elucidation problem utilizes a number of

chemical tags that can unambiguously identify the chemical entities with which
they are associated. The tags should be incorporated on the same bead on which
the compound they encode is synthesized. Therefore, the tagging process should
not interfere with the synthesis. The tags should not occupy much of the bead ca-
pacity. It should be possible to cleave the synthesized compounds from the bead
selectively in the presence of the encoding elements. The decoding process should
be quick and reliable, while the chemical nature of the tags should permit their
rapid determination in small quantities using conventional analytical technologies.
Time-consuming methods may defeat the purpose of the encoding.
5.2.1
Oligonucleotide Tags
In 1992, Brenner and Lerner [3] were the rst to suggest in the literature the con-
cept of chemical encoding when they proposed a method for producing an oligo-
nucleotide-encoded peptide library. Addition of each amino acid to the polymeric
bead is followed by the attachment of two preselected oligonucleotides to a dier-
ent tag site on the same bead. Each base pair encodes one, and only one, amino
acid. In the split-and-pool strategy, the oligonucleotide chain grows in parallel
with the peptide chain; thus, each unique peptide sequence is encoded by a
unique oligonucleotide. The decoding process starts by amplifying the encoding
oligonucleotide using the polymerase chain reaction (PCR). To reveal the primary
172 5 Encoding Technologies
structure, the encoding oligonucleotide is sequenced, unambiguously unveiling

the amino acid sequence of the satellite peptide.
Oligonucleotide encoding was reported by Nielsen and colleagues [4], who
used the construct presented in Scheme 5.1. a-Amino functionality of the serine
residue was used as an attachment point for the growing peptide chain, while the
b-hydroxyl of the side-chain was used for the encoding oligonucleotide assembly.
Therefore, the tag-to-peptide ratio used in this work was 1:1. Synthesis was carried
out on controlled porous glass (CPG) beads.
Scheme 5.1. Nielsen construct for oligonucleotide encoding [4].
Gallop and coworkers from the Aymax Research Institute used the oligo-
nucleotide tagging strategy for the encoding of a library containing 823,543 hepta-
peptides [5]. The synthesis was carried out on 10-mm-diameter monodisperse
beads. The beads were used in sucient number to synthesize 200 copies of each
sequence in the library. The beads were made of polystyrene crosslinked with di-
vinylbenzene and derivated with a 1,12-diaminododecane linker. The capacity of
the resin was 10 mmol g1 , corresponding to 10 fmol per bead. The resin was fur-
ther functionalized with two chemical linkers: a mixture of 9-uorenylmethoxy-
carbonyl (Fmoc)Thr(t-Bu)OBt and succinimidyl activated ester of 4-O-(dimeth-
oxytrityl) oxobutyrate. The former is introduced to support the growing peptide
chain; the latter to support the synthesis of the encoding oligonucleotide. The re-
sulting construct contained a 20:1 ratio of peptides to oligonucleotides on the bead.
The structure of the construct is shown in Scheme 5.2.
Scheme 5.2. Aymaxs construct for oligonucleotide encoding [5].
The peptides were synthesized using Fmoc-protecting groups for a-amino func-
tionalities and t-butyl-type protection for the side-chains of amino acids. Oligo-
nucleotides were assembled using dimethoxytrityl-protected 3 0 -O-methyl-N,N-
diisopropyl phosphorimidates. To protect the encoded oligonucleotides from the
depurination side reaction upon triuoracetic acid (TFA)-mediated side-chain de-
protection of t-butyl-type protecting groups, the susceptible 2 0 -deoxyguanosine
(dG) unit was not used. 2 0 -Deoxyadenosine (dA) was substituted with 7-deaza-2
deoxyadenosine (c7dA), which is stable to TFA treatment. To make the encoding
compatible with the peptide synthesis, phosphorimidites carried 3 0 -O-methyl pro-

tection, which is, contrary to the b-cyanomethyl protective group, stable to piper-
idine used for Fmoc-deprotection.
The library was built to construct 7 7 analogs of the C-terminal heptapeptide
RQFKVVT of opioid peptide dynorphin B. Amino acids Arg, Gln, Phe, Lys, Val,
Thr and d-Val were used in a seven-step split-and-pool synthesis. Each amino
acid was encoded by a unique dinucleotide. Thus, each heptapeptide was syn-
thesized with the corresponding sequence of 14 nucleotide bases. At the end of
the synthesis, the encoding sequences were framed by the degenerate DNA PCR
primer sequence (55 bases). The library was screened against the uorescently
labeled anti-dynorphin B antibody, D32.39, with the fully deprotected peptides at-
tached to the beads. A sample containing a sucient number of beads to represent
all synthesized sequences with high statistical certainty was analyzed. The beads
containing binding sequences became uorescent. The top 0.17% of the beads
with the most intense uorescence was collected using a uorescence-activated
cell-sorting (FACS) instrument. The collected beads were subjected to PCR ampli-
cation and subsequent sequencing of the encoding oligonucleotides. The se-
quences of the binding peptides were revealed from their primary structures.
Oligonucleotide tagging was developed and used successfully for the synthesis
of peptides; many methodological issues, related mostly to the chemical compati-
bility of the approach, were solved. However, the compatibility of the encoding
strategy with the synthesis of other classes of organic molecules remains limited.
5.2.2
Peptide Tags
The technology for automated Edman degradation of peptides to determine their

sequence is well developed. Therefore, peptides can be used similarly to oligonu-
cleotides as encoding molecules. Several groups have reported using peptide en-
coding [6, 7]. Unfortunately, applications of the peptide encoding are very limited
because of severe restrictions imposed on the scope of chemical methods that
are compatible with this approach. With the development of alternative encoding
strategies, peptide encoding has very limited applications in the modern approaches
to the synthesis of small organic molecules.
5.2.3
Haloaromatic Binary Coding
Several laboratories have worked on the development of robust encoding strategies

that can be used for combinatorial synthesis of pharmacologically appealing chem-
ical libraries. In 1993, Still and colleagues were the rst to report binary encoding
[8] using chromatographically resolvable haloaromatic reagents as tagging mole-
cules. The tags are attached to the beads during library synthesis in a binary coding
strategy intended to keep a molecular record of all chemical transformations to
which the beads are subjected. The tags are incorporated via amide bond forma-
Scheme 5.3. Haloaromatic tags on a photolinker [8].
tion as part of a construct with a photolabile linker (Scheme 5.3) at the expense of
the ligand synthesis sites. Each compound in the library is encoded by a limited
set of tags. The presence, as well as the absence, of each member of the set carries
information about the specic encoded structure. In a binary code, a set of n tags
can encode 2 n 1 dierent structures. For example, 20 tags can encode 20 20 1
1,048,575 dierent library members. After being released from the beads by pho-
tolysis, the tags are detected by capillary gas chromatography using electron cap-
ture detection (ECGC), a detection method that is particularly sensitive to heavily
chlorinated aromatics. The haloaromatic compounds were selected to ensure reli-
able and reproducible separation by ECGC, which is capable of detecting sub-
picomolar amounts of the tags. Consequently, the beads can be tagged at only 0.5
1% of the resin loading (0.51 pmol per bead) without detectable interference with
the library synthesis.
Later, Still and coworkers modied the original strategy by developing a new
type of tagging reagent TnC [9], presented in Scheme 5.4. A derivative of vanillic
acid (3-methoxy-4-hydroxybenzoic acid) was chosen as a linker. Synthesis of the
tagging reagent TnC begins with a Mitsunobu reaction of a tag alcohol Tn with
methyl vanillate, followed by LiOH hydrolysis of the methyl ester. This produces
free acid TnA, which is converted to acid chloride TnB. Excess of diazomethane
converts acid chloride TnB into the tagging diazoketone TnC. In the presence of
rhodium reagents Rh2 (OAc)4 or Rh2 (O2 CCF3 )4 TnC forms an acylcarbene, which
rapidly and cleanly reacts with benzene, forming a derivative of cycloheptatriene
Tn1. Benzene was used as a soluble analog of polystyrene resin. Derivatives of TnC
containing dierent numbers of methylene groups n have been prepared. The re-
searchers found that diazoketones TnC are stable solids and can be stored at room
temperature for months. They react easily with polystyrene resin, providing a
means for binary encoding. At the decoding stage, the tags are oxidatively cleaved
by ceric ammonium nitrate and analyzed by ECGC.
The acylcarbene tagging strategy does not require any specic functional group
for tag attachment, and the tags and linkers are generally compatible with a wide
Scheme 5.4. Acylcarbene-generating tagging reagents [9].
range of chemical reactions. The acylcarbenes can unselectively add to some of

the synthesized compounds. However, the bulk of the library is represented by the
polymeric support, which accepts the major portion of the tag molecules. Because
tags are added at molar levels corresponding to 1% or less of the library members,
interference with the synthesis is minimal [10].
5.2.4
Secondary Amine Binary Coding
In 1996, Gallop and coworkers developed another robust encoding strategy [11,
12], based on secondary amine tags, which are incorporated into a polyamide back-
bone. The secondary amine binary coding scheme utilizes an amine-based poly-
meric resin that is dierentially functionalized with sites for both ligand synthesis
and tag addition (Scheme 5.5). The ligand synthesis site is derivatized with a N-
Fmoc-protected photocleavable linker group [13]. This linker allows for the release
of the ligand from the resin by exposure to ultraviolet (UV) light. The amino group
of the tag site is protected with orthogonal to the Fmoc group functionalities (e.g.
Boc or Alloc). The tag site occupies only 10% of the total number of amino groups
on the resin. Each 130-mm-diameter bead of the TentaGel S resin, which is recom-
mended by the authors of this methodology, contains about 300 pmol of amino
groups. Therefore, the theoretical yield of the ligand is 270 pmol per bead. Such
Scheme 5.5. Resin construct for secondary amine binary coding [11, 12].
quantities being photo-released in 100 ml of a solvent would be adequate for the

concentration of the ligand in most biological assays.
The tags are a set of relatively hydrophobic amines, such as HN(Et)(Bu),
HNMe(C6 H13 ), HNBu2 , HNMe(C7 H15 ), and HN[CH2 CH(Et)C4 H9 ]2 . The set is
selected to ensure reliable separation of the dansyl derivatives of the amines by
reversed-phase high-performance liquid chromatography (HPLC). The tagging
monomer units are synthesized by reaction of an N-protected iminodiacetic anhy-
dride with a secondary amine from the set (Scheme 5.6).
Scheme 5.6. Preparation of tag monomers for secondary amine coding.
The resulting N-protected N-[(dialkylcarbamoyl)methyl]glycines are assembled

into binary mixtures, which are incorporated into the tag sites of the resin beads
by using HATU or other peptide-coupling reagents (Scheme 5.7). Addition of each
new building block at the ligand synthesis site in the course of a split-and-pool
combinatorial synthesis is accompanied by the incorporation of the preselected
mixture of the monomer units at the tag addition site. Selection of the protecting
groups allows for the addition of the tags either before or after the addition of the
building block to the ligand. The ability to choose dierent protecting groups for
the N-protected tag monomers helps to resolve potential chemical compatibility
issues.
Scheme 5.7. Coupling of secondary amine tag constructs to solid support.
Upon completion of the library synthesis, each bead is distributed into a sepa-
rate well of a microtiter plate. The ligands are released from the beads into the
assay medium by exposure to UV light at 365 nm. The tag residues remain coval-
ently attached to the beads. After screening, beads from the wells containing active
compounds are collected for decoding. The decoding process is shown schemati-
cally in Scheme 5.8, and begins with the acid hydrolysis of the beads in 6 N hy-
drochloric acid. Under these conditions all amide bonds are hydrolyzed, releasing
free secondary amine tags into the solution. After evaporation of the HCl, the
amines are converted into the corresponding dansyl derivatives by treatment with
dansyl chloride. Analysis of the resulting mixture of dansylated tags is carried out
Scheme 5.8. The decoding process for secondary amine binary coding.
by reversed-phase HPLC on a microbore column. Fluorescence detection allows

for the reliable analysis of 2030 fmol of a dansylated tag. Only 25% of the entire
dansylated hydrolyzate from a single bead is sucient to obtain unambiguous
results.
The secondary amine encoding method was used in the synthesis of a library of
pyrrolidine-based inhibitors of angiotensin converting enzyme (ACE) via [2 3]
cycloaddition [14].
5.2.5
Mass Encoding
As mentioned previously, conventional methods of characterization of chemical

compounds cannot be applied to most combinatorial technologies owing to the
insucient quantities of the analytes. One fortunate exception is mass spectros-
copy. Matrix-assisted laser desorption and electrospray ionization mass spectros-
copy (MS) have been used [15, 16] to identify compounds synthesized on a single
bead. For beads with diameters larger than 100 mm, a mass spectrum can be ac-
quired in less than 1 min. In 1996, Geysen and colleagues from Glaxo-Wellcome
proposed a novel encoding method [17], which takes advantage of modern MS
techniques. In general, when recording the chemical history of a compound syn-
thesized on a bead mass encoding incorporates stable isotopes that give distinct
isotopic patterns in mass spectra.
In one of the proposed strategies, the resin is derivatized with a linker (Scheme
5.9) to which an MS code is attached. The mass of the coding block is designed to
appear in a convenient region of the mass spectrum. As an example, the code can
be a dipeptide built from the combinations of the natural amino acids glycine (Gly)
and alanine (Ala), and their 13 C-labeled derivatives: [ 13 C]Gly, [ 13 C]2 Gly, [ 13 C]Ala,
and [ 13 C]4 Ala. As an example, the authors present mass spectra recorded in the
295330 MW range for the following ten mass codes: GlyGly, Gly[ 13 C]Gly,
[ 13 C]Gly[ 13 C]Gly, Gly[ 13 C]2 Gly, GlyAla, Gly[ 13 C]Ala, [ 13 C]2 GlyAla,
[ 13 C]2 Gly[ 13 C]Ala, and[ 13 C]2 Gly[ 13 C]4 Ala. After the code (Scheme 5.10), an ad-
ditional linker is introduced; this should be orthogonal to the rst one and is used
for the release of the synthesized compound ABC. In a split-and-pool synthesis,
the code denes the identity of the rst building block A. The third building block
C can be known from the nal pool in which its addition was carried out. The
identity of the building block B can be calculated from the molecular weight of the
ligand and the molecular weight of monomers A and C.
For unambiguous results, the set of building blocks used at the second step of
the library synthesis should not contain any compounds with the same mass as
building block B.
Scheme 5.9. Resin construct for mass encoding.

Scheme 5.10. Principle of light-directed, spatially addressable synthesis.
The code block can also consist of equimolar mixtures built from a set of isotopi-
cally labeled dipeptides: GlyGly, Gly[ 13 C]Gly, Gly[ 13 C]2 Gly, [ 13 C]Gly[ 13 C]Gly,
[ 13 C]Gly[ 13 C]2 Gly, and [ 13 C]Gly[ 13 C]2 Gly. These dipeptides incorporate equal to
their content in the mixture, because isotopic labeling does not aect chemical re-
activity. The resulting mass spectra of these mixture codes serve as bar codes.
In the ratio-encoding strategy, the encoded information is derived from just
two peaks in the mass spectrum. A mixture of a reagent, common to all members
of the library, is prepared from dierent ratios of the isotopic isomers of the
reagent. The resulting mass spectrum will reveal two distinct peaks corresponding
to each of the isomers. The relative heights of the peaks provides the encoded in-
formation.
The mass encoding strategy was used by Wagner and coworkers [18] for the
synthesis of a peptoid library. A set of 20 14 N: 15 N ratio-encoded imidazoles was
synthesized to investigate pharmacokinetic applications of isotopic labeling.
5.3
Non-Chemical Encoding Methods
Chemical methods of encoding combinatorial libraries can be used for synthesis

on very small elements of solid supports (i.e. 10-mm-diameter beads). However,
none of the procedures developed so far is totally compatible with all chemical
transformations that might be necessary for the implementation of successful
drug discovery programs. In principle, physical methods of encoding are fully
compatible. Unfortunately, none of the conventionally used labeling techniques
(bar codes, labels, etc.) is small enough to be used with resin beads. It is often
necessary to obtain compounds via combinatorial chemistry approaches in sub-
stantially larger quantities than the single-bead approach is capable of. As an alter-
native, macroscopic pieces of a solid support can be used, the larger physical
dimensions allowing for the application of more space-demanding encoding strat-
egies.
5.3.1
Positional Encoding
Positional, or spatial, encoding directly links the reaction history of a compound

to the particular location of the corresponding synthesis compartment (reactor) in
a spatially arrayed, xed matrix of reactors, i.e. the 8 12 two-dimensional (2D)
matrix in a 96-well plate or special chip formats.
5.3.1.1 Light-directed Synthesis

In 1991, Fodor and colleagues combined photolithography, photochemistry, and
solid-phase synthesis in a new technology [1922] called light-directed, spatially
addressable parallel synthesis or VLSIPS (very-large-scale immobilized polymer
synthesis). The principal points of the technology are illustrated in Scheme 5.10.
The synthesis occurs on a at glass surface modied with an appropriate linker
(e.g. 3-aminopropyl-triethoxysilane) to allow for the covalent attachment of pro-
tected amino acids. The entire synthesis area of the slide is derivatized with a pho-
tolabile protecting group (PG). At the rst step of the synthesis, selected sites of
the synthesis area (typically three squares per slide, 1.28 cm 1.28 cm each) are
exposed to UV light through photolithographic mask A. The variety of patterns
available for photolithography is essentially unlimited. The exposure to light causes
removal of the photolabile groups, thus elaborating amino functionality. At the
next step, the synthesis area is treated with the reagents necessary for the elonga-
tion of the peptide chain. Only the sites that were previously photodeprotected will
participate in a coupling reaction; the rest of the synthesis area remains protected
and intact. Synthesis continues by illuminating another part of the surface
through photolithographic mask B, followed by the next chain elongation reaction.
By repeating the photodeprotection and coupling steps, highly dense arrays, each
consisting of thousands of peptides, can by synthesized. Importantly, the primary
structure of each peptide in the array is suciently dened by the sequence of
coupling and photolysis steps, and by photolithography mask patterns. Therefore,
the structure can be easily deduced from the (x, y) coordinates of the peptide on
the slide. This eliminates the need for encodingdecoding procedures required by
some other combinatorial technologies. After completion of the synthesis, the syn-
thesis area is exposed to reagents necessary for the elimination of side-chain pro-
tecting groups. To assess the binding properties of all synthesized peptides, the
entire array is incubated with a uorescently labeled target molecule and scanned
using a stage-scanning confocal uorescence microscope. Sites, containing pep-
tides that bind to the target, become uorescent. Anity data on all peptides in the
entire array are obtained in one step.
The consumption of chemical reagents required for the synthesis of thousands
of peptides composing the array, together with the biological reagents necessary
for bioassay, is very small, because the capacity of the at glass surface is only 5
20 pmol cm2 . Biological reagents used in this technology are recoverable and can
be reused. Moreover, after performing an assay with one target molecule, the
bound target can be easily dissociated from the array (e.g. by treating it with 6 M
guanidine hydrochloride), making the array available for subsequent screening
with other targets. These arrays are reusable for at least 6 months.
With special (orthogonal) masking strategies the number of synthetic regions on
the glass surface can be increased until the limit of photolithographic resolution is
achieved (1020 mm). With this resolution, 250,0001,000,000 compounds can be
synthesized in 1 cm 2 . Routinely, 50-mm resolution is practiced and allows for the
production of 40,000 compounds in the same area.
Light-directed, spatially addressable synthesis is a powerful technology for gen-
erating chemical diversity. Unfortunately, the technique is limited to peptides, oli-
gonucleotides and other linear oligomeric structures.
5.3.1.2 Microtiter Plate-based Positional Encoding

The 96-well microtiter format has been a common platform for high throughput
screening (HTS) for many years, and also oers many advantages as a platform for
parallel synthesis. There are multiple liquid-handling devices (multichannel pipettes,
robotic systems, etc.) that signicantly simplify and accelerate the process of the
reagent delivery to the wells on the plate. Moreover, all 96 compounds can be handled
as one synthesis entity. Their structures are spatially encoded by their location on
the plate. Contemporary analytical instrumentation, such as mass spectrometers
and HPLC systems, can also easily handle compounds in the 96-well microtiter
format. Combined with the commonly used 96-well-based systems for screening, this
eliminates the need for time-consuming redistributing and relabeling of a large
number of synthesized compounds for analytical and biological characterization.
Synthesis on multipins In 1984, Geysen and coworkers [23] introduced an alter-

native to the synthesis on polymeric beads. As a solid support, they proposed the
use of pins; these are reusable polyethylene rods, which have a diameter of 4
mm and a length of 40 mm, and are grafted with polyacrylic acid. The pins are at-
tached to a supporting block arranged in an 8 12 array to t into a 96-well mi-
crotiter plate. The 96-well plate is used as 96 separate reaction vessels. Each well
can be used for the attachment of a dierent building block. Washing and de-
protection steps can be carried out in a separate common reaction vessel. After the
synthesis is completed and side-chain protecting groups are removed, peptides or
small organic molecules can be assayed while attached to the pins [24, 25]. If a
cleavable linker was used, individual peptides are separated from the solid support
in a 96-well microtiter plate containing appropriate reagents [26], or by exposing
the array to vapor-phase ammonolysis [27, 28]. Originally, the capacity of each pin
was 10100 nmol. Later, a much greater variety of multipins of dierent capacities
with a wide selection of linkers became commercially available from Chiron Tech-
nologies Pty. Ltd. In the latest development, the pins can be attached to the radio-
frequency tags to allow for encoding in the split-and-pool mode.
HiTOPS system Over time, original approaches have been developed by many
companies to perform the synthesis of organic compounds on the footprint of a
96-well plate. The HiTOPS (high-throughput organic parallel synthesis) system
[29] (Scheme 5.11) utilizes a variety of 96-deep-well ltration microtiter plates
available from Polyltronics/Whatman.
The plates are made of polypropylene and other polymers, and are available with
a selection of dierent lters. The volume of each well is 2 mL and allows the use
of up to 50 mg of resin. For larger scale syntheses, several wells or even the entire
row or the entire column can be used for the preparation of the same compound.
Reactants are retained in wells by the positive pressure of an inert gas.
Scheme 5.11. HiTOPS system. Synthesis device (left) and cleavage device (right).
5.3.2
Non-Positional Encoding
5.3.2.1 Tea-Bag Approach

In 1985, Houghten [30] reported on peptide synthesis carried out on a resin sealed
in porous polypropylene packets. The pore size of the polypropylene mesh (74 mm)
allows the free access of chemicals to and from the contained resin. Each packet
or tea-bag can be individually labeled to identify the peptide synthesized on
the entrapped polymer. Many tea-bags can be combined in the same reaction to
carry out common synthetic steps, such as washing and deprotection. The packets
are sorted in separate reaction vessels according to the specic amino acid that will
be coupled next. Cleavage, depending on the amount of used resin, can be carried
out in separate vessels or in a 96-well microtiter plate with a 2-mL well volume. In
the original paper, 248 dierent tridecapeptides were synthesized in 10- to 20-mg
quantities and characterized in less than 4 weeks.
The tea-bag method is very practical as it does not require any special tools,
except a sealing device to make the tea-bags. A number of mesh materials of
dierent porosity are available form Spectrum Medical Industries. Almost all
commercially available resins can be used, as long as the size of the beads is larger
than the mesh size; in addition, the mesh should be stable to reaction conditions.
The scale of the synthesis is easy to control by the size of the packet chosen
to contain the desired amount of a polymer support. Multiple synthesis can be
carried out manually or on a synthesizer. The tea-bags can be mechanically
labeled, or radiofrequency tags can be used for this purpose.
5.3.2.2 Cellulose and Laminar Supports

Similarly to the tea-bag approach, pieces of any solid-phase support suitable
for solid-phase synthesis can be used for parallel peptide preparation. One of the
rst materials used in this manner was paper. Frank used paper disks [31, 32]
(Whatman 3MM, 1.5 cm diameter) packed into columns of a multicolumn contin-
uous ow synthesizer. Prior to the synthesis, the paper was derivatized with p-
alkoxybenzyl linkage to allow for the cleavage with triuoroacetic acid. The disks
can easily be labeled with a pencil, sorted, and combined depending on the com-
mon amino acid to be coupled at the next step.
Cotton has mechanical properties superior to those of paper, and was used in
a similar way by Lebl and colleagues [33, 34]. Researchers from the Rockefeller
University used polystyrene-grafted polyethylene lm [35, 36], whereas scientists
from Pzer used material prepared from two sheets of polypropylene mesh with
resin sandwiched in between [37]. The sandwich was fused together with a
polymer with a low melting point.
5.3.2.3 Radiofrequency Tags

One of the most successful automated solutions for the synthesis of encoded
chemical libraries is utilizing electronic identication devices. Scheme 5.12 illus-
trates one such device the radiofrequency (RF) identication (ID) tag. Similar
Scheme 5.12. Schematic of an RF memory chip useful for encoded synthesis.
devices have been used for years to tag laboratory mice subcutaneously, and more
recently these have been used to provide security for automobile ignition keys, to
secure building entrance identication, and for a variety of other functions. The
application of RF tags to combinatorial syntheses was reported in 1995 by two
groups, one working at IRORI [38] and the other at Ontogen [39]. The RF ID tag
is about the size of a ea stirbar and is encased in a thick-walled glass shell. As
shown in Scheme 5.12, the essential components are an antenna (the largest
component) and a microelectronic chip. Each chip has a unique, nonvolatile 40-bit
ID code laser-etched into it. With 40 bits available, a total of 2 40 (over 1 trillion)
unique ID codes is possible. The virtually inexhaustible range allows one to guar-
antee the uniqueness of all present and future RF tag ID codes. Additional bits are
used to perform extensive digital error detection, which prevents incorrect report-
ing. (Bar codes are a more common graphical embodiment of encoding, but of
course one that is substantially less information-rich.)
A transceiver controlled by a computer is used to interrogate and receive the ID
code of each RF tag. The transceiver antenna transmits a specially modulated, 125-
kHz electromagnetic eld. This eld is of very low energy and is not harmful.
When an RF tag is held within about 1 cm from the transceivers antenna, energy
is picked up by the RF tags antenna. A rectier in the chip converts this energy to
microwatt levels of direct current (DC) power, which is enough to power-up the
logic circuitry on the chip. In a very real sense, the RF tag is similar to a crystal
radio (which does not require an external power source), except that the device
serves as both receiver and transmitter. It is self-contained, in that the chip used
no internal batteries and has no external metallic connections.
A synchronization signal modulated onto the transceivers signal allows the chip
to respond with its ID code (a serial sequence of ID bits) and error-checking bits.
The time elapsed between placing the chip on the transceiver and seeing the ID
code on the interfaced computer screen is about 0.5 s.
If one could physically associate this chip with a compound undergoing syn-
thetic transformations, then the ID code on the chip would permit one to pick up
a sample at any point of the combinatorial synthesis and know which reaction(s)
it had already been through. Of course, just knowing the reaction history of a
sample is not equivalent to knowing the chemical concept of a sample, but it is
much better than nothing. If each reactor (compound-carrying unit) must be
present in a series of reaction asks containing lots of other reactors, then having
them tagged makes it possible to put them into the right ask for each step of the
synthesis. Moreover, if that tag can be read easily, then that movement of reactors
can be automated. Electronic tagging permits all of these benets.
How this works in practice is detailed as follows. After a compound has been
identied for which several hundred to several thousand derivatives would be of
value, a synthetic route is chosen that: (i) permits linkage to a solid-phase support;
(ii) utilizes reaction steps that appear possible to optimize to b90% yield; and (iii)
aords reagents in each step for which desirable variants can be purchased (or,
less optimally, can be made trivially). In the synthesis itself, one of the signicant
advantages of the microreactor approach becomes evident: one can use standard
laboratory glassware and equipment to accomplish the library synthesis. There is
no need for the automation of liquid-handling steps, and indeed there is no need
for automation at all until rather large libraries are desired.
IRORI oers several miniature reactors MicroKans9 and MicroTubes9
(Scheme 5.13). MicroKans9 is a small cylindrical container with mesh walls; the
internal volume of the container is 330 ml. In addition to the RF tag, the container
hold up to 30 mg of any commercially available resin.
Scheme 5.13. MicroKans9 and MicroTubes9.
Manual sorting of microreactors can become tedious when a large number

(more than 10002000) of them is used. IRORI designed the AutoSort TM 10-K
microreactor sorting system (Scheme 5.14) to solve this problem. The system ac-
commodates up to 10,000 microreactors that can be distributed between chemical
steps into 48 dierent containers. The distribution rate is 1000 microreactors per
hour. The device is also very useful for sorting MicroKrans9 and MicroTubes9 into
microreactor carriers for further cleavage, which takes place on the Accu-Cleave-96
Scheme 5.14. IRORI AutoSort TM 10-K microreactor sorting system.
cleavage station. Twelve 8 12 microreactor carriers can be used simultaneously

on the sorting system.
One of the rst applications of the RF tagging technology was demonstrated by
the synthesis of a 432-member library (18 8 3 array) of tyrphostins (Scheme
5.15) [40].
5.3.2.4 Laser Encoding

Another example of encoding that does not interfere with chemistry was suggested
in 1997 by Xiao et al. [41]. The coding structure is an inert ceramic plate with a
two-dimensional, laser-etched bar code. The encoded plate, which is a 3 mm
3 mm square, is placed in the center of a laser optical synthesis chip (LOSC). The
chip is a 1 cm 1 cm square made of polypropylene grafted with polystyrene. The
smallest possible size of the encoding ceramic plate is 0.5 mm 0.5 mm. Un-
fortunately, the bar code cannot be modied during the course of the synthesis.
5.4
Conclusion
The development of various encoding methods for combinatorial chemistry played

a crucial role in the chemists ability to synthesize large numbers of organic mol-
References 187
Scheme 5.15. A combinatorial synthesis of 432 tyrphostins

(prepared using 29 reaction vessels) [40].
ecules rapidly in distinct formats. If the focus in library synthesis is on single

compounds, milligram quantities, automated handling, exibility and eciency
radiofrequency encoding being broadly applied in pharmaceutical companies is
considered to be the most promising technology.
References
1 a) V. V. Antonenko, N. V. Kulikov, 3 S. Brenner, R. A. Lerner, Proc. Natl.

R. Mortezaei, F. Gualtieri (eds) Acad. Sci USA 1992, 89, 53815383.
Methods and Priniples in Medicinal 4 J. Nielsen, S. Brenner, K. D. Janda,
Chemistry: New Trends in Medicinal J. Am. Chem. Soc. 1993, 115, 9812
Chemistry, Wiley-VCH, Weinheim 9813.
2000, pp. 3980; b) A. W. Czarnik, F. 5 M. C. Needels, D. G. Jones, E. H.
Gualtieri (eds) Methods and Priniples Tate, G. L. Heinkel, L. M. Kocher-
in Medicinal Chemistry: New Trends in sperger, W. J. Dower, R. W. Barrett,
Medicinal Chemistry, Wiley-VCH, M. A. Gallop, Proc. Natl. Acad. Sci.
Weinheim 2000, pp. 8196. USA 1993, 90, 1070010704.
2 A. W. Czarnik, Curr. Opin. Chem. 6 V. Nikolaev, A. Stierandova, V.
Biol. 1997, 1, 6066. Krchnak, B. Seligmann, K. S. Lam,
S. E. Salmon, M. Lebl, Pept. Res. Fodor, L. Stryer, US Patent No.

1993, 6, 161170. 5,143,854, 1992.
7 J. M. Kerr, S. C. Banville, R. N. 21 J. W. Jacobs, S. P. A. Fodor, Trends.
Zuckermann, J. Am. Chem. Soc. Biotechnol. 1994, 12, 1926.
1993, 115, 25292531. 22 M. C. Pirrung, Chem. Rev. 1997, 97,
8 M. H. J. Ohlmeyer, R. N. Swanson, 473488.
L. W. Dillard, J. C. Reader, G. 23 H. M. Geysen, R. H. Meloen, S. J.
Asouline, R. Kobayashi, M. Wigler, Barteling, Proc. Natl. Acad. Sci. USA
W. C. Still, Proc. Natl. Sci. USA 1984, 81, 39984002.
1993, 90, 1092210926. 24 H. M. Geysen, S. J. Rodda, T. J.
9 H. P. Nestler, P. A. Bartlett, W. C. Mason, Mol. Immunol. 1986, 23, 709
Still, J. Org. Chem. 1994, 59, 4723 715.
4724. 25 H. M. Geysen, S. J. Rodda, T. J.
10 W. C. Still, Acc. Chem. Res. 1996, 29, Mason, G. Tribbick, P. G. Scoofs,
155163. J. Immunol. Methods 1987, 102, 259
11 Z.-J. Ni, D. Maclean, C. P. Holmes, 274.
M. M. Murphy, B. Ruhland, J. W. 26 A. M. Bray, N. J. Maeji, R. M.
Jacobs, E. M. Gordon, M. M. Valerio, R. A. Campbell, H. M.
Gallop, J. Med. Chem. 1996, 39, Geysen, J. Org. Chem. 1991, 56,
16011608. 66596666.
12 Z.-J. Ni, D. Maclean, C. P. Holmes, 27 A. M. Bray, N. J. Maeji, A. G.
M. M. Gallop in: Methods in Jhingran, R. M. Valerio,
Enzymology, vol. 267, Combinatorial Tetrahedron Lett. 1991, 32, 61636166.
Chemistry. Abelson, J. N. (ed.). 28 A. M. Bray, A. G. Jhingran, R. M.
Academic Press, San Diego 1996, pp. Valerio, N. J. Maeji, J. Org. Chem.
261272. 1994, 59, 21972203.
13 C. P. Holmes, D. G. Jones, J. Org. 29 V. V. Antonenko in: Combinatorial
Chem. 1995, 60, 23182319. Chemistry and Combinatorial
14 D. Maclean, J. R. Schullek, M. M. Technologies Methods and Appli-
Murphy, Z.-J. Ni, E. M. Gordon, M. cations. Miertus, S., Fassina, G.
A. Gallop, Proc. Natl. Acad. Sci. USA (eds), Marcel Dekker 1998, pp.
1997, 94, 28052810. 205232.
15 M. Stankova, O. Issakova, N. F. 30 R. A. Houghten, Proc. Natl. Acad.
Sepetov, V. Krchnak, K. S. Lam, M. Sci. USA 1985, 82, 51315135.
Lebl, Drug. Dev. Res. 1994, 33, 146 31 R. Frank, R. Doring, Tetrahedron
156. 1988, 44, 60316040.
16 R. A. Zambias, D. A. Boulton, P. R. 32 B. Blankenmayer-Menge, R. Frank,
Griffin, Tetrahedron Lett. 1994, 35, Tetrahedron Lett, 1988, 29, 5871
42834286. 5874.
17 H. M. Geysen, C. D. Wagner, W. M. 33 M. Lebl, V. Gut, J. Eichler in:
Bodnar, C. J. Markworth, G. J. Peptides 1990. Giralt, E., Andreu,
Parke, F. J. Schoenen, D. S. D. (eds), ESCOM, Leiden 1991, pp.
Wagner, D. S. Kinder, Chem. Biol. 10591060.
1996, 3, 679688. 34 M. Lebl, J. Eichler, Peptide Res. 1989,
18 D. S. Wagner, C. J. Markworth, 2, 297300.
C. D. Wagner, F. J. Schoenen, C. E. 35 R. H. Berg, K. Almdal, W. Wats-
Rewerts, B. K. Kay, H. M. Geysen, berg Pedersen, A. Holm, J. P. Tam,
Comb. Chem. High Throughput R. B. Merrield, J. Am. Chem. Soc.
Screening 1998, 1, 143153. 1989, 111, 80248026.
19 S. P. A. Fodor, L. J. Read, M. C. 36 R. H. Berg, K. Almdal, W. Watsberg
Pirrung, L. Stryer, A. T. Lu, D. Pedersen, A. Holm, J. P. Tam, R. B.
Solas, Science 1991, 251, 767773. Merrield in: Innovation and
20 M. C. Pirrung, J. L. Read, S. P. A. Perspectives in Solid Phase Synthesis:
References 189
Peptides, Polypeptides and Oligo- Angew. Chem. Int. Ed. 1995, 3, 2289
nucleotides, Macro-Organic Reagents 2291.
and Catalysts-1990. Epton, R. (ed.), 39 E. J. Moran, S. Sarshar, J. F.
SPCC, Birmingham 1990, pp. 453 Cargill, M. M. Shabaz, A. Lio, A. M.
459. M. Mjalli, R. W. Armstrong, J. Am.
37 N. K. Terrett, M. Gardner, Chem. Soc. 1995, 117, 1078710788.
D. W. Gordon, R. J. Kobylecki, 40 T. Czarnik, M. Nova, Chem. Britain
J. Steele, Chem.-Eur. J. 1997, 3, 1997, 33, 3941.
19171920. 41 X. Y. Xiao, C. Zhao, H. Potash, M.
38 K. C. Nicolaou, X. Y. Xiao, Z. P. Nova, Angew. Chem. Int. Ed. Engl.
Parandoosh, A. Senyei, M. Nova, 1997, 36, 780782.
190
6
Instrumentation for Combinatorial Chemistry
Marcus Bauser and Hubertus Stakemeier
6.1
Automation in Combinatorial Synthesis
6.1.1
General Remarks
Economic pressure to speed up the drug discovery process has had a huge impact
on all elds of medicinal chemistry [1], therefore automation has increasingly be-
come one of the main strategies to fulll this demand [2]. While automation was
successful in high-throughput screening (HTS) [3] and peptide synthesis, it played
a minor role in mainstream organic synthesis. Automated systems are recom-
mended for procedures that are highly predictable and repetitive [4]. However, or-
ganic chemistry is seldom dened in this way. The successful synthesis of organic
molecules depends strongly on the chemical properties of the reagents and react-
ants. Within the library production process solubility and reactivity of synthons
can be highly dierent, therefore it is very dicult to nd one protocol that works
for every building block. Since multiple parallel synthesis began, there has been a
wide range of dierent approaches and concepts for the design of automated sys-
tems to overcome these problems [57]. The rst attempts at automation were the
simple parallelization of commercially available reaction vessels. Secondly, reaction
blocks were designed and used in combination with existing liquid-handling sys-
tems. Another approach uses stand alone systems that mimic the typical action of
a chemist. Today, modern automated systems are modular workstation approaches.
An overview is given in Table 6.1.
6.1.2
Fully Automated Systems for Solid- and Solution-phase Synthesis
6.1.2.1 Robot-arm-based Systems

The main advantage of fully automated robot-arm-based systems is that they oer
customized solutions similar to HTS equipment [8]. The individual user needs to
dene the architecture, the layout, and the processes of the robotic system. Within

ISBN: 3-527-30509-2
Tab. 6.1. Automated systems for solid- and solution-phase chemistry.
Accelab Acrosyn98 ACT BenchMark Omega ACT Vantage ACT Venture

Series
Automation
Type Unit Unit Unit Unit
Arm Cylindric arm Two multiprobe XYZ arms Two multiprobe XYZ arms Two multiprobe XYZ arms
Chemistry Solid phase Solid phase Solid phase Solid phase
Solution phase Solution phase Solution phase Solution phase
Reaction block (RB) Monomer rack Ares reactor
Array 20 (4 5) 8-, 16-, 40-, 96-well reactor 40, 96, 384 40, 96, 384
Number of possible RBs Up to 5 RBs Up to 4 RBs (Omega 384) 1 Multiple
Type Fixed during synthesis Fixed during synthesis Fixed during synthesis Fixed during synthesis
Reaction vessels
Number/volume 20/5 ml Solid phase: 96/3.5 ml; 40/9 384/0.5 ml; 96/2 ml; 40/6 384/0.5 ml; 96/2 ml; 40/6
ml; 16/15 ml; 8/30 ml ml ml
Solution phase: 96/6 ml;
40/14.5 ml
Material Polypropylene or glass Multiple-well teon reactor Teon block with fritted Teon block with fritted
syringes with frit or block with frits for solid wells wells
customized blocks phase
Reaction procedures
Reux (condenser module) Completely sealed reaction Completely sealed reaction
block block
Filtration Bottom Bottom Bottom
Evaporation in rv
Agitation Magnetic levitation stirring Orbital shaking Orbital shaking
Temperature range 80 to 160 C 70 to 150 C 70 to 150 C
Pressure Up to 150 psi Up to 150 psi
6.1 Automation in Combinatorial Synthesis
Inert atmosphere In rv (rv reaction vessel) In rv In rv In rv

191
192
Accelab Acrosyn98 ACT BenchMark Omega ACT Vantage ACT Venture

Series
Work-up
Liquidliquid extraction
Solid-phase extraction
Analysis HPLC upgradable
Special features . Fully enclosed robot-arm- . Automatic on-board . Heating above boiling . Conductometric detection
based system (SCARA) cleavage of all products point is possible of phase boundry
with balance, vortexer, . Multiple segregation of . Multichannel solvent/ . Up to 10,000 parallel
vacuum centrifuge reactor waste for hazard reagent delivery reactions
. Flexible control software classication or reagent . Fully enclosed . Fully enclosed
6 Instrumentation for Combinatorial Chemistry
recovery
. Fully enclosed
Argonaut Trident Charybdis Technologies Illiad Chemspeed ASW200 Irori

PS 2
Automation
Type Modular Unit Unit Modular
Arm XYZ arm Two XYZ arms XYZ arm (Gilson 222)
Chemistry Solid phase Solid phase Solid phase Solid phase
Solution phase Solution phase Solution phase
Reaction block (RB) Trident Reaction Cassette TM Calypso Reaction Block
Array (wells/vials) 48 (6 8) Microplate footprint e.g. 16 (8 2)
96 (8 12)
Number of possible RBs Up to 4 RBs Up to 4 RBs 7
Type Flexible during synthesis Fixed during synthesis Fixed during synthesis
Reaction vessels KANTM
Number/volume 48/5 m, 24/14 ml 6/50 ml; 12/25 ml; 24/10 112/13 ml; 64/27 ml; 32/75 Kans for 30 mg, 60 mg and
ml; 48/5 ml; 96/2 ml ml; 16/100 ml 300 mg resin capacity
are available
Material Glass vessels Multiple-well teon reactor Individual glass vials Polypropylene
block with frits
Reaction procedures
Reux (Sealed vessels) (Sealed vessels) Reux condensers for each (standard glassware)
vial
Filtration Top Bottom Parallel vessel to vessel
Evaporation in rv (online)
Agitation Orbital shaking Orbital shaking Orbital shaking
Temperature range 40 to 150 C 70 to 150 C 60 to 120 C
Pressure (upgradable up to 10 bar)
Inert atmosphere In rv In rv In rv In rv
Work-up
Liquidliquid extraction (Trident Processing (by volume)
Station)
Solid-phase extraction (Trident Processing
Station)
Analysis HPLC upgradable Online TLC; online HPLC
possible valve preinstalled
Special features . Fully enclosed . Modular bench layout . Reagent additions while . Modular, expandable
. Temperature and and format shaking or stirring and system
agitation speed exible heating or cooling . AutoSortTM10K
for each reaction cassette . Closure of the reactors by automatically sorts
. Rvs sealed with rotatable a ceramic valve allowing microreactors between
Teon valve for ecient evaporation reaction steps
(DMSO, DMF) . Sort 1000 microreactors
. Fully enclosed per hour
. Handling of slurries and

suspensions
193
194
ISRA Mettler Toledo Myriad Core MultiSyn Tech Syro II Perkin-Elmer Solaris 530
system
Automation
Type Unit Modular Unit Unit
Arm Articulated arm Transfer of RBs by a Two XYZ arms XYZ arm (TECAN)
conveyor belt
Chemistry Solution phase Solid phase Solid phase Solid phase
Solution phase Solution phase
Reaction block (RB) Minitray
Array (wells/vials) 12 (2 6) 96; 60; 40 48 (6 8)
Number of possible RBs Multiple 1 Up to 4 RBs
Type Flexible during synthesis Fixed during synthesis Fixed during synthesis
Reaction vessels
Number/volume 50/35 ml 12/10 ml 96/2 ml; 60/5 ml, 40/10 ml 48/10 ml
Material Glass vessels Glass vessels Glass or polypropylene Single glass reactors
syringes
Reaction procedures
Reux Closed reactors Closed rvs with (reux channel)
overpressure value
Filtration Bottom Bottom Top
Evaporation in rv (online)
Agitation Magnetic stirring Magnetic stirring, gas Magnetic levitation stirring Orbital shaking
bubbling
Temperature range 40 to 150 C 60 to 150 C 60 to 150 C 30 to 150 C
Pressure
Inert atmosphere In rv In rv In rv In rv
Work-up
Liquidliquid extraction (Allex TM )
Analysis Online HPLC
Special features . Detection of phase . Modular, expandable . Fully enclosed . Oine incubator
boundary via a camera system . Reagent and solvent available
system . Automated scheduling addition under agitation . Seven sensors to monitor
. Online error detection and simultaneous module possible critical instrument
operation functions
. Compatibility with the . Fully enclosed
Myriad Discoverer series
. Septumless rvs with twist
cap
Zenyx Magellan Zymark Zinsser Sophas
Automation
Type Unit Unit Unit
Arm XYZ arm Cylindrical arm XYZ arm
Chemistry Solid phase Solid phase Solid phase
(Solution phase) Solution phase
Reaction block (RB) Stem Block
Array (wells/vials) 98 Customized
Number of possible RBs 1 Customized
Type Fixed during synthesis Fixed during synthesis Fixed during synthesis
Reaction vessels
Number/volume 96/10 ml Customized 96/2 ml; 60/5 ml, 40/10 ml
Material Glass vessels Glass vessels Teon, glass vessels
195
196
Zenyx Magellan Zymark Zinsser Sophas
Reaction procedures
Reux Closed reactors Closed reactors Optional
Filtration Top Top
Evaporation in rv (online) Optional
Agitation Orbital shaking Orbital shaking Orbital shaking
Temperature range Ambient to 150 C Ambient to 150 C 80 to 150 C
Pressure
Inert atmosphere In rv In rv
Work-up
Liquidliquid extraction
Analysis Optional
Special features . Oine incubation . Modular, expandable . Oine incubation possible
possible system . Reaction vessels are moved
. 96-channel ltration head . Fully enclosed between functional unit on
workbench
the typical workow of an organic synthesis every step can be fully automated via
specialized devices that work totally independently but are at the same time con-
nected and controlled through an intelligent and easy-to-use software program.
Therefore, robotic systems are one of the most exible solutions to laboratory au-
tomation, and established systems can be further developed or redesigned if nec-
essary. Once a robotic system is established it is subject to constant optimization,
which is in contrast to workstation approaches where xed hardware and software
subroutines are usually used. In customized robotic systems, the control software
is used with a wide range of devices from dierent suppliers, and subroutines for
the specialized stations can be easily redened. With exible control software, au-
tomated error identication mechanisms and correction tasks are possible that
allow an unattended round-the-clock operation. But maximum versatility comes
at a price, which is one of the main disadvantages of customized robotic systems.
The size of the instrument requires custom-built ventilation cabinets and safety
installations such as a re extinguisher system, therefore the timeline for the suc-
cessful implementation of an automated robotlab is often a critical point for
pharmaceutical companies. The reliability of the equipment is dicult to predict
and can only be tested during installation, which can be a time-intensive process.
The key components of robot-arm systems are industrial robots that are used
extensively in many areas of industry, such as the car industry, for a wide range of
dierent tasks. Some of the main suppliers of robots are CRS [9], Beckman
Coulter [10], Mitsubishi [11], and Zymark [12] (robot-arm features are shown in
Table 6.2).
Isra system A one-arm-based system for solution-phase synthesis was manufac-

tured by Isra (Darmstadt, Germany). This system was developed in cooperation
with dierent companies, among them Bayer [13], at the beginning of 1997. The
system was designed for the synthesis, work-up, and analysis of arrays of 50 com-
pounds per run in amounts of up to 2 g. In this system, the CRS robot arm is used
for transport functions. It can be easily programmed via access tasks by using get-
and-put commands. Synthesis planning and navigation of the robotic system as
Tab. 6.2. Robot arm features.
Physical characteristics
Travel length Up to 5 m
Height to enclosure 138.7 mm
Height to saddle mounting 201 mm
surface
Weight approximately 50 kg/m
Performance specications
Speeds 0.010.9 m s1
Acceleration 3 m s2
Repeatability 0.08 mm
198 6 Instrumentation for Combinatorial Chemistry
Fig. 6.1. Layout of the Isra robot-arm-based system.

Implemented at Bayers central research center.
well as documentation of the chemistry undertaken are also very important fea-
tures of the control software. Therefore, a software concept was developed that of-
fers complete and legally admissible documentation of all substances which are to
be prepared by the robotic system. The data generated can easily be transferred
into widely used electronic laboratory journals. The whole system has a footprint
of 5 m long by 2 m wide and is divided into three functional parts for the synthe-
sis, work-up, and analysis; the layout is outlined in Fig. 6.1.
The individual components for the synthesis are a needle XYZ-pipetting robot,
heating and cooling reaction blocks with magnetic stirrers, a rack for reagents, and
a rack for starting materials. These devices have been successfully used in many
dierent syntheses under various conditions. The largest part of the machine is
used for storage and work-up procedures. The main devices for work-up are a lter
station, a drying station, a balance, a centrifuge, a solvent evaporator, and a phase
separation and a phase boundary recognition station. The analytic part of the robot
is represented by a Shimadzu high-performance liquid chromatography/ultraviolet
(HPLC-UV) system. Via an interface it can be used for online analytical character-
ization of the synthesized products. The main features of the system are:
. liquid capability per vial: 35 ml;

. all manipulations under argon;
Fig. 6.2. Phase separation.
. classical laboratory procedures:

mixing, vortexing, and ltration,
liquidliquid extraction, centrifugation,
drying, evaporation;
. online analysis of purity and yield.
The system contains a specially designed phase-separation station. An integrated

camera (Fig. 6.2) system is able to measure the z-height; the registered value is
used as the input command for the phase-separation device.
Zymark One of the most widely used robot arms in fully automated systems for
process development and organic synthesis is the Zymate XP arm [14], which has
been commercially available since the early 1980s. The example shown uses a
cylindrical Zymark robot with interchangeable eectors for performing dierent
manipulations (Fig. 6.3).
This system was developed as a result of collaboration between Zeneca and
Zymark (Runcorn, UK) [15]. Depending on the individual components, the main
features of the system are:
. synthesis of 4050 reactions at a time in gram scale;

heating, cooling, mixing, vortexing,
ltration, liquidliquid extraction;
. sample preparation for analytical purposes [16].
Fig. 6.3. Layout of a Zymark robot-arm-based system.
The customized synthesizer has an open architecture with considerable exibil-

ity. Based on a Zymark synthesizer, SmithKline Beecham developed a system for
synthesis and online purication via column chromatography [17].
Accelab Arcosyn98 The Arcosyn98 manufactured by Accelab [18] is a fully auto-

mated system for solid- and solution-phase synthesis. A xed Scara [19] robot arm
is equipped with a gripper change system, enabling it to change its eector tool.
Based on this technology, the Scara arm is in charge of all vessel transfers. In ad-
dition, other functions such as pipetting and vial opening/closing mechanisms can
be performed without an in-built peripheral station (Fig. 6.4).
To achieve high throughput, the system includes devices for heating and cooling,
evaporation, dissolution, liquidliquid extractions, yield determination, and sam-
ple preparation for analytical purposes, as shown. The Arcosyn98 can be used with
ve reaction blocks at a time, therefore 100 parallel reactions are possible in one
run (Fig. 6.5).
The whole system can be controlled and programmed with a software package
Fig. 6.4. Layout of Accelabs Arcosyn98 robot system.
using one master computer. The multifunctional software can also be used for
planning, scheduling, and administration of data entries and results.
6.1.2.2 Fully Automated Workstation Systems
Chemspeed ASW2000 system Chemspeed [20] was founded in 1997 by a team of

chemists who had previously worked in a medicinal chemistry laboratory at Roche.
Fig. 6.5. Reaction block Arcosysn98.

Fig. 6.6. ASW2000 layout.
Their main objective was to develop an unattended automated system that allowed
parallel preparation of compounds in glassware reactors with online purication
and analysis in a compact workstation approach (Fig. 6.6).
Chemspeed delivers the system on a trolley (footprint 1.4 m 0.8 m) covered
with a hood. Because of this compact design, the very exible system can be used
in nearly every laboratory. Within one run, 80 parallel reactions (with an option of
112) can be performed that have the following features:
. liquid capability of 13, 27, 75 or 100 ml per vial;

. fully inert environment inside and outside the reactors;
. reagent additions while shaking or stirring and while heating or cooling;
mixing, vortexing, ltration,
liquidliquid extraction,
drying, evaporation, cold nger reuxing;
. solid-phase extraction (SPE);

. temperature range from 70 to 150 C, measured and controlled in the reac-
tion mixture;
. online analysis of purity and yield by thin layer chromatography (TLC) or ana-
lytical HPLC (optional);
. rheodyne valves for preparative HPLC.
The whole system can be upgraded into the ASW2000P workstation, which
allows pressurized reactions that integrate work-up and analysis procedures during
the synthesis. The pressure capabilities of the system are:
. up to ve reactor blocks (80 parallel reactions at maximum);

. up to 12 bar;
. pressure sensor;
. autosecurity system to provide optimum seal performance.
Advanced ChemTech Since 1985, Advanced ChemTech (ACT) [21] has supplied
systems for organic synthesis, which in the beginning were especially for peptide
synthesis. Today ACT oers a broad family of manual, semiautomated, and au-
tomated synthesizers for solution- and solid-phase synthesis (Table 6.1).
The Venture 576 (launched in May 1999) is designed to be a platform for fully
automated high-throughput synthesis (Fig. 6.7).
The heart of the Venture 576 is a special reaction block combined with two
multiprobe XYZ arms. The microplate reactor block contains 96 wells and is con-
structed of glass-impregnated polytetrauoroethylene (PTFE) constructions. The
usable reaction well volume is approximately 3 ml compared with a total volume of
6 ml and allows parallel reactions in milligram scale even under a reactive gas at-
mosphere because reaction vessels can be pressurized up to 150 psi. The system is
capable of up to 10,000 simultaneous reactions that are determined by the cus-
tomer. The following description summarizes the main features of the system:
. inert atmosphere for reactor, reactants, and the whole platform;

vortexing, ltration, liquidliquid extraction;
. reactor block with integrated condenser module;
. temperature range from 70 to 150 C, electric resistive heating, cooling by
nitrogen gas generated from liquid nitrogen.
The oor-standing cabinet is equipped with connections for a ventilation system.

Because the system is capable of performing up to 10,000 reactions per run, it is
recommended for combinatorial laboratories producing large numbers libraries.
MultiSyn Tech Syro II MultiSyn Tech [22] oers manual, semiautomated, and fully
automated systems for combinatorial chemistry. The fully automated Syro system
Fig. 6.7. ACT Venture 576.
(Fig. 6.8) consists of two independent XYZ robot arms and a specially designed
reaction block. The system can be equipped with dierent reaction vessels. For
solid-phase synthesis the removable reaction vessels (number/volume: 96/2 ml;
60/5 ml; 40/10 ml) in glass or polypropylene with glass or PTFE frits are rec-
Fig. 6.8. Syro by MultiSyn Tech.

Fig. 6.9. Levitation mechanism.
ommended. Owing to the reaction block design all manipulations can be per-
formed under inert gas atmosphere using reaction temperatures between 60 and
150 C.
The system has a specially designed agitation mechanism. Each reaction tube is
circumvented by electric coils that are used to generate a magnetic eld. The coils
are placed in a movable levitation plate, the center of the magnetic eld is about
6 mm above the frit of the reaction tubes. This special set-up ensures that, during
agitation, the resin is not crushed between the stirring bar and the frit (Fig. 6.9).
Zenyx Magellan synthesizer In 1996, Zeneca Pharmaceuticals entered into a col-

laboration with Zenyx Scientic to design and build an instrument for multiple
parallel synthesis [23]. The new system was intended to fulll the following main
objectives:
. access to libraries containing up to 1000 single compounds;

. scale: up to 30 mg for primary screening and repository;
. microplates should be used as transfer racks.
The Magellan system is a fully automated synthesizer controlled by a computer.
An Excel interface within the control software allows substance data to be im-
ported for the reprogramming of standard protocols. With this system 96 reactions
can be performed within one run, using a Stem [24] reaction block. The set-up is
very exible because the layout of the workstation can easily be changed. The XYZ
robot arm is in charge of all pipetting jobs. After cleavage from the resin, the com-
pounds can be delivered directly into disposable vials using a special 96-lter sta-
tion with 96 individual needles with a lter frit at the end.
Perkin-Elmer Solaris 530 The Solaris TM 530 [25] organic synthesizer for auto-
mated combinatorial chemistry was introduced in late 1998 by PE Biosystems, a
division of the PE Corporation (Fig. 6.10).
The system is able to synthesize 48 discrete molecules per run in parallel. The
portable synthesis module contains an array of 8 6 reaction vessels with a vol-
ume of 10 ml per vial (Fig. 6.11). A reux channel is built in the chemically inert
module to provide reux conditions. The dual septa secures an inert atmosphere.
Fig. 6.10. Solaris.
Key features of the system include:
. eight liquid-handling tips;

. seven sensors to monitor critical instrument functions;
. completely enclosed system with ow-through ventilation;
. multiple instrument sensors;
. oine workstation for heating, mixing, and cooling.
An oine incubation workstation enables multiuser access and staggered syn-
thesis runs, which increases throughput. The system is designed for the auto-
mated lead optimization using solid-phase synthesis techniques.
Zinsser Sophas In 1998 Zinsser [26] launched the Sophas system, which is spe-
cially designed for solid-phase synthesis. The synthesizer uses a robotic XYZ arm
with four independent probes that are manufactured by Rosys [27]. All liquid-
handling tasks are controlled via a personal computer. The easy-to-use software is
very exible, can import data from any database, and allows customized layouts to
Fig. 6.11. Glass vials.
be dened. The automated workbench oers the opportunity to choose from a set
of movable reactors that range from 96-well plates to 25-ml reaction vessels.
Charybdis Technologies Illiad PS 2 Charybdis Technologies [28] was founded in

1996, and provides solutions in the areas of high-throughput organic synthesis,
laboratory automation, and chemical discovery. The Iliad PS 2 Series are multi-
tasking robotic workstations for solid- and solution-phase chemistry. The two in-
dependent XYZ robotic arms work in parallel and are controlled via the OASys
software. The heart of all Charybdis synthesizers is the Calypso reaction block sys-
tem, which consists of a top frame with a specially designed top cover plate and a
base frame with a base cover plate. The reaction block accepts any array with the
standard footprint of a microplate with well volumes of 50, 25, 10, 5, and 2 ml. The
Iliad systems can be upgraded to provide online ltration and agitation.
6.1.2.3 Modular Systems
Argonaut Trident Argonaut Technologies [29] was founded in 1994, and provides
systems for parallel solution- and solid-phase chemistry. The Trident [30] family
consists of a reaction cassette, a library synthesizer, a workstation, and a process-
ing station. The core of the system is the Trident Reaction Cassette TM that contains
48 5-ml vessels or 24 14-ml vessels which are made from glass. The reaction cas-
sette ts into every member of the Trident family and can be easily removed dur-
ing synthesis for spot checks on the reactions.
With one run, the fully automated Trident library synthesizer can prepare up to
192 reactions in parallel. The whole system is controlled via the Trident software,
which controls, for example, the temperature, solvent deliveries, or product collec-
tion. The synthesizer can handle up to four dierent reaction cassettes, and each
cassette position can be set to a dierent temperature and agitation speed.
The Trident workstation is a straightforward supplement to the synthesizer, be-

cause it can be used for the manual delivery of solvent and reagent, so it performs
parallel resin washing and sample collection in a very eective way. The work-
station is ideal for development chemistry, because the methods are developed and
adopted in the same cassette as that used for library production. The Trident Pro-
cessing Station completes the family. It is a multipurpose liquid handler with a
special interface to the reaction cassette. The key features of the station are:
. liquidliquid extraction;
. solid-phase extraction;
. clean up with scavenger resins;
. reverse ltration;
. dry solid loading to open vessels;
. reformatting (e.g. from tubes to microplates).
Mettler Toledo Myriad Core System The Myrid TM Core System (MCS) [31] was de-
veloped by a consortium of pharmaceutical companies (SmithKline Beecham,
Pzer, BASF, Novartis, Merck, Takeda, and Chiroscience) and The Technology
Partnership [32]. In December 1998 the MCS was sold to Mettler Toledo [33].
The MCS was created as a synthesis system based on a series of robotic pro-
cessing modules combined with a unique reaction vessel design, fullling the fol-
lowing objectives:
. solid- and solution-phase chemistry should be possible;

. synthesis of large numbers of compounds for high-throughput screening;
. multistep directed synthesis of pure compounds;
. method development should be possible;
. modular, expandable design;
. automatic transfer of vessels between processing modules;
. automated scheduling and simultaneous module operation.
The reaction block consists of an array of 12 reaction vessels with twist caps. The
whole blocks can be transferred to the dierent units (incubator and processing
module) by a conveyor belt. The system is controlled by the chemist using software
that allows the processing of four completely independent batches (48 reactions).
Irori In 1996 Irori [34] introduced the AccuTag TM -100 Combinatorial Chemistry
System. With this system, large numbers of discrete compounds can be produced
using the directed sorting split-and-pool technique [35]. The reactions are per-
formed in single microreactors which are identied using miniature electronic
tags. The Irori Kan TM reactor family is specially designed for solid-phase synthesis.
Three dierent Kans the MicroKan TM , the MiniKan TM , and the MacroKan TM
with a resin capacity of up to 30, 60, and 300 mg are available, therefore com-
pounds can be synthesized in approximately 10-, 20- and 100-mg batches (Fig.
Fig. 6.12. Irori Kans.
6.12). Another big advantage of this approach is that standard glassware can be
used for performing the library synthesis.
To achieve high throughput, the Kans are used together with the AutoSort-10K.
This workstation has been designed to extend the directed sorting technique for
use with libraries in the range of 1000 to 10,000 compounds. The AutoSort TM -10K
Microreactor Sorting System (Fig. 6.13) automatically sorts microreactors between
reaction steps.
The key features of the system are:
. accommodates up to 10,000 microreactors;

. sorts 1000 microreactors per hour;
. automatically sorts for cleavage into the AccuCleave-96;
. standard glassware applicable.
6.2
Purication of Combinatorial Libraries
In the early days of combinatorial chemistry [36], mixtures derived from solid-
phase split-and-mix libraries [37] as well as nonpuried compounds from solution-
Fig. 6.13. Autosort.
phase synthesis played an important role as test compounds for biological screen-
ing, basically because it was a very easy way to produce the promised numbers
of compounds. It was soon recognized that those compounds often led to false-
positive test results, and that the deconvolution of mixtures and extraction of bio-
logically active molecule in an HTS mode are dicult tasks [38]. This problem re-
sulted in the synthesis of single compounds fullling properties such as diversity,
drug likeness, and a high degree of purity [39]. Classical purication procedures
such as liquidliquid extraction and chromatography were automated, solid-phase
extractions with ion exchangers were adopted, and scavenger reagents for trapping
excess starting material or reagents were developed. Automated preparative re-
versed phase HPLC systems were set up to address high-throughput purication
issues.
6.2.1
Automated LiquidLiquid Extraction
Liquidliquid extraction is one of the standard methods for removing hydrophilic

byproducts, reactants, or reagents. Several examples of the parallel usage of this
technique for purication of combinatorial libraries have been described [40]. This
6.2 Purification of Combinatorial Libraries 211
method is only appropriate for very simple separation problems and can be per-
formed in an automated fashion by using a liquid handler. The method totally fails
when polar compounds have to be puried because emulsions can appear or prod-
ucts remain in the aqueous phase. Coupled to a solid-phase extraction system, au-
tomated liquidliquid extraction can be performed together with a 96-needle pi-
petting system such as Quadra 96 [41]. Separation problems, for example removal
of amines from a combinatorial library, were solved by applying several extraction
cycles. Dichloromethane and dilute HCl were mixed and separated through ltra-
tion using solid-phase diatomaceous earth. The phase separation was achieved via
vacuum ltration through a 96-well lterplate carrying a hydrophobic membrane
which held the aqueous phase back. Liquidliquid extraction can be easily auto-
mated by using pipetting workstations. Reaction mixtures are mixed with buers
and the upper or lower phase, depending on the density, is removed. Ecient
mixing can be achieved through redispensing, which can be repeated several
times. The use of a capacity sensor represents a more sophisticated approach. This
sensor type is available for several liquid handlers (Zinsser, Tecan). A drawback
of this method is when phase separation is not complete or undetectable, erratic
results are obtained.
6.2.2
Solid-phase Extraction
Solid-phase extraction is widely used in bio- or environmental analyses in order

to enrich or discover organic molecules from complex aqueous matrices. It can
also be very useful for the purication of combinatorial libraries. There are rather
simple desktop instruments available which are designed for this application
Zymark Benchmate TM , Gilson Aspec TM , and Hamilton Microlab TM in addition to
integrated devices in automated systems (e.g. Chemspeed); simple self-constructed
systems have also been reported [42]. One of the big advantages of solid-phase
extraction is the availability of various solid phases for the separation of diverse
molecules, which range from hard and soft anion or cation exchangers to reversed
phase silica columns which are all available in prepacked formats. One disadvan-
tage of the system is that the separation problem has to be evaluated very carefully
to achieve optimal results. This becomes a problem when the library is diverse in
terms of biophysical behavior and limits the universality of this methodology. An
example of the successful application of solid-phase extraction is the synthesis of
225 basic amines which were adsorbed on an acidic ion exchanger. Neutral side
products were eluted, and after several washing steps the products were cleaved
using ammonia in methanol [43]. Another example is the separation of a library
containing neutral compounds from basic and acidic side products via inline solid-
phase extraction using ion exchangers. The neutral products were not aected by
the solid phases and only side products were absorbed. Excess isocyanates were
also successfully removed by trapping them as ureas using an excess of a basic
amine. This side product was then eciently absorbed to an acidic solid-phase ab-
sorber [44]. An enormous increase in the versatility of this methodology can be

achieved with scavenging reagents. Scavenging reagents oer the opportunity to
use chemical reactivity as a mode of irreversible absorption to a solid support. This
allows the selective and ecient removal of many excess reagents. Examples are
the removal of excess electrophiles such as acid chlorides, sulfonic chlorides, and
isocyanates as well as the trapping of excess nucleophiles such as amines [45].
Despite these simple separation problems rather complex multistep transforma-
tions have been performed using this separation technique [46]. Several of these
polymer-supported reagents are commercially available [47]. Furthermore, solid-
phase reagents prepacked in columns or microplates would be a great advantage
in performing parallel reactions.
6.2.3
Normal Phase Chromatography
Together with crystallization and liquidliquid extraction, normal phase chroma-

tography is one of the most important purication operations in organic synthesis.
For automation and parallelization normal phase chromatography is also appro-
priate and several systems are commercially available, e.g. CombiFlash TM from
Isco [48], Quad3 TM from Biotage [49], and FlashMaster TM from Jones Chroma-
tography [50]. Parallel ash chromatography ranging from 4 to 12 single-use col-
umns is widely used. The Isco and Biotage systems provide time-triggered fraction-
ation; the system from Jones chromatography collects fractions via UV detection,
which minimizes the number of fractions. Prepacked columns are available and
have to be exchanged after each run, therefore only batchwise working is possible.
If salts and other polar byproducts are carefully removed before chromatography,
the columns can be used several times. The commercially available columns can
also be self-packed with very simple equipment. The loading of these columns is
usually very high: a 20-g cartridge can be used for the purication of up to gram
quantities of product.
6.2.3.1 CombiFlashTM from Isco [48]

This instrument is designed for parallel separation with ten columns and is
equipped with an injection system in which dissolved samples or samples ab-
sorbed on silica gel can be loaded. Besides the commercially available Isco Red-
Sep TM columns all other columns with luer ttings can be used. Fractionation is
time guided, and a maximum of 40 fractions per run can be collected. An advan-
tage of this system is the very small hood space of 50 cm which is required.
6.2.3.2 Quad3TM from Biotage [49]

With the Quad3 TM 12 columns can be used in parallel together with a fraction
collector which is able to handle dierent vial types as well as microplates. The
microplates simplify the evaporation process because vacuum centrifuges can be
used. A step gradient can be applied, and an injection system for the delivery of
Tab. 6.3. Common stationary phases for reversed phase preparative HPLC.
Material Application
C18 endcapped Drug-like compounds

C18 hydropylic endcapped Drug-like compounds especially for polar compounds injected
in DMSO
C8 Drug-like compounds, amines, lipids
CN Polar compounds
dissolved samples or samples absorbed on silica gel is available. In addition to this

system a simple desktop version, the MultiElute TM system for 12 columns with
fraction collector, is also available.
6.2.3.3 FlashMasterTM from Jones Chromatography [50]

FlashMaster TM is a computer-controlled desktop system for automated ash chro-
matography of ten columns, which allows gradient elution. With an integrated UV
detector, UV-triggered fractionation minimizes identication logistics. Together
with postrun reporting of chromatograms, product identication can be easily real-
ized. In addition to this system, Jones Chromatography also oers simple solutions
for parallel ash chromatography.
6.2.4
Reversed Phase Chromatography
Reversed phase chromatography (RP-HPLC) is widely used in analyses and puri-

cation of combinatorial libraries (Tables 6.3 and 6.4). The method is very univer-
sal in terms of polarity of the analytes and a wide range of compound types can be
puried with RP-HPLC. This makes RP-HPLC a favorable method for purifying
combinatorial libraries, mostly because no method development is necessary.
The available equipment is very rugged and has been developed for high through-
put. Columns can be used up to 1000 times and continuous working is applicable,
enabling fairly high throughput which compensates for the serial nature of HPLC.
In theory, HPLC can be used 24 h per day, but normally this does not happen be-
cause of solvent delivery and removal, sample supply, and fraction removal. Lim-
ited throughput because of the serial nature of the system is compensated by very
Tab. 6.4. HPLC columns, dimensions, and applicable loading.
Dimension (mm)/material/particle size (mm) Loading (mmol) Flow rate (ml min1 )
8 75/C18/5 10 814
20 50/C18/5 50 2540
30 125/C18/5 75100 5070
fast chromatography, which allows the semipreparative separation of one sample

within minutes and a daily throughput of approximately 200 samples is possible.
Fractions are usually triggered via UV and only compound-containing fractions
are collected. Diculties can be encountered in the identication of the target
product-containing fraction, which is usually done oine with FIA-MS (FIA
ow injection analysis) or HPLC-MS. Column switching is desirable for speeding
up cycle times. One column is used for the chromatography while the other col-
umn is equilibrated to starting conditions, saving about 1020% of the cycle time.
There are systems on the market which are able to run two columns. This doubles
throughput and also the price of the system because further pumps, a detector,
and fraction collector must be used. The advantage of running two columns is
small compared with running two individual systems.
Because of the complexity of the whole set-up consisting of HPLC plus down-
stream processing large eorts are required for the implementation of this tech-
nology in a laboratory workow in order to run the system in an optimal fashion.
Depending on the separation problem, and on the number of byproducts, up to
ten fractions can easily be obtained per injection. For identication of the target
product, each fraction must be analyzed with FIA-MS. This issue consequently
demands very close interaction with the analytical group performing these experi-
ments. RP-HPLC is complementary to RP-HPLC-MS and the information from
analytical HPLC-MS can be directly used for identication of the desired product
fraction without any FIA-MS [51]. For every kind of set-up the logistics are com-
plex, and adoption or development of useful software solutions are desirable for
tracking the large amounts of data and to prevent bottlenecks. A reduction in
the amount of solvent used may be achieved through supercritical uid chroma-
tography (SFC). This method oers the opportunity to use a supercritical gas, for
example CO2 , as a mobile phase. CO2 is cheap, it has high ow rates because of
low backpressure, and it evaporates when external pressure is removed [52].
6.2.4.1 Biotage [49]

The Parallex TM System from Biotage is a four times parallel HPLC-UV work-
station. The system has four channels with four individual fraction collectors, de-
tectors, and pump heads. Throughput lies in the range of 40 injections per hour
and the injection system can handle up to 768 samples per run. Loading can be
from 1 mg up to 200 mg depending on the column used. The system is fully soft-
ware controlled and a detailed reporting software package is available.
6.2.4.2 Gilson [53]

Gilson oers a very rugged preparative HPLC system named Nebula Series TM .
The pumps especially are outstanding. Flow rates of 200 ml min1 and pressure
limits of 400 bar can be achieved. The fraction collector 215 TM has a capacity of up
to 12 microplates and completes the high-throughput system. The system is totally
software controlled and detailed reporting allowing fraction tracking is also in-
cluded.
6.2.4.3 Merck [54]

Merck oers an automated preparative HPLC for parallel chromatography of two
columns named the High Throughput Purier TM (HTP). Four columns are in-
tegrated: two are conditioned while the other pair is used for chromatography. The
optionally available Merck-Hitachi Ion Trap MS oers online or oine product
identication. The MS is fully integrated into the workow and oers very simple
reporting to Excel, which is essential for integration into a laboratory workow.
6.2.4.4 Varian [55]

Varian distributes an HPLC equipped with Dynamax HPLC Pumps. Flow rates of
up to 200 ml min1 with a pressure limit of 410 bar are applicable. High through-
put is not possible because the system lacks a useful fraction collector that can
handle microplates. In addition to this, the Apple software is hard to integrate with
Microsoft-based laboratory environment.
6.2.4.5 Shimadzu [56]

Shimadzu is one of the leading companies in preparative HPLC. The systems
oered are very robust and the equipment, such as the UV detector and pumps,
can be very easily controlled. A disadvantage is the fraction collector, which cannot
handle microplates this feature minimizes throughput and capacity.
6.2.5
Preparative HPLC-MS
The search for more powerful techniques for the purication of combinatorial li-
braries using HPLC led to collaboration between researchers from the pharma-
ceutical and analytical industries, namely PE Sciex and Micromass, with the goal
of developing preparative HPLC-MS [57, 58]. The advantage of this technique is
that the molecular mass of the target molecule triggers the fraction collector. This
allows the collection of the desired compounds and the online identication of the
target molecules. Furthermore, this method oers logistical benets. If just the
target molecules are collected, fraction collector capacity is not critical and down-
stream processing can be performed very eciently. This enables the technique to
work very eciently in terms of throughput. For setting up such a system integra-
tion of the mass spectrometer and a reliable software platform which ensures
fraction collecting and sample tracking are necessary. This application is now of-
fered from more vendors than the pioneers Micromass and PE Sciex, e.g. Merck-
Hitachi, Gilson in collaboration with Thermoquest and Shimadzu.
6.2.5.1 PE Sciex [59]

PE Sciex, the rst vendor with this application type on the market, oers a prepa-
rative HPLC-MS/UV system with Shimadzu pumps and a Gilson 215 as a fraction
collector. The hardware components, especially the API 150EX mass spectrometer,
are very rugged, and from this point of view the system is very useful for high
throughput. One of the main disadvantages is the Apple-based software and the
unstable fraction collector script used for tracking fractions. Besides lacking soft-
ware stability, it is also not easy to integrate an Apple-based system into a usually
Microsoft-based laboratory environment.
6.2.5.2 Waters Micromass [60]

Micromass merged with Waters and was the second vendor oering this applica-
tion. As HPLC components, Waters devices can be integrated with equipment
from other HPLC providers. The Gilson 215 is used as a fraction collector device
that is fully integrated in the software platform. The Masslynx TM software is fairly
well adapted to high throughput, making it easy to integrate these systems into
laboratory workow.
6.2.5.3 Merck-Hitachi
As already mentioned above, Merck-Hitachi oers a system that is designed for
this application. By using a special valve as an interface, it is possible to switch
between two ows running into the MS inlet. Therefore two preparative separa-
tions at a time can be performed and analyzed, thus doubling the throughput and
reducing hardware costs. Merck-Hitachi devices together with Gilson fraction col-
lectors are compatible HPLC components.
6.2.5.4 Shimadzu
Shimadzu oers a preparative HPLC-MS/UV system with a Gilson 215 fraction
collector. Besides being good HPLC equipment, a reliable and exible software
package is available. In addition to the software package operating the instrument,
a Shimadzu LIMS (LIMS laboratory information management system) system
is available which can also be used for documentation of data other than those
from the HPLC-MS.
6.2.5.5 Gilson ThermoQuest

Gilson, one of the leading experts in HPLC, has established a preparative HPLC-
MS system in collaboration with Thermoquest. The HPLC part of the system,
supplied by Gilson, is controlled by Uni Point software (Gilson); the ThermoQuest
MS however is controlled by Excalibur software (Thermoquest). Both software ap-
plications are controlled via special interface software, which has the consequence
that the MS detector is only marginally controlled by the HPLC part of the equip-
ment, by pulsing externally, and the two independent software packages always
have to run on a single PC.
6.3
Analysis of Combinatorial Libraries
Combinatorial syntheses need fast and reliable analyses in order to determine the
identity of products and intermediates in each step of a parallel reaction sequence.
6.3 Analysis of Combinatorial Libraries 217
Tab. 6.5. Analytical methods and their applications in combinatorial chemistry.
Method Application
FT-IR Characterization of resin-bound intermediates in reection (ATR (ATR

attenuated total reectance) DRIFTS (DRIFTS diuse reectance infrared
fourier transform spectroscopy))
NMR Characterization and quantication of combinatorial libraries with fast FIA or
sample exchanger devices
ESI-MS Characterization of libraries in coupling to HPLC or CE. Identication of fractions
from preparative HPLC in FIA mode
Consequently, analyses were adopted that operate at the same speed as combina-
torial methodologies when these methods became popular for synthesis. The
analysis of the nal products from solid- and solution-phase synthesis usually
compounds for biological testing are the same because similar purity criteria are
applicable. Because of the nature of solid-phase synthesis, the analysis of polymer-
bound intermediates is rather dicult. Special nuclear magnetic resonance (NMR)
and FT-IR methods (Table 6.5) have been developed for the purpose of character-
izing polymer-bound intermediates. In the case of FT-IR techniques, reection
measurements are usually used, e.g. ATR and DRIFTS [61]. These methods can be
performed directly on bead and no KBr solids have to be made, as is the case in
transmission experiments. In the case of NMR, magic angle spinning can be used
to suppress signals from the polymer matrix [62]. All these special analytical tech-
niques are usually used for developing the method owing to the fact that they are
very time-consuming and therefore have a fairly low throughput.
The minimal requirements for combinatorial libraries are usually purity, iden-
tity, and quantity.
6.3.1
Purity of Combinatorial Libraries
Purity assessment is historically carried out using chromatographic methodologies.

Thin layer chromatography (TLC), reversed phase (RP)-TLC, and HPLC are there-
fore widely used; these methods may also be used for spot tests in parallel synthe-
sis. For a purity check of a whole library, methods with a higher throughput such
as automated HPLC, supercritical uid chromatography (SFC) [63], and capillary
electrophoresis (CE) are applicable. In addition to chromatographic separation, de-
tection plays an important role. Standard detection is UV absorption at dierent
wavelengths. In addition, another optical detector the light-scattering detector
(ELSD) can be used [64]. Light-scattering detectors have a more linear signal
to mass response and are more likely to be quantitative. For use in quantitative
analysis of combinatorial libraries, a nitrogen chemoluminescence detector is even
more appropriate because the nitrogen signal is proportional to the amount of ni-
trogen present in the sample [65]. HPLC-MS coupling is the most widely used
method of purity assessment in parallel synthesis, mainly because separation and
identication of the target molecules is carried out in a parallel fashion. Mild ion-
ization techniques such as ESI and APCI are used. They almost always show the
molecular ion peak, which can be directly taken from the synthesis protocol. Cycle
times are highly optimized. It is possible to perform 400 HPLC-MS runs per day
[66]. The resulting data have to be stored in an appropriate LIMS system. Tools are
available from hardware suppliers for the semiautomatic processing of these data.
Using these tools, further steps such as adaptation to the laboratory workow are
additional issues, and eorts to optimize these interfaces are necessary [67]. The
widespread use of HPLC-MS for purity evaluation gives a limited insight into the
actual purity of a product because only UV-absorbing side products and those on
RP-absorbable compounds can be detected. Salts and polymer fragments are usu-
ally not detected. One should take this feature into account when assessing the
purity of combinatorial libraries if they are not puried chromatographically before
biological testing. Many suppliers sell fast HPLC-MS applications especially de-
signed for library purity checks, and all have semiautomated software packages
available for data processing.
6.3.2
Identity of Combinatorial Libraries
Besides purity, determination of the identity of the individual library member

is one of the important analytical tasks in combinatorial chemistry. Usually, classi-
cal methods such as NMR and mass spectrometry are used. NMR has a disadvan-
tage in that it is possible to measure hundreds of NMR spectra daily but the auto-
matic processing of data is still a bottleneck. Therefore, NMR is mostly used
during method development, especially when stereochemical aspects have to be
addressed. As already mentioned ESI (ESI electro spray ionisation) and APCI
(APCI atmospheric pressure chemical ionisation) mass spectrometry are widely
used ionization methods. The advantages of these ionization techniques are that
detection from a liquid spray is possible and that an FIA system or an HPLC sys-
tem can be directly coupled. Additionally almost always a molecular peak is ob-
tained which makes the semiautomatic processing of the data very easy. Classical
ionization methods such as EI (EI electron ionisation) and CI (CI chemical
ionisation) are not applicable for polar molecules in the mass range of 300 to 500.
MALDI is also very popular, especially for peptides and proteins in bioanalyses
[68]. Critical sample preparation procedures and the impossibility of coupling to
an HPLC system limit the methodology. For mass analyses, the highly robust
quadruple technique is widely used, as are TOF [69] and FT-ICR [70]. The advan-
tage of TOF and especially FT-ICR is the very good mass resolution of 5 ppm in the
case of TOF (TOF time of ight) and better than 1 ppm in the case of FT-ICR
(FT-ICR fourier transform ion cyclotron resonance spectroscopy). Owing to this
high resolution, the molecular composition can be obtained directly from the mass
signal.
For fast analysis of combinatorial libraries and for identication of products in
fractions coming from preparative HPLC, FIA-ESI-MS is the method of choice [71,
72]. Cycle times below 10 s can be achieved even with standard equipment. Prob-
lems can arise because of the vast amounts of data, but software packages are avail-
able from all suppliers of ESI mass spectrometers for automated processing. The
implementation of these data into the workow of combinatorial laboratories is of
course another issue and is only achievable with programming resources which
can be limited to automated reformatting of Excel tables. FIA-ESI-MS does not
give any results concerning purity, and if mixtures are obtained ionization yields
can vary dramatically and lead to false results if the product is suppressed, e.g. by
basic impurities. In addition to FIA-ESI-MS, MALDI-MS (MALDI matrix aided
laser desorption ionisation) in an oine FIA mode can also be performed.
Through an automated process MALDI targets have been coated and prepared for
measurement [73]. This application is rather complex because it is impossible to
work directly from solution. The advantage however is that it is the only method
which gives a molecular peak from larger molecules such as proteins.
6.3.3
Quantication of Combinatorial Libraries
In addition to purity and identity, quantication of combinatorial libraries is one

of the major issues in combinatorial analyses because it is essential to know
the amount of compound in order to quantify the biological eects. Unfortunately,
there is no simple way to automate quantication. The best way to quantify the
system, but also the worst way to automate it, is by weighing. Besides weighing, it
is also possible to use a nitrogen detector, but accuracy can be very low for diverse
sets of compounds. Therefore weighing as the method of choice must be auto-
mated. This can be achieved with liquid handlers carrying a small robotic arm.
These systems, which are commercially available from Zinsser Calli TM and Mettler
Toledo Bodan TM , can handle single vials. The bar-coded vials are weighed empty
and the weight is recorded in a database. After weighing all the vials, the dispenser
transfers solutions of the synthesized compounds into the vials. After evaporation
of the solvent in a vacuum centrifuge, the robot arm again weighs the vials and the
quantity of compound is determined.
6.4
Automated Sample Processing
6.4.1
Sample Logistics
Parallel high-throughput synthesis is a mass production process. The process con-

sists of several stages that must operate in an interlocking way. It is very important
to identify and remove bottlenecks in order to obtain optimal throughput. A very
important role that is often regarded as a bottleneck is played by the sample logis-
tics (Fig. 6.14).
Fig. 6.14. Flow chart of an automated processes in parallel synthesis.
After evaluation of a synthesis that is considered useful for library production,

the production process begins with weighing of the starting materials. The weigh-
ing process cannot be performed in an automated fashion because of the diverse
physical nature of common starting materials, which can be liquids, solids, or oils.
After weighing the starting materials, they can be dissolved in an appropriate sol-
vent and then transferred very eciently to the reaction vessels by using liquid
handlers; some four- or eight-needle systems are described in Table 6.6. When the
reaction is complete, the work-up protocols described in Chapter 6.2 are used for
purication of the library. For liquidliquid extractions or solid-phase extractions,
the samples are produced in ratios of 1:1, which simplies the sample logistics for
reformatting and analysis. Samples can be taken directly with pipetting robots and
then diluted or ltered for analysis. After analysis, those samples that are to be
processed further to determine their biological activity are selected. This decision
is based on the analytic results, usually those from HPLC-ESI-MS. Qualitatively
acceptable compounds are taken through a quantication and reformatting step.
Sometimes further analytical and quality control steps are necessary. When HPLC
or HPLC-MS are used for purication of the library, the logistics are much more
dicult than for the 1:1 purication strategies. The raw products from synthesis
have to be ltered and dissolved in an HPLC-compatible solvent. Additionally, all
of them have to be reprocessed into an HPLC-suitable format, usually a micro-
plate. After chromatographic purication a large number of fractions have to be
identied and evaporated. A pooling step is necessary for those fractions that give
Tab. 6.6. Liquid handlers suitable for sample processing in parallel synthesis.
Liquid handler Application
Tecan Four- and eight-needle systems suitable for reformatting and

synthesis in MTPs. A robot arm can also be adopted for use in
vial handling, weighing, etc. Further equipment for evaporating
of lter plates, etc. available
Myriad Mettler Toledo Four-needle system with robot arm specially designed for weighing,
SPE
Zinsser Lissy Four-needle system for reformatting and synthesis. Robot arm and
further equipment for weighing, SPE and synthesis available
Packard Eight-needle system, second arm with disposable tips, evaporation
manifold available
MTP, microtiter plate; SPE, solid-phase extraction.

Fig. 6.15. Flow chart of sample logistics if preparative HPLC is used for purication.
a positive result. This step can be performed before or after evaporation of

the fractions. Reformatting before evaporation has the advantage that only the
product-containing fractions are evaporated, thus saving capacity in the vacuum
centrifuges. After evaporation, the fractions are pooled and analyzed and normally
redissolved and processed into vials or microplates (MTPs), from where biological
testing can be performed. The whole process is described in Fig. 6.15. The HPLC
system distributes the fractions from one injection into dierent cavities of the
collecting MTP. After identication of the products a software tool, usually an Ex-
cel macro, produces a run le for the liquid handler, which pools the fractions
back into a 96-well MTP. From there, further analysis and reformatting steps are
performed after the Excel macro has produced the second run le pooling the
quality-controlled samples into the desired nal formats.
6.4.2
Evaporation
Solvent removal is one of the most important downstream processes in parallel

synthesis. Several attempts to address this issue have been made, and vacuum
centrifuges and freeze-drying for water-containing mixtures are the most appro-
priate methods. Besides these techniques, shakers using infrared (IR) radiation
[74] or stirrers in combination with air or nitrogen streams [75] are also in use.
The main advantages of freeze-drying are that no thermal stress is applied to the
sample and the loading of liquid can be fairly high. Also, carrier formats are not
limited and almost every type of carrier, for example microplates, racks, and single
vials, can be loaded into the freeze-dryer. The disadvantages are that the evapora-
tion time can be long and that the methodology is limited to aqueous solutions.
Tab. 6.7. Vacuum centrifuges commonly used in parallel synthesis.
Centrifuge Advantages/disadvantages
Genevac Robust in terms of imbalance, high capacity, fast evaporation/price, stability

Christ Price, fast evaporation/capacity, unstable in case of imbalance
Savant Vapor stability/capacity
Vacuum centrifuges have the advantage that almost every solvent can be evapo-
rated, even those with very high boiling points such as dimethylsulfoxide (DMSO).
Evaporation times are usually fast and the samples are concentrated and centri-
fuged at once, which results in all the material ending up at the bottom of the vial.
Disadvantages are the thermal stress, which can lead to degradation of the prod-
ucts, and the possibility of imbalance due to the dierent concentrations of solvent
mixtures.
Several suppliers sell vacuum centrifuges for evaporation of HPLC fractions or
cleaving solutions from solid-phase chemistry. Usually, carrier formats are xed or
limited. The microplate footprint is the most common, which makes it necessary
to optimize the whole workow to this footprint. Advantages and disadvantages of
several commercially available instruments are shown in Table 6.7.
References
1 a) W. Harrison, Drug Discovery Today J. P. (ed.), New York, Basel, Decker

1998, 3, 343349; b) J. Drews, S. 1997, pp. 209221.
Ryser, Drug Discovery Today 1997, 2, 8 http://www.robocon.com
365372. 9 http://www.crsrobotics.com
2 a) A. T. Merrit, Drug Discovery Today 10 http://www.beckmancoulter.com
1998, 3, 505510; b) J. S. Lindsey, 11 http://www.mitsubishi-automation.de
Lab. Information Manage. 1992, 17, 12 http://www.zymark.com
1545; c) J. F. Cargill, M. Lebl, Curr. 13 H. Brummer, R. L. M. Markert, C.
Opin. Chem. Biol. 1997, 1, 6771. Schwemler, GIT Laborfachzeitschrift,
3 a) D. Harding, M. Banks, S. 1999, 43, 598601.
Fogarty, A. Binnie, Drug Discovery 14 a) T. E. Weglarz, S. C. Atkin in:
Today 1997, 9, 385390; b) J. R. Advances in Laboratory Automation
Broach, J. Thorner, Nature 1996, 7, Robotics, vol. 6. Strimaitis, J. R.,
1416. Helfrich, J. P. (eds), Zymark,
4 N. W. Hird, Drug Discovery Today Hopkintion 1990, pp. 435461; b) R.
1999, 4, 265274. Matsuda, M. Ishibashi, Y. Takeda,
5 S. H. DeWitt, A. W. Czarnik, Curr. Chem. Pharm. Bull. 1988, 36, 3512
Opin. Biotechnol. 1995, 6, 640645. 3518.
6 J. H. Hardin, F. R. Smietana in: 15 B. G. Main, D. A. Rudge in:
High Througput Screening. Devli, ISLAR93 Proceedings, http://
J. P. (ed.), New York, Basel, Decker www.islar.com
1997, pp. 251261. 16 E. Wegrzyniak et al. in: ISLAR98
7 A. M. M. Mjali, B. E. Toyonaga in: Proceedings, http://www.islar.com
High Througput Screening. Devli, 17 D. A. Rudge, M. L. Crowther in:
References 223
ISLAR97 Proceedings, http:// 39 H. N. Weller, Mol. Diversity 1999, 4,

www.islar.com 4752.
18 http://www.accelab.de 40 S. Cheng, D. D. Corner, J. P.
19 http://www.Sankyo.com Williams, P. L. Meyers, D. L. Boger,
20 http://www.chemspeed.com J. Am. Chem. Soc. 1996, 118, 2567
21 http://www.peptide.com 2573
22 http://www.multisyntech.com 41 S. X. Peng, C. Henson, M. J.
23 J. Coope, Zeneca Pharmaceuticals in: Strojnowsky, A. Golebiowski, S. R.
High Throughput Multiple Parallel Klopfstein, Anal. Chem. 2000, 72,
Synthesis using the Zenyx Magellan 261266.
Synthesizer, on MipTec-ICAR99, 42 B. Kaye, W. J. Herron, P. V. Macrae,
1999. S. Robinson, D. S. Stopher, R. F.
24 http://www.prosence.net Venn, W. Wild, Anal. Chem. 1996,
25 a) http://www.appliedbiosystems.com/ 68, 16581660.
pa/solaris/index_.html; b) http:// 43 R. M. Lawrence, S. A. Biller, O. M.
www.appliedbiosystems.com/ Fryszman, M. A. Poss, Synthesis 1997,
molecularbiology/press_releases/ 553558.
solaris/081098.html 44 M. G. Siegel, P. J. Hahn, B. A.
26 http://www.zinsser-analytic.com Dressman, J. E. Fritz, J. R.
27 http://www.qiageninstruments.com/ Grunwell, S. W. Kaldor, Tetrahedron
automation Lett. 1997, 38, 33573360.
28 http://www.charybdis.com 45 R. J. Booth, J. C. Hodges, J. Am.
29 http://www.argotech.com Chem. Soc. 1997, 119, 4882.
30 J. Labadie, Argonaut Technologies 46 S. V. Ley, I. R. Baxendale, R. N.
Inc. in: The Trident System: A Bream, P. S. Jackson, A. G. Leach,
Flexible Approach to Automated D. A. Longbottom, M. Nesi, J. S.
Synthesis, on MipTec-ICAR99, Scott, R. I. Storer, S. J. Taylor, J.
1999. Chem. Soc. Perkin Trans. 1 2000,
31 a) http://www.techprt.co.uk/ttp/ 38154195.
m-t_myriad.htm; b) B. MacLachlan, 47 Calbiochem-Novabiochem AG,
SmithKline Beecham in: Automated Weidenmattweg 4, CH-4448
Chemical Synthesis using Myriad Lauingen.
System, on MipTec-ICAR99, 1999. 48 http://www.isco.com
32 http://www.techprt.co.uk/ttp/ 49 http//www.biotage.com
index.html 50 http://www.joneschrom.com
33 http://www.mt.com/home/ 51 I. Hughes, J. Assoc. Lab. Autom. 2000,
mettlertoledo.asp 5, 6971.
34 a) http://www.irori.com; b) X. Xiao, 52 W. C. Ripka, G. Barker, J. Krakover,
C. Zhao, H. Potash, M. P. Nova, Drug Discovery Today 2001, 6, 471
Angew. Chem. 1997, 109, 799 477.
801. 53 http//www.gilson.com
35 N. K. Terret, M. Gardner, D. W. 54 http//www.hii-hitachi.com
Gordon, R. J. Kobylecki, J. Steel, 55 http://www.varianinc.com
Tetrahedron 1995, 51, 81358173. 56 http://www.shimadzu.com
36 M. A. Gallop, R. W. Barett, W. J. 57 L. Zeng, L. Burton, K. Yung, B.
Dower, S. P. A. Fodor, E. M. Shushan, D. B. Kassel, J.
Gordon, J. Med. Chem. 1994, 37, Chromatogr. A 1998, 794, 313.
12331236. 58 J. P. Kiplinger, R. S. Ware, E.
37 J. S. Fruchtel, G. Jung, Angew. Roskamp, P. Dorf, R. G. Cole, S.
Chem. 1996, 108, 1946. Robinson, A. Brailsford, R. Raso,
38 R. H. Griffey, A. Haoyun, L. C. Frey in: Pittcon97 Conference,
Cummins, H.-J. Gaus, B. Haly, R. Atlanta 1997.
Herrmann, P.-D. Cook, Tetahedron 59 http://www.appliedbiosystems.com
1998, 54, 40674076 60 http://www.waters.com
61 T. Y. Chan, R. Chen, M. J. Soa, B. 68 R. J. Cotter, Anal. Chem. 1999, 71,

C. Smith, D. Glennon, Tetrahedron 445A451A.
Lett. 1997, 38, 28212824. 69 U. Selditz, S. Nilsson, D. Barnidge,
62 R. Warras, J.-M. Wieruszeski, C. K. E. Markides, Chimia 1999, 53,
Boutillon, G. J. Lippens, J. Am. 506510.
Chem. Soc. 2000, 122, 17891795. 70 M. Wigger, J. P. Nawrocki, C. H.
63 M. C. Ventura, W. P. Farrell, C. M. Watson, J. R. Eyler, S. A. Benner,
Aurigemma, M. J. Greig, Anal. Rapid Commun. Mass Spectrom. 1997,
Chem. 1999, 71, 24102416. 11, 17491752.
64 B. H. Hsu, E. Orton, S.-Y. Tang, R. 71 R. Richmond, E. Gorlach, Anal.
A. Carlton, J. Chrom. B 1999, 725, Chimica Acta 1999, 394, 3342.
103112. 72 R. Richmond, E. Gorlach, J.-M.
65 E. W. Taylor, M. K. Qian, G. D. Seifert, J. Chrom. A 1999, 835, 29
Dollinger, Anal. Chem. 1998, 70, 39.
33393347. 73 D. A. Lake, V. Johnson, C. N.
66 W. K. Gotzinger, J. N. Kyranos, Am. McEwen, B. S. Larsen, Rapid
Lab. 1998, 30, 27. Commun. Mass Spectrom. 2000, 14,
67 B. D. Dulery, J. Verne-Mismer, E. 10081013.
Wolf, C. Kugel, L. Van Hijfte, J. 74 http://www.hettlab.ch/IRclancer.htm
Chrom. B 1999, 7, 25, 3947. 75 http://www.comgenex.hu
225
Part II
Synthetic Chemistry

ISBN: 3-527-30509-2
227
7
Radical Reactions in Combinatorial Chemistry
A. Ganesan and Mukund P. Sibi
7.1
Introduction
Organic synthesis is dominated by polar transformations, in which an electron-

rich center reacts with an electron-decient center. By contrast, homolytic pro-
cesses involving organic radicals were largely unexploited for many years. The
general belief was that such free radicals would be undisciplined in their
reactions, and prone to undesirable pathways such as premature radicalradical
recombination or hydrogen atom abstraction from the solvent. Even under suc-
cessful chain-propagating conditions, the chemistry seemed best suited to poly-
merization. More recently, a deeper understanding of the kinetics of radical re-
actions has enabled [1] the orchestration of a complicated series of elementary
steps, and there is now a vast number of synthetically useful radical reactions
which are complementary to traditional polar processes. For example, the reaction
conditions are relatively mild, avoiding strongly acidic or basic reagents, and many
functional groups are tolerated without requiring protection. Additionally, the
product of a radical abstraction reaction or a radical addition to an unsaturated
center is a new radical that can participate in further tandem reactions. Such reac-
tion cascades can represent strategically powerful disconnections, as a relatively
complex product is derived from a much simpler starting material in one step.
Combinatorial chemistry is also heavily dominated by polar reactions. Early ef-
forts were predominantly based around peptides and nucleotides, as their syn-
thesis was adaptable to the preparation of large libraries and compatible with ex-
isting automated equipment. Solid-phase synthesis techniques for such oligomers
were already highly advanced [2], with nearly quantitative coupling yields at each
cycle. However, the emphasis in combinatorial libraries rapidly shifted toward
drug-like small molecules. The resultant need to assemble diverse nonoligo-
meric carbocyclic and heterocyclic scaolds has led to an intense eort to devise
combinatorial versions of more sophisticated organic reactions, including those in
which carboncarbon bonds [3] are made. In recent years, the potential of radical
reactions for combinatorial purposes has become apparent.
The majority of radical reactions explored for combinatorial applications have

ISBN: 3-527-30509-2
228 7 Radical Reactions in Combinatorial Chemistry
been reported on solid phase. While this does not change the actual chemistry
compared with traditional solution-phase radical reactions, there are contexts in
which the solid-phase environment may be advantageous. Even in the swollen gel
phase, reactions are kinetically slower than in homogeneous solution-phase con-
ditions, which may be helpful in determining the relative partitioning of a radical
intermediate into various pathways. A second unique feature is the loading of poly-
meric resins, typically a1 mmol g1 of beads, thus eectively placing an upper
limit on the maximum concentration attainable with solid-phase reactions. This
enforced dilution can be useful for radical reactions, although gel-phase polymer
chains do exhibit signicant freedom of motion and certainly do not approach
innite dilution. A further variable is the spacer length between the substrate
and the matrix. Many reactions, including Merrields original peptide synthesis,
were carried out with the substrate attached directly to the polystyrene matrix.
Today, it is more common to include a linker [4] between the polymer and the
substrate. The linker can profoundly inuence chain mobility as well as the poly-
mer microenvironment where the reaction is taking place. Linkers are often used
for solid-phase radical reactions, although the reasons for selecting a particular
linker are seldom described. Finally, the ability to lter o reagents and byproducts
can certainly be a bonus for solid-phase radical reactions, especially those mediated
by tin reagents, whose removal is not always trivial in solution phase (see below).
7.2
Intramolecular Radical Additions to sp 2 and sp Carbon
The rst carboncarbon bond-forming radical reactions reported on solid phase

were intramolecular aryl radical 5-exo cyclizations, which have ample solution-
phase precedents [5]. Routledge et al. [6] investigated the formation of dihydro-
benzofuran (2) from an aryl halide precursor (Scheme 7.1). The eciency of the
reaction was found to depend on the resin: with polystyrene, more than 1 equiva-
lent of AIBN was required as radical initiator, whereas the reaction was complete
within 20 h using 6 mol% of AIBN on TentaGel resin. The intermediate alkyl rad-
ical underwent two dierent types of reactions: a b-elimination or a H-atom ab-
straction from tributyltinhydride. The b-elimination process could be suppressed
Scheme 7.1. Aryl halide cyclizations by Routledge et al. [6].

7.2 Intramolecular Radical Additions to sp 2 and sp Carbon 229
by the addition of t-butanol. An attempt to make the b-elimination the major

pathway by switching to thiyl linker (3) only yielded a small amount of 4. 5-Exo
cyclizations of an alkyl radical onto an acetylene group leading to exomethylene
furans were also reported in this study.
Du and Armstrong [7] reported similar cyclizations of aryl iodides attached
to polystyreneRink resin using SmI2 for radical generation (Scheme 7.2). The
reactions can be carried out under mild conditions without the solvent degass-
ing. However, a large excess of HMPA was found to be necessary for ecient
reaction. Use of a TentaGel-type resin allowed polymer swelling in aqueous sol-
vents, enabling Sm(III) impurities in the beads to be removed by saturated
NaHCO3 prior to resin cleavage. The feasibility of radicalpolar crossover reactions
by anionic capture of the intermediary Sm(III) species by electrophiles was at-
tempted [8]. The reaction was unsuccessful when the carboxylic acid was immobi-
lized on polystyreneRink resin as an amide, possibly due to quenching of the
anion by the amide proton. On the other hand, when substrate 7 on TentaGel
Wang resin was treated with HMPA, 3-pentanone, and SmI2 , the crossover prod-
uct 8 was obtained in moderate yield after resin cleavage. Reaction eciency with
the TentaGelWang-supported substrate (33% yield) was similar to that in solu-
tion phase (40% yield), although perhaps still too low for reliable generation of
libraries.
Scheme 7.2. Aryl iodide cyclizations by Du and Armstrong [7, 8]. THF, tetrahydrofuran.
De Mesmaeker and coworkers have reported a series of aryl radical cyclizations

[9], and compared them with Pd-mediated Heck cyclization of the same substrates.
Radical cyclization of iodo alkenes immobilized on polystyrene resin through a
Wang-like linker (9) using tributyltinhydride (Scheme 7.3) gave dihydrobenzofur-
ans (10) [10]. A tandem cyclization using allyltributyltin gave the allylated products
(11) in low to moderate yields. Formation of isomeric dihydrobenzofurans (13)
could be accomplished by radical cyclization onto b-alkoxy esters [11]. For best
results, the tributyltinhydride and AIBN were added portionwise every 58 h. The
impressive 95% yield was in fact higher than that for the solid-phase Heck cycli-
zation of 12.
Scheme 7.3. Aryl iodide cyclizations by the Novartis group [10, 11].
The Novartis group has also studied [12] the radical cyclization of cyclohexene-
diols, immobilized by a ketal linkage on polystyrene (Scheme 7.4). The reaction of
14 gave the desired dihydrobenzofuran (15) and the uncyclized product of direct
reduction (16). Jia et al. [13] have reported a related cyclization with allylamine (17)
immobilized on polystyreneWang resin. The reaction was monitored by acetyla-
tion and cleavage to yield 18, as a mixture of free and Boc-protected amines. This
solid-phase synthesis of seco-CBI (18, R H), related to the pharmacophore of the
CC-1065 and duocarmycin class of cyclopropylindole antitumor antibiotics, has
potential for the preparation of analog libraries, and an example of further conver-
sion of resin-bound 18 to a polyamide has been presented.
A series of bromoacetals (19) (Scheme 7.5) linked to polystyrene was cyclized to
the corresponding acetals by Watanabe et al. [14]. Oxidative cleavage of the resin
using Jones reagent gave easy access to g-butyrolactones (20).
7.3
Intermolecular Radical Additions
The carboncarbon bond-forming steps of intramolecular reactions are facilitated

by entropic acceleration. Intermolecular reactions oer a more stringent test of the
Scheme 7.4. Aryl and vinyl iodide cyclizations by Berteina et al. and Jia et al. [12, 13].
Scheme 7.5. Intramolecular cyclizations by Watanabe et al. [14].
feasibility of solid-phase radical reactions. Sibi and Chandramouli [15] reported the
rst examples of intermolecular radical allylations. The polymer-bound electro-
philic C-radicals generated from a-bromo esters (21) gave g; d-unsaturated acids
(22) (Scheme 7.6). Large excesses of allylstannane and AIBN were required for
good yields. Radical initiation at room temperature using Et3 B/O2 was less e-
cient. The yields were similar to those for solution-phase reactions, while reduc-
tion of 21 with tributyltin deuteride gave @93% deuterium incorporation, implying
<7% hydrogen atom transfer from the polymer matrix. Electron-withdrawing
Scheme 7.6. Intermolecular allylations by Sibi and Chandramouli [15].

groups at the 2-position of the allylstannane were also found to improve the reac-
tion yield, as in the formation of 23.
Enholm et al. have reported the rst example of a diastereoselective radical re-
action on a polymer (Scheme 7.7) [16]. A sugar-based auxiliary attached to a non-
crosslinked soluble polystyrene polymer (24) as the support was used in the
experiments. Allylation under standard conditions gave 25 in high yield and dia-
stereoselectivity (97%). Use of Lewis acids for the allylation was detrimental in that
chiral auxiliary cleavage was observed.
Scheme 7.7. Polymer-supported diastereoselective allylation [16].
Although organotin reagents are the most popular reagents for generating radi-
cals in solid-phase reactions, other methods are also being explored. Zhu and Ga-
nesan have investigated [17] the conjugate addition of radicals generated from
Barton esters. Acrylic acid was immobilized as the ester (26) (Scheme 7.8) using
the Wang linker on both polystyrene and TentaGel resins. Conjugate radical addi-
tion and cleavage gave acids (27) in high yields. Also noteworthy, as in the tin-
mediated reactions, is the ability to use large excesses of reagent without problems
in product isolation. The yields with polystyrene resin were similar to solution-
phase results with methyl acrylate and appear to be relatively insensitive to the
nature of the radical: primary, secondary, or tertiary. Benzyl radical gave 27 in only
32% yield, presumably due to its highly stabilized nature. The TentaGel resin gave
consistently lower yields than polystyrene, suggesting interference from the poly-
ether spacer. When acrylic acid was immobilized as the amide on polystyrene
Rink resin, yields were also lower, which is consistent with the lower solution-
phase yields with acrylamide than with methyl acrylate.
An interesting cascade reaction was observed with the Barton ester (28) of
cyclopent-2-enylacetic acid. Radical generation and addition to the acrylate resin
results in electrophilic acyl-substituted radical 29, which can undergo chain trans-
fer to produce 30 (after cleavage and esterication). The major pathway is intra-
molecular 5-exo cyclization to provide radical 29a. The intermediate nucleophilic
radical 29a gave two dierent products depending on the termination step. Chain
transfer gave 31 as a minor product. Alternatively, addition of a second acrylate
followed by thiyl transfer gave 32 as the major product. Formation of 32 requires
the crosslinking of two polymer chains and shows that site isolation is not signi-
cant.
Scheme 7.8. Intermolecular conjugate additions by Zhu and Ganesan [17].
Barton ester chemistry also featured in the work by Attardi and Taddei [18].
Irradiation of a solid-phase-bound Barton ester derived from aspartic acid (Scheme
7.9) gave the corresponding alkyl radical, which could be trapped by CBrCl3 pro-
vided it was in very large excess, to give the alkyl bromide (34) after cleavage. Also
presented were examples in which the alkyl bromide was displaced by an amine,
providing a route to the solid-phase synthesis of unnatural amino acids. Trapping
the alkyl radical by intermolecular conjugate addition to methyl acrylate or a nitro-
olen was also attempted, although desired products such as 35 were contami-
nated by 1020% of 36.
A route to a-amino acids by conjugate radical addition to the dehydroalanine
derivative (37) on solid phase has been reported by Yim et al. [19]. Organo-
mercurials as radical precursors (Giese method) gave better yields of 38 in contrast
to the standard conditions of reaction between alkyl halides with tributyltinhydride
(Scheme 7.10). The intermolecular addition of tosyl radicals to an unactivated al-
kene and alkyne (39) has also been reported [20], and the reaction has been found
to be quite sensitive to solvent toluene giving optimum results. The related free
radical addition of thiols to unactivated alkenes has been described by Plourde
et al. [21]. An inositol derivative was directly immobilized on carboxypolystyrene
Scheme 7.9. Intermolecular radical additions by Attardi and Taddei [18].
Scheme 7.10. Intermolecular alkene additions [19, 20].
resin and reacted with aliphatic thiyl radicals generated by AIBN, yielding 42
(Scheme 7.11) after cleavage. The reaction was not observed with arylthiyl radicals,
possibly because of their increased stability. Similarly, functionalization of an ami-
nocyclitol linked to the Wang resin to give 44 was accomplished.
Amines can be readily prepared by intermolecular radical additions to oxime
ethers. In a nice extension of its work in solution-phase chemistry, Naitos group
has published several papers on amine synthesis on solid support. Immobilized
glyoxylic oxime ether (45) underwent radical addition to give amino acid deriva-
tives (46) in moderate to good yields (Scheme 7.12) [22]. Preparation of enan-
tioenriched amino acids by this strategy has also been reported. Chirality was in-
corporated in the form of Oppolzers camphorsultam and the solid support was
attached on the oxime hydroxyl (47). Ethyl radical addition to 47 using either tri-
ethylborane or diethylzinc as radical initiators gave product (48a) with >95% dia-
stereoselectivity [23]. This was better than the analogous solution-phase reaction,
suggesting that the immobilized oxime is less reactive. The addition of isopropyl
Scheme 7.11. Intermolecular alkene additions [21].
Scheme 7.12. Intermolecular oxime ether additions by Miyabe et al. [22, 23].
and cyclohexyl radicals by atom transfer from the corresponding iodide, to furnish
48b,c, has also been demonstrated. In these cases, the product was contaminated
by the competing addition of initiating ethyl radical, and this was avoided by using
a large excess of the alkyl iodide.
Pyrrolidines have been synthesized on solid phase by a combination of an inter-
molecular radical addition followed by an intramolecular oxime ether cyclization,
as exemplied in the preparation of 50 [24] and 52 [25] (Scheme 7.13). The solid-
phase reactions were sluggish with triethylborane as an initiator at room tempera-
ture, while the analogous solution-phase process was kinetically much faster. Rad-
Scheme 7.13. Intermolecular oxime ether additions by Miyabe et al. [24, 25].
ical addition to chiral substrate 53 using triethylborane as an initiator gave mostly

the ethyl addition product 54 (R Et). Successful incorporation of the alkyl radical
generated from the alkyl iodide required the reaction to be performed almost neat
in the latter, and proceeded with decent diastereoselectivity.
Radical additions to the phenylsulfonyl oxime ether 55 (Scheme 7.14) have been
reported by Jeon et al. [26]. Yields were better with primary and secondary alkyl
Scheme 7.14. Intermolecular oxime ether additions by Jeon et al. [26].

7.4 Functional Group Removal 237
iodides, and the tandem cyclization sequence with iodide (57) to aord bicyclic 58
has been accomplished, albeit in modest yield.
7.4
Functional Group Removal
Solid-phase synthesis necessarily requires attachment to the polymer matrix by a

functional group, which will be unmasked at the end of the synthetic sequence
upon cleavage from the resin. In peptide and nucleotide synthesis, this respec-
tively reveals the C-terminus carboxylic acid and the 5 0 alcohol. As these groups
are inherently part of the nal biopolymer, this does not pose a problem. For
small-molecule synthesis, however, it is not always desirable to have a dangling
functional group whose sole purpose had been to enable immobilization. One
possible solution is to devise traceless linkers [27] that produce CaH bonds
upon cleavage, as realized by Plunkett and Ellman [28] with an arylsilane cleaved
by protodesilylation.
Homolytic carbonheteroatom bond ssion followed by quenching of the or-
ganic radical represents an alternative means of achieving a traceless solid-phase
synthesis. A pioneering eort by Sucholeiki [29] involved the photochemical irra-
diation of resin-bound thioethers (Scheme 7.15) attached via two dierent linkers
to TentaGel resin. The isolated yields of biphenyl 60 were reportedly low owing to
product volatility, and degassed solvent was crucial to minimize the formation of
byproduct aldehyde 61.
Scheme 7.15. Thioether cleavage by Sucholeiki [29].
More recently, several groups have explored the homolytic cleavage of resin-
bound selenides as a route to traceless synthesis. Nicolaou et al. [30] started with
lithiated polystyrene, which was trapped by dimethyl diselenide to furnish the
alkylselenide resin. Reaction with bromine generated selenylbromide resin (63)
(Scheme 7.16), which could be reduced to the selenide anion (64). This resin can
Scheme 7.16. Traceless selenide cleavage by Nicolaou et al. and Ruhland et al. [30, 31].
then be reacted with alkyl halides, followed by traceless reductive cleavage with
tributyltinhydride. A similar dealkylation was simultaneously reported by Ruhland
et al. [31], in which a chloro- and a bromoalcohol were immobilized by the sele-
nide resin (70). The free alcohol was then functionalized by a Mitsunobu reaction
prior to traceless cleavage. Nicolaou also described the use of resin 63 in pro-
moting the glycosidations of sugar glycals, resulting in a polymer-bound selenide
whose radical cleavage yields 2-deoxyglycosides. The Nicolaou group has since re-
ported a number of further applications with these selenide resins.
In the previous sections, many solid-phase radical reactions were described that
had an extended linker between the substrate and the polymer matrix, unlike the
Nicolaou and Ruhland examples. Fujita et al. were the rst to report [32] a trace-
less selenide cleavage with a linker. However, the yield from 73 (Scheme 7.17)
was poor, and the authors suggest that the tinhydride reagent is reacting with the
linker itself. A more robust ether-based selenide linker (76) has recently been de-
scribed by Li et al. [33], and an example of homolytic cleavage proceeded with good
yields.
7.5
Polymer-supported Reagents for Radical Chemistry
As was illustrated in the above sections, radical reactions are feasible on solid sup-
port and are relatively new entrants to the eld. In contrast, the use of polymer-
Scheme 7.17. Traceless selenide cleavage by Fujita et al. and Li et al. [32, 33].
supported organic reagents has a much longer history in radical chemistry. Devel-
opments in this area can be attributed to the diculty in removal of organotin by-
products, since tin-derived compounds are used extensively for radical chemistry.
Use of polymer-supported reagents alleviates most of the diculties associated
with product purication. The tin-containing polymer can be easily removed by
simple washing.
7.5.1
Polymer-supported Tinhydrides
Most of the activity in polymer-supported reagents has been in the preparation of

tinhydride derivatives. Early work in this area was carried out by Neumann and
coworkers [34]. A polystyrene-derived reagent (80), which mimics tributyltinhy-
dride, was prepared and evaluated as a reducing and chain transfer reagent. Rep-
resentative examples are shown in Scheme 7.18. Similar chemical eciency in the
cyclization of 81 and in the reductions of 8284 demonstrated that the polymeric
tinhydride has similar reaction characteristics to tributyltinhydride.
Dumartin and coworkers have evaluated several polystyrene-supported tinhy-
drides prepared from Amberlite XE305 in reductions [35]. These reagents (8586)
contain dierent spacers between the tin atom and the phenyl group. The amount
of residual tin was determined by ICP-MS for the reduction of 87 (Scheme 7.19).
The polymer hydride produced 45 ppm of residual tin compared with 7000 ppm
Scheme 7.18. Reductions using polystyrene-supported tinhydride [34].
Scheme 7.19. Reductions using polystyrene-supported tinhydride [35].
from tributyltinhydride. In situ generation of the polymer-supported reagent from

the corresponding halide and sodium borohydride and reactions without mechan-
ical stirring signicantly reduced the tin pollution level. The Dumartin group has
also reported BartonMcCombie deoxygenation of secondary alcohols using cata-
lytic amounts of polymer-supported tinhydride [36].
Deluze and coworkers [37] have prepared a new type of macroporous polymer-
supported tinhydride using suspension copolymerization (Scheme 7.20). The au-
thors have determined the swelling characteristics of the resin in dierent solvents
as well as the specic surface areas. The organotin chloride-functionalized beads
showed good stability and reactivity in reductions using sodium borohydride as the
co-reductant.
Recently, Enholm and Schulte [38] prepared a soluble tinhydride on a non-
crosslinked polystyrene support (89) and demonstrated its utility in reductions
Scheme 7.20. A macroporous polymer-supported tinhydride precursor [37].
(Scheme 7.21). The reductions use only catalytic amounts of the polymeric tinhy-
dride and sodium borohydride as the co-reductant. Several examples (9094) of
chemoselective reductions have been reported. The tin contents in the products
were also determined and shown to be in the ppm range.
Scheme 7.21. Reductions with polymer-supported tinhydride [38].
Curran and coworkers [39] have developed novel alternatives for polymer-
supported reagents. They have successfully demonstrated the use of very versatile
uorous reagents (95) for free radical chemistry [39]. The uorous tinhydrides
(Scheme 7.22) are commercially available and have the advantages of ease of prod-
uct purication by simple separation and high reaction rates since the reactions
are carried out in the solution phase.
Scheme 7.22. Fluorous tinhydride [39].
7.5.2
Polymer-supported Allyl Stannane
Enholm and coworkers [40] have prepared a soluble noncrosslinked polystyrene-

supported allyltin reagent (96) (Scheme 7.23). The reagent is quite successful in
transferring an allyl group to a variety of substrates in moderate to good yields.
The products (98101) obtained from allylation show reasonable structural diver-
sity. The selective allyl transfer to the more electrophilic site in 101 is noteworthy.
Ryu, Curran, and coworkers [41] have demonstrated the utility of uorous allyltin
reagents in organic synthesis.
Scheme 7.23. Polymer-supported allylating agent [40].
7.5.3
Polymer-supported Reagents for Atom-transfer Reactions
Atom- and group-transfer radical reactions have enjoyed a lot of popularity in re-
cent years. Clark and coworkers [42] have prepared solid-supported catalysts for
atom-transfer radical cyclizations (Scheme 7.24). Functionalized aminopropyl sili-
cagel was coupled to pyridine 2-carboxaldehye to provide an orange solid (102).
The catalyst (103) was prepared by stirring a mixture of 102 and copper halide
in acetonitrile. Atom transfer cyclization of several N-allyl amides using 30 mol%
of the catalyst gave the product in high yields. The catalyst could be recovered by
simple ltration. Recently, a soluble copper catalyst supported on poly(ethylene)-
block-poly(ethylene glycol)-polymer (108) has been eectively used for atom-
transfer radical polymerizations [43]. Marsh and coworkers [44] have reported
Cu(I)-mediated radical polymerization of nucleoside monomers on silica support.
The preparation of polystyrene-block-polymethylmethacrylate lms by a sequential

carbocationic polymerization of styrene followed by radical polymerization of
methylmethacrylate has been reported previously [45].
Scheme 7.24. Atom-transfer radical cyclizations and poly-

merizations with polymer-supported catalysts [42, 43].
7.5.4
Photochemical Generation of Radicals
O-Acyl and O-alkylthiohydroxamates are convenient precursors for C- and O-

centered radicals. Product purication at times is dicult because of the sulfur
byproducts. De Luca and coworkers [46] have reported a solution to this problem.
The polymer support with appropriate functionality was prepared from N-hydroxy-
thiazole 2(3)-thione and functionalized Wang resin (109). A Hunsdicker reaction
of 110 furnished the corresponding bromide (111) cleanly. Similarly, the cycliza-
tion of the O-centered radical under reductive conditions furnished ether 113. In
both cases, product purication was simple (Scheme 7.25).
Scheme 7.25. Photochemical generation of radicals [46].

Tab. 7.1. Methods used in solid-phase radical reactions.
Radical precursor Method of radical generation
Alkyl/aryl halide RBr or RI AIBN, Bu3 SnH

Me3 SnSnMe3 , hn
SmI2
Et3 B, O2
Et2 Zn, O2
Organomercurial RHgCl NaBH4
Thioether RSR hn
Thiol RSH AIBN
Sulfonyl bromide ArSO2 Br AIBN
Alkyl selenide RSeAr AIBN, Bu3 SnH
Barton ester RCO2 aNAr hn
7.6
Summary
Radical reactions have yet to be applied to the synthesis of compound libraries,

whether in combinatorial fashion or as parallel arrays. This is perhaps not sur-
prising, as it is only in the last few years that the feasibility of carrying out radical
reactions at all on solid phase has been demonstrated. The examples in this chap-
ter convincingly illustrate that there is no intrinsic limitation to such processes.
Now that the gestation period is over, one can predict that radical reactions will be
part and parcel of the combinatorial chemists toolkit of organic reactions. The
various precursors to radicals used in solid-phase reactions, and the methods of
generation, are summarized in Table 7.1.
The early preponderance of solid-phase reactions in combinatorial chemistry has
also evolved to a more equal weighting with solution-phase synthesis. Here also,
the eld of radical reactions has not been left out. A number of polymer-supported
reagents and scavenger resins are now available that facilitate radical reactions in
parallel, with the potential for considerably simplied work-up and purication
compared with the original procedures. Further advances in combinatorial radical
chemistry, both solution and solid phase, can certainly be anticipated.
References
1 P. Renaud, M. P. Sibi (eds) in: M. J. Kurth, Chem. Rev. 1999, 99,

Radicals in Organic Synthesis, Wiley- 15491581; b) R. E. Sammelson, M. J.
VCH, Weinheim, 2001. Kurth, Chem. Rev. 2001, 101, 137
2 For an account of the early history of 202.
solid-phase synthesis, see: a) D. 4 For reviews, see: a) I. W. James,
Hudson, J. Comb. Chem. 1999, 1, Tetrahedron 1999, 55, 48554946;
333360. b) D. Hudson, J. Comb. b) F. Guillier, D. Orain, M.
Chem. 1999, 1, 403457. Bradley, Chem. Rev. 2000, 100, 2091
3 For reviews, see: a) B. A. Lorsbach, 2157.
References 245
5 For a review, see: B. K. Banik, Curr. Dahmen, Chem. Eur. J. 2000, 6, 1899
Org. Chem. 1999, 3, 469496. 1905.
6 A. Routledge, C. Abell, S. 28 M. J. Plunkett, J. A. Ellman, J. Org.
Balasubramanian, Synlett 1997, 61 Chem. 1995, 60, 60066007.
62. 29 I. Sucholeiki, Tetrahedron Lett. 1994,
7 X. Du, R. W. Armstrong, J. Org. 35, 73077310.
Chem. 1997, 62, 56785679. 30 K. C. Nicolaou, J. Pastor, S.
8 X. Du, R. W. Armstrong, Tetrahedron Barluenga, N. Winssinger, Chem.
Lett. 1998, 39, 22812284. Commun. 1998, 19471948.
9 For a review, see: S. Wendeborn, A. 31 T. Ruhland, K. Anderson, H.
De Mesmaeker, W. K. D. Brill, S. Pedersen, J. Org. Chem. 1998, 63,
Berteina, Acc. Chem. Res. 2000, 33, 92049211.
215224. 32 K. Fujita, K. Watanabe, A. Oishi, Y.
10 S. Berteina, A. De Mesmaeker, Ikeda, Y. Taguchi, Y. Synlett 1999,
11 S. Berteina, S. Wendeborn, A. De 33 Z. Li, B. A. Kulkarni, A. Ganesan,
Mesmaeker, Synlett 1998, 12311233. Biotechnol. Bioeng. 2001, 71, 104106.
12 S. Berteina, A. De Mesmaeker, S. 34 a) U. Gerigk, M. Gerlach, W. P.
Wendeborn, Synlett 1999, 1121 Neumann, R. Vieler, V. Weintritt,
1123. Synthesis 1990, 458452; b) M.
13 G. Jia, H. Iida, J. W. Lown, Synlett Gerlach, F. Jordens, H. Kuhn,
2000, 603606. W. P. Neumann, M. Peerseim, J.
14 Y. Watanabe, S. Ishikawa, G. Takao, Org. Chem. 1991, 56, 59715972;
T. Toru, Tetrahedron Lett. 1999, 40, c) C. Bokelmann, W. P. Neumann,
34113414. M. Peterseim, J. Chem. Soc., Perkin
15 M. P. Sibi, S. V. Chandramouli, Trans. 1 1992, 3165.
Tetrahedron Lett. 1997, 38, 89298932. 35 a) G. Dumartin, M. Pourcel, B.
16 E. J. Enholm, M. E. Gallagher, S. Delmond, O. Donard, M. Pereyre,
Jiang, W. A. Batson, Org. Lett. 2000, Tetrahedron Lett. 1998, 39, 46634666;
2, 33553357. b) G. Dumartin, G. Ruel, J.
17 X. Zhu, A. Ganesan, J. Comb. Chem. Kharboutli, B. Delmond, M.-F.
1999, 1, 157162. Connil, B. Jousseaume, M. Pereyre,
18 M. E. Attardi, M. Taddei, Tetra- Synlett 1994, 952954; c) G. Ruel, N.
hedron Lett. 2001, 42, 35193522. K. The, G. Dumartin, B. Delmond,
19 A.-M. Yim, Y. Vidal, P. Viallefont, J. M. Pereyre, J. Organomet. Chem.
Martinez, Tetrahedron Lett. 1999, 40, 1993, 444, C18C20.
45354538. 36 P. Boussaguet, B. Delmond, G.
20 S. Caddick, D. Hamza, S. N. Dumartin, M. Pereyre, Tetrahedron
Wadman, Tetrahedron Lett. 1999, 40, Lett. 2000, 41, 33773380.
72857288. 37 a) A. Chemin, H. Deleuze, B.
21 R. Plourde Jr, L. L. Johnson Jr, Maillard, Eur. Polym. J. 1998, 34,
R. K. Longo, Synlett 2001, 439441. 1395; b) A. Chemin, H. Deleuze, B.
22 H. Miyabe, Y. Fujishima, T. Naito, J. Mailard, J. Chem. Soc., Perkin Trans.
Org. Chem. 1999, 64, 21742175. 1, 1999, 137142.
23 H. Miyabe, C. Konishi, T. Naito, 38 E. J. Enholm, J. P. Schulte, II, Org.
Org. Lett. 2000, 2, 14431445. Lett. 1999, 1, 12751277.
24 H. Miyabe, H. Tanaka, T. Naito, 39 a) D. P. Curran, S. Hadida, S.-Y.
Tetrahedron Lett. 1999, 40, 83878390. Kim, Z. Luo, J. Am. Chem. Soc. 1999,
25 H. Miyabe, K. Fujii, H. Tanaka, T. 121, 66076615; b) D. P. Curran, S.
Naito, Chem. Commun. 2001, 831 Hadida, J. Am. Chem. Soc. 1996, 118,
832. 25312532; c) I. Ryu, T. Niguma, S.
26 G.-H. Jeon, J.-Y. Yoon, S. Kim, S. S. Minakata, M. Komatsu, S. Hadida,
Kim, Synlett 2000, 128130. D. P. Curran, Tetrahedron Lett. 1997,
27 For a review, see: S. Brase, S. 38, 78837886.
40 E. J. Enholm, M. E. Gallagher, Smith, J. Org. Chem. 1999, 64, 8954

K. M. Moran, J. S. Lombardi, J. P. 8957.
Schulte, II, Org. Lett. 1999, 1, 689 43 Y. Shen, S. Zhu, R. Pelton,
691. Macromolecules 2001, 34, 3182
41 a) I. Ryu, T. Niguma, S. Minakata, 3185.
M. Komatsu, Z. Luo, D. P. Curran, 44 A. Marsh, A. Khan, M. Garcia, D.
Tetrahedron Lett. 1999, 40, 23672370; M. Haddleton, Chem. Commun.
b) see also: D. P. Curran, S. Hadida, 2000, 20832084.
M. He, J. Am. Chem. Soc. 1997, 119, 45 B. Zhao, W. J. Brittain, J. Am.
67146715. Chem. Soc. 1999, 121, 35573558.
42 A. J. Clark, R. P. Filik, D. M. 46 L. De Luca, G. Giacomelli, G.
Haddleton, A. Radigue, C. J. Porcu, M. Taddei, Org. Lett. 2001, 3,
Sanders, G. H. Thomas, M. E. 855857.
247
8
Nucleophilic Substitution in Combinatorial and
Solid-phase Synthesis
8.1
Introduction
Nucleophilic substitution (SN ) reactions are widely used in combinatorial chemis-

try. Two reasons account for this prevalence: rst the potential to combine build-
ing blocks by SN and second the availability of building blocks that can participate
in SN reactions. In addition, SN reactions are typically very reliable transforma-
tions, robust, and thus ideally suited for high-throughput synthesis of organic com-
pounds.
In this chapter the application of SN reactions to combinatorial chemistry using
both solution- and solid-phase formats will be discussed. The sections on aliphatic
and aromatic substrates are subdivided by the classes of nucleophiles that par-
ticipate in the reaction. Reactions used to form medium-sized or large rings are
treated separately owing to their signicance in macrocyclic ring chemistry. This
chapter will not cover nucleophilic substitution reactions at acyl carbons, reactions
of organometallic reagents, reactions of carbon nucleophiles, and transition metal-
catalyzed substitution reactions of nucleophiles (see other Chapters).
8.2
Nucleophilic Substitution at Aliphatic Carbons
8.2.1
General Remarks
Nucleophilic substitutions (SN ) at aliphatic carbons play an important role in the

combinatorial synthesis of diverse classes of compounds. The reactions have had
great impact right from the beginning of combinatorial chemistry. R. B. Merrield
used SN of chloromethyl-polystyrene with cesium carboxylates as a means to attach
amino acids to a solid support (see Scheme 8.1) [1].

ISBN: 3-527-30509-2
248 8 Nucleophilic Substitution in Combinatorial and Solid-phase Synthesis
Scheme 8.1. Immobilization of amino acids by Merrield.
A broad range of electrophilic substrates can be used in SN reactions. Alkyl

chlorides and bromides are fairly common whereas alkyl iodides are used less
often [2]. Alkyl chlorides are usually activated with catalytic amounts of iodide salts
such as potassium iodide or tetrabutylammonium iodide (TBAI). Alkyl esters of
sulfonic acids such as alkyl tosylates or alkyl mesylates are also common electro-
philes. They are prepared from a sulfonyl halide and the corresponding alcohol.
The alcohol itself can be employed as an electrophilic substrate when activated in
situ. The Mitsunobu reaction [3] and related transformations are frequently uti-
lized for this purpose. Recently, the activation of alcohols as trichloroacetimidates
has been applied to parallel synthesis [4].
Epoxides and cyclic sulfates [5] are synthetically valuable substrates for library
generation since the reaction with a nucleophilic building block liberates another
hydroxyl function ready for further derivatization.
8.2.2
Halogen Nucleophiles
Benzylic alcohols are converted into the corresponding benzyl chlorides or bro-
mides by reaction with phosphorus trihalides or under milder conditions with
triphenylphosphine (TPP) and tetrahalogenomethanes. The reaction has found
widespread application in the activation of benzyl alcohol-type linkers for subse-
quent attachment of nucleophilic substrates to a solid support [6].
The reaction was also applied to one of the masterpieces of multistep solution-
phase synthesis involving polymer-supported reagents and scavengers. During
Leys pyrrole synthesis, all six reaction steps to the highly diverse pyrroles used
these reagents. In those cases where the benzylic halides are not commercially
available, the alkyl halides used for N-alkylation are prepared from the corre-
sponding alcohols. In the bromination step, a reagent combination of polymer-
supported TPP and tetrabromomethane is used (see Scheme 8.2) [7].
Scheme 8.2. Solution-phase benzyl bromide synthesis.

8.2.3
Oxygen Nucleophiles
Carboxylate alkylation by alkyl halides can be used both on solid phase (see above)
and in solution [8] to give alkyl carboxylic acid esters. For optimum results, cesium
salts are employed. Alternatively, carboxylate alkylation can be performed under
Mitsunobu conditions using alcohols as electrophiles. For solid-phase applications
the common reagents TPP and diethyl azodicarboxylate (DEAD) can be used. In
solution-phase parallel synthesis, it is advantageous to use reagents that do not re-
quire a chromatographic product isolation. A combination of polymer-bound TPP
[9] and di-tert-butyl azodicarboxylate has been found to be particularly useful (see
Scheme 8.3) [10]. While the former reagent is ltered o easily, the latter (and its
byproduct di-tert-butylhydrazodicarboxylate) is readily converted into volatile com-
pounds by treatment with triuoroacetic acid (TFA).
Scheme 8.3. Solution-phase Mitsunobu carboxylate alkylation.
Cesium carbonate in the presence of an alcohol and carbon dioxide can be alky-
lated by Merrield resin to give solid-supported carbonates (see Scheme 8.4). Add-
ing an amine instead of an alcohol gives rise to carbamate formation [11].
Scheme 8.4. Solid-phase carbonate formation.
Alcohols are transformed into ethers by reaction with an alkylating agent in the
presence of a very strong base such as sodium hydride. The reaction, known as the
Williamson ether synthesis, is frequently used for attaching alcoholic substrates to
Merrield-type resins (see Scheme 8.5) [12].
Scheme 8.5. Solid-phase Williamson ether synthesis.

In a similar reaction, Wang resin is converted into a trichloroacetimidate de-

rivative and used as a polymer-bound benzylating agent. Attachment of alcohols to
this resin is achieved under acid catalysis [4].
Ether-forming reactions involving phenolate nucleophiles proceed much more
readily. All types of electrophiles have been used in both solution- and solid-phase
chemistry. Usually, the phenolates are generated in situ from phenols and bases
such as 1,8-diazabicyclo[5.4.0]undecene-7 (DBU) or potassium carbonate (see
Scheme 8.6) [13].
Scheme 8.6. Solid-phase phenolate alkylation.
The solution-phase synthesis of alkyl aryl ethers is simplied by using ion-

exchange resins. The reaction of various phenolates loaded on Amberlite IRA-900
with alkyl bromides gives alkyl aryl ethers in solution. Thereby the ammonium
bromide byproduct remains on the Amberlite resin [14].
Aryl alkyl ethers are also obtained by Mitsunobu reaction of phenols and alco-
hols. For solid-phase applications, the standard reagents TPP and DEAD have been
used successfully. In some cases, Castros sulfonamide betaine 1 (see Scheme 8.7)
[15] oers cleaner reactions and is easier to handle especially with automated
equipment. Since the betaine decomposes upon exposure to air into inactive com-
ponents without a change of appearance, care should be taken to ensure pure ma-
terial is used.
Scheme 8.7. Castro and Matassas sulfonamide betaine (1) [15].
The solid-phase Mitsunobu reaction has been employed for linker attachment
[16] as well as diversity generation [17]. In solution-phase chemistry, specially
designed reagents are used to facilitate product separation (see above). Thus,
polymer-bound TPP and DEAD derivatives that are easily ltered o are commer-
cially available. Also, ionophoric side-chains have been attached to both TPP and
DEAD to make them (and the corresponding byproducts) easily separable using
ion-exchange resins [18]. This technique is an example of a general concept called
phase tagging or phase labeling [19].
The solution-phase reaction of phenols with epoxides is catalyzed by polymer-
supported Co(salen) complexes [20]. Using chiral catalysts the corresponding 1-
aryloxy-2-alcohols are obtained in high yields, purities, and enantiomeric excesses.
8.2.4
Sulfur Nucleophiles
The reactions of sulfur nucleophiles show similarities to those of oxygen nucleo-

philes. The greater nucleophilicity of sulfur compounds, however, makes a range
of unique additional transformations possible.
A convenient way to prepare the thiol function involves thioacetate alkylation.
This method has been adapted to polymer-supported solution-phase synthesis.
Displacement of halides or tosylates with a polymer-supported thioacetate reagent
aords an intermediate thioester, which can be reduced to the thiol by the addition
of borohydride exchange resin [21].
As expected, alkane thiols [22] and thiophenols [23] are readily alkylated by alkyl
halides. The substitution proceeds at room temperature in the presence of a base
(DIEA for aromatic and DBU for aliphatic thiols).
Thioether formation can also be used for synthesis of heterocycles, as shown in
the preparation of 2,4,5-trisubstituted thiomorpholin-3-ones [24].
Dithiocarbamates, which are formed in situ from the reaction of carbon disulde
with amines, are alkylated by Merrield resin to obtain resin-bound dithiocarba-
mates (see Scheme 8.8). These compounds are intermediates in a reaction se-
quence leading to guanidines carrying three dierent side-chains [25].
Scheme 8.8. Solid-phase dithiocarbamate alkylation.
Similarly, thiourea is attached to Merrield resin by S-alkylation to give a S-alkyl-

isothiouronium salt, which is further transformed into guanidine derivatives [26]
and pyrimidines (see Sect. 8.3.2).
Thiourea alkylation is also involved in the classical Hantzsch thiazole synthesis.
N-Substituted thioureas are alkylated with a-bromoketones, and after immediate
cyclization aminothiazoles are obtained (see Scheme 8.9). The reaction has been
adapted to a solution-phase library synthesis by simply mixing the components as
dimethylformamide (DMF) solutions and heating the mixtures to 70 C [27].
Scheme 8.9. Solution-phase Hantzsch thiazole synthesis.
8.2.5
Nitrogen Nucleophiles
The direct N-alkylation of primary amines is in general not the method of choice
for the synthesis of secondary amines because of potential of overalkylation. There-
by a reductive alkylation with a carbonyl compound is to be preferred. Most often

the primary amine is reacted with an aldehyde in the presence of a water-removing
agent such as trimethyl orthoformate (TMOF) or molecular sieves to form an
imine intermediate. This is reduced to the secondary amine with a suitable boro-
hydride agent, preferably tris(acetoxy)sodiumborohydride.
A dierent situation occurs in solid-phase synthesis when the alkylating agent
is attached to the solid support. Upon reaction with a primary amine usually
applied in great excess a clean conversion to the immobilized secondary amine
is observed. The reaction can be used for the attachment of amines to the resin
[28]. The most important application of this reaction is in the solid-phase synthesis
of N-substituted glycine (NSG) oligomers, so-called peptoids [29]. These oligomers
resemble peptides. Their side-chains are not attached at the a-carbon as in peptides
but rather at the nitrogen atom. Peptoids are synthesized by a repeated sequence
of acylation with bromoacetic acid followed by SN reaction with a primary amine
(see Scheme 8.10). Iodoacetic acid can also be used, but chloroacetic acid gives in-
ferior results.
Scheme 8.10. Solid-phase peptoid synthesis.
The straightforward synthesis has mostly been developed by Chiron researchers.

Exploiting the great number of available amines, they were able to identify rapidly
nanomolar ligands for a1-adrenergic and opiate receptors out of huge peptoid li-
braries.
Peptoids oer a good example of the evolution of methods that mimic natural
oligomers with easy-to-make unnatural compounds. A recent similar development
has been peptide nucleic acids (PNAs). PNAs resemble DNA with the phospho-
diester backbone of the DNA being replaced by an oligo-[N-(2-aminoethyl)glycine]
motif. They have been investigated for diagnostic and antisense purposes [30].
The SN reaction of alkylating agents with secondary amines can be controlled to
give tertiary amines selectively. Thus, reaction of polymer-bound alkyl sulfonates
with secondary amines gives immobilized tertiary amines [31]. In solution-phase
synthesis, selective monoalkylation of secondary amines has been achieved mostly
with monosubstituted piperazine substrates (see Scheme 8.11) [32]. The reaction
can be performed with an excess of piperazine or with an additional base. To facil-
itate product isolation in solution-phase chemistry, either a water-soluble base in
combination with an aqueous work-up [33] or a polymer-bound base [34] can be
employed.
Scheme 8.11. Solution-phase piperazine alkylation.

Intramolecular amine alkylation does not usually bear the risk of overalkyla-
tion and is an excellent way to close heterocyclic rings. An Epibatidine synthesis
using polymer-supported reagents provides an example that involves a mesylate
substitution [35]. Even strained rings such as aziridines can be formed (Gabriel
Cromwell reaction) [36].
Epoxide opening with amine nucleophiles is frequently used in combinatorial
chemistry since it leads to the attractive aminoalcohol substructure. When cata-
lyzed with Lewis acids, for example lithium perchlorate, the reaction proceeds
smoothly with a range of alkyl amines, anilines, and heteroaromatic amines. The
reaction is useful in solution-phase synthesis (see Scheme 8.12) [37] as well as in
solid-phase synthesis [38].
Scheme 8.12. Solution-phase epoxide opening by amines.
The nucleophilic attack of an epoxide by amines can be followed by reactions

involving the newly generated hydroxyl function. In Scheme 8.13 a carbamate
group at a suitable distance is attacked by the hydroxyl group that is exposed dur-
ing epoxide opening. The resulting oxazoline formation occurs with concomitant
cleavage o the resin [39].
Scheme 8.13. Solid-phase oxazolidinone synthesis.
Other nucleophiles that are readily alkylated on the solid phase by alkyl halides
or sulfonates include hydroxyl amine [40], O-benzyl hydroxylamine [41], hydrazine
derivatives [42], azide ion [43], and sulfonamides [44].
Nitrogen compounds bearing hydrogens of sucient acidity can also be alky-
lated under Mitsunobu conditions (see above). Thus, a polymer-bound imidodicar-
bonate can be alkylated with primary and secondary alcohols using the standard
reagents TPP and DEAD. After cleavage o the resin, primary amines are obtained
(see Scheme 8.14) [45].
Scheme 8.14. Solid-phase Mitsunobu reaction of imidodicarbonate.

8.2.6
Ring-closing Reactions
The formation of medium-sized or large rings in combinatorial synthesis is fre-

quently accomplished with SN reactions. Especially S-alkylation reactions are used
in the ring-closing step. Representative examples involve the syntheses of b-turn
mimetics containing nine- or ten-member rings [46] and a cyclic oligocarbamate
consisting of a 26-membered ring [47].
An unusual case of macrocyclization is observed in solid-phase synthesis of
[Arg-8]-vasopressin. The thiol groups of two cysteines of the peptide can be linked
by a methylene unit to form a macrocyclic methylenedithioether [48]. The trans-
formation is achieved by simply treating the resin with tetrabutylammonium uo-
ride in dichloromethane.
8.3
Nucleophilic Substitution at Aromatic Carbons
8.3.1
General Remarks
Nucleophilic aromatic substitution (SN Ar) is an attractive approach to the func-

tionalization of electron-decient aromatic systems, in solution phase as well as on
solid support. It has become an invaluable part of combinatorial transformations,
particularly for the installation of nitrogen- or oxygen-linked substituents. A wide
range of readily accessible nucleophiles can be introduced, making SN Ar reactions
as popular as amide formations and outstanding for the synthesis of combinatorial
libraries.
The large majority of these reactions is based on two classes of reactive scaolds.
Di- and trihalogenated heterocycles with two or more heteroatoms in the hetero-
cyclic ring (mostly nitrogen atoms) have been used extensively. In these mole-
cules the halogen atoms can be replaced selectively and sequentially with various
nucleophiles, making the reaction ideal for combinatorial library production. On
the other hand, there is a large number of examples for attractive and practical
methods to cleanly and eciently prepare novel libraries using substituted halo-
geno-nitrobenzenes as templates. First, the nitro group activates the aromatic sys-
tem for nucleophilic attack. After halogen substitution the nitro group can be
reduced easily and used in an excellent way for further diversication of the
libraries. If the chloro derivatives prove not to be reactive enough in the SN Ar re-
actions, the chloro substrates can be transformed into the uoro analogs by halex
reaction (which is a SN Ar reaction in itself ). Fluoroaromatics are signicantly
more reactive toward nucleophiles [49].
8.3.2
Nitrogen Nucleophiles
From a historical point of view, the rst template for SN Ar reactions was cyanuric
chloride (2,4,6-trichloro-1,3,5-triazine), which is commercially available and inex-
pensive [50]. Compounds containing this core element have shown biological
activity, e.g. as herbicides (Atrazin).
A research group at ArQule showed that the selective and sequential derivati-
zation of cyanuric chloride could be achieved by simply controlling the reaction
temperature. The generality of the research groups method has been proven by
the solution-phase synthesis of a large combinatorial library of over 40,000 indi-
vidual compounds (see Scheme 8.15) [51]. The rst chloride substitution proceeds
at 20 C using N,N-diisopropylethylamine (DIPEA) as the base and acetonitrile
as the solvent. Even anilines react with the very reactive cyanuric chloride in the
proposed way. Usually, the arylation of the primary amine reduces its nucleophi-
licity strongly. Therefore, no bis-arylation occurs at this position and the second
chlorine atom can be substituted at room temperature. Owing to the relatively low
reactivity of the third position, heating is required for the last exchange and only
strong nucleophiles such as secondary amines give pure products and high con-
versions. Besides amines and anilines, also carbohydrates, dipeptides, amidines,
and a-ketoamides can be incorporated, giving access to more complex structures.
Upon screening of these compounds, a series of hits in the cardiovascular area has
emerged.
Scheme 8.15. Sequential displacement of the chlorines of cyanuric chloride.
Using the cyanuric chloride template for solid-phase synthesis has become a
very ecient method for the production of large combinatorial libraries. This was
also demonstrated by the synthesis of a 12,000-compound library by Stankova and
Lebl [52]. The rst chlorine atom was selectively substituted by coupling the tem-
plate to a resin loaded with amino acids (see Scheme 8.16). Taking advantage of
the decreasing reactivity of tri-, di-, and monochlorotriazines, various nucleophiles
(amines, anilines, hydrazines) were introduced at dierent temperatures [53].
Likewise, an 8000-membered library on a cellulose-based polymeric membrane
has been synthesized [54].
Scheme 8.16. Solid-phase library based on the triazine template.
The reaction sequence can be extended to related starting materials such as 2,6-
dichloropurines, although the reaction conditions need to be harsher [55]. In a
representative example, the dichloropurine was treated with a primary amine at
elevated temperature. For the second substitution, reux conditions and ve equiv-
alents of amine were necessary. Excess amine was removed by the use of formyl-
polystyrene beads. The compounds could be benzylated at the N-9 position by an
alkylation protocol or by using the Mitsunobu reaction (see Scheme 8.17) [56].
Scheme 8.17. Liquid-phase synthesis of a purine-based library.
SN Ar reactions on perhalogenated heterocyclic systems are well established in

solution phase and these reactions have been well adapted to solid-phase synthesis.
They have been shown to be useful indeed, more advantageous in many cases
than their solution-phase counterparts. Special attention in this area should be
given to purine templates as purines are involved in signal pathways and meta-
bolic processes in all living organisms (see Scheme 8.18). For example, the discov-
Scheme 8.18. Natural products containing the purine core.
ery of the biologically active natural product olomoucine stimulated attempts to

generate diverse analogs based on the adenosine template on solid support [57].
First an aldehyde-functionalized resin preloaded with benzylamines was reacted
with the purine scaold. The authors chose N-9-SEM (SEM: trimethylsilylethoxy-
methylene)-protected 2-uoro-6-chloropurine as the starting material because of
the activating potential of the SEM group in the amination reaction. After removal
of this group using tetrabutylammonium uoride in tetrahydrofuran (THF), a
Mitsunobu reaction introduces the isopropyl moiety. A second nucleophilic sub-
stitution and nal cleavage from the resin led to the desired purine analogs (see
Scheme 8.19). Since the molecules were attached to the resin via the amino group
at position 6, only primary amines could be introduced into the reaction sequence
[58]. As a result, myoseverin, a novel microtubule-binding molecule, was identied
upon screening these libraries [59].
Scheme 8.19. Synthesis of myoseverin on solid support.

The production of new compound libraries from polyhalogenated heterocycles is

very common in combinatorial chemistry for example reactions involving nucle-
ophilic amines. Besides cyanuric chloride and chloropurines, many other tem-
plates have been used as starting materials (see Scheme 8.20) [50b] [60]. For ex-
ample, for the synthesis of a library of 160 pyrimidine carboxamides, Suto et al.
[61b] took advantage of the dierence in reactivity between the two reactive sites of
the substituted 2-chloropyrimidine-5-carboxylic acid chloride core (see Scheme
8.21). After amidation of the carboxylic function, some of the products were
treated with amines to increase the polarity [61].
Scheme 8.20. Useful templates for SN Ar reactions.
Scheme 8.21. Liquid-phase synthesis of a pyrimidine-based library.
Alternatively, structurally diverse pyrimidines can be obtained by a de novo syn-

thesis. The synthesis commencing with isothiouronium salts (R1 Ar-CH2 or
resin-CH2 , see Section 2.3) is amenable to solution as well as to solid-phase ap-
plications. When condensing the isothiouronium salts with ketene derivatives, a
pyrimidine skeleton with versatile functional groups is obtained. Oxidation of the
alkylthio-linkage with m-chloroperbenzoic acid (m-CPBA) activates the molecule
for SN Ar derivatization (see Scheme 8.22). The corresponding sulnyl or sulfonyl
compounds are then easily substituted with various amines [62].
In a very similar approach, the solution- and solid-phase synthesis of libraries of
trisubstituted 1,3,5-triazines has been described previously [63].
Arylpiperazines have been identied as a privileged structural element in vari-
ous biologically active compounds. Besides strategies involving the cyclization of a
Scheme 8.22. De novo synthesis of pyrimidines.
substituted aniline with bis-(2-chloroethyl)amine, a synthetic route based on nu-

cleophilic aromatic substitutions was also required. Dierent uorobenzenes with
a nitro group either at the ortho or para position underwent SN Ar reactions with
N-Boc-piperazine (see Scheme 8.23). After removal of the protection group, acyla-
tion under SchottenBaumann conditions with a set of eight carboxylic acid chlo-
rides gave 48 N-alkyl-N 0 -acylpiperazines [64]. This methodology has been well
adapted to solid-phase chemistry, as reected in recent reviews.
Scheme 8.23. Synthesis of an arylpiperazine library.
Resin-bound 4-uoro-3-nitrobenzoic acid is also an outstanding template for

nucleophilic aromatic substitution reactions with nitrogen nucleophiles. An enor-
mous number of publications report the syntheses of benzodiazepin-2-ones, ben-
zimidazoles, and related structures. Not surprisingly, only a short selection of ex-
amples can be described here.
Owing to the importance of benzodiazepines in many therapeutic areas, funda-
mental work in the area of solid-phase synthesis has been carried out using this
structural element [65].
The 4-uoro-3-nitrobenzoic acid has been immobilized via the acid group and
reacted with a variety of a- and/or b-substituted b-amino esters in DMF in the
presence of DIEA. The reduction of the arylic nitro compound to the aniline was
carried out using standard conditions [2 M SnCl2 H2 O in DMF, room temperature
(rt)] (see Scheme 8.24). After hydrolysis of the ester with a mixture of 1 N NaOH/
Scheme 8.24. Benzodiazepine synthesis on solid support.

THF, the resulting compound was cyclized with DIC and HOBt and the 1,5-
benzodiazepin-2-one was obtained. Alternatively, selective alkylation at the N-5 po-
sition adds further diversity to the library [66].
Using a-amino acids in the place of the b-amino acids, the [6,6]-fused ring sys-
tem of quinoxalin-2-ones has been accessed [67]. The synthetic strategy is an
adaptation of TenBrinks and coworkers solution-phase synthesis on solid phase
[68]. Variably substituted tetrahydroquinoxalin-2-ones can also be prepared based
on 4-uoro-3-nitrobenzoic acid. After substitution of the uorine with primary ali-
phatic amines at room temperature and reduction of the nitro group, double acy-
lation with chloroacetic anhydride has been shown to be the key step in the syn-
thesis [69].
Further ring contraction to [6,5]-fused systems such as benzimidazoles has
been the aim of other synthetic eorts in solution and in solid-phase synthesis.
Again, 4-uoro-3-nitroarenes were linked to a solid support via an ether linkage
[70] or via a carboxylic acid [71]. Commonly, both strategies use a SN Ar displace-
ment reaction of the uorine atom by an amine with subsequent reduction of
the nitro group. Whereas Phillips and Wie [70] achieved immediate cyclization by
condensation with benzimidates, a research group at Aymax acylated the inter-
mediate with an activated bromoacetic acetic acid rst (see Scheme 8.25). After
displacement of the bromide groups by nucleophiles, cyclization occurred upon
cleavage with a concomitant dehydration [72].
Scheme 8.25. Solid-phase synthesis of benzimidazoles.
Finally, benzimidazolones can also be prepared from solid-supported 4-uoro-

3-nitrobenzoic acid. The key step in the synthesis was again the displacement
of uorine by a nitrogen nucleophile. The nitro group was reduced as described
above and the resulting molecules underwent cyclization with the phosgene
equivalent disuccinimidocarbonate [73].
An ecient liquid-phase synthesis of substituted benzimidazolones has also
been described using a soluble polymer support [MeO-PEG, molecular weight
(MW) 5000] [74]. This polymer support dissolves in many organic solvents (e.g.
DMF, THF) and precipitates in particular solvents (e.g. diethyl ether) (see Scheme
8.26). Again, 4-uoro-3-nitrobenzoic acid was loaded onto the support and was
then allowed to react with a variety of amines. After reduction of the nitro group,
cyclization was achieved with trichlorophosgene.
Scheme 8.26. Benzimidazolones via solid-phase chemistry.
Recently, a synthetic route to substituted 7-azabenzimidazoles was published. As

a key template the highly reactive 6-chloro-5-nitro-nicotinyl chloride was used. The
sequential alkylation with dierent amines by replacement of the strongly acti-
vated chloro atoms proceeds easily at room temperature [75].
Another scaold well suited to the generation of huge libraries by combinatorial
methods is 1,5-diuoro-2,4-dinitrobenzene. The two uoro groups in the ortho
positions of two aromatic nitro groups can be sequentially substituted with two
amines. As the scaold is planar and symmetrical, no problems with regio-
selectivity occur. Lam and coworkers [76] demonstrated the viability of this concept
by the production of a 2485-membered library designed for screening for antibac-
terial activity (see Scheme 8.27) whereas the rst substitution takes place within
hours, the second runs overnight [76]. The authors then used the same concept
for a solid-phase synthesis on 2-chloro-trityl resin, demonstrating that the two
methods are complementary.
Scheme 8.27. 1,5-Diuoro-2,4-dinitrobenzene as a scaold for combinatorial libraries.
The displacement of activated halides with nucleophilic amines such as piper-

azines is also a key step in the synthesis of antiviral quinolones and other phar-
maceutically relevant compounds [77].
The starting materials, suitably substituted 3-oxo-3-phenyl-propanoates, are con-
verted into enamines and cyclized to the quinolone core via an intramolecular
SN Ar reaction (see Scheme 8.28). After ester hydrolysis, a wide range of amines
can be introduced by displacement of an activated halogen, e.g. a uorine atom.
A library of related compounds was synthesized and screened for human im-
munodeciency virus (HIV) suppression [78].
A solid-phase approach to quinolones was published using the same cyclo-
arylation procedure (see Scheme 8.29). A resin-bound b-keto ester was transferred
Scheme 8.28. Synthesis of quinolones.
Scheme 8.29. Solid-phase approach to Ciprooxacin.
into the enamine and cyclized using tetramethylguanidine (TMG). Many amines
can be incorporated by displacement of the uorine atom at C-7 before the prod-
ucts are cleaved o the resin [79].
8.3.3
Oxygen Nucleophiles
Reactive arenes such as uoro-nitroarenes, halopyridines, halopyrimidines, and

halotriazines are preferred for reactions with oxygen nucleophiles [80]. Diary-
lethers can be prepared by simply reacting the well-known 4-uoro-3-nitrobenzoic
acid template with a wide range of functionalized phenols in a solid-phase reaction
(see Scheme 8.30) [81].
Scheme 8.30. Diaryl ether via SN Ar reaction on solid support.

In solution-phase chemistry, diarylethers can be produced utilizing a polymer-

supported guanidine base. The reaction requires an excess of phenol to achieve
complete conversion. The polymer-supported base deprotonates the phenol and
also traps unreacted starting material (see Scheme 8.31). Since numerous phenols
are commercially available, the method is well suited to library synthesis in an au-
tomated and parallel manner [82].
Scheme 8.31. Diaryl ether synthesis using polymer-supported reagents.
The seven- and eight-member ring systems of dibenzoxazepins and dibenzox-

azocines, respectively, have been well investigated in combinatorial chemistry
using solution- and solid-phase synthesis [83]. The target heterocycles are e-
ciently assembled via intramolecular aromatic substitution of the uorine in 2-
uoro-5-nitroarenes with the OH function of various phenols (see Scheme 8.32).
For the solid-phase approach, the cyclization step was achieved using a 5% solu-
tion of DBU in DMF. DBU was found to give superior results when compared
with TMG or N-methylmorpholine. The authors preferred a solid-phase approach
rather than a solution-phase approach because yields were generally better while
purities were identical.
Scheme 8.32. Solution- and solid-phase synthesis of medium-sized rings.
The value of trichlorotriazine as a template for library synthesis by sequential

substitution of the chloro atoms is discussed in Section 8.3.2. Besides this, tri-
chlorotriazine can react with a soluble polymer support (MeO-PEG-OH, MW 5000)
to give PEG-bound dichlorotriazine, a new soluble electrophilic scavenger (see
Scheme 8.33). Because of the high reactivity of the scavenger toward nucleophiles,
it was used to remove alcohols at the end of ester or silyl ether-forming reactions
[84].
Scheme 8.33. Ester synthesis using dichlorotriazine scavenger.
8.3.4
Sulfur Nucleophiles
The uoro-nitroarene motif is also the most preferred template for SN Ar for
sulfur nucleophiles. In many applications, a suitably protected form of cysteine as a
b-mercapto acid is reacted with 4-uoro-3-nitrobenzoic acid to form 1,5-benzothia-
zepin-4-ones, an important class of drugs in the treatment of cardiovascular dis-
orders. For example, 4-uoro-3-nitrobenzoic acid was treated with 1.5 equivalents
of 9-uorenylmethoxycarbonyl (Fmoc)-l-cysteine in DMF to be converted to the 2-
nitro-thioether (see Scheme 8.34) [85]. After the reduction of the nitro group and a
subsequent reductive alkylation (dicult because of the poor nucleophilicity of
some anilines), the resulting secondary anilines were cyclized to form the seven-
member thiazepine ring.
Scheme 8.34. Solid-phase synthesis of 1,5-benzothiazepin-4-ones.
Fmoc-homocysteine reacts with similar eectiveness to a nucleophile in the same

reaction sequence. Shortening the side-chain from b-mercapto acid to a-mercapto
acids, the SN Ar reaction is also reliable in this case. However, the synthetic utility
is limited owing to the fact that only a very small number of a-mercapto acids are
commercially available.
Using a reversed synthetic strategy, a great variety of other fused heterocycles is
accessible [86]. Wang resin loaded with cysteine via a carbamate linker can be re-
acted with numerous halo-nitroarenes bearing diverse functional groups.
Recently, immobilized 4-uoro-3-nitrobenzoic acid was transformed into 2-

amino-4-carboxythiophenol as an intermediate for the synthesis of several classes
of heterocyclic compounds such as benzothiazoles or 3,4-dihydro-1,4-benzothia-
zines (see Scheme 8.35) [87]. The resin-bound 2-amino-4-carboxythiophenol was
prepared by displacement of the uorine atom with triphenylmethylmercaptan,
reduction of the nitro group, and removal of the sulfur-protecting group.
Scheme 8.35. Solid-phase synthesis of 2-amino-4-carboxythiophenol.
8.3.5
Macrocyclization Reactions
In this section the reaction for closing large rings by nucleophilic substitution of
activated arenes will be discussed. Cyclorelease reactions such as those used in the
well-established syntheses of hydantoins [88] or diketopiperazines [89] will not be
covered.
At rst sight, the closure of medium-sized or large rings by nucleophilic dis-
placement does not meet the demands of combinatorial synthesis. No new sub-
stituents are incorporated and therefore no diversication is achieved. On closer
inspection, the great importance of this reaction becomes obvious in view of the
immense dierence between the three-dimensional structure of a linear oligopep-
tide and the corresponding cyclic analog. So SN Ar macrocyclizations have become
an important part of solid-phase organic synthesis, especially for the preparation of
libraries of b-turn mimics.
Based on the experiences presented earlier in this chapter, suitably substituted
uoro-nitrobenzoic acids are the substrates of choice for intramolecular SN Ar re-
actions [90].
Small libraries of 14-membered macrocyclic diaryl ethers and thioethers can be
produced using a very similar procedure. Precursors are synthesized by the acyla-
tion reaction of solid-supported peptides with 3-uoro-4-nitro benzoic acid. The
substrates undergo cyclization by displacement of the uorine with the phenolic
oxygen of a tyrosine derivative [91] or with the thiol group of cysteines [92] under
exceptionally mild conditions (see Scheme 8.36). Diversity could be increased via
postmodication reactions of the nitro group.
Recently, Burgess and coworkers reported in detail on their research on libraries
of peptide turn mimetics [93]. The eects on nucleophilicity, product ring size,
resins, and other reaction conditions were examined. Optimized procedures to
produce 13- to 16-membered ring systems are described [93].
Larger rings are synthesized by the replacement of the uorine atom in three
regioisomeric uoro-nitrobenzoic acids to prepare analogs of tocinoic acid (see
Scheme 8.37) [94]. In this synthesis the amino group of lysine serves as an inter-
nal nucleophile for the closure of the macrocycle.
Scheme 8.36. Macrocyclizations using SN Ar reactions.
Scheme 8.37. Synthesis of large-ring systems.
References
1 R. B. Merrield, J. Am. Chem. Soc. 9 M. Bernard, W. T. Ford, J. Org.

1963, 85, 21492154. Chem. 1983, 48, 326332.
2 P. Karoyan, A. Triolo, R. 10 J. C. Pelletier, S. Kincaid, Tetra-
Nannicini, D. Giannotti, M. hedron Lett. 2000, 41, 797800.
Altamura, G. Chaissaing, E. 11 R. N. Salvatore, V. L. Flanders, D.
Perrotta, Tetrahedron Lett. 1999, 40, Ha, K. W. Jung, Org. Lett. 2000, 2,
7174. 27972800.
3 O. Mitsunobu, Synthesis 1981, 128. 12 See for example W.-R. Li, N.-M. Hsu,
4 S. Hanessian, F. Xie, Tetrahedron Lett. H.-H. Chou, S.-T. Lin, Y.-S. Lin,
1998, 39, 733736. Chem. Commun. 2000, 401402.
5 N. Bouloc, N. Walshe, M. Bradley, 13 D. P. Matthews, J. E. Green, A. J.
J. Comb. Chem. 2001, 3, 68. Shuker, J. Comb. Chem. 2000, 2, 19
6 G. A. Morales, J. W. Corbett, W. F. 23.
DeGrado, J. Org. Chem. 1998, 63, 14 J. J. Parlow, Tetrahedron Lett. 1996,
25832589. 37, 52575260.
7 M. Caldarelli, J. Habermann, S. V. 15 J. L. Castro, V. G. Matassa, J. Org.
Ley, J. Chem. Soc., Perkin Trans. 1 Chem. 1994, 59, 22892291.
1999, 107110. 16 E. E. Swayze, Tetrahedron Lett. 1997,
8 H. Perrier, M. Labelle, J. Org. Chem. 38, 84658468.
1999, 64, 21102113. 17 M. G. Johnson, D. D. Bronson, J. E.
References 267
Gillespie, D. S. Gifford-Moore, K. 34 M. G. Organ, C. E. Dixon, Biotech.

Kalter, M. P. Lynch, J. R. McCowan, Bioeng. 2000, 71, 7177.
C. C. Redick, D. J. Sall, G. F. Smith, 35 J. Habermann, S. V. Ley, J. S. Scott,
R. F. Foglesong, Tetrahedron 1999, J. Chem. Soc., Perkin Trans. 1 1999,
55, 1164111652. 12531256.
18 G. W. Starkey, J. J. Parlow, D. L. 36 S. N. Filiheddu, S. Masala, M.
Flynn, Bioorg. Med. Chem. Lett. 1998, Taddei, Tetrahedron Lett. 1999, 40,
8, 23852390. 65036506.
19 D. P. Curran, Angew. Chem., Int. Ed. 37 a) B. L. Ching, A. Ganesan, Bioorg.
1998, 37, 11751196. Med. Chem. Lett. 1997, 7, 15111514;
20 S. Peukert, E. N. Jacobsen, Org. Lett. b) R. Maltais, D. Poirier, Tetrahedron
1999, 1, 12451248. Lett. 1998, 39, 41514144.
21 J. Choi, N. M. Yoon, Synth. Commun. 38 R. Maltais, M. R. Tremblay, D.
1995, 25, 26552663. Poirier, J. Comb. Chem. 2000, 2, 604
22 J. Rademann, R. R. Schmidt, J. Org. 614.
Chem. 1997, 62, 36503653. 39 H.-P. Buchstaller, Tetrahedron 1998,
23 A. Bhandari, D. G. Jones, J. R. 54, 34653470.
Schullek, K. Vo, C. A. Schunk, L. L. 40 W. J. Haap, D. Kaiser, T. B. Walk,
Tamanaha, D. Chen, Z. Y. Yuan, M. G. Jung, Tetrahedron 1998, 54, 3705
C. Needels, M. A. Gallop, Bioorg. 3724.
Med. Chem. Lett. 1998, 8, 23032308. 41 S. Hanessian, R.-Y. Yang, Tetrahedron
24 A. Nefzi, M. Giulianotti, R. A. Lett. 1996, 37, 58355838.
Houghten, Tetrahedron Lett. 1998, 39, 42 A. Lohse, K. B. Jensen, K.
36713674. Lundgren, M. Bols, Bioorg. Med.
25 L. Gomez, F. Gellibert, A. Wagner, Chem. 1999, 7, 19651971.
C. Mioskowski, Chem. Eur. J. 2000, 6, 43 H. S. Oh, H.-G. Hahn, S. H. Cheon,
40164020. D.-C. Ha, Tetrahedron Lett. 2000, 41,
26 D. S. Dodd, O. B. Wallace, Tetra- 50695072.
hedron Lett. 1998, 39, 57015704. 44 B. Raju, T. P. Kogan, Tetrahedron Lett.
27 N. Bailey, A. W. Dean, D. B. Judd, D. 1997, 38, 49654968.
Middlemiss, R. Storer, S. P. 45 C. Subramanyam, Tetrahedron Lett.
Watson, Bioorg. Med. Chem. Lett. 2000, 41, 65376540.
1996, 6, 14091414. 46 A. A. Virgilio, A. A. Bray, W.
28 S. Brase, D. Enders, J. Kobberling, Zhang, L. Trinh, M. Snyder, M. M.
F. Avemaria, Angew. Chem., Int. Ed. Morrissey, J. A. Ellman, Tetrahedron
1998, 37, 34133415. 1997, 53, 66356644.
29 a) R. N. Zuckermann, J. M. Kerr, S. 47 C. Y. Cho, R. S. Youngquist, S. R.
B. H. Kent, W. H. Moos, J. Am. Paikoff, M. H. Beresini, A. H. Hebert,
Chem. Soc. 1992, 114, 1064610647; L. T. Berleau, C. W. Liu, D. E. Wemmer,
b) R. N. Zuckermann, E. J. Martin, T. Keough, P. G. Schultz, J. Am.
D. C. Spellmeyer, G. B. Stauber, Chem. Soc. 1998, 120, 77067718.
K. R. Shoemaker, J. M. Kerr, J. Med. 48 M. Ueki, T. Ikeo, M. Iwadate, T.
Chem. 1994, 37, 26782685. Asakura, M. P. Williamson, J.
30 G. Aldrian-Herrada, A. Rabie, R. Slaninova, Bioorg. Med. Chem. Lett.
Wintersteiger, J. Brugidou, J. Pept. 1999, 9, 17671772.
Sci. 1998, 4, 266281. 49 B. Langlois, L. Gilbert, G. Forat,
31 J. K. Rueter, S. O. Nortey, E. W. Ind. Chem. Libr. 1996, 8, 244292.
Baxter, G. C. Leo, A. B. Reitz, 50 a) J. T. Thurston, J. R. Dudley, D.
Tetrahedron Lett. 1998, 39, 975978. W. Kaiser, I. Hechenbleikner, F. C.
32 C. N. Selway, N. K. Terret, Bioorg. Schaefer, D. J. Holm-Hansen, J.
Med. Chem. 1996, 4, 645654. Am. Chem. Soc. 1951, 73, 29812983;
33 Y. F. Xie, J. P. Whitten, T. Y. Chen, b) C. R. Johnson, B. Zhang, P.
Z. Liu, J. R. McCarthy, Tetrahedron Fantauzzi, M. Hocker, K. M. Yager,
1998, 54, 40774084. Tetrahedron 1998, 54, 40974106; c) P.
J. Hajduk, J. Dinges, J. M. M. Legraverend, O. Ludwig, E.

Schkeryantz, D. Janowick, M. Bisagni, S. LeClerc, L. Meijer, N.
Kaminski, M. Tufano, D. J. Augeri, Giocanti, R. Sadri, V. Favaudon,
A. Petros, V. Nienaber, P. Zhong, Bioorg. Med. Chem. 1999, 7, 1281
R. Hammond, M. Coen, B. Beutel, L. 1293; e) Z. Wu, J. Kim, R. M. Soll, D.
Katz, S. W. Fesik, J. Med. Chem. 1999, S. Dhanoa, Biotechnol. Bioeng. 2000,
42, 38523859. 71, 8790; f ) L. F. Hennequin, S.
51 G. R. Gustafson, C. M. Baldino, Piva-Le Blanc, Tetrahedron Lett. 1999,
M.-M. E. ODonnell, A. Sheldon, 40, 38813884.
R. J. Tarsa, C. J. Verni, D. L. Coffen, 61 a) R. W. Sullivan, C. G. Bigam, P. E.
Tetrahedron 1998, 54, 40514065. Erdman, M. S. S. Palaski, D. W.
52 M. Stankova, M. Lebl, Mol. Diversity Anderson, M. E. Goldman, L. J.
1996, 2, 7580. Ransone, M. J. Suto, J. Med. Chem.
53 J. L. Silen, A. T. Lu, D. W. Solas, 1998, 41, 413419; b) M. J. Suto, L.
M. A. Gore, D. Maclean, N. H. Shah, M. Gayo-Fung, M. S. S. Palaski, R.
J. M. Coffin, N. S. Bhinderwala, Y. Sullivan, Tetrahedron 1998, 54, 4141
Wang, K. T. Tsutsui, G. C. Look, D. 4150.
A. Campbell, R. L. Hale, M. Navre, 62 a) D. Obrecht, C. Albrecht, A.
C. R. DeLuca-Flaherty, Antimicrob. Grieder, M. J. Villalgordo, Helv.
Agents Chemother. 1998, 42, 14471453. Chim. Acta 1997, 80, 6572; b) T.
54 D. Scharn, H. Wenschuh, U. Masquelin, D. Sprenger, R. Baer, F.
Reineke, J. Schneider-Mergener, L. Greber, Y. Mercadal, Helv. Chim.
Germeroth, J. Comb. Chem. 2000, 2, Acta 1998, 81, 646660; c) L. M. Gayo,
361369. M. J. Suto, Tetrahedron Lett. 1997, 38,
55 M. T. Fiorini, C. Abell, Tetrahedron 211214.
Lett. 1998, 39, 18271830. 63 a) T. Masquelin, N. Meunier, F.
56 A. S. Fraser, A. M. Kawasaki, P. D. Gerber, G. Rosse, Heterocycles 1998,
Cook, Nucleosides Nucleotides 1999, 18, 48, 24892504; b) T. Masquelin, Y.
10871089. Delgado, V. Baumle, Tetrahedron Lett.
57 T. C. Norman, N. S. Gray, J. T. Koh, 1998, 39, 57255726.
P. G. Schultz, J. Am. Chem. Soc. 64 L. Neuville, J. Zhu, Tetrahedron Lett.
1996, 111, 74307431. 1997, 38, 40914094.
58 Y.-T. Chang, N. S. Gray, G. R. 65 a) B. A. Bunin, J. A. Ellman, J. Am.
Rosania, D. P. Sutherlin, T. C. Chem. Soc. 1992, 114, 1099710998; b)
Kwon, R. Sarohia, M. Leost, L. C. G. Boojamra, K. M. Burow, L. A.
Meijer, P. G. Schultz, Chem. Biol. Thompson, J. A. Ellman, J. Org.
1999, 6, 361375. Chem. 1997, 62, 12401256.
59 N. S. Gray, L. Wodicka, A.-M. W. H. 66 a) J. Lee, D. Gauthier, R. A. Rivero,
Thunnissen, T. C. Norman, S. Kwon, J. Org. Chem. 1999, 64, 30603065; b)
F. H. Espinoza, D. O. Morgan, G. M. K. Schwarz, D. Tumelty, M. A.
Barnes, S. LeClerc, L. Meijer, S.-H. Gallop, Tetrahedron Lett. 1998, 39,
Kim, D. J. Lockhart, P. G. Schultz, 83978400.
Science 1998, 281, 533538. 67 a) J. Lee, W. V. Murray, R. A.
60 a) C. Chen, R. Dagnino Jr, E. B. De Rivero, J. Org. Chem. 1997, 62, 3874
Souza, D. E. Grigoriadis, C. Q. 3879; b) G. A. Morales, J. W.
Huang, K.-I. Kim, Z. Liu, T. Moran, Corbett, W. F. DeGrado, J. Org.
T. R. Webb, J. P. Whitten, Y. F. Xie, Chem. 1998, 63, 11721177.
J. R. McCarthy, J. Med. Chem. 1996, 68 R. E. TenBrink, W. B. Im, V. H.
39, 43584360; b) A. D. Baxter, E. A. Sethy, A. H. Tang, D. B. Carter, J.
Boyd, P. B. Cox, V. Loh Jr, C. Med. Chem. 1994, 37, 758768.
Monteils, A. Proud, Tetrahedron Lett. 69 F. Zaragoza, H. Stephensen, J. Org.
2000, 41, 81778181; c) R. Di Chem. 1999, 64, 25552557.
Lucrezia, I. H. Gilbert, C. D. Floyd, 70 G. B. Phillips, G. P. Wie, Tetrahedron
J. Comb. Chem. 2000, 3, 249253; d) Lett. 1996, 37, 48874890.
References 269
71 a) D. Tumelty, M. K. Schwarz, M. C. 83 a) X. Ouyang, N. Tamayo, A. S.

Needels, Tetrahedron Lett. 1998, 39, Kiselyov, Tetrahedron 1999, 55, 5827
74677470; b) J. P. Mayer, G. S. 5830; b) X. Ouyang, A. S. Kiselyov,
Lewis, C. McGee, D. Bankaitis- Tetrahedron 1999, 55, 82958302; c) X.
Davis, Tetrahedron Lett. 1998, 39, Ouyang, Z. Chen, L. Longbin, C.
66556658; c) J. Lee, D. Gauthier, R. Dominguez, A. S. Kiselyov,
A. Rivero, Tetrahedron Lett. 1998, 39, Tetrahedron 2000, 56, 23692377.
201204; d) Z. Wu, P. Rea, G. 84 a) A. Falchi, M. Taddei, Org. Lett.
Wickham, Tetrahedron Lett. 2000, 41, 2000, 2, 34293431; b) H. Deleuze, D.
98719874. C. Sherrington, J. Chem. Soc., Perkin
72 J. P. Kilburn, J. Lau, R. C. F. Jones, Trans. 2 1995, 22172221; c) C. R.
Tetrahedron Lett. 2000, 41, 54195421. Johnson, B. Zhang, P. Fantauzzi,
73 G. P. Wie, G. B. Phillips, Tetrahedron M. Hocker, K. M. Yager, Tetrahedron
Lett. 1998, 39, 179182. 1998, 54, 40974106.
74 a) P.-C. Pan, C.-M. Sun, Tetrahedron 85 a) B. Yan, G. Kumaravel, Tetrahedron
Lett. 1999, 40, 64436446; b) P.-C. 1996, 52, 843848; b) M. K. Schwarz,
Pan, C.-M. Sun, Biorg. Med. Chem. D. Tumelty, M. A. Gallop, J. Org.
Lett. 1999, 9, 15371540. Chem. 1999, 64, 22192231.
75 E. Farrant, S. S. Rahman, Tetra- 86 a) G. C. Morton, J. S. M. Salvino, R.
hedron Lett. 2000, 41, 53835386. F. Labaudiniere, T. F. Herpin,
76 G. Liu, Y. Fan, J. R. Carlson, Z.-G. Tetrahedron Lett. 2000, 41, 30293030;
Zhao, K. S. Lam, J. Comb. Chem. b) A. Nefzi, N. A. Ong, M. A.
2000, 2, 467474. Giulianotti, J. M. Ostresh, R. A.
77 U. Petersen, T. Schenke in: Houghten, Tetrahedron Lett. 1999, 40,
Quinolone Antibacterials. Kuhlmann, 49394942.
J., Dalhoff, A., Zeiler, H.-J. (eds), 87 T. S. Yokum, J. Alsina, G. Barany, J.
Springer Verlag, Berlin 1998, pp. 63 Comb. Chem. 2000, 2, 282292.
118. 88 a) S. Hobbs-DeWitt, J. S. Kiely, C. J.
78 a) Y.-S. Oh, S.-H. Cho, J Heterocyclic Stankowic, M. C. Schroeder, D. M.
Chem. 1998, 35, 1723; b) K. E. Reynolds-Cody, M. R. Pavia, Proc.
Frank, P. V. Devasthale, E. J. Natl. Acad. Sci. USA 1993, 90, 6909
Gentry, V. T. Ravikumar, A. 6913; b) S. Hobbs-DeWitt, A. W.
Keschavarz-Shokri, L. A. Mitscher, Czarnik, Acc. Chem. Res. 1996, 29,
A. Nilius, L. L. Shen, R. Shawar, W. 114122.
R. Baker, Comb. Chem. High 89 A. K. Szardenings, T. S. Burkoth,
Throughput Screening 1998, 1, 8999. H. H. Lu, D. W. Tien, D. A. Campbell,
79 a) A. A. MacDonald, S. H. DeWitt, Tetrahedron 1997, 53, 65736593.
E. M. Hogan, R. Ramage, Tetrahedron 90 E. A. Jefferson, E. E. Swayze,
Lett. 1996, 37, 48154818; b) A. M. Tetrahedron Lett. 1999, 40, 77577760.
Hay, S. Hobbs-DeWitt, A. A. 91 A. S. Kiselyov, S. Eisenberg, Y. Luo,
MacDonald, R. Ramage, Tetrahedron Tetrahedron 1998, 54, 1063510640.
Lett. 1998, 39, 87218724; c) A. M. 92 A. S. Kiselyov, S. Eisenberg, Y. Luo,
Hay, S. Hobbs-DeWitt, A. A. Tetrahedron Lett. 1999, 40, 24652468.
MacDonald, R. Ramage, Synthesis 93 a) Y. Feng, K. Burgess, Chem. Eur. J.
1999, 11, 19791985. 1999, 5, 32613272; b) Z. Wang, S.
80 R. Mohan, W. Yun, B. O. Buckman, Jin, Y. Feng, K. Burgess, Chem. Eur.
A. Liang, L. Trinh, M. M. J. 1999, 5, 32733278; c) A. J. Zhang,
Morrissey, Biorg. Med. Chem. Lett. S. Khare, K. Gokulan, D. S.
1998, 8, 18771882. Linthicum, K. Burgess, Bioorg. Med.
81 J. C. H. M. Wijkmans, A. J. Culshaw, Chem. Lett. 2001, 11, 207210.
A. D. Baxter, Mol. Diversity 1998, 3, 94 C. Fotsch, G. Kumaravel, S. K.
117120. Sharma, A. D. Wu, J. S. Gounarides,
82 W. Xu, R. Mohan, M. M. Morrissey, N. R. Nirmala, R. C. Petter, Biorg.
Tetrahedron Lett. 1997, 38, 73377340. Med. Chem. Lett. 1999, 9, 21252130.
270
9
Electrophilic Substitution in Combinatorial and
9.1
Introduction
Reactions in which an electron-decient reagent attacks a substrate and an

electron-decient leaving group is displaced are called electrophilic substitutions
(SE ). The most common leaving group is the proton. While the reaction is typical
for aromatic systems, aliphatic substrates only react when hydrogens of sucient
acidity are available. This chapter focuses on the application of SE in the genera-
tion of chemical diversity.
Compared with nucleophilic substitution reactions (see Chapter 8) the use of
SE in the context of combinatorial chemistry is rare. Much still remains to be done
in this area of research. Although a number of functional group transformations
involving SE mechanisms have been applied to solution- and solid-phase synthesis,
the potential of the reaction to link building blocks in a combinatorial sense is re-
stricted to very special cases. The wide application of acid-labile linkers in solid-
phase synthesis often prohibits the use of electrophilic reagents since the linkers
are electron-rich aromatics and thus highly susceptible to aromatic SE .
Reactions involving SE mechanisms are frequently used in building-block syn-
thesis. Despite its importance in the overall workow of combinatorial chemistry,
this aspect is beyond the scope of this chapter and will not be covered. Reference
will only be made to the use of SE in the preparation of linkers and solid supports
(see also Chapter 4). SE reactions involving organometallic reagents or carbon nu-
cleophiles will be dealt with in the appropriate chapters. Traditional synthetic
methods involving SE have been supplemented by modern transition metal-cata-
lyzed substitution reactions. Please refer to other Chapters for their applications in

ISBN: 3-527-30509-2
9.2 Electrophilic Substitution at Aliphatic Carbons 271
9.2
Electrophilic Substitution at Aliphatic Carbons
9.2.1
Halogen Electrophiles
Halogenated carbonyl compounds are important synthetic intermediates, espe-

cially in the formation of heterocycles. Suitable reaction conditions have been de-
vised for the transformation of enolizable carbonyl compounds into the corre-
sponding a-bromo derivatives. The reagent of choice is pyridinium perbromide,
which can be employed in both solid-phase [1] and solution-phase synthesis. In
the latter case the commercially available polymer-bound version of the reagent
has been frequently used [2].
As an example of this transformation the solution-phase bromination of aceto-
phenones to a-bromo-acetophenones will be discussed. The transformation has
been incorporated in an oxidation, bromination, and nucleophilic substitution re-
action sequence (see Scheme 9.1). Notably, this sequence is performed by adding
all the necessary polymer-supported reagents to the starting phenylethanol at
the same time in a single reaction vessel. The nal yield in this multistep/one-
chamber solution-phase synthesis is higher than the combined yields of the three
steps performed sequentially [3].
Scheme 9.1. Solution-phase bromination of acetophenones.
9.2.2
Nitrogen Electrophiles
The formation of hydrazones by the reaction of diazonium salts with activated

methylene compounds can be adapted to parallel synthesis by linking either of the
reactants to a polymer support. Polymer-supported aryl diazonium cations have
been treated with the potassium salt of Meldrums acid at 25 C to give the corre-
sponding 5-phenylhydrazone derivatives of Meldrums acid in good yield [4]. Al-
ternatively, polymer-supported Meldrums acid anion reacts with various aryl di-
azonium uoroborates at 25 C in acetonitrile, yielding the same products [5].
Aliphatic diazo compounds are obtained on solid support from the reaction of
tosyl or mesyl azide with immobilized activated methylene compounds. The sub-
strates used are b-ketoesters [6], b-ketoamides [7] (see Scheme 9.2), or malonic
acid derivatives [8]. Typically, the reaction is carried out at room temperature using
an excess of the azide and an even larger excess of triethylamine or diisopropyle-
thylamine.
272 9 Electrophilic Substitution in Combinatorial and Solid-phase Synthesis
Scheme 9.2. Solid-phase diazotation.
9.2.3
Carbon Electrophiles
Enamines react with a number of electrophiles such as electron-poor olens. The

reaction is used in heterocycle chemistry, as shown in a solid-phase synthesis of
dihydropyridines (see Scheme 9.3) [9].
Scheme 9.3. Solid-phase enamine substitution and cyclization.
9.3
Electrophilic Substitution at Aromatic Carbons
9.3.1
General Remarks
Almost all kinds of SE reactions involving arene substrates are used in solution-
phase chemistry as a powerful synthetic tool. In solid-phase chemistry the use of
this reaction is limited owing to its incompatibility with electron-rich linkers. With
the exception of a few examples mentioned below, aromatic SE is restricted to the
functionalization of polystyrene-based supports [10].
Polystyrene can be brominated, nitrated, and acylated or alkylated applying
FriedelCrafts conditions in solvents such as carbon tetrachloride or nitrobenzene.
For example, in 1988 Ajayaghosh and Pillai [11] demonstrated the preparation of a
photosensitive resin using SE reactions (see Scheme 9.4). Commercially available
Scheme 9.4. Solid-phase FriedelCrafts acylation.

polystyrene (crosslinked with 1% divinylbenzene) was rst acylated with acetyl

chloride under typical FriedelCrafts conditions. The resulting ketone was reduced
to the corresponding alcohol and then halogenated. Using a second SE reaction, a
nitro group was introduced with fuming nitric acid at low temperature.
Higher reaction temperatures applied during acylation of solid-supported mate-
rial may lead to side-reactions such as partial dealkylation of phenyl groups and
hence to soluble polymers. Although FriedelCrafts alkylations on polystyrene are
possible under harsh conditions (strong acids), there are more suitable methods
for this kind of CaC bond formation. Reaction of an immobilized organometallic
compound (most commonly lithiated by a halogenlithium exchange reaction)
[12] with alkyl halides can be considered as the method of choice.
9.3.2
Halogen Electrophiles
In accordance with their inherent preference for electrophilic substitutions, many

heterocycles are easily halogenated. For example, a simple bromination can serve
as a starting point for further diversication when followed by palladium-catalyzed
CaC bond formation (see Scheme 9.5). In addition to Suzuki couplings, the 6-
bromonalidixic acid derivative obtained in the bromination step can also undergo
Heck reaction [13].
Scheme 9.5. Solution-phase arene bromination and subsequent Suzuki coupling.
There are only a few examples of arene brominations on solid support in the
literature. Using N-bromosuccinimide in dimethyl formamide at room tempera-
ture, electron-rich arenes such as thiophenes can be brominated (see Scheme 9.6).
Combination with a Stille coupling and reiteration of the reaction sequence leads
to oligothiophenes new materials with interesting optical and electronic prop-
erties [14].
Scheme 9.6. Solid-phase arene bromination and subsequent Stille coupling.

A rare example of direct halogenation on a solid support has been reported for
phenols. The phenolic moiety of tyrosine undergoes iodination when treated with
bis-(pyridine) iodonium(I) tetrauoroborate (Ipy2 BF4 ) for no more than 10 min
(see Scheme 9.7) [15].
Scheme 9.7. Solid-phase iodination.
The only example in this chapter in which the leaving group in an SE reaction is
not a proton involves germanium-based linkers. These linkers have been devel-
oped for solid-phase synthesis as a means of traceless linkage (see Chapter 4).
However, reaction of germanium-linked substrates with bromine rapidly releases
the corresponding aryl bromides by ipso substitution of the germanium by bro-
mine (see Scheme 9.8). Aryl iodides can be prepared by the same method using
iodomonochloride [16].
Scheme 9.8. Solid-phase ipso substitution of germanium by bromine.
9.3.3
Nitrogen Electrophiles
Very recently the diazotization of aromatic compounds has found applications in

combinatorial chemistry. The formation of diazonium salts and the coupling to
electron-rich aromatics to give azo dyes can be performed using polymer-supported
reagents (see Scheme 9.9) [17].
Polymer-bound aryl diazonium salts also play a pivotal role in the chemistry of
triazene linkers.
Scheme 9.9. Solution-phase diazotation and azo coupling.
9.3.4
Carbon Electrophiles
FriedelCrafts chemistry is rarely used to generate diversity. One of the few

examples is the superacid-induced solution-phase synthesis of a small library of
3,3-diaryloxindoles (see Scheme 9.10) [18]. The reaction proceeds smoothly in pure
triic acid at room temperature.
Scheme 9.10. Solution-phase FriedelCrafts alkylation.
The PictetSpengler reaction is a very well-established method for the synthe-

sis of tetrahydroisoquinolines and tetrahydro-b-carbolines both in solution and on
solid support [19]. The molecules are easily prepared by intramolecular reaction of
an iminium ion with an arene usually under acidic conditions. The imines are
typically formed by condensing amines with (aromatic) aldehydes (see Scheme
9.11), cyclohexanones, or aryl methyl ketones [20].
Scheme 9.11. Solution-phase PictetSpengler reaction.

Using tryptophan as the starting material, the synthesis of tricyclic carbolines

has been reported in numerous examples in the literature. Whereas reactions with
aldehydes are normally complete within hours, less reactive ketones require up to
several days to reach complete conversion (see Scheme 9.12) [21].
Scheme 9.12. Solid-phase PictetSpengler reaction.
A PictetSpengler reaction has been used as the key step during the synthesis of
indolyl diketopiperazine-based libraries of Fumitremorgin C analogs (see Scheme
9.13). This natural product, isolated by fermentation of the fungi Aspergillus fumi-
gatus, appears to be of interest in the area of central nervous system (CNS) and
cancer research and has therefore resulted in the preparation of some solid-phase
combinatorial libraries [22].
Scheme 9.13. Solid-phase synthesis of Fumitremorgin C analogs.
The PictetSpengler reaction is not limited to the synthesis of six-member

ring systems. Also the class of seven-member rings present in the pharmaceuti-
cally important diazepine class of compounds is easily accessed by condensing al-
dehydes with suitably substituted aminomethylfurans (see Scheme 9.14) [23].
Scheme 9.14. Solution-phase PictetSpengler reaction yielding seven-member rings.

References 277
In the closely related BischlerNapieralski reaction dihydroisoquinolines are

formed. The intramolecular condensation of an acylated amine with an arene is
mediated by the action of a strong dehydrating agent, usually phosphoryl chloride.
It leads to dihydroisoquinolines, which can be transformed either into isoquino-
lines by oxidation or into tetrahydroisoquinolines by reduction (see Scheme 9.15).
The harsh reaction conditions are not generally amenable to solid-phase reactions
since most linkers are not stable to a large excess of phosphoryl chloride in toluene
at 80 C [24].
Scheme 9.15. Solid-phase BischlerNapieralski reaction.
The reaction has also been applied to solution-phase synthesis, but has found
little application in library production to date [25].
In a Reissert-type reaction involving pyrrole derivatives, CaC bond formation is
achieved by aromatic SE on solid support using N-oxides (see Scheme 9.16). The
reaction also works with indoles and with enamines [26].
Scheme 9.16. Solid-phase Reissert reaction.
References
1 A. Barco, S. Benetti, C. De Risi, Thomas, J. Chem. Soc. Perkin Trans. 1

C. Marchetti, C. P. Pollini, 1999, 24252427.
V. Zanirato, Tetrahedron Lett. 1998, 3 J. J. Parlow, Tetrahedron Lett. 1995,
39, 75917594. 36, 13951396.
2 a) J. Habermann, S. V. Ley, J. S. 4 B. P. Bandgar, J. V. Totare, J. N.
Scott, J. Chem. Soc. Perkin Trans. 1 Nigal, Ind. J. Heterocycle Chem. 1998,
1998, 31273130; b) J. Habermann, 8, 7778.
S. V. Ley, R. Smits, J. Chem. Soc. 5 B. P. Bandgar, A. M. Tavhare, S. S.
Perkin Trans. 1 1999, 24212423; Pandit, Ind. J. Chem., Sect. B 2000,
c) J. Habermann, S. V. Ley, J. J. 38, 721723.
Scicinski, J. S. Scott, R. Smits, A. W. 6 M. Cano, F. Camps, J. Joglar,
Tetrahedron Lett. 1998, 39, 9819 19 P. P. Fantauzzi, K. M. Yager,

9822. Tetrahedron Lett. 1998, 39, 1291
7 F. Zaragoza, S. V. Petersen, 1294.
Tetrahedron 1996, 52, 59996002. 20 M. G. Siegel, M. O. Chaney, R. F.
8 a) D. L. Whitehouse, K. H. Nelson Bruns, M. P. Clay, D. A. Schober,
Jr, S. N. Savinov, D. J. Austin, A. M. Van Abbema, D. W. Johnson,
Tetrahedron Lett. 1997, 38, 71397142; B. E. Cantrell, P. J. Hahn, D. C.
b) M. R. Gowravaram, M. A. Gallop, Hunden, D. R. Gehlert, H.
Tetrahedron Lett. 1997, 38, 69736976; Zarrinmayeh, P. L. Ornstein, D. M.
c) D. L. Whitehouse, K. H. Nelson Zimmerman, G. A. Koppel, Tetra-
Jr, S. N. Savinov, R. S. Lowe, D. J. hedron 1999, 55, 1161911639.
Austin, Bioorg. Med. Chem. 1998, 6, 21 a) J. P. Mayer, D. Bankaitis-Davis,
12731282. J. Zhang, G. Beaton, K. Bjergarde,
9 M. F. Gordeev, D. V. Patel, J. Wu, C. M. Andersen, B. A. Goodman,
E. M. Gordon, Tetrahedron Lett. 1996, C. J. Herrera, Tetrahedron Lett. 1996,
37, 46434646. 37, 56335637; b) L. Yang, L. Guo,
10 a) J. H. Adams, R. M. Cook, D. Tetrahedron Lett. 1996, 37, 50415044;
Hudson, V. Jammalamadaka, M. H. c) L. Yang, Tetrahedron Lett. 2000, 41,
Lyttle, M. F. Songster, J. Org. Chem. 69816984; d) X. Li, L. Zhang, W.
1998, 63, 37063716; b) G. Orosz, Zhang, S. E. Hall, J. P. Tam, Org.
L. P. Kiss, Tetrahedron Lett. 1998, 39, Lett. 2000, 2, 30753078.
32413242. 22 a) A. van Loevezijn, J. H. van
11 A. Ajayaghosh, V. N. R. Pillai, Maarseveen, K. Stegman, G. M.
Tetrahedron Lett. 1988, 21, 66616666. Visser, G.-J. Koomen, Tetrahedron
12 a) S. Havez, M. Begtrup, P. Vedso, Lett. 1998, 39, 47374740; b) H.
J. Org. Chem. 1998, 63, 74187420; Wang, A. Ganesan, Org. Lett. 1999, 1,
b) Z. Li, A. Ganesan, Synlett 1998, 16471649.
405406. 23 a) X. Feng, J. C. Lancelot, A. C.
13 C. Plisson, J. Chenault, Heterocycles Gillard, H. Landelle, S. Rault,
1999, 51, 26272637. J. Heterocycle Chem. 1998, 35, 1313
14 P. R. L. Malenfant, J. M. Frechet, 1316; b) S. Vega, M. S. Gil, V. Darias,
Chem. Commun. 1998, 26572658. C. C. Sanchez Mateo, M. A.
15 G. Arsequell, G. Espuna, G. Exposito, Pharmazie 1995, 50, 2733.
Valencia, J. Barluenga, R. P. 24 a) K. Rolng, M. Thiel, H. Kunzer,
Carlon, J. M. Gonzalez, Tetrahedron Synlett 1996, 10361038; b) W. D. F.
Lett. 1998, 39, 73937396. Meutermans, P. F. Alewood,
16 a) A. C. Spivey, M. C. Diaper, Tetrahedron Lett. 1995, 36, 77097712.
H. Adams, J. Org. Chem. 2000, 65, 25 a) V. Jullian, J. C. Quirion, H. P.
52535263; b) M. J. Plunkett, J. A. Husson, Eur. J. Org. Chem. 2000, 7,
Ellman, J. Org. Chem. 1997, 62, 2885 13191325; b) S. Deprets, G. Kirsch,
2893. Eur. J. Org. Chem. 2000, 7, 1353
17 M. Caldarelli, I. R. Baxendale, S. V. 1357.
Ley, Green Chem. 2000, 4345. 26 M. Z. Hoemann, M. Melikian-
18 D. A. Klumpp, K. Y. Yeung, G. K. S. Badalian, G. Kumaravel, J. R.
Prakash, G. A. Olah, J. Org. Chem. Hauske, Tetrahedron Lett. 1998, 39,
1998, 63, 44814484. 47494752.
279
10
Elimination Chemistry in the Solution- and
Solid-phase Synthesis of Combinatorial
Libraries
Demosthenes Fokas and Carmen Baldino
10.1
Introduction
One of the challenges for organic chemists involved in the burgeoning eld of
combinatorial chemistry is to rediscover new uses and applications of old reactions
and subsequently adapt them to either solid- or solution-phase chemistry. Elimi-
nation reactions, which have been studied thoroughly and used extensively by the
chemistry community in the synthesis of several complex molecules, fall into this
category [1]. Among them, b-eliminations prevail in organic synthesis with nu-
merous applications in the preparation of olens. Although olens are versatile
and useful intermediates for combinatorial chemistry, the synthesis of libraries of
olenic substrates by adaptation of the classical b-elimination reaction has not re-
ceived much attention so far, presumably because of the lack of convergence in the
synthesis and diversity of the nal products. Instead, b-eliminations along with
other elimination reactions are gaining favor in solid-phase synthesis as a release
strategy of the desired products from solid support.
In this chapter we will address elimination reactions from a mechanistic
rational including: (1) b-eliminations, (2) conjugate eliminations, and (3) addition
elimination reactions. We will also discuss the utility of these transformations
in combinatorial chemistry. Olenation reactions such as the Wittig, Horner
Emmons, and ring-closing olen metathesis, which could fall into the addition
elimination category, will not be discussed herein since they will be addressed in
dierent chapters.
10.2
b-Eliminations in Combinatorial Chemistry
b-Elimination has been used for peptide synthesis since 1967. However, broader
applications have been limited, presumably because the cleavage conditions as de-
scribed needed to be tightly controlled [2]. The expanded utility of b-elimination
reactions in combinatorial chemistry and solid-phase synthesis has been realized

ISBN: 3-527-30509-2
280 10 Elimination Chemistry in the Solution- and Solid-phase Synthesis of Combinatorial Libraries
very recently with the advent of new linkers [3]. The design of traceless linkers that
leave no residue on the cleaved product enabled chemists to envision b-elimination
reactions as an eective release strategy of the desired products from solid sup-
port. The term traceless usually denes linkers that leave no obvious residue on
the cleaved molecule. A traceless linker is dened as one where a new CaH or
CaC bond is formed at the linkage site of the cleaved molecule. However, this def-
inition has been expanded to linkers that include other cleavage reactions. Al-
though there are several transformations in combinatorial chemistry that involve
an intermediate b-elimination step, we will focus on release-based b-eliminations
and their application to combinatorial chemistry.
10.2.1
The Hofmann Elimination Solid-phase Synthesis of Tertiary Amines
10.2.1.1 Via a Regenerated Michael Acceptor (REM) Resin

The Hofmann elimination can be traced back to 1851 when Hofmann rst re-
ported the elimination of quaternary ammonium compounds [4]. The reaction is
usually considered to be a useful method for the synthesis of alkenes and indeed
has been previously used by Blettner and Bradley to synthesize dehydroalanine
derivatives on resin [5]. The utility of this reaction in combinatorial chemistry was
not realized until 1996 when Rees and coworkers introduced this reaction as part
of a traceless linker strategy for the solid-phase synthesis of libraries of tertiary
amines (Scheme 10.1) [6].
Scheme 10.1. Synthesis of tertiary amines on a REM resin.
This strategy utilizes a hydroxymethylpolystyrene resin (1) derivatized as the

acrylate ester (2) which upon a Michael addition of a primary or secondary amine
gives the secondary or tertiary resin-bound amine (3) respectively. In the case
where a primary amine is added, the resulting resin-bound secondary amine can
be converted into tertiary amine (3) by a reductive alkylation, thus introducing a
new element of diversity. Quaternization of the tertiary amine with an alkyl halide
to give ammonium salt (4) introduces another site of diversity and activates the
linker for cleavage by a facile Hofmann elimination reaction. Then, NiPr2 Et at
room temperature liberates the tertiary amine (5) into solution and regenerates the
acrylate resin (2). Similarly, tertiary amines with the general structure 5 and with
three sites of diversity can result from a resin-bound equivalent of ammonia (6),
which can be derived from the coupling of 9-uorenylmethoxycarbonyl (Fmoc)-b-
alanine to hydroxymethylpolystyrene resin followed by Fmoc deprotection. Since
the resin linker 2 is regenerated after elimination of the product and is function-
alized via a Michael reaction, this resin was referred to as a REM (regenerated Mi-
chael acceptor) resin.
The REM resin system can be used in the monoalkylation of diamines without
the use of protecting groups (Scheme 10.2). For example, piperazine can be added
to resin 2 to give the monoalkylated derivative 7, which can then be acylated or al-
kylated cleanly at the second nitrogen [7]. Treatment of resin-bound piperazine (7)
with isocyanates or alkyl halides can generate compounds of the general structure
8 or 9 respectively. Quaternization and elimination provides disubstituted piper-
azine adducts 10 and 11 in high purity. A library of 125 piperazines with the gen-
eral structure 11 was prepared and a few of the compounds were found to be active
against d-opioid receptors [8]. The high purity of substrate 11 demonstrates that
although quaternization at the undesired nitrogen in piperazine (9) is possible, it
does not reduce the purity of the nal product since only the desired product can
be cleaved from the resin.
Scheme 10.2. Immobilization and derivatization of diamines on a REM resin.
The overall yield for the three-step sequence ranges from 40% to 80% and is
substrate dependent. The purity of the isolated products is good because only the
desired tertiary resin-bound amine will be susceptible to the elimination condi-
tions. The method works well when the quaternization step can be conducted at
ambient temperature using reactive alkyl halides (i.e. allyl, benzyl, and methyl).
The quaternization step only requires heat when less reactive alkylating agents are
used. However, quaternization at elevated temperatures can cause the Hofmann

elimination to occur prematurely, releasing the tertiary amine into solution where
it is susceptible to quaternization by a second equivalent of alkylating agent [7].
Therefore, a more thermally stable linker needs to be developed in order to prevent
premature cleavage when less reactive alkyl halides are used. Quaternization can
also be problematic with sterically hindered alkylating agents or when sterically
hindered resin-bound amines are involved.
Although the Michael addition of primary and secondary alkyl amines to resin
2 works well, there are no examples describing the addition of anilines to resin 2
and, consequently, the synthesis of tertiary anilines. Addition of anilines would
presumably require more vigorous reaction conditions.
The REM linker is stable to both mildly acidic and basic conditions, making
possible Fmoc protection of amines and tert-butyl ester protection of carboxylic
acids. Boc protection of amines is also likely to be compatible with the resin, since
the cleavage conditions are likely to be similar to those used for deprotecting tert-
butyl esters. The amount of racemization occurring during the synthesis of N-
alkylated a-amino ester derivatives on REM resin is likely to be minimal. Further-
more, the REM resin 2 can be recycled and used successfully with no substantial
loss of its reactivity. No decrease in yield or purity of products was observed even
after ve synthesis cycles [7]. However, the ester linkage is not compatible with
Grignard reagents, metal hydride reducing agents, or transesterication condi-
tions, which limits the scope of reactions that can be performed on solid phase.
However, this problem can be addressed through the use of the more stable sul-
fone REM resins 1214, which have been successfully used in the synthesis of
amine libraries. These sulfone REM resins provide enhanced chemical stability
and compatibility with a wider range of chemical reagents and reaction conditions
[9]. Recently, the amide REM resin derivatives have emerged and two of these res-
ins (15, 16) are currently under evaluation for the automated preparation of amine
libraries (Scheme 10.3) [10].
Scheme 10.3. Other REM resins used in the synthesis of tertiary amines.
10.2.1.2 Via a Safety-catch Resin

A small library of 13 G-coupled protein receptor agonists and antagonists was
produced by Wade et al. using the sulde safety-catch resin 17 (Scheme 10.4) [11].
Quaternization of resin 17 followed by oxidation gave resin-bound sulfone 18,
which resembles those derived from the corresponding vinyl sulfone REM resins
via a Michael additionquaternization sequence [9]. Sulfone 18 underwent a Hof-
Scheme 10.4. Hofmann elimination on a safety-catch resin.
mann elimination, upon treatment with Me 2 NH, to furnish vinyl sulfone resin 20
and release in solution the desired tertiary amine with general structure 19 in a
25% average yield for the six-step sequence. However, all of the nal compounds
had to be puried by reversed phase high-performance liquid chromatography
(HPLC) owing to a minor 3-chlorobenzoic acid impurity. This problem can be cir-
cumvented by extended washing of the activated resin with 2 N HCl in tetrahy-
drofuran (THF), presumably exchanging the anions of the ammonium salt for
chloride. The advantage of the sulde safety-catch resin is the decreased sensitivity
of the alkylated product to b-elimination, which could be utilized to increase the
yield or extend the scope of alkylating agents to less activated systems. However,
oxidation of the sulde resin prior to amine synthesis would be necessary for more
oxidation-sensitive systems.
10.2.1.3 Via a Hydroxylamine Resin

A Hofmann-type elimination has also been utilized independently by both Grigg
(Scheme 10.5, route a) and Andersson (Scheme 10.5, route b) in the synthesis of
tertiary methylamines using an extremely robust and versatile traceless linker [12].
Polystyrene resin (21) with a hydroxylamine linker attached can be converted to
resin-bound tertiary hydroxylamine 22. Quaternization of 22 with MeOTf resulted
in the alkoxyammonium intermediate 23, which upon treatment with NEt3 in
CH2 Cl2 furnished the resin-bound aldehyde 25 and released into solution the ter-
tiary methylamine with the general structure 24. An alternative route involving the
exposure of 23 to much milder reagents such as lithium iodide (in dioxane or ace-
Scheme 10.5. Hofmann elimination on a hydroxylamine resin.

tonitrile) or samarium iodide (in THF) also resulted in highly ecient cleavage
delivering tertiary methylamines of high purity in good overall yields.
The quaternization works only with methyl triate as the alkylating reagent,
thus limiting the diversity of the produced library. Although other triates pre-
pared in situ via AgOTf/alkyl halide exchange gave the corresponding quaternary
salts in solution, this approach is unsuitable for the solid-phase sequence because
of interference of reaction kinetics from the silver halide precipitate. Both routes
are amenable to solution-phase parallel synthesis by careful selection of reaction
conditions and work-up methods starting from O-benzylhydroxylamine. Although
this hydroxylamine resin (22) is more stable than the ester REM resin (2) toward a
variety of nucleophilic reagents, it limits a library design to tertiary methylamines.
Furthermore, this resin cannot be recycled once it is used an advantage of the
REM resins.
10.2.1.4 Alternative Cleavage Techniques

A major challenge associated with the cleavage of amines from resins is the re-
moval of any excess cleavage reagents and byproducts from the reaction mixture.
The process generally requires extraction or chromatography, which could render
the synthesis of large libraries cumbersome. The pursuit of other cleavage strat-
egies that would allow for the direct isolation of pure compounds has become
necessary. Murphy and coworkers introduced a novel two-resin system in which
the resin-bound quaternary ammonium compounds were treated with an excess of
a second resin-bound amine such as the weakly basic ion-exchange resin Amber-
lite IRA-95 in dimethylformamide (DMF) and a catalytic amount of Et3 N (Scheme
10.6) [13]. Under these conditions, highly pure products were recovered with good
yields after ltration and evaporation of the solvent.
Scheme 10.6. Proposed mechanism for the two-resin system-promoted Hofmann elimination.
Similar results were obtained by treating the resin-bound quaternary ammo-

nium compounds with Amberlite weakly basic ion-exchange resin in DMF in the
absence of any additional base. The basic resin is sucient to achieve cleavage and
avoid the need for an aqueous work-up. These surprising two-resin results may be
explained by a thermal elimination of the amine from the resin as the HBr salt.
The basic resin then desalts the amine to catalyze the b-elimination. Alternatively,
it may also be due to trace amounts of base, present either from previous steps or
from trace dimethylamine in the DMF. It was found that yield was a function of
reaction time with an optimal length of 18 h for a 14-member library production.
Identical results generating highly pure products were obtained using a depro-
tected Rink amide resin, albeit at lower yield [13].
A novel Wang resin-bound piperazine base (26) that resembles Murphys two-
resin system was introduced by Yamamoto et al. (Scheme 10.7) [14]. It was used
successfully (2 equiv., loading 1.62 mmol g1 ), in the absence of any other external
base, to cleave N-aryl-N 0 -benzylpiperazines from the resin by treating the quater-
nary ammonium compounds with resin 26 in CH2 Cl2 for 16 h at room tempera-
ture. However, the caveat of this reagent and the ion-exchange resin is that they
complicate the reusability of the REM resin since at the end of the sequence both
resins are mixed together.
Scheme 10.7. Polymer-supported bases used in Hofmann elimination.
A soluble noncrosslinked polystyrene-bound basic reagent (NCPS-NEt2 ) (27) has

been developed recently by Janda and coworkers (Scheme 10.7) [15]. Use of base
27 (3 equiv., loading 0.85 mmol g1 ) in CH2 Cl2 eliminates the need for purica-
tion and allows the direct isolation of a library of pure tertiary amines through
simple ltration and concentration operations. The advantage of this method over
the ion-exchange resin and the polymer-supported base methods is that it allows
for the recycling of the REM resin by taking advantage of the insolubility of cleav-
age reagent 27 in methanol. Once the cleavage is complete, ltration of the reac-
tion mixture separates the REM resin from the tertiary amine and the soluble re-
agent 27. Concentration of the ltrate followed by trituration with cold MeOH
results in precipitation of 27. Filtration of the resulting slurry eectively separates
the noncrosslinked polystyrene reagent and evaporation of the ltrate leaves be-
hind the tertiary amine in good yields and high purity. However, a large amount of
MeOH might be required to triturate the soluble reagent 27, which could render
the synthesis of large libraries cumbersome.
Alternatively, Brown has reported a vapor-phase elimination approach as a rapid
method for the cleavage of tertiary amines from REM resins 2 and 12 in Irori
MacroKans TM [16]. The MacroKans TM were placed in a glass peptide vessel, which
was then sealed under a slight positive pressure of ammonia gas. Products were
isolated cleanly in good yields after evaporation, resin sorting, and washing with
CH3 CN or dimethylsulfoxide (DMSO). This is a particularly suitable method of
parallel processing for the synthesis of large libraries, thus minimizing or elimi-
nating the impurities due to the cleavage reagent.
10.2.2
b-Elimination on Selenyl Resins
The oxidation of selenides to selenoxides and their thermal elimination to alkenes

has been studied extensively and has found numerous applications in synthesis
[17]. The chemistry was rst adapted to solid phase in 1976 when Heitz and co-
workers prepared a polymer-supported selenide and oxidatively eliminated it to re-
lease an a; b-unsaturated ketone [18]. However, its application in solid-phase syn-
thesis as a cleavage method was realized with the advent of the polymer-bound
selenium reagents used in cyclization reactions to construct resin-bound carbo-
cyclic scaolds [19]. Recently, Nicolaou et al. utilized it in a strategy to generate
a 10,000-compound benzopyran library by a solid-phase split-and-pool technique
using Iroris NanoKan TM technology [20].
This novel strategy involves immobilization of an o-prenylated phenol (28)
through cycloloading with a polystyrene-based selenyl bromide resin [21] to give
resin-bound benzopyran scaold 29 via a precedented 6-endo-trig cyclization
(Scheme 10.8) [22]. Further elaboration of 29 to 30 and subsequent cleavage from
solid support via oxidation and spontaneous syn-elimination of the selenoxide
tether provides benzopyran 31. This is an example of a traceless release from solid
support where functionality is generated at the released molecule instead of any
linker residue being incorporated at the cleavage site.
Scheme 10.8. Release of benzopyrans via a resin-bound selenoxide elimination.

Indeed, the newly formed double bond can serve as a starting point for the gen-
eration of secondary libraries or more focused libraries, thus introducing addi-
tional elements of diversity. For example, epoxidation of the released benzopyran
31 followed by ring opening of the intermediate epoxide 32 with a variety of nu-
cleophiles provides access to a new series of benzopyran derivatives with the gen-
eral structure 33. Additionally, benzopyrans with the general structure 34 can
result from further elaboration of the secondary hydroxyl group of 33 with a series
of electrophiles [20c]. Taking into consideration the current advances in asymmet-
ric epoxidation of olenic substrates, this sequence could provide entry to chiral
benzopyran libraries starting from chiral benzopyran epoxides [23].
The loading to the selenium solid support is compatible with a great variety of
prenylated phenols except for substrates with electron-withdrawing groups adja-
cent to the prenyl group or adjacent to the phenol hydroxyl group participating in
the cyclization step. Therefore, these scaolds have to be loaded with the electron-
withdrawing groups masked. The elimination of the selenoxide resin tether pro-
ceeds smoothly at room temperature and seems to be independent of the substi-
tution pattern of the benzopyran scaold.
A similar resin-bound selenoxide elimination on 2-seleno carbohydrates (35)
was utilized by Nicolaou et al. in the synthesis of a small library of carbohydrate
orthoesters representing novel regions of the potent antibiotic everninomicin
(Scheme 10.9) [24]. Oxidation of glycoside 35 with meta-chloroperbenzoic acid (m-
CPBA) gave the corresponding resin-bound selenoxide, which underwent a ther-
mal syn-elimination. This thermal selenoxide elimination to the intermediate ke-
tene acetal 36 introduces the desired functionality for the formation of orthoesters
37 and 38 and can release the desired products in a traceless manner from solid
support. Orthoester 37 is formed from glycoside 35a and 2,3-allyl orthoester 38 is
formed from deprotected glycoside 35b. However, unlike the solution-phase selen-
oxides, it was observed that the resin-bound selenoxide was more prone to elimi-
nate at room temperature and therefore necessitated the use of lower temperatures
in the oxidation step. Thus, treatment of selenide 35 with m-CPBA in CH2 Cl2 at
78 C, followed by rapid ltration and transfer to a sealed tube, was found to give
the best results. Although the chemistry has been developed in both solution- and
solid-phase chemistry, it is well suited to the solid-phase synthesis of novel semi-
synthetic everninomicins and other carbohydrate libraries.
Scheme 10.9. Carbohydrate orthoesters via a resin-bound selenoxide elimination.

10.2.3
b-Elimination on Sulfone Resins
Sulfone elimination has the potential to be a preferred strategy for solid-phase

compound cleavage. While no linker and cleavage strategy can be stable to the full
range of conditions available to the synthetic chemist, the oxidative activation
elimination strategy promises to increase substantially the variety of options.
Schwyzer et al. rst described a 2-(4-carboxyphenylsulfonyl)ethanol linker for
the synthesis of peptides and oligonucleotides [25]. However, the application and
utility of a sulfone-type linker in peptide synthesis was demonstrated in 1992 by
Katti et al. with the introduction of a new and readily available linker in the solid-
phase synthesis of C-terminal peptides (Scheme 10.10) [26]. For example, Leu-
enkephalin (40) was released from resin 39 in 54% or 60% overall yields, using
either Boc or Fmoc chemistries respectively, after cleavage from the solid support
with dioxane/MeOH/4 N NaOH followed by re-acidication.
Scheme 10.10. Release of C-terminal peptides via a b-elimination from a sulfone resin.
Apart from being used successfully in the area of peptide chemistry, sulfone
linkers have gained favor in the solid-phase synthesis of small molecules. For
example, 4-aminobenzenesulfonamides with the general structure 44 were pre-
pared from 2-mercaptoethanol resin 42 (Scheme 10.11) [27]. Resin 42 was con-
verted to sulfone 43, which underwent a facile b-elimination to release the desired
Scheme 10.11. Release of arylsulfonamides via a b-elimination from a sulfone resin.

4-aminobenzenesulfonamides, in good yields and purities, upon treatment with

aqueous NH4 OH.
A small library of seven dehydroalanine derivatives has been prepared by a b-
elimination of a sulnate resin (Scheme 10.12). Anchoring of cysteine onto Merri-
eld resin through the side-chain thiol group gave a resin-bound sulde (46).
Modication of both C- and N-termini and oxidation of the sulde with m-CPBA
followed by a b-elimination of the sulnate resin 48 furnished the dehydroalanine
derivatives 47 in 3186% yields with high purities after aqueous work-up [28].
Scheme 10.12. Dehydroalanine derivatives via a sulfone elimination.
Elimination of a sulnate resin has also been utilized in heterocyclization chem-

istry for the synthesis of a few 2-substituted-4-piperidone derivatives (50) from
resin-bound sulfone 49, which serves as a divinyl ketone synthon (Scheme 10.13).
The amine reagent can act both as a nucleophile and as a base, thus promoting a
Michael addition to resin 49 and inducing elimination of the sulnate resin fol-
lowed by a second Michael addition to the newly formed enone [29].
Scheme 10.13. 2-Substituted-4-piperidones via a sulfone elimination.
10.2.4
b-Elimination on Silyl Resins
b-Elimination was utilized in the cleavage of several silyl amide linkers (SAL) and
trimethylsilylethyl ester linkers for the facile release of peptide fragments from the
solid support (Scheme 10.14). Stabilization of a carbocation by a b-trialkylsilyl
group, as shown in intermediate 52, seems to facilitate the release of C-terminal
Scheme 10.14. Release of peptides via a b-silyl elimination on silyl amide linkers.
amides (53) from silyl resin 51 [30]. b-Elimination of the trialkylsilyl group neu-
tralizes the transient carbocation to give a stable styrene derivative (54). These silyl
amide linkers gave improved yields of C-terminal tryptophan amides over conven-
tional linkers since an irreversible alkylation of the tryptophan indole nucleus
by such carbocations is suppressed. However, acid scavengers (1,2-ethanedithiol/
phenol/thioanisole, 5:3:2) were needed as the styrene moiety is sensitive to proto-
nation. Therefore, purication of the nal product is required in order to remove
the scavenger byproducts.
Similarly, linker 55 was designed to be cleaved by a b-elimination mechanism
based on the 2-(trimethylsilyl)ethylester protecting group (Scheme 10.15) [31].
Fluoridolysis or dilute acid cleavage enabled the preparation of protected peptide
fragments such as 56. C-Terminal tryptophans or prolines could be successfully
anchored with this linker and no undesired alkylation or diketopiperazine forma-
tion was observed upon cleavage.
Scheme 10.15. Release of peptides via b-silyl elimination on 2-(trimethylsilyl)ethyl ester linkers.
A b-elimination mechanism is also involved in the release of olens 60 from

resin-bound allyl silanes such as 59, the product of a solid-phase cross-olen
metathesis between allylsilane 58 and an olen (Scheme 10.16) [32].
Scheme 10.16. Release of olens from an allyl silane resin via a b-silyl elimination.
10.2.5
b-Elimination on Fluorenyl Resins
b-Elimination was also implemented in the cleavage of several uorene-based

linkers for the facile release of peptide fragments from solid support (Scheme
10.17) [33]. Quantitative cleavage of the Merrield peptide 62 and peptide 63,
which corresponds to the sequence 3138 of uteroglobin, was achieved from the
uorene resin 61 in good yields and high purities with 20% morpholine in DMF
or 10% piperidine in DMF. Resin 61 proved to be superior to other uorene-
derived resins where incomplete removal of the protected peptide from the resin
has been described [33b]. Also, slight lability to N,N-diisopropylethylamine, which
was used at the neutralization step after Boc deprotection in peptide synthesis, and
basic amino groups of the growing peptide has been detected occasionally in other
uorene-derived resins [33c]. The uorene nucleus in resin 61 has been con-
veniently substituted with an electron-donating N-amide group to ne-tune its base
lability in order to prevent any premature cleavage of the growing peptide chain.
Scheme 10.17. Release of C-terminal peptides via a b-elimination from a uorenyl resin.
10.2.6
b-Elimination on 2-(2-Nitrophenyl)ethyl Resins
b-Elimination was also utilized with 2-(2-nitrophenyl)ethyl (NPE) linkers. Release

of 3 0 -hydroxy-and 3 0 -phosphateoligonucleotides 66 and 67 from CPG (controlled
pore glass) support was achieved through carbonate and phosphate linkers 64 and
65 respectively (Scheme 10.18) [34]. The conditions used were either 0.5 M 1,8-
diazabicyclo[5.4.0]undecene-7 (DBU) in dioxane, pyridine for 1 h, and ammonia
for 5 h at 55 C or 20% piperidine in DMF for 3 h. The linkage was found to be
resistant to 40% Et3 N in pyridine for 16 h, conditions commonly used to remove
the 2-cyanoethylphosphate protecting group. An important application of 2-(2-
nitrophenyl)ethyl linkages is that these supports can be used together with p-
nitrophenylethyl-protected nucleoside 2-cyanoethylphosphoramidites for the prep-

aration of oligonucleotides without using ammonia during the nal deblocking,
because all protecting groups will be cleaved by DBU. This strategy will be of in-
terest for the preparation of oligonucleotides containing ammonia-sensitive com-
pounds such as base analogs, uorescent compounds, and so on.
Scheme 10.18. Release of oligonucleotides via a b-elimination.
10.2.7
Radical-based b-Eliminations
10.2.7.1 b-C,O Bond Scission

Peukert and Giese devised the original photolabile linker (68) based on the radical-
induced b-C,O bond scission of a 2-pivaloylglycerol group for the release of immo-
bilized acids (Scheme 10.19) [35]. Upon irradiation, an a-hydroxyalkyl radical in-
termediate (69) is generated via a Norrish type I reaction with release of carbon
monoxide and a t-butylradical that leads to isobutene. Elimination then takes place
where the glycerol radical is converted into an enolate radical (70) and a carboxylic
acid (71) is released. The reaction is not solvent dependent but selection of the ir-
radiation wavelength is crucial. The pivaloyl linker 68 was found to cleave aromatic
Scheme 10.19. Release of carboxylic acidspeptides by a radical b-C,O scission.

carboxylic acids and peptides with high yields (6593%) and purities in various
solvents such as THF, CH2 Cl2 , dioxane, and DMSO by irradiation with light above
320 nm. The photo byproducts are either volatile (CO and isobutene/isobutane) or
inert resin-bound acetone. The linker proved to be stable upon treatment with
acids and bases and to be compatible with many reagents and reaction conditions,
such as palladium-catalyzed cross-coupling and epoxidation, with broad applicabil-
ity in combinatorial chemistry.
10.2.7.2 b-C,Se Bond Scission-Release of Olens

Release of olens from solid support can also be achieved under mild reductive
conditions. Olens can be loaded onto polymer support by treatment with the
polymer-bound selenium bromide resin and released reductively under the inu-
ence of Bu3 SnH-AIBN (cat). A radical b-elimination is responsible for producing
the release. For example, once olen 72 is loaded onto solid support as the resin-
bound bromoselenide (73), reductive debromination of 73 followed by a homolytic
cleavage of the CaSe bond and subsequent elimination of resin-bound selenol (74)
will regenerate the starting olen (72) (Scheme 10.20) [21]. However, purication
would be required to isolate the released olen from tin byproducts. Alternatively,
Curran and coworkers uorous hydrides in uorinated solvents could be utilized
as well in order to isolate the released olen in pure form from tin byproducts
through a liquidliquid extraction [36]. In addition, Barton et al.s buered N-
ethylpiperidine hypophosphite reagent in conjuction with Et3 B as the radical initi-
ator instead of AIBN could provide a viable alternative for this reductive release
[37]. Although this radical-based release strategy has not been implemented for li-
brary synthesis, it is well suited to the solid-phase synthesis of small molecules.
Scheme 10.20. Release of olens by a radical b-C,Se scission.
10.3
Conjugate Eliminations
10.3.1
1,6-Conjugate Eliminations
Conjugate eliminations were also envisioned as a release strategy of the desired

products from solid support, thus leading to the development of new linkers.
Waldmann and coworkers developed an enzyme-labile 4-acyloxybenzyloxy linker

system (75), which was hydrolyzed with lipase RB 00105 on TentaGel resin
(Scheme 10.21) [38]. The linker is attached through a carboxyl group as an amide
to the solid support. The resulting resin contains an acyl group, such as acetate,
which can be cleaved by lipases or esterases. A phenolate is thus generated
which fragments to give a quinone methide (76) and releases compound 77, the
desired product. The quinone methide remains bound to the solid support and is
quenched by water or an additional nucleophile.
Scheme 10.21. Enzymatic release based on a conjugate 1,6-elimination.
In this way, amines (bound as urethanes), alcohols (bound as carbonates), and

carboxylic acids (bound as esters) can be detached from the polymeric carrier
under very mild conditions (pH 57, room temperature (rt)) and with complete
selectivity. The substrate specicity of the enzyme guarantees that only the in-
tended ester is cleaved, and the mild conditions of the biocatalyzed transforma-
tions ensure that the compounds constructed on the solid support remain intact
during cleavage. The applicability of the enzyme-labile group to multistep synthe-
sis on solid support was proven by the synthesis of tetrahydro-b-carboline car-
boxylic acids (79) by means of the PictetSpengler reaction and their subsequent
enzyme-mediated release from resin 78.
A similar 1,6-conjugate elimination mechanism is also involved in the release
of carboxylic acids, peptides, amines, and alcohols in good yields by the uoride-
induced cleavage of several labile silyl linkers, such as 8082 (Scheme 10.22) [39].
Apart from the desired carboxylic acid, linker 82 also releases a quinone methide,
which is scavenged by thiophenol. Consequently, the nal products have to be pu-
ried to remove the thiophenol byproduct.
Scheme 10.22. Fluoride-induced release based on a conjugate elimination.
10.3.2
1,4-Conjugate Eliminations
A conjugate 1,4-elimination of a phenylsulnate anion yielding functionalized 3-

arylbenzofurans in a traceless manner was observed in a novel cyclofragmentation
pathway involving epoxides (85) (Scheme 10.23) [40]. Sulfone anion 85a undergoes
a 5-exo-trig cyclization to alkoxide 85b, which next collapses to benzofuran 86 by a
concomitant expulsion of both formaldehyde and a phenylsulnate anion. This
cyclofragmentation-release pathway has been developed in both solution and solid
phase. It is well suited to solid-phase synthesis and can lead to the generation of a
diverse family of 3-arylbenzofurans starting from commercially available or pro-
prietary 2-hydroxybenzophenones.
Scheme 10.23. 3-Arylbenzofurans by a 1,4-conjugate cyclofragmentation-release assay.
Greater structural diversity can be introduced by starting from a series of 2-

hydroxybenzophenones (84) or made directly from the addition of arylmagnesium
bromides to resin-bound salicaldehydes (83), followed by an oxidation of the inter-
mediate carbinol. All cleavage products are remarkably clean since the mechanism
only allows for the release of products generated through intermediate 85. The
limitation of this novel fragmentation pathway lies in the necessity for epoxides
derived from 2-hydroxybenzophenones, since both aryl groups are required for the
regioselective epoxide opening.
10.4
AdditionElimination Reactions
Additionelimination reactions in which a CaC or CaX bond (X heteroatom) is

formed by the combination of two or more reactive centers, in an intra- or inter-
molecular fashion, followed by an elimination or extrusion of a small molecule can
be useful in combinatorial chemistry for the convergent synthesis of diverse li-
braries. The structural diversity, which originates directly from the starting mate-
rials or building blocks, is retained through the library synthesis. If a polymer
support is directly linked to the eliminated molecule, then a traceless release of the
desired compounds from solid support can be achieved. Although there are several
mechanistically dierent additionelimination transformations, here we will iden-
tify those utilized in the synthesis of libraries where the additionelimination step
is the nal process that completes the synthesis of the desired scaold.
10.4.1
AdditionElimination on Vinylogous Systems
10.4.1.1 Entry to Aminomethyleneoxazolones

Aminomethyleneoxazolones are recognized as a class of serine protease inhibitors,
and therefore have been the focus of library synthesis [41]. The synthesis involves
the addition of a primary or secondary amine to an ethoxymethyleneoxazolone
(EMO) (87) followed by elimination of a molecule of ethanol (Scheme 10.24). The
convergent nature of this scheme greatly facilitates its execution starting from
either commercially available or proprietary amines and ethoxymethyleneox-
azolones. Baldino et al. reported the automated parallel synthesis of 1600 amino-
Scheme 10.24. Solution-phase synthesis of aminomethyleneoxazolones.

10.4 Addition--Elimination Reactions 297
methyleneoxazolones (89) starting from 20 EMOs and 80 secondary amino a-

ketoamide intermediates (88), prepared in situ from ten a-ketoesters and eight
diamines under equimolar reagent combinations [42].
The chemistry works well in a wide range of solvents such as CH3 CN, DMF,
THF, and dioxane. Ultimately, the choice of the appropriate solvent depends
mainly on the solubility of the starting oxazolones. The corresponding products
were isolated as E,Z isomers, in good yields and high purities, after evaporation of
the solvent. Although there are no examples illustrating the solid-phase imple-
mentation of this chemistry, it could be amenable to solid phase as well (i.e. via a
resin-bound EMO). However, mild cleavage conditions would be required, since
strong acidic or basic conditions might disrupt the oxazolone ring system.
10.4.1.2 Entry to Benzopyrones

Substituted benzopyrones encompass an important class of molecules that possess
a wide range of interesting biological activities [43, 44]. Although there are nu-
merous literature methods for the synthesis of the benzopyrone ring system, they
are not ideally suited for combinatorial approaches owing to harsh reaction con-
ditions, poor yields, and limited substituent tolerance. A method that is amenable
to solution-phase parallel synthesis was developed by Brueggemeier and coworkers
for the preparation of a seven-member benzopyrone library (Scheme 10.25) [44].
This sequence utilizes chlorination of a bis-silylated salicylic acid (90) with oxalyl
chloride to generate the corresponding acid chloride (91) followed by a Sonoga-
shira coupling with a terminal alkyne to give cleanly alkynone 92. Treatment of al-
kynone 92 with a secondary amine such as diethylamine in reuxing ethanol pro-
vides an intermediate enaminone (94a) which undergoes a disilylation and an
intramolecular Michael addition followed by elimination of volatile diethylamine to
give the benzopyrone 95. Removal of silyl impurities along with the palladium and
copper catalysts and any triphenylphosphine requires purication.
Scheme 10.25. Entry to benzopyrones via an additionelimination sequence.
The problems identied above were circumvented by a resin capture strategy.

Indeed, capturing alkynone 92 with a vefold excess of piperazinyl Merrield resin
(93) (loading 0.7 mmol g1 ) eliminates the need for any further purication [45].
Thus, the resin-bound enaminone 94b could be easily separated from the excess
reagents and byproducts of the reaction mixture by a simple ltration. On-resin
cyclization of the enaminone 94b released the benzopyrone 95 in good yields and
good purities and regenerated the piperazinyl resin. This resin capture would fa-
cilitate a one-pot conversion of silylated salicylic acids to benzopyrones without re-
quiring any intermediate purication steps an attractive feature for the synthesis
of large libraries. Furthermore, this method can be applied to the synthesis of
benzopyrones with no residual functionalities required for linkage to the solid
support. The solid-supported capture reagent can be regenerated and recycled for
additional rounds of resin capture.
10.4.1.3 2,3-Dihydro-4-pyridone Libraries

The reaction of Danishefskys diene with imines leading to 2,3-dihydro-4-
pyridones has been studied extensively by the chemistry community and has nu-
merous applications in the synthesis of piperidine alkaloids [46]. The reaction is
postulated to proceed via a Mannich reaction followed by an intramolecular Mi-
chael reaction with a subsequent elimination of a molecule of methanol [46ac].
The large number of readily available aromatic aldehydes and amines prompted
chemists to adapt this reaction to both solid- and solution-phase automated syn-
thesis of large libraries of 2,3-dihydro-4-pyridones. Application of this chemistry to
solution-phase parallel synthesis was demonstrated recently by Yu et al. in the
construction of a 4320-member library (Scheme 10.26) [47a]. Condensation of
benzaldehydes with anilines in the presence of a Yb resin [48] gave the intermedi-
ate imine, which upon immediate treatment with Danishefskys diene gave the
corresponding dihydropyridones (96) in good yields and purities after ltration of
the resin-bound catalyst.
Scheme 10.26. Solution-phase synthesis of a 2,3-dihydro-4-pyridone library.
Adaptation of this chemistry to solid phase was demonstrated by Wang and

Wilson starting from Wang resin-bound benzaldehyde and anilines or aliphatic
amines [47b]. Several dierent Lewis acids were found to be compatible with
the reaction conditions, including ZnCl2 , AlCl3 , Et2 AlCl, TiCl 4 , BF3 Et2 O, and
Yb(OTf )3 . However, the water-tolerant Yb(OTf )3 gave the highest yield. The nal
products were obtained after cleavage with triuoroacetic acid (TFA)/CH2 Cl2 (1:1)
in relatively high yields and purities.
10.4.2
Cycloreversions
10.4.2.1 Pyrrole Libraries

A cycloreversion reaction with loss of CO2 is involved in the pyrrole synthesis via
a 1,3-dipolar cycloaddition of alkynes to munchnones. Mjalli and coworkers and
Armstrong and coworkers reported independently the solid-phase synthesis of
pyrroles where the munchnone precursors N-acyl-N-alkyl-a-amino amides
were generated in a single step via an Ugi four-component condensation (U-4CC)
instead of relying upon individual acylated amino acids (Scheme 10.27) [49].
Treatment of the N-acyl-N-alkyl-a-amino acid 97a with Ac2 O or treatment of Arm-
strongs cyclohexenamide precursor 97b with HCl in the presence of an acetylenic
dipolarophile resulted in the bicyclo intermediates 98a and 98b, which rapidly
aromatized to pyrroles 99a and 99b, respectively, with loss of CO2 .
Scheme 10.27. Entry to pyrroles via a dipolar cycloadditioncycloreversion pathway.
Pyrroles 99a were isolated in 40% overall yield with high purities, according to
Mjalli and coworkers protocol, after release from solid support. Armstrong and
coworkers four-step protocol, although not optimized, gave pyrroles 99b with 4
17% yields. Although this chemistry is amenable to solution-phase synthesis, low
yields of the tetra-substituted pyrroles are usually observed [50]. This may be at-
tributed to the substitution pattern of the acetylenic dipolarophile and to the ten-
dency of munchnones to self-condense. Furthermore, it would require the use of
the corresponding N-acyl-N-alkyl-a-amino acids as building blocks in order to in-
crease the purity of the nal products.
10.4.2.2 Imidazole Libraries

Application of the same cycloadditioncycloreversion strategy described above
resulted in the solid-phase synthesis of a 12-member library of 2,4,5-
triarylimidazoles by employing an aryltosylimine as the dipolarophile (Scheme
10.28) [51]. Treatment of the resin-bound acid 100 with N 0 -(3-dimethylamino-
propyl)-N-ethylene carbodiimide (EDC) in CH2 Cl2 at ambient temperature for 24
48 h followed by a cycloaddition of the intermediate munchnone 101 with a tosyli-
mine gave bicyclo compound 102. Cycloreversion of 102 with elimination of tolue-
nesulnic acid and CO2 provided the polymer-linked imidazole 103, which was
next washed with TFA, without any observed cleavage, to remove any unreacted
starting materials. Release from resin upon treatment with AcOH at 100 C gave
the free imidazole 104. All reagent combinations provided the desired products in
good yields and high purities with a 73% average yield over the six-step sequence.
However, low yields of imidazoles were observed when this chemistry was carried
out in solution phase [52b]. This is at least partly the result of the potential for
munchnones to self-condense, which can be suppressed in a solid-phase approach
[52].
Scheme 10.28. Entry to imidazoles via a dipolar cycloadditioncycloreversion pathway.
10.4.2.3 Traceless Solid-phase Synthesis of Furans

Isomunchnones readily undergo a [3 2] cycloaddition with acetylenes to give bi-
cyclo intermediates, which can lead to furans after a cycloreversion and elimina-
tion of isocyanate [53]. This strategy was applied to the solid-phase synthesis of
furan libraries independently by Gowravaram and Gallop and by Austin and co-
workers (Scheme 10.29) [54]. a-Diazocarbonyl 107 can react with Rh(II) catalysts
to form a highly reactive rhodium carbenoid that collapses to a mesoionic dipole
intermediate the isomunchnone 108 which in the presence of an acetylenic
dipolarophile can lead to a bicyclo intermediate (109). Cycloreversion of 109 and
extrusion of the resin-bound isocyanate liberates the tetrasubstituted furan 110
into solution, in good yields and high purities, and leaves no obvious remnant of
polymer tethering in the desired product.
Scheme 10.29. Tetrasubstituted furans via a cycloadditioncycloreversion pathway.
The cleavage rate from solid support, at similar temperatures, is highest in polar
protic solvents, which could allow for the cleavage to be carried out directly in
aqueous media. The chemistry could be amenable to solution-phase parallel syn-
thesis since furans were recovered in good yields but would require a special work-
up or purication to remove the rhodium catalyst. The released isocyanate could
be eectively scavenged with a resin-bound amine.
10.4.2.4 1,2-Diazines
Access to a small library of functionalized 1,2-diazines can be provided by the in-
verse electron demand DielsAlder reactions of 3,6-substituted-1,2,4,5-tetrazines
on solid phase (Scheme 10.30) [55a]. Treatment of an immobilized azadiene (111)
with a variety of electron-rich olens in dioxane at room or elevated temperatures
gave bicyclo intermediate 112, which underwent a cycloreversion with loss of N2
and concomitant loss of HX to give resin-bound diazine 113. Removal of the Boc
group rst, followed by cleavage from solid support under basic conditions, gave
the corresponding 3-amino-6-thiomethyl-1,2-pyridazines (114) in good to moderate
yields. The chemistry can be extended with the azadienes bearing a sulfone group
in the 6-position. The sulfone substrate is more reactive than the corresponding
thiomethyl substrate in a DielsAlder reaction as more ecient conversion is
generally achieved with the less reactive alkynes. A wide range of electron-rich di-
enophiles can be used which permits the introduction of two diversity elements on
Scheme 10.30. Entry to diazines via a [4 2] cycloadditioncycloreversion pathway.

heteroaromatic scaolds. Subsequent nucleophilic aromatic substitution of the C-6

methylsulde/sulfone and acylation/alkylation of the C-3 amine will introduce the
third and fourth diversity elements. This chemistry could be amenable to solution
phase although library purication might be required for the less reactive ena-
mines or enol ethers derived from acetophenones [55b].
10.5
Summary
b-Elimination has been successfully used in solid-phase synthesis as a release

strategy of the desired products from solid support. However, it has not been
broadly applied in the synthesis of diverse libraries as the nal step that de-
termines the synthesis of the desired scaold. This is presumably because of the
lack of convergence in the synthesis and diversity of the nal products. On the
contrary, additionelimination reactions, apart from also being used as a release
method of the nal products from solid support, can be utilized in the convergent
synthesis of diverse libraries. However, b-elimination could be very well utilized in
the synthesis of functionalized intermediates where the generated functionality
(i.e. double bond) could serve as a handle for the introduction of additional di-
versity elements. Although elimination reactions can be very useful to the high-
throughput synthesis of small molecules by either solid- or solution-phase parallel
synthesis, their potential has not been fully realized yet.
References
1 J. March in: Advanced Organic 6 J. R. Morphy, Z. Rankovic, D. C. Rees,

Chemistry, 4th edn, Wiley-Interscience, Tetrahedron Lett. 1996, 37, 32093212.
New York 1992, pp. 9821050. 7 A. R. Brown, D. C. Rees, Z.
2 a) G. I. Tesser, J. T. W. A. R. M. Buis, Rankovic, J. R. Morphy, J. Am.
E. T. M. Wolters, E. G. A. M. Bothe- Chem. Soc. 1997, 119, 32883295.
Helmes, Tetrahedron 1976, 32, 1069 8 J. Cottney, Z. Rankovic, J. R.
1072; b) G. I. Tesser, B. W. J. Morphy, Bioorg. Med. Chem. Lett.
Ellenbroek in: Eighth European 1999, 9, 13231328.
Peptide Symposium. Beyerman, H. 9 For synthesis of tertiary amines via
C., Linde, A. v. d., Brink, W. M. v. d. vinyl sulfone REM resins, see: a) F. E.
(eds), Amsterdam 1967. K. Kroll, R. Morphy, D. Rees, D.
3 For a review on linkers, see: a) F. Gani, Tetrahedron Lett. 1997, 38,
Guillier, D. Orain, M. Bradley, 85738576; b) P. Heinonen, H.
Chem. Rev. 2000, 100, 20912157; b) I. Lonnberg, Tetrahedron Lett. 1997, 38,
W. James, Tetrahedron 1999, 55, 4855 85698572.
4946. 10 M. J. Plater, A. M. Murdoch, J. R.
4 A. W. Hofmann, Annalen 1851, 78, Morphy, Z. Rankovic, D. C. Rees, J.
253286. Comb. Chem. 2000, 2, 508512.
5 C. Blettner, M. Bradley, Tetrahedron 11 W. S. Wade, F. Yang, T. J. Sowin, J.
Lett. 1994, 35, 467470. Comb. Chem. 2000, 2, 266275.
References 303
12 a) P. Blaney, R. Grigg, Z. Rankovic, Nicolaou, Z. Lysenko, J. Am. Chem.

M. Thoroughgood, Tetrahedron Lett. Soc. 1977, 99, 31853187.
2000, 41, 66356638; b) M. Gustafs- 23 For asymmetric epoxidation of
son, R. Olsson, C.-M. Andersson, benzopyran systems with a polymer-
Tetrahedron Lett. 2001, 42, 133136. bound chiral salen manganese (III)
13 X. Ouyang, R. W. Armstrong, M. M. complex, see: C. E. Song, E. J. Roh,
Murphy, J. Org. Chem. 1998, 63, B. M. Yu, D. Y. Hi, S. C. Kim, K.-J.
10271032. Lee, Chem. Commun. 2000, 615616.
14 Y. Yamamoto, K. Tanabe, T. 24 K. C. Nicolaou, H. J. Mitchell, K. C.
Okonogi, Chem. Lett. 1999, 103104. Fylaktakidou, H. Suzuki, R. M.
15 P. H. Toy, T. S. Reger, K. D. Janda, Rodrguez, Angew. Chem. Int. Ed.
Org. Lett. 2000, 2, 22052207. 2000, 39, 10891093.
16 A. R. Brown, J. Comb. Chem. 1999, 1, 25 R. Schwyzer, E. Felder, P. Faili,
283285. Helv. Chim. Acta 1984, 67, 1316
17 Y. Nishibayashi, S. Uemura in: 1326.
Topics in Current Chemistry. Wirth, 26 S. B. Katti, P. K. Misra, W. Haq, K.
T. (ed.), Springer Verlag, Berlin 2000, B. Mathur, J. Chem. Soc., Chem.
vol. 208, pp. 201214. Commun. 1992, 843844.
18 R. Michels, M. Kato, W. Heitz, 27 C. G. Echeverra, Tetrahedron Lett.
Makromol. Chem. 1976, 177, 2311 1997, 38, 89338934.
2320. 28 M. Yamada, T. Miyajima, H.
19 For cyclizations mediated by resin- Horikawa, Tetrahedron Lett. 1998, 39,
bound selenium reagents, see: a) K. 289292.
Fujita, K. Watanabe, A. Oishi, Y. 29 A. Barco, S. Benetti, C. De Risi, P.
Ikeda, Y. Taguchi, Synlett 1999, Marchetti, G. P. Pollini, V.
17601762; b) K. C. Nicolaou, J. A. Zanirato, Tetrahedron Lett. 1998, 39,
Pfefferkorn, G.-Q. Cao, S. Kim, 75917594.
J. Kessabi, Org. Lett. 1999, 1, 807 30 H.-G. Chao, M. S. Bernatowicz, G.
810. R. Matsueda, J. Org. Chem. 1993, 58,
20 a) K. C. Nicolaou, J. A. Pfeffer- 26402644.
korn, A. J. Roecker, G.-Q. Cao, S. 31 H.-G. Chao, M. S. Bernatowicz,
Barluenga, H. J. Mitchell, J. Am. P. D. Reiss, C. E. Klimas, G. R.
Chem. Soc. 2000, 122, 99399953; b) Matsueda, J. Am. Chem. Soc. 1994,
K. C. Nicolaou, J. A. Pfefferkorn, 116, 17461752.
H. J. Mitchell, A. J. Roecker, S. 32 M. Schuster, N. Lucas, S. Blechert,
Barluenga, G.-Q. Cao, R. L. Affleck, Chem. Commun. 1997, 823824.
J. E. Lillig, J. Am. Chem. Soc. 2000, 33 a) F. Rabanal, E. Giralt, F.
122, 99549967; c) K. C. Nicolaou, J. Albericio, Tetrahedron Lett. 1992, 33,
A. Pfefferkorn, S. Barluenga, H. J. 17751778; b) M. Mutter, D. Bellof,
Mitchell, A. J. Roecker, G.-Q. Cao, Helv. Chim. Acta 1984, 67, 20092016;
J. Am. Chem. Soc. 2000, 122, 9968 c) Y. Z. Liu, S. H. Ding, J. Y. Chu, A.
9976. M. Felix, Int. J. Pept. Prot. Res. 1990,
21 K. C. Nicolaou, J. Pastor, S. 35, 9598.
Barluenga, N. Winssinger, Chem. 34 a) R. Eritja, J. Robles, D.
Commun. 1998, 19471948. Fernandez-Forner, F. Albericio, E.
22 For a solution-phase precedent of Giralt, E. Pedroso, Tetrahedron Lett.
selenium-mediated 6-exo-trig 1991, 32, 15111514; b) F. Albericio,
cyclizations of ortho-prenylated E. Giralt, R. Eritja, Tetrahedron Lett.
phenols and related systems, see: a) D. 1991, 32, 15151518.
L. J. Clive, G. Chittattu, N. J. 35 S. Peukert, B. Giese, J. Org. Chem.
Curtis, W. A. Kiel, C. K. Wong, J. 1998, 63, 90459051.
Chem. Soc., Chem. Commun. 1977, 36 D. P. Curran, S. Hadida, S.-Y. Kim,
725727; b) P. B. Anzeveno, J. Org. Z. Luo, J. Am. Chem. Soc. 1999, 121,
Chem. 1979, 44, 25782580; c) K. C. 66076615.
37 D. H. R. Barton, D. O. Jang, J. Cs. e) S. Kobayashi, H. Ishitami, S.

Jaszberenyi, J. Org. Chem. 1993, 58, Nagayama, Synthesis 1995, 11951202.
68386842. 47 a) L. Yu, C. M. Baldino, M. S.
38 B. Sauerbrei, V. Jungmann, H. Harris, E. Marler, B. Carr, J.
Waldmann, Angew. Chem. Int. Ed. Troth, M. Kearny, J. Mills, J.
1998, 37, 11431146. Brochu, J. Gordon, D. L. Coffen,
39 a) R. Ramage, C. A. Barron, S. paper presented at the 217th ACS
Bielecki, D. W. Thomas, Tetrahedron National Meeting, Anaheim, March
Lett. 1987, 28, 41054108; b) A. 1999, Organic Division, abstract no.
Routledge, H. T. Stock, S. L. 335; b) Y. Wang, S. R. Wilson,
Flitsch, N. J. Turner, Tetrahedron Tetrahedron Lett. 1997, 38, 40214024.
Lett. 1997, 38, 82878290; c) D. G. 48 L. Yu, D. Chen, J. Li, P. G. Wang,
Mullen, G. Barany, J. Org. Chem. J. Org. Chem. 1997, 62, 35753581.
1988, 53, 52405248. 49 a) A. M. M. Mjalli, S. Sarshar, T. J.
40 K. C. Nicolaou, S. A. Snyder, A. Baiga, Tetrahedron Lett. 1996, 37,
Bigot, J. A. Pfefferkorn, Angew. 29432946; b) A. M. Strocker, T. A.
Chem. Int. Ed. 2000, 39, 10931096. Keating, P. A. Tempest, R. W.
41 N. L. Benoiton, F. Hudesz, F. M. F. Armstrong, Tetrahedron Lett. 1996,
Chen, Int. J. Pept. Prot. Res. 1995, 45, 37, 11491152.
266271. 50 T. A. Keating, R. W. Armstrong, J.
42 C. M. Baldino, D. S. Casebier, J. Am. Chem. Soc. 1996, 118, 25742583.
Caserta, G. Slobodkin, C. Tu, D. L. 51 M. T. Bilodeau, A. M. Cunningham,
Coffen, Synlett 1997, 488490. J. Org. Chem. 1998, 63, 28002801.
43 E. S. C. Wu, J. T. Loch, B. H. Toder, 52 a) K. T. Potts in: 1,3-Dipolar Cyclo-
A. R. Borrelli, D. Gawlak, L. A. addition Chemistry. Padwa, A. (ed.),
Radov, N. P. Gensmantel, J. Med. Wiley-Interscience, New York 1984,
Chem. 1992, 35, 35193525. vol. 2, pp. 182; b) R. Consonni,
44 A. S. Bhat, J. L. Whetstone, R. W. P. D. Croce, R. Ferraccioli, C. La
Brueggemeier, Tetrahedron Lett. 1999, Rosa, J. Chem. Res., Synop. 1991,
40, 24692472. 188189.
45 A. S. Bhat, J. L. Whetstone, R. W. 53 M. H. Osterhout, W. R. Nadler, A.
Brueggemeier, J. Comb. Chem. 2000, Padwa, Synthesis 1994, 123141.
2, 597599. 54 a) M. R. Gowravaram, M. A. Gallop,
46 a) H. Kunz, W. Pfrengle, Angew. Tetrahedron Lett. 1997, 38, 69736976;
Chem. Int. Ed. 1989, 28, 10671068; b) b) D. L. Whitehouse, K. H. Nelson,
H. Waldmann, M. Braun, M. Jr, S. N. Savinov, D. J. Austin,
Drager, Angew. Chem. Int. Ed. 1990, Tetrahedron Lett. 1997, 38, 71397142.
29, 14681471; c) H. Waldmann, M. 55 a) J. S. Panek, B. Zhu, Tetrahedron
Braun, J. Org. Chem. 1992, 57, 4444 Lett. 1996, 37, 81518154; b) S. M.
4451; d) H. Yamamoto, K. Hattori, Sakya, K. K. Groskopf, D. L. Boger,
Tetrahedron 1993, 49, 17491760; Tetrahedron Lett. 1997, 38, 38053808.
305
11
Addition to CC Multiple Bonds
(Except for CC Bond Formation)
Adrian L. Smith
11.1
Introduction
The last decade has witnessed the birth and maturation of combinatorial chemistry
as a technique for synthesizing large numbers of compounds. Much of the early
emphasis was on synthesizing large (mixtures) libraries for screening and lead
generation, and this was almost exclusively based upon solid-phase chemistry.
However, the technologies developed during this work were also applicable to the
more traditional medicinal chemistry lead optimization process, and this has led to
a rethink in the ways in which the medicinal chemist can most eciently optimize
a lead series, both in vitro and in vivo. Whilst this initially resulted in many people
developing solid-phase synthetic routes for the parallel synthesis of arrays of single
compounds (whether it be to make 10 or 10,000 compounds), the co-development
of postsynthesis sample-handling techniques (particularly in the area of purica-
tion) has signicantly broadened the scope of chemistries which can be used. In
particular, the initial advantages of solid-phase chemistry (primarily related to pu-
rication) are now less compelling in many cases where solution-phase chemistry
will require less chemistry development time and where crude synthetic products
can be puried in an automated fashion.
Today, the term combinatorial chemistry is loosely used to describe a very
broad range of techniques including solid- and solution-phase chemistry and the
synthesis of discrete (single) compound arrays and mixtures. Whilst the dierent
techniques each have their pros and cons, their unifying factor when properly
applied is the ability to address a particular problem (e.g. a medicinal chemistry
problem) by making and testing a larger and more diverse set of compounds than
would have been the case by more traditional methods. Therefore, although a large
number of publications have appeared in the area of solid-phase chemistry, the
purpose of this chapter is not to act as a comprehensive review of solid-phase
chemistry per se, but rather to highlight key areas in which chemists may prac-
tically utilize these techniques in chemical transformations involving overall
addition to carboncarbon multiple bonds. It should be noted that certain trans-
formations such as carboncarbon bond formation, heterocycle formation, cyclo-

ISBN: 3-527-30509-2
306 11 Addition to CC Multiple Bonds (Except for CC Bond Formation)
addition reactions, and transition metal-catalyzed formation of single bonds are

covered in other chapters and will not be duplicated here.
11.2
Addition to C=C Double Bonds
Additions to CbC double bonds fall into two broad main categories dependent
upon the electronic nature of the double bond. The main focus of this section will
deal with electrophilic addition to isolated double bonds, whilst nucleophilic 1,4-
addition to conjugated a; b-unsaturated systems will be briey touched upon at the
end.
The reactivity of the isolated CbC double bond arises from the nucleophilic na-
ture of the p-bond, with the majority of reactions involving some form of electro-
philic addition. This may result in formal oxidation (e.g. epoxidation) or reduction
(e.g. hydrogenation). It may be expected that more electron-rich double bonds will
generally exhibit greater reactivity than electron-decient double bonds in the ab-
sence of overriding steric factors. Whilst the CbC double bond is also frequently
encountered in radical reactions, this is usually implicated in CaC bond formation
and is outside the scope of this chapter. This section aims to summarize some of
the key transformations which can be eected by addition to the CbC double bond,
emphasizing applicability to combinatorial chemistry.
11.2.1
Epoxidation and Subsequent Epoxide Opening
The epoxidation of an olen represents one of the more versatile transformations

available to the aspiring combinatorial chemist, generating a reactive epoxide in-
termediate which can be opened by a range of nucleophiles (Scheme 11.1). In par-
ticular, opening with amines gives rise to the (hydroxyethyl)amine isostere (3),
which mimics the tetrahedral intermediate for amide hydrolysis [1], making this a
very powerful two-step transformation of an olen.
Scheme 11.1. Epoxidation and subsequent epoxide opening of an olen.
Epoxidation is most usually carried out with meta-chloroperbenzoic acid (m-

CPBA) in a solvent such as dichloromethane and, being a very ecient and mild
reaction in the absence of competing functionalities, generally gives clean and full
11.2 Addition to C=C Double Bonds 307
conversion with a minimal excess of reagent. As such, it is suitable for use in both
solid- and solution-phase chemistry. It should be noted that there is often little
diastereoselectivity with this reagent. Scheme 11.2 shows an example of an epox-
idation carried out on solid phase [2]. Here, the author experienced instability of
the urethane linker to the generated 3-chlorobenzoic acid byproduct and buered
the reaction with NaHCO3 . Another side-reaction sometimes observed is open-
ing of the epoxide by the generated 3-chlorobenzoic acid, and in these cases more
success may be possible with reagents such as dimethyldioxirane [3]. It is also
possible to use a range of solid-supported reagents for epoxidation (see Table 11.1)
[4].
Scheme 11.2. Epoxidation on solid phase.
The two-step processes shown in Scheme 11.1 are very well suited to solution-
phase parallel synthesis. Generally, the intermediate (2) is prepared in bulk, puri-
ed, and then split into individual reactors for parallel ring opening by a range of
nucleophiles. For reactions with amines to give 3, we nd a small excess of the
amine (typically 1.5 equiv.) in isopropyl alcohol heated at 65 C for 16 h usually
gives clean conversion, even with relatively non-nucleophilic amines such as ani-
line. It is important that no epoxide remains in nal products, since this can give
misleading data in biological assays by acting as a suicide inhibitor. It is there-
fore generally preferred to use the epoxide as the limiting reagent. For reactions
with secondary amines to give tertiary amine products, it may be possible to scav-
enge excess amine with an appropriate resin [9]. Alternatively, we nd automated
preparative high-performance liquid chromatography (HPLC) to be a convenient
method for purication.
Examples of larger solution-phase combinatorial mixtures libraries are known
utilizing a similar approach. A library of over 6000 b-amino alcohols was prepared
using LiClO4 in acetonitrile and 1.2 equiv. of amine [10]. In such cases, care is
needed to validate the reactivity of reagents properly in order to avoid misleading
bioassay data since purication is more dicult. A solid-phase mixtures library of
Tab. 11.1. Polymer-supported epoxidation reagents.
Reagents Reaction Yield Comments Ref.

Time
48 h 1397% TentaGel resin (2 5

equiv.). 5 equiv.
Oxone8. Generates
dioxirane resin in situ
Oxone8/NaHCO3/THF/H2 O
60 h 7090% 2 equiv. of dioxirane 6
resin used. Resin is
CHCl3 prepared by treatment
of polystyrene 2-
oxoalkyl resin with
Oxone8 and NaHCO3
in THF/H2 O and
isolated prior to use.
Shelf stability of
dioxirane resin not
reported
4h 80% AG 50W-X8 ion 7
exchange resin (Bio-
THF/D
Rad), converted to
persulfonic acid with
potassium persulfate
4h 5095% Resin prepared by 8
treatment of 1%
THF/40 C crosslinked
carboxypolystyrene
with 85% H2 O2 in
MeSO3 H for 16 h.
Peracid resin stable to
storage at 20 C.
THF is vastly superior
to CH2 Cl2 as solvent
5800 phenoxypropanolamines, prepared via a split-and-mix strategy, has also been

reported [11]. Here, a resin-bound epoxide was opened with excess amine in ace-
tonitrile at 80 C for 18 h.
Opening of epoxides on solid phase with alternative nucleophiles to amines is
illustrated in Scheme 11.3 [12]. In this example, which includes experimental pro-
cedures, azides (10) were prepared using buered sodium azide in dimethylform-
amide (DMF) at 100 C for 2 h, whilst thiols (11) were prepared by reaction with
sodium thiophenoxide in DMF at 0 C. In these systems, lactonization occurred
under the cleavage conditions.
Scheme 11.3. Epoxidation, epoxide opening, and lactonization during cleavage from resin.
An elegant and potentially very versatile extension to the utility of epoxides is

demonstrated in Scheme 11.4 [13]. Here, a range of olens (14) was converted in
a one-pot procedure to the immobilized a-sulfonated ketones (17) by epoxidation
with dimethyldioxirane, epoxide opening with a sulfonic acid resin, and subse-
quent oxidation with DessMartin periodinane. The activated sulfonyloxy moiety is
an excellent leaving group, and 20 ecient functionalizing cleavage options were
demonstrated for resin 17.
Scheme 11.4. One-pot epoxidation and conversion to a-sulfonated ketones.
11.2.2
Dihydroxylation
The dihydroxylation of an olen is most eciently carried out using osmium tetr-
oxide, giving rise to vicinal diols (Scheme 11.5) [14]. The catalytic variant of the
reaction is usually employed owing to the toxic and volatile nature of the reagent,
and the facile regeneration of the catalyst with oxidants such as N-methylmorpho-
line N-oxide (NMO), potassium ferricyanide, hydrogen peroxide, or tert-butyl hy-
droperoxide. Osmium(III) chloride is sometimes used as the osmium source in
the catalytic reaction, being less volatile than the tetroxide and therefore easier to
weigh out safely. It is converted in situ to the tetroxide by the oxidant. High levels
of enantioselectivity can be achieved in the reaction using catalytic amounts of os-
mium tetroxide in the presence of cinchona alkaloid derivatives [15].
Scheme 11.5. Dihydroxylation of an olen.
Osmium tetroxide is a very mild reagent and compatible with many functional
groups, making it suitable for combinatorial synthesis, at least in principle. There
have, however, been few reported uses in library synthesis. For solution-phase li-
brary synthesis, perhaps the most practical methods will involve the use of solid-
supported osmium tetroxide [4] since this will minimize handling problems for
the toxic osmium reagent, allowing recovery by simple ltration. One such exam-
ple is osmium tetroxide microencapsulated in polystyrene [16]. This work high-
lighted one potential practical problem associated with such reagents. The dihy-
droxylation is usually carried out in acetonewater or tert-butanolwater mixed
solvent systems. Not only does this raise the possibility of solubility issues for re-
actants, but also solvent/reactant access within the solid-supported reagent may be
restricted since polymers such as polystyrene are poorly solvated and not swelled
well by these solvents. In this work, acetonitrile was added as a cosolvent in order
to achieve good conversion. Good results have been obtained in the area of sup-
ported asymmetric dihydroxylations. The OsO4 copolymer of 20 [an analog of
(DHQ)2 -PHAL] behaves well under standard conditions [t-BuOH/H2 O (1:1) at 10

C using K3 Fe(CN)6 -K2 CO3 (3 equiv.) as secondary oxidant], giving high yields and
enantioselectivities (Scheme 11.6) [17]. The copolymer is easily recovered by ltra-
tion.
Scheme 11.6. Poly((QN)2 -PHAL-co-MMA) used in asymmetric dihydroxylation of olens.

An example of solid-phase parallel synthesis employing asymmetric dihydroxy-

lation is shown in Scheme 11.7 [18]. For this work, ArgoGel Wang resin was em-
ployed for the synthesis because of its compatibility with the solvent system, al-
lowing standard Sharpless asymmetric dihydroxylation reaction conditions to be
used which would have been less compatible with polystyrene Wang resin as dis-
cussed above. A second example demonstrating the use of osmylation in solid-
phase chemistry is shown in Scheme 11.8 [19]. Here, a polystyrene-based resin
was used and the solvent conditions were modied to tetrahydrofuran (THF)/H2 O
(5:1) in order to promote resin swelling.
Scheme 11.7. Synthesis of khellactone derivatives.
Scheme 11.8. Solid-phase dihydroxylation using T2 triazine linker.
11.2.3
Oxidative Cleavage
In situ oxidative cleavage of olens to carbonyl compounds can be eciently

achieved by inclusion of sodium periodate as the oxidant in the osmium tetroxide
dihydroxylation of olens (the LemieuxJohnson reagent) [20]. There have, how-
ever, been few if any reports on the use of this reagent combination in combinato-
rial synthesis, owing to either environmental/handling concerns or possible com-

patibility problems with resin systems.
More use has been made of ozonolysis (Scheme 11.9) [21], primarily for the
solid-phase synthesis of peptide aldehydes (Scheme 11.10) [2224]. A simple al-
kenyl ester linkage to Merrield hydroxy resin may conveniently be used for teth-
ering small molecules [21]; an a; b-unsaturated g-amino acid linker to polystyrene
[22, 24] or direct vinyl linkage to polystyrene (prepared by Wittig reaction) [23] has
been used in the preparation of peptide aldehydes.
Scheme 11.9. Oxidative cleavage of olens by ozonolysis.
Scheme 11.10. Solid-phase synthesis of peptide aldehydes.
The procedure usually involves bubbling a stream of ozone through a dichloro-

methane solution of the olen at 78 C until a blue coloration remains, followed
by quenching of the ozonide with a reducing agent such as dimethylsulde, tri-
phenylphosphine, or thiourea to give the carbonyl compound. Quenching with a
reducing agent such as sodium borohydride gives rise to the corresponding alcohol
[21], and a variation on this approach has been used for the preparation of a lac-
tone (Scheme 11.11) [25]. There are certain logistical questions to be addressed in
carrying out a large number of such reactions in parallel which may limit the
overall utility of the reaction for combinatorial chemistry in the absence of spe-
cialist equipment. Additionally, there is a general tendency for swollen polystyrene-
based resins to collapse when cooled to the low temperatures usually utilized in
this reaction. This may limit reagent diusion into the resin and will need to be
borne in mind.
Scheme 11.11. Lactone formation via ozonolysis.

11.2.4
Electrophilic Addition of A--X
The examples above represent electrophilic addition of oxygen to a carboncarbon

double bond. Additionally, other powerful electrophiles most notably sources of
I , Br, ArSe , and H are also able to add (Scheme 11.12). The formation of
the intermediate onium species such as 35 can then be followed by nucleophilic
attack of the counterion X , by addition of some external nucleophile (e.g. water),
or by an intramolecular process such as lactonization. Examples of such reactions
are reported for both solution-phase and solid-phase chemistry and can be very ef-
cient, although their reported use in library synthesis is somewhat limited.
Scheme 11.12. Electrophilic addition of AaX to olens.
An example of solid-phase iodolactonization and concomitant resin release is

shown in Scheme 11.13 [26]. In this case, a modest degree of diastereofacial con-
trol (2:1 mixture of enantiomers) was achieved in the iodolactone 38. Similarly,
Scheme 11.14 demonstrates an example of iodoetherication on solid phase with
concomitant oxidative cleavage to give the 2,5-disubstituted tetrahydrofuran deriv-
ative 40 [27]. Both of these examples provide functional groups which could, in
principle, be used for postcleavage derivatization in solution phase.
Scheme 11.13. Solid-phase intramolecular iodolactonization.
Scheme 11.14. Solid-phase intramolecular iodoetherication.
Perhaps most use has been made of organoselenium reagents in this area of re-
search, providing mild and extremely versatile reactivity [28, 29]. A resin-bound
version of phenylselenyl bromide (43) has been developed which provides a conve-
nient and odorless way of handling this toxic and smelly reagent (Scheme 11.15)
[30]. This reagent can also be converted to polymer-supported phenylselenyl phtha-
limide (44), which provides a convenient method for hydration of olens (Scheme
11.16) [30]. A polymer-supported version of phenylselenyl cyanide is readily pre-
pared from Merrield resin and potassium selenocyanate [31].
Scheme 11.15. Synthesis of polymer-supported phenylselenyl bromide.
Scheme 11.16. Synthesis and use of polymer-supported phenylselenyl phthalimide.
The polymer-supported phenylselenyl bromide 43 eciently adds to olens in

the manner depicted in Scheme 11.12 [30]. However, most use has been made of
the way in which these selenium reagents facilitate intramolecular cyclizations
such as cyclic ether formation (Scheme 11.17) [30], lactonization (Scheme 11.18)
[32], and cyclic amine formation (Scheme 11.19) [33]. Reductive hydrodeselenation
can be achieved with tributyltinhydride or, alternatively, oxidation results in the
formation of an olen via selenoxide elimination. The use of such reactions in the
formation of benzopyran libraries (Scheme 11.20) [3436] and polycyclic indoline
libraries 53 [33] is described in more detail in Chapter X.
Scheme 11.17. Intramolecular etherication/selenoxide

elimination using polymer-supported PhSeBr.
Scheme 11.18. Intramolecular lactonization using polymer-supported PhSeCN.
Scheme 11.19. Intramolecular selenoamination of o-allylamines in the presence of SnCl4 .
Scheme 11.20. Polymer-supported synthesis of benzopyrans.
11.2.5
Hydrogenation
The catalytic hydrogenation of olens is, in the absence of sensitive functionalities

and with the use of an appropriate catalyst, a very ecient transformation. Cata-
lysts such as 10% Pd on activated carbon were in widespread use long before
polymer-supported reagents became fashionable, and are easily removed from re-
action mixtures by simple ltration. The parallel processing of multiple samples
introduces certain complexities such as addition of hydrogen gas which may be
overcome with specialist equipment [37] or, alternatively, catalytic transfer hydro-
genation from reagents such as ammonium formate [38] may be considered. Car-
rying out hydrogenation during a solid-phase synthesis adds yet another layer of
complexity since, by necessity, the catalyst must be soluble in order to gain access
to the polymer-bound reactant [39]. Additionally, the reaction conditions must be
compatible with the resin and linker, which often contain functionalities such as
benzyl ethers that are themselves sensitive to hydrogenation. Consequently, this is
an underutilized reaction in combinatorial chemistry. Diimide oers an alternative
for reduction of alkenes (and alkynes) on solid phase, and excellent conversions
have been observed using benzene sulfonylhydrazide in DMF at 100 C as diimide
source [40].
11.2.6
Hydrometallation
Of the hydrometallation processes available, the hydroboration of an olen repre-

sents one of the more useful, not only allowing access to alkylboranes but also the
formal hydration of the double bond to an alcohol through a subsequent oxidation
step.
The utility of in situ hydroborated alkenes as coupling partners in the Suzuki
reaction for library generation was demonstrated through the parallel synthesis of
an array of 26 prostaglandin analogs on solid phase (Scheme 11.21) [41]. In this
work, terminal olens (57) were hydroborated with 9-BBN dimer in vials and then
directly transferred to resin 59 contained within the reaction vessels of a parallel
synthesizer, eciently converting it to resin 60 under standard Suzuki conditions.
Subsequent elaboration provided the prostaglandin E1 analogs (61) in 1856%
overall yield.
Scheme 11.21. Parallel synthesis of prostaglandin E1 analogs,

utilizing hydroborated alkenes as coupling partners in a Suzuki
reaction.
The hydroboration/oxidation of alkenes to alcohols is a potentially useful trans-

formation for the combinatorial chemist, particularly on solid phase. This reaction
eectively allows the use of a terminal alkene as a protecting group for the hy-
droxyethyl moiety, which can then be further functionalized. This was demon-
strated during the course of some synthetic studies toward mniopetals (Scheme
11.22) [42]. The triene 62 was selectively hydroborated with 9-BBN to give the pri-
mary alcohol 63. IBX oxidation and a subsequent BaylissHillman reaction using
PhSeLi as nucleophile provided the key intermediate 64 which, upon oxidation to
the corresponding ketone, underwent an intramolecular DielsAlder reaction.
Cleavage from the resin then gave the polycyclic compound 65 in 35% overall
yield.
Scheme 11.22. Solid-phase hydroboration/oxidation of a

terminal alkene and subsequent elaboration.
11.2.7
1,4-Addition to a; b-Unsaturated Carbonyl Systems
The reactions described above all make use of the electron-rich nature of isolated
carboncarbon double bonds and their consequent reactivity toward electrophiles.
By contrast, when the carboncarbon double bond is conjugated to a carbonyl
or sulfonyl group, the electronic character of the double bond changes, making
it susceptible to 1,4-nucleophilic addition (also known as Michael addition in
the case of carbon nucleophiles). Pioneering work in this area of combinatorial
chemistry is shown in Scheme 11.23, in which secondary amines 68 add to resin-
bound acrylate (67 ! 69), are quaternized with alkyl halides, and then undergo
a Hofmann-type b-elimination in the presence of triethylamine to give tertiary
amines 72 [43]. When primary amines 68 are used in this sequence (R2 H), a
reductive amination step has been used prior to quaternization to prepare terti-
ary amine libraries (72) with three points of diversity [43, 44]. Subsequent work
has shown that replacement of triethylamine with Amberlite weakly basic ion-
exchange resin in DMF simplies work-up procedures since it overcomes the ne-
cessity to remove triethylamine salts from cleaved products, and this procedure
has been used to generate large libraries of trisubstituted amines (> 10,000 com-
pounds) [44]. A similar approach has been employed utilizing a vinylsulfone resin
in place of the acrylate resin 67 [45].
Scheme 11.23. REM linker 1,4-addition of amines to acrylate,

quaternization, and b-elimination to give tertiary amines.
DIPEA, N,N-diisopropylethylamine.
11.3
Addition to C C Triple Bonds
The acetylenic group displays a versatile range of reactivities for use in com-
binatorial chemistry. Its use in cycloaddition reactions, palladium-mediated reac-
tions, and radical reactions is well documented and covered here in the relevant
chapters. Prominent examples on solid phase include their use in the palladium-
mediated syntheses of heterocyclic templates such as indoles [4649] and benzo-
furans [50].
The discussion above (Sect. 11.2.5) on hydrogenation of olens applies equally
to the hydrogenation of acetylenes the diimide reduction of an acetylene on solid
phase is one of the few reported examples [40]. Hydrometallation is another area
References 319
where addition to acetylenes could be a very powerful transformation for further

functionalization, although there are few reported examples. One such example is
the hydrostannylation of a terminal acetylene using a polymer-supported tinhy-
dride to give a vinyl stannane (74 ! 75, Scheme 11.24) [51]. The vinyl stannane 75
was obtained as a mixture of E:Z isomers and was taken through to compound 76
in order to carry out a cyclorelease palladium-mediated Stille coupling to give 77.
There is, however, relatively little to report of relevance to this chapter at present,
although there is scope for future work in this area.
Scheme 11.24. Solid-phase hydrostannylation of an acetylene

and subsequent synthesis of a macrocyclic system.
References
1 E. K. Kick, D. C. Roe, A. G. Waddington, Tetrahedron Lett. 1998,

Skillman, G. Liu, T. J. A. Ewing, Y. 39, 18391842.
Sun, I. D. Kuntz, J. A. Ellman, 6 A. Shiney, P. K. Rajan, K.
Chem. Biol. 1997, 4, 297307. Sreekumar, Polym. Int. 1996, 41,
2 D. P. Rotella, J. Am. Chem. Soc. 1996, 377381.
118, 1224612247. 7 C. S. Pande, N. Jain, Synth. Commun.
3 H. M. C. Ferraz, R. M. Muzzi, T. de 1989, 19, 12711279.
O. Vieira, H. Viertler, Tetrahedron 8 C. R. Harrison, P. Hodge, J. Chem.
Lett. 2000, 41, 50215023. Soc., Perkin I 1976, 605609.
4 S. V. Ley, I. R. Baxendale, R. N. 9 G. M. Coppola, Tetrahedron Lett. 1998,
Bream, P. S. Jackson, A. G. Leach, 39, 82338236.
D. A. Longbottom, M. Nesi, J. S. 10 B. L. Chng, A. Ganesan, Bioorg. Med.
Scott, R. I. Storer, S. J. Taylor, J. Chem. Lett. 1997, 7, 15111514.
Chem. Soc., Perkin Trans. I 2000, 11 W. M. Bryan, W. F. Huffman, P. K.
38154196. Bhatnagar, Tetrahedron Lett. 2000, 41,
5 T. R. Boehlow, P. C. Buxton, E. L. 69977000.
Grocock, B. A. Marples, V. L. 12 C. L. Hetet, M. David, F. Carreaux,
B. Carboni, A. Sauleau, Tetrahedron Soc., Chem. Commun. 1998, 1947

Lett. 1997, 38, 51535156. 1948.
13 K. C. Nicolaou, P. S. Baran, Y.-L. 31 K. Fujita, K. Watanabe, A. Oishi, Y.
Zhong, J. Am. Chem. Soc. 2000, 122, Ikeda, Y. Taguchi, Synlett 1999,
1024610248. 17601762.
14 M. Schroder, Chem. Rev. 1980, 80, 32 K.-i. Fujita, H. Taka, A. Oishi, Y.
187213. Ikeda, Y. Taguchi, K. Fujie, T.
15 R. A. Johnson, K. B. Sharpless in: Saeki, M. Sakuma, Synlett 2000,
Catalytic Asymmetric Synthesis. 15091511.
Ojima, I. (ed.), VCH, New York 1993, 33 K. C. Nicolaou, A. J. Roecker, J.
pp. 227272. A. Pfefferkorn, G.-Q. Cao, J.
16 S. Nagayama, M. Edo, S. Kobayashi, Am. Chem. Soc. 2000, 122, 2966
J. Org. Chem. 1998, 63, 60946095. 2967.
17 C. E. Song, J. W. Yang, H. J. Ha, S. 34 K. C. Nicolaou, J. A. Pfefferkorn,
Lee, Tetrahedron: Asymmetry 1996, 7, G.-Q. Cao, Angew. Chem., Int. Ed.
645648. Engl. 2000, 39, 734739.
18 Y. Xia, Z.-Y. Yang, A. Brossi, 35 K. C. Nicolaou, G.-Q. Cao, J. A.
K.-H. Lee, Org. Lett. 1999, 1, 2113 Pfefferkorn, Angew. Chem., Int. Ed.
2115. Engl. 2000, 39, 739743.
19 S. Brase, S. Dahmen, M. Pfeffer- 36 K. C. Nicolaou, J. A. Pfefferkorn,
korn, J. Comb. Chem. 2000, 2, 710 A. J. Roecker, G.-Q. Cao, S.
715. Barluenga, H. J. Mitchell, J.
20 R. Pappo, D. S. Allen, R. U. Lemieux, Am. Chem. Soc 2000, 122, 9939
W. S. Johnson, J. Org. Chem. 1956, 9953.
21, 478479. 37 T. Bruckdorfer, H. Linnertz, GIT
21 C. Sylvain, A. Wagner, C. Labor-Fachz 2000, 44, 58.
Mioskowski, Tetrahedron Lett. 1997, 38 B. C. Ranu, A. Sarkar, S. K.
38, 10431044. Guchhait, K. Ghosh, J. Indian
22 C. Pothion, M. Paris, A. Heitz, L. Chem. Soc. 1998, 75, 690694.
Rocheblave, F. Rouch, J.-A. 39 I. Ojima, C.-Y. Tsai, Z. Zhang,
Fehrentz, J. Martinez, Tetrahedron Tetrahedron Lett. 1994, 35, 5785
Lett. 1997, 38, 77497752. 5788.
23 B. J. Hall, J. D. Sutherland, 40 P. Lacombe, B. Castagner, Y.
Tetrahedron Lett. 1998, 39, 6593 Gareau, R. Ruel, Tetrahedron Lett.
6596. 1998, 39, 67856786.
24 M. Paris, A. Heitz, V. Guerlavais, 41 D. R. Dragoli, L. A. Thompson, J.
M. Cristau, J.-A. Fehrentz, J. OBrien, J. A. Ellman, J. Comb.
Martinez, Tetrahedron Lett. 1998, 39, Chem. 1999, 1, 534539.
72877290. 42 U. Reiser, J. Jauch, Synlett 2001, 90
25 S. Hanessian, F. Xie, Tetrahedron Lett. 92.
1998, 39, 737740. 43 A. R. Brown, D. C. Rees, Z.
26 H. S. Moon, N. E. Schore, M. J. Rankovic, J. R. Morphy, J. Am.
Kurth J. Org. Chem. 1992, 57, 6088 Chem. Soc. 1997, 119, 32883295.
6089. 44 X. Ouyang, R. W. Armstrong, M. M.
27 X. Beebe, N. E. Schore, M. J. Kurth, Murphy, J. Org. Chem. 1998, 63,
J. Org. Chem. 1992, 57, 10061 10271032.
10062. 45 F. E. K. Kroll, R. Morphy, D. Rees,
28 K. C. Nicolaou, N. A. Petasis, D. Gani, Tetrahedron Lett. 1997, 38,
Selenium in Natural Product Synthesis. 85738576.
CIS Inc., Philadelphia, PA, 1984. 46 A. L. Smith, G. I. Stevenson, C. J.
29 D. Liotta, Organoselenium Chemistry, Swain, J. L. Castro, Tetrahedron Lett.
Wiley, New York 1986. 1998, 39, 83178320.
30 K. C. Nicolaou, J. Pastor, S. 47 H.-C. Zhang, B. E. Maryanoff, J.
Barluenga, N. Winssinger, J. Chem. Org. Chem. 1997, 62, 18041809.
References 321
48 H.-C. Zhang, K. K. Brumeld, B. E. 50 D. Fancelli, M. C. Fagnola, D.

Maryanoff, Tetrahedron Lett. 1997, 38, Severino, A. Bedeschi, Tetrahedron
24392442. Lett. 1997, 38, 23112314.
49 M. C. Fagnola, I. Candiani, G. 51 K. C. Nicolaou, N. Winssinger,
Visentin, W. Cabri, F. Zarini, N. J. Pastor, F. Murphy, Angew.
Mongelli, A. Bedeschi, Tetrahedron Chem., Int. Ed. Engl. 1998, 37, 2534
Lett. 1997, 38, 23072310. 2537.
322
12
Addition to CarbonHetero Multiple Bonds
Philipp Grosche, Jorg Rademann, and Gunther Jung
12.1
Introduction
Carbonhetero multiple bonds play a central role in synthetic organic chemistry.

They possess a polar character and react with various nucleophiles as well as with
electrophiles in numerous addition reactions. They form valuable substrates for
the synthesis of structurally diverse and pharmacologically important compounds,
such as tetrahydro-b-carbolines, ureas, and guanidines. Many of the addition reac-
tions to CX multiple bonds have found wide application in combinatorial chemis-
try such as the synthesis of ureas via isocyanates, the PictetSpengler reaction, and
several Mannich-type reactions. In the literature, most articles in the eld of com-
binatorial chemistry deal with solid-phase reactions, however, solution-phase pro-
tocols are in many instances also suited to parallel synthesis.
In this chapter addition reactions to CN double bonds, CS double bonds, and
CN triple bonds are discussed. The chapter will not include cycloaddition reactions
of CX multiple bond systems and reactions of isocyanides typically employed in
multiple component reactions.
This chapter reviews those transformations of the CX multiple bonds that are
suitable for combinatorial chemistry, either in solution or on solid phase. To assure
clarity and readability, the reactions are grouped according to the number of bonds
between the C atom and the heteroatom, the hybridization of the carbon center,
and the nature of the attacking agent.
12.2
Additions to CN Double Bonds in sp2 Systems
CN double bonds are the structural motif of various functional groups. This sec-
tion refers to CN double bonds in sp2 systems such as imines, iminium ions, acyl-
iminium ions, and N-oxides of nitrogen heterocycles (pyridine, quinoline, iso-
quinoline). The reacting CN double bond can be isolated; however, the reactions
are often performed as a three-component reaction consisting of an amine, a car-

ISBN: 3-527-30509-2
bonyl compound and the attacking nucleophile, with in situ formation of the reac-
tive CN double bond.
12.2.1
Attack by Hydride (Reductive Alkylation)
Reductive alkylation, or reductive amination, is one of the most commonly used

reactions in combinatorial chemistry. It is a convenient method for the preparation
of secondary and tertiary amines and is one of the easiest ways to generate diver-
sity, as usually the substrate tolerance is very broad. The monoalkylation of pri-
mary or secondary amines is aected by condensation with aldehydes or ketones
and the subsequent reduction of the imine species. In the case of primary amines,
the reaction can be performed either in a two-step procedure by rst synthesizing
and isolating the imine followed by reduction, or in a one-pot procedure by adding
the carbonyl partner together with the reducing agent. Secondary amines are typi-
cally converted in a one-pot synthesis because of the low stability of the intermedi-
ary iminium ion. The use of primary amines in a one-pot procedure carries the
risk of dialkylation as the formed secondary amine can react with another carbonyl,
thus forming the tertiary amine. As a reducing agent, NaBH3 CN, NaBH(OAc)3 ,
Me4 NBH4 , LiBH4 , NaBH4 , BH3 py, and BH3 THF can be employed. In solution
phase, both the one-pot synthesis [1] and the reduction of preformed imine spe-
cies [2] were used. Anilines were, for example, converted upon treatment with al-
dehydes and NaBH(OAc)3 in dichloromethane at room temperature (rt) to give the
respective secondary amines [3]. The degree of dialkylation in the one-pot proce-
dure increases with less-hindered amines and aldehydes and with more electron-
rich amines. To avoid double alkylation an excess of amine is often used [4].
Polymer-bound reducing agents have found wide application in solution-phase
combinatorial synthesis mostly in the form of ion-exchange resins loaded with
borohydride or cyanoborohydride (Scheme 12.1). Polymer-bound ammonium cya-
noborohydride was used for the reductive alkylation of primary and secondary
amines with aromatic aldehydes in MeOH at rt (Scheme 12.1) [5, 6], or for the
reduction of preformed imines in toluene/MeOH under reux conditions [7].
Polymer-supported borohydride was utilized for the reduction of preformed imines
in MeOH at rt. An excess of amine relative to the aldehyde was applied in order
to drive the imine formation to completion and to suppress dialkylation. Excess
amine was readily scavenged from the desired secondary amine by selective imine
formation using a polymer-supported aldehyde [8]. Tertiary amines were formed
by treating aldehydes with an excess of secondary amine and polymer-supported
Scheme 12.1
324 12 Addition to Carbon--Hetero Multiple Bonds
cyanoborohydride in acetic acid/dichloromethane. In this case excess secondary

amine was removed using polymer-supported benzoyl chloride [8].
In solid-phase chemistry, both of the components forming the imine species can
be linked to the solid phase. Both approaches, the reduction of isolated imines
(Scheme 12.2) [9, 10] and the one-pot synthesis [11], can be used. Polymer-bound
primary amines can be partly overalkylated using the one-pot strategy, as reported
for solution-phase chemistry. Reactions using secondary amines are always carried
out as a one-pot procedure. Imines can easily be hydrolyzed, especially under
acidic conditions. Thus, with isolated imines the condensation and reduction step
can be repeated to achieve complete conversion [12].
Scheme 12.2
Usually NaBH3 CN in AcOH/dimethylformamide (DMF) is used as the reducing

agent. However, several other reagents have also been used in solid-phase chemis-
try: NaBH(OAc)3 [13], Me4 NBH4 [14], LiBH4 [15], NaBH4 [10], BH3 py [16], and
BH3 THF [17]. The boranepyridine complex was found to be an excellent reagent
for the in situ reduction of iminium ions on solid phase [16]. The reaction was
performed in DMF/EtOH (3:1) using an excess of aldehyde or ketone respectively.
However, this reagent is not suitable for primary amines as it leads to dialkylation.
In contrast to imines, oximes required harsher conditions for ecient reduction.
In a recent example, resin-bound oximes were reduced using BH3 THF in 4 M
HCl in dioxane, tetrahydrofuran (THF)/MeOH at rt [17].
12.2.2
Addition of Carbon Nucleophiles
A broad range of C-nucleophiles could be added to CN double bonds, namely eno-

lates, ketene acetals, C,H-acidic compounds, electron-rich heterocycles, organo-
metallic compounds, boronic acids, and silanes. The reactions are sorted according
to the nature of the nucleophile. In several cases there are only a few examples of
solution-phase combinatorial chemistry, which does not necessarily reect the
suitability of solution-phase protocols to library synthesis.
12.2.2.1 Imino Aldol Reaction

Imines react readily with silyl enolates, silyl ketene acetals, and silyl thioketene
acetals to aord N-substituted b-amino ketones, b-amino esters, and b-amino thio-
esters. The reaction is catalyzed typically by Lewis acids, preferably with the lan-
thanide triates Ln(OTf )3 , Sc(OTf )3 , and Yb(OTf )3 . It can also be performed as
a three-component reaction between amine, aldehyde or ketone, and the silyl
component where the imine is formed in situ. In this case, a dehydration agent
such as trimethyl orthoformate is normally added to support imine formation and
to prevent degradation of the ketene silyl acetals by H2 O. This Mannich-type reac-
tion has attracted a lot of interest in solution-phase as well as in solid-phase
chemistry.
A typical procedure in solution applies equimolar (or nearly equimolar) amounts
of imine (or amine and aldehyde) and silyl component and 0.050.3 mol%
Ln(OTf )3 . The reaction is performed in dichloromethane (DCM), acetonitrile
(ACN), or mixtures of both solvents at rt. The suitability of this reaction for library
synthesis was exemplied by the generation of a small library of 40 2,3-dihydro-4-
pyridones using Danishefskys diene as the silyl component and Yb(OTf )3 as the
Lewis acid catalyst [18]. Byproducts and unreacted aldehyde were removed with
polyamine resin and the products were obtained in good to excellent purities and
yields. Although this reaction was often described as an aza-DielsAlder reaction
in the literature, other authors favored a tandem MannichMichael mechanism [19].
Another solution-phase approach utilizes a polymer-bound scandium catalyst
(polyallyl-scandium-triylamide ditriate) (Scheme 12.3). The reaction is conducted
as a three-component reaction, with silyl enolates, ketene silyl acetals, and cya-
notrimethyl silane as nucleophiles [20]. Treatment with cyanotrimethyl silane
as the nucleophile aords a-aminonitriles in a Lewis acid-catalyzed variation of
the classical Strecker synthesis. This reaction is performed in dichloromethane/
acetonitrile (2:1) at rt for 19 h. When ketene silyl acetal is used, MgSO4 is added
to prevent decomposition of the ketene silyl acetal by traces of water. A cation-
exchange resin has also been used for the promotion of the imino-aldol reaction
[21].
In the imino-aldol reaction at least one asymmetric C atom is generated. Thus, a
procedure for enantioselective addition is of special interest. Catalysis of the reac-
tion with polymer-supported palladium BINAP m-hydroxo complex (BINAP 2,2 0 -
bis(diphenylphorphino)-1,10 -binaphthyl) yields an ee of 81% [22].
Scheme 12.3
This Mannich-type reaction is very suitable for combinatorial chemistry and has
also been adapted to solid-phase chemistry, thus pursuing both possible strategies:
the immobilization of the imine and the immobilization of the silyl component.
Polymer-supported silyl thioketene acetals obtained by silylation of immobilized
thioesters were converted to b-aminoesters by treatment with imines in the pres-
ence of Sc(OTf )3 using dichloromethane as solvent [23, 24]. Alternatively, a three-
component protocol can be employed (Scheme 12.4) [25]. In both cases reductive
cleavage of b-amino acid thioesters with LiBH4 yields b-amino alcohols.
Scheme 12.4
In the second approach, a polymer-supported imine was treated with silyl enol
ethers or silyl ketene acetals in the presence of Yb(OTf )3 in dichloromethane to
yield b-amino ketones and esters respectively [26, 27]. Instead of imines, polymer-
supported acyl hydrazones can also be used as substrates [28].
2,3-Dihydro-4-pyridones were synthesized by tandem MannichMichael reaction
in good yields. Resin-supported imines were reacted with Danishefskys diene in
THF using Yb(OTf )3 (Scheme 12.5) [29] or ZnCl2 [30] as catalyst.
Scheme 12.5
A more classical example of Mannich chemistry is the solid-phase variant of the

Robinson tropanone synthesis. Starting from immobilized primary amines, tropa-
none derivatives are formed upon treatment with 1,3-acetonedicarboxylic acid and
succinic aldehyde under acidic conditions at rt [31].
12.2.2.2 Reaction with Boronic Acids

The Petasis reaction is a three-component condensation reaction between an alde-
hyde, an amine (usually secondary amine), and a boronic acid. It is also referred to
as a boronic acid Mannich reaction. The reaction mechanism is not yet completely
elaborated, however, a mechanism involving iminium species is likely and there-
fore this reaction is discussed here. A wide range of building blocks is accepted in
this reaction, but the limited number of suitable aldehydes is remarkable. Besides
glyoxylic acid, only a few aldehydes react satisfactorily, e.g. a-hydroxyaldehydes and
aldehydes bearing an a-heteroatom. In solution-phase chemistry the condensation
is performed using equimolar amounts of the components in THF or acetonitrile
at rt. By using 1,2-diamines, glyoxylic acid, and boronic acids, piperazinones and
benzopiperazinones are accessible (Scheme 12.6) [32]. The Petasis reaction has
also been adapted to solid-phase chemistry. Each of the required components can
Scheme 12.6
be linked to the solid support. Typically, the components in solution are employed
in large excess. Polymer-bound N-substituted amino acids have been treated with
glyoxylic acid and boronic acids in dichloromethane at rt for 18 h, and the reaction
was repeated for additional 60 h. The carboxylic acids obtained were further modi-
ed by coupling with amines. After cleavage from the resin, products were ob-
tained in good purity and yield [33, 34]. This reaction was also carried out at 50 C
for 12 days in DMF/1,2-dichloroethane (DCE), and these reaction conditions have
also been successfully applied to immobilized phenyl boronic acid, glyoxylic acid
(Scheme 12.7), and proline or piperazine [35].
Scheme 12.7
12.2.2.3 Addition of Allylsilanes (Imino-Sakurai Reaction)

Allylsilanes add to CN double bonds in an imino-Sakurai reaction. Both the imine
species and the allylsilane can be the immobilized component. Polymer-bound
acyl imines have been generated in situ by reaction of immobilized carbamate with
aromatic and heteroaromatic aldehydes under Lewis acid conditions. These inter-
mediates reacted directly with allylsilanes to yield homoallylic amines. The reac-
tion was performed as a one-pot procedure in acetonitrile using BF3 OEt2 as Lewis
acid (Scheme 12.8) [36]. A variation employing cyclic N-acyliminium ion inter-
mediates has also been performed [37].
Scheme 12.8
In another approach immobilized allylsilanes were treated with Boc-protected

aldimines in dichloromethane using BF3 OEt2 as Lewis acid. This reaction yielded
Boc-protected homoallylic amines [38].
12.2.2.4 Reaction with Grignard Reagents, Lithium Organyles, and Zinc Organyles
Imines and iminium species are converted to amines upon treatment with
Grignard reagents, lithium reagents, and zinc organyles. This reaction is often
used in solution-phase chemistry and has been adapted to solid-phase chemistry.
Resin-immobilized aldimines, derived from condensation of Rink amide poly-
styrene resin with aldehydes, reacted with Grignard reagents at 60 C or lithium
reagents at 78 C to 20 C to yield after cleavage primary amines in good to ex-
cellent purity (Scheme 12.9) [15]. Since the aldimines of ammonia are unstable,
similar approaches to primary amines in solution phase need protecting groups
at the N atom to improve the stability. In this example, the function is fullled by
the resin. If the imines are not immobilized via the N atom, secondary amines are
obtained after cleavage [39, 40]. Enantiopure immobilized aldimines have been
converted diastereoselectively to homoallylamines upon treatment with allyl zinc
reagents in THF. The latter were obtained from allylbromide and zinc using
CeCl3 7H2 O as an additive [41].
Scheme 12.9
Another kind of CN double bond-containing substrate are the N-acyl-pyridinium

or N-acyl-quinoline intermediates. These are generated by the reaction of the
heterocycle with acylchlorides or chloroformates. Activation of 4-methoxypyridine
can be achieved by reaction with a resin-bound chloroformate. Addition of the
Grignard reagent was performed at 20 C in THF and yielded 2,3-dihydro-4-
pyridones in high purity following basic cleavage [42, 43].
Another possibility to generate acyl-pyridinium intermediates is the immobili-
zation of hydroxypyridine and subsequent acylation. Conversion with a Grignard
reagent and acidic cleavage aords N-acyl-2,3-dihydro-4-pyridones (Scheme 12.10)
[44, 45]. In a similar approach, quinolines were converted to 2-substituted N-
acyl-dihydroquinolin-4-ones [46]. A related reaction is the solid-phase variant of the
Reissert reaction, which is an ecient activation method for introducing substi-
tuents at the C-1 position of isoquinolines. Polymer-bound N-acyl-isoquinolinium
intermediates generated in situ from immobilized benzoyl chloride react with tri-
methylsilyl cyanide to form N-acyl-1-cyanodihydroisoquinolines. These Reissert in-
termediates possess increased acidity at the C-1 position and are smoothly alky-
lated [47, 48].
Scheme 12.10
12.2.2.5 Addition of Copper Alkynes

Aldehydes, amines, and alkynes react in a Mannich-type reaction yielding prop-
argylic amines. As in other examples the reactive imine species is formed in situ.
The reaction is catalyzed by CuCl and proceeds presumably via copper alkynes.
Each of the three components can be linked to the solid support.
Propargylamine was immobilized on 2-chlorotrityl chloride resin and was re-
acted with secondary amines and paraformaldehyde in the presence of CuCl to
give the aminomethylated products in high purity. The reaction was performed in
dioxane at 7075 C for 3 h [49]. Solid-supported alkynes can also be prepared via
the Sonogashira reaction [50] and have been employed in the addition of alkyne
cuprates on solid phase.
Besides the amino alkynes, resin-bound piperazine and benzaldehydes have
served as substrates for this reaction (Scheme 12.11) [51].
Scheme 12.11
12.2.2.6 Addition of Electron-rich Aromatic and Heteroaromatic Cycles

Electron-rich heterocycles can add to CN double bonds. The most famous example
in this eld is the PictetSpengler reaction. In this reaction 3-(20 -aminoethyl)-
indoles are condensed with aldehydes or ketones and subsequently cyclized to yield
1,2,3,4-tetrahydro-b-carbolines.
This reaction has often been used in solid-phase chemistry. Tryptophan deriva-
tives serve as substrates and are immobilized via the carboxy group. Condensation
with the carbonyl compound and cyclization is performed in one pot. Aliphatic
and aromatic aldehydes as well as ketones have been used. Neutral or acidic con-
ditions are suitable for the PictetSpengler reaction. However, the acid-catalyzed
route using 125% triuoroacetic acid (TFA) in dichloromethane is most often
used, and under neutral conditions the reaction can be conducted at 50110 C.
A typical procedure employs tryptophan immobilized on Merrield resin, with a
tenfold excess of aldehyde in 10% TFA/dichloromethane at rt for 16 h (Scheme
12.12). The tetrahydro-b-carbolines were obtained with high purity after cleavage
via aminolysis with ethylamine [52]. N-Substituted tryptophan derivatives can also
be used for the PictetSpengler reaction [53]. In an alternative approach the imine
obtained from the condensation of various aldehydes with tryptophan immobilized
on Wang-polystyrene resin was isolated. Treatment with uorenylmethoxycarbonyl
(Fmoc)-protected amino acid chloride results in the formation of an N-acylimi-
nium intermediate which undergoes PictetSpengler condensation. Fmoc depro-
tection leads to resin cleavage through cyclization to yield diketopiperazines in
high purity (Scheme 12.13) [54].
Scheme 12.12
Scheme 12.13
Instead of tryptamine derivatives, electron-rich m-tyramine and histamine de-

rivatives can be linked to the support. Condensation and cyclization proceeds well
with aliphatic, aromatic, and heteroaromatic aldehydes in pyridine at 100 C for 14
h. Tetrahydroisoquinolines and tetrahydroimidazopyridines are obtained with high
purity after cleavage (Scheme 12.14).
Scheme 12.14
Another reaction of this type is the aminomethylation of resin-supported indoles

with formaldehyde and secondary amines, aording 3-aminomethylindole in high
yield and purity. The reaction is conducted as a three-component reaction in
AcOH/1,4-dioxane (1:4) at rt for 1.5 h. The iminium intermediate is formed in situ
and is trapped by the indole [55].
Immobilized heterocyclic N-oxides, such as quinoline-N-oxide or isoquinoline-
N-oxide react with various nucleophiles, for example indoles, pyrroles, and enam-
ines, in the presence of benzoylchloride to aord 2-substituted quinolines or 1-
substituted isoquinolines, respectively [118]. The reaction proceeds via an addition
to the CN double bond followed by cleavage of benzoic acid.
12.2.2.7 Radical Reactions

CN double bonds can participate in radical reactions. Radical reactions are covered
in detail in Chapter 7, however, some typical examples are also discussed here.
In solid-phase chemistry the intermolecular and intramolecular carbon radical ad-

ditions to CN double bonds have been established.
In the intermolecular reaction, radicals generated from alkyl iodides in the pres-
ence of Et3 B and Bu3 SnH have been added to resin-bound glyoxylic oxime ethers
in dichloromethane at rt to yield a-hydroxylamino acid derivatives in moderate to
good yields (Scheme 12.15) [56]. Another approach uses phenylsulfonyl oxime
ethers that react with alkyl iodides and hexamethylditin in benzene under irradia-
tion at 300 nm at rt to aord alkylated a-oxime ethers in moderate to good yields
[57].
Scheme 12.15
Resin-bound allylamino acetaldoxime and propargylamino acetaldoxime were

employed as substrates for an intramolecular radical reaction using Et3 B and
Bu3 SnH in toluene at 80 C. Functionalized pyrrolidines were formed via a carbon
carbon bond-forming process [58].
12.2.3
Addition of Nitrogen Nucleophiles
The addition of N-nucleophiles to CN double bonds is typically conducted

as a three-component reaction between amines, carbonyl compounds, and N-
nucleophiles. The active imine species is formed in situ and trapped by the N-
nucleophile. Benzotriazoles add readily to imines. This approach was adapted to
solid-phase chemistry as a linker strategy using polymer-bound benzotriazole and
excess aldehyde and amine in THF/trimethyl orthoformate (TMOF) at 2060 C
(Scheme 12.16) [59, 60]. The adducts can be released in solution with nucleophiles
such as hydride ions, Grignard reagents, and organo zinc compounds.
Scheme 12.16
In a second group of addition reactions used in heterocycle synthesis, the

reactions proceed presumably via CN double bond intermediates. Phenylenedi-
amines obtained from immobilized nitroanilines via reduction condense with al-
dehydes to form benzimidazoles. The reaction is performed at 50 C [61] or with
2,3-dichloro-5,6-dicyanobenzoquinone (DDQ) at rt [62]. The reaction can also

be conducted in a one-pot procedure treating nitroaniline with aldehyde and
SnCl2 2H2 O [63].
Polymer-bound 2-aminobenzamides (immobilization via the amide nitrogen)
react with aldehydes in N,N-dimethylacetamide (DMA) in the presence of 5%
acetic acid at 100 C to form dihydroquinazolinones via an imine intermediate.
The relatively harsh reaction conditions are required because of the low activity of
the N-nucleophile [64].
12.2.4
Addition of Phosphorus Nucleophiles
Various P-nucleophiles react with imines or iminium ions in Mannich-type reac-

tions. Protocols have been developed for solution-phase combinatorial as well as
for solid-phase chemistry.
Condensation of a secondary phosphine with an aromatic or heteroaromatic al-
dehyde and an amine proceeds in THF at rt to yield aminomethylphosphines in
good yields (Scheme 12.17). Owing to the air sensitivity of the phosphines the re-
action has to be conducted under inert conditions. The protocol was utilized for
the synthesis of a 96-member library [65].
Scheme 12.17
The addition of dialkyl phosphite to imines can be eectively promoted with

polymer-supported TBD (1,5,7-triazabicyclo[4.4.0]dec-1-ene) as base to aord a-
aminophosphonates [66].
A solid-phase approach to a-amino phosphonates and phosphonic acids starts
from polymer-bound H-phosphonates, which were obtained in a three-step pro-
cedure. Wang-PS resin was treated with 2-chloro-4H-1,3,2-benzodioxaphosphorin-
4-one followed by hydrolysis and esterication. Addition of imines using either
sonication or Yb(OTf )3 catalysis followed by cleavage aorded the correspond-
ing a-amino phosphonates in high yield and purity [67]. Cleavage of the p-nitro-
phenylethyl group using 1,8-diazabicyclo[5.4.0]undecene-7 (DBU) followed by TFA
cleavage from the resin yielded a-amino phosphonic acids.
Aminophosphonites were synthesized by nucleophilic addition of bis-(trime-
thylsilyl)phosphonite (BTSP) to polymer-supported imine in dichloromethane/
DMF. The silyl groups are cleaved upon treatment with methanol to produce
amino-phosphinic acid (Scheme 12.18). N-Fluorenylmethoxy-carbonyl-9-amino-
xanthen-3-yloxymethyl polystyrene was used as support and cleavage was per-
formed using TFA/CH2 Cl2 /triisopropylsilane. Aromatic, heteroaromatic, aliphatic,
and sterically hindered aldehydes can be used for imine formation [68].
Scheme 12.18
12.2.5
Reactions with Oxygen Nucleophiles
There are only few addition reactions of O-nucleophiles to CN double bonds re-
ported in solid-phase chemistry. 1,2-Aminoalcohols were cyclized with aldehydes
to form oxazolidines via an imine intermediate. This reaction has been exploited
for the immobilization of aldehydes. Polymer-bound serine or threonine was
treated with an aldehyde in 1% N,N-diisopropylethylamine (DIPEA)/MeOH for 2 h
at 60 C. This oxazolidine linker is stable to the conditions of Fmoc peptide syn-
thesis and is cleaved by heating with 5% AcOH/water for 30 min at 60 C [69].
A similar approach was chosen for the synthesis of disubstituted 1,3-
oxazolidines [70]. 1,2-Aminoalcohols linked to the polymeric support were con-
densed with aldehydes in TMOF at rt to yield the corresponding imines that were
converted to N-acyl-1,3-oxazolidines by treatment with acyl chlorides, isocyanates,
or isothiocyanates (Scheme 12.19). Cleavage of the Wang-PS resin was performed
using DDQ and aorded 1,3-substituted 4-(40 -formylphenoxymethyl)oxazolidines
in good yields. In this example, the cleavage using 1% TFA led to the decomposi-
tion of the heterocycles. Thus, an oxidative method was required for smooth isola-
tion of the products.
Scheme 12.19
12.2.6
Addition of Sulfur Nucleophiles
Thiols can readily add to imines, which is exploited in combinatorial chemistry for
the formation of several heterocycles, namely thiazolidinones, metathiazanones,
thiazolines, and benzothiazoles. Imines react with mercapto acids under addition
of the thiol followed by acylation of the resulting N,S-acetal. a-Mercaptocarboxylic
acids are used for the synthesis of thiazolidinones; b-mercaptocarboxylic acids for
the synthesis of metathiazanones. The latter reaction is most conveniently per-
formed as a three-component condensation of a primary amine, an aldehyde, and
a mercapto carboxylic acid, but a stepwise approach is also possible.
Solid-phase procedures of this reaction [71, 72] start from immobilized amines
that are treated with excess aldehyde and mercapto carboxylic acids in THF at 70 C
for 2 h (Scheme 12.20). Molecular sieves or TMOF are used to remove H2 O that
formed during the condensation as well as during the cyclization step [72].
Whereas thiazolidinones are obtained in high purities, the formation of meta-
thiazanones is more problematic. Besides immobilized amines, immobilized
glyoxylic acid has also been used as a substrate [73].
Scheme 12.20
The solid-phase synthesis of thiazolines and benzothiazoles begins from related

compounds. 2-Substituted thiazole-4-carboxylic acids were obtained by reaction of
aldehydes with unprotected cysteine attached to the polymeric support via an ester
bond. The condensation and cyclization step is performed under acidic conditions
(toluene/acetonitrile/AcOH; 45:45:10). The thiazolidines formed can be acylated
and obtained in good yield after cleavage from the resin [74].
If immobilized 3-amino-4-mercaptobenzoic acid is used instead of cysteine, the
reaction with aldehydes in reuxing ethanol for 4 h aords benzothiazoles in good
to high purities and similar yields. The reaction proceeds presumably via an imine
intermediate, which is subsequently attacked by the mercapto group followed by
oxidation. This pathway is analogous to that of the benzimidazole formation from
phenylenediamines [75].
12.3
Additions to CN Double Bonds in sp-Systems
In this section, transformations of carbodiimides, isocyanates, and isothiocyanates

are discussed. These functional groups have a common feature in that the C atom
is highly reactive against nucleophiles because of the two neighboring electron-
withdrawing heteroatoms.
12.3.1
Additions to Carbodiimides
Besides their importance as coupling reagents in amide and ester formation,

(Chapter 13.3.1) carbodiimides are important synthetic intermediates. They are
easily attacked by primary and secondary amines to form guanidines. The carbo-
diimides are generated commonly by eliminating water or H2 S from ureas or
thioureas using suitable dehydrating agents such as Mukaiyamas reagent or p-
toluenesulfonyl chloride together with Et3 N. Alternatively, the aza-Wittig reaction
of iminophosphoranes with isocyanates or isothiocyanates is employed. Often, the
carbodiimides are not isolated.
In the solid-phase synthesis of guanidines, the carbodiimide is most often the
immobilized component. There are several examples of carbodiimide formation
from iminophosphoranes with either isocyanates [76] or with isothiocyanates [77,
78] via an aza-Wittig reaction. Another approach to carbodiimides is the elimina-
tion of H2 S from thioureas using Mukaiyamas reagent [79]. The addition of pri-
mary and secondary amines to carbodiimides is typically performed at rt. Higher
temperatures are used if the formed guanidines are to react further as nucleo-
philes. This strategy has been exploited for the syntheses of several heterocycles
employing a cyclization-release approach. Polymer-supported carbodiimides that
are obtained by the reaction of immobilized a-amino acids with isothiocyanates
followed by treatment with Mukaiyamas reagent are converted to guanidines upon
treatment with amines. These guanidines cyclize to release 2-aminoimidazolinones
[79]. A similar cyclization-cleavage approach has been used for the synthesis of 3H-
quinazolin-4-ones using immobilized 2-azido-benzoic acid as substrate (Scheme
12.21) [80]. If polymer-supported 20 -amino-cinnamic acid is employed, guanidine
formation is followed by a Michael addition to yield 3,4-dihydroquinazolines [76].
Scheme 12.21
12.3.2
Reaction of Isocyanates and Isothiocyanates
The chemistry of these two groups is very similar. There is a vast number of ar-
ticles describing the addition of nucleophiles to isocyanates and isothiocyanates.
12.3.2.1 Addition of Carbon Nucleophiles

CH acidic compounds react with isothiocyanates to form thioamides. This reaction
has been adapted to solid-phase chemistry. Both components required for this
synthesis can be linked to the solid support. Resin-bound cyanoacetamide was re-
acted with aliphatic and aromatic isothiocyanates in DMF at rt using DBU as base
to yield thioamides [81]. Also resin-bound cyanoacetic acid has been used as a
substrate, employing DIPEA as a base (Scheme 12.22) [82].
Scheme 12.22
Resin-bound isothiocyanates are alkylated with acceptor-substituted acetonitriles,

such as malononitrile and methanesulfonylacetonitrile, under basic conditions to
yield the respective thioamides [83].
12.3.2.2 Addition of Nitrogen Nucleophiles

Amines readily react with isocyanates or isothiocyanates to form ureas or thiour-
eas. Both ureas and thioureas are of interest as nal products and as precious
synthetic intermediates which, among other reactions can be further converted to
carbodiimides, guanidines, hydantoins, and quinazoline-2,4-diones. Typically, het-
erocycle formation proceeds via an intramolecular acylation of the urea. In accor-
dance with their importance, these reactions were soon adapted to combinatorial
solution- and solid-phase chemistry.
In solution-phase chemistry, each of the two components may be used in excess.
Treatment of the reaction mixture with an appropriate scavenger resin yields pure
products (Scheme 12.23). When there is an excess of the amine, a scavenger resin
functionalized with isocyanate, aldehyde, or carboxy groups is used. An excess
of isocyanate or isothiocyanate has best been removed with amino resins [4, 6]. In
solid-phase chemistry either of the components has been linked to the resin; most
often, resin-bound primary and secondary aliphatic amines or anilines are used.
Typically an excess of the solution component is used in dichloromethane, THF,
or DMF at rt. Polymer-bound isocyanates have to be generated on solid support.
They are accessible by reaction of immobilized Fmoc-protected amino acids with
methyltrichlorosilane [84] or by Curtius rearrangement of acyl azides [85]. The
Scheme 12.23
reaction of resin-bound amines with p-nitrophenyl chloroformate under basic con-

ditions yields isocyanates via the active carbamate.
Ureas are often formed as intermediates in reaction sequences leading to het-
erocycles. Several syntheses of this kind have been established on solid phase,
namely the syntheses of hydantoins, thiohydantoins, and quinazoline-2,4-diones.
Often, a cyclizing cleavage strategy is pursued which guarantees high purities. For
example, quinazoline-2,4-diones are obtained in >90% purities if the route de-
picted in Scheme 12.24 is followed [85].
Scheme 12.24 DPPA Diphenylphosphorylazide; TEA Triethyl amine.
12.3.2.3 Addition of Oxygen Nucleophiles

Isocyanates form carbamates when treated with alcohols. Alcohols linked to a solid
support or to soluble polymers have been reacted with isocyanates at rt using Et3 N
as a base (Scheme 12.25) [86, 87]. Highly activated isocyanates have been reacted
with hydroxy resins without base at 0 C [88, 89]. The carbamates obtained using
this approach are cleaved either under acidic conditions to yield the amines via the
carbamic acid or by nucleophiles. Carbamates have also been accessed from im-
mobilized secondary alcohols using isocyanates in DMF in the presence of cata-
lytic amounts of CuCl at rt. This procedure was embedded in a multistep library
synthesis, in which the products were obtained in good to excellent purity [90].
Scheme 12.25
12.3.3
Addition to CS Double Bonds in sp2 Systems
Thioamides and thioureas are the most frequently used synthons bearing CS
double bonds. Owing to its high nucleophilicity, the sulfur is readily alkylated. The
alkylated species is often used as an intermediate to facilitate subsequent substitu-
tion with amines to aord amidines and guanidines. Furthermore, the alkylated
species can be exploited for the synthesis of heterocycles such as thiazoles from
thioamides and a-halo ketones. These reactions are well established in solution
and have also been employed successfully on solid phase.
The alkylation of benzimidazol-2-thiones with various alkyl halides was per-
formed using MeO-PEG-OH as soluble polymeric support. The reaction proceeds
in dichloromethane using Et3 N as a base and yields the 2-alkylthiobenzimidazoles
in good to high purity [91].
S-Alkylation has been conducted on solid phase using, for example, immobilized
benzimidazolthiones and quinazoline-2-thioxo-4-ones as substrates. The reaction is
typically performed in DMF or N-methyl-2-pyrrolidone using a tertiary base and
various alkyl or aryl halides as alkylating agents [92, 93].
As already mentioned, S-alkylations can be a key step in heterocycle syntheses.
Thiazoles are formed by the Hantzsch synthesis by reaction of resin-bound thio-
amides with a-halo ketones [94]. 2,4-Diaminothiophenes are obtained by alkylation
of immobilized a-cyano thioamides with a-halo ketones followed by cylization (see
Sect. 12.4.1).
Formation of guanidines from thioureas via S-alkylation and substitution with
amines has been performed using methyl iodide, Mukaiyamas reagent, or carbo-
diimides as alkylating agents. Merrield resin can also act as an alkylation reagent
and yields immobilized S-alkyl isothioureas. These are typically cleaved as guani-
dines when treated with amines [95, 96]. For carbodiimides, the alkylated species
is not isolated but is directly substituted with amines [97, 98], whereas the alky-
lation products of methyl iodide [99, 100] or Mukaiyamas reagent are isolated
(Scheme 12.26) [101].
Scheme 12.26
Treatment of thioureas with Mukaiyamas reagent, Et3 N in dichloromethane, or

MeCN aorded carbodiimides [79, 102]. Thioamides react in a similar way to
thioureas with N 0 -(3-dimethylaminopropyl)-N-ethylene carbodiimide (EDC) and
amines to yield amidine derivatives (Scheme 12.22) [82].
12.3.4
Reaction of CS Double Bonds in sp Systems
CS double bonds occur as part of sp systems in isothiocyanates and in carbon di-

sulde. Additions of isothiocyanates have been discussed previously together with
additions of isocyanates.
Carbon disulde reacts with amines and Merrield resin in a three-component
reaction to give resin-bound dithiocarbamates. In the rst step, the amine adds
to carbon disulde to form dithiocarbamates which are subsequently trapped by
the Merrield resin (Scheme 12.27). The reaction proceeds at rt using DIPEA as
the base. The dithiocarbamates obtained with primary amines and anilines can be
cleaved with primary and secondary amines in toluene at 60 C to yield thioureas
in good to excellent yield [103].
Scheme 12.27
A similar approach to dithiocarbamates uses resin-bound amines. Carbon disul-

de was added to the amine in 1,4-dioxane using aqueous KOH as a base. This
dithiocarbamate was converted upon treatment with formaldehyde and amino
acids to yield tetrahydro-2H-1,3,5-thiadiazin-2-thiones in good to excellent purity
and yield [104].
12.4
Additions to CN Triple Bonds (Cyanides, not Isocyanides)
Cyanides and isocyanides participate in numerous inter- and intramolecular addi-

tion reactions. Most reactions in which cyanides are transformed lead to amino-
substituted heterocycles. Isonitriles are typically converted in multicomponent re-
actions that are discussed in Chapter 23 and will not be discussed here.
12.4.1
Addition of Carbon Nucleophiles
Nitriles can be attacked by CH acidic compounds. This feature was exploited in the
synthesis of aminothienopyridine libraries in a solution-phase approach [105, 106].
Treatment of 3-cyanopyridine-2-thiones with acceptor-substituted bromomethylene
compounds and aqueous KOH in DMF at rt resulted in S-alkylation. Cyclization
was carried out again with aqueous base to yield aminothienopyridines (Scheme
12.28) [106].
Scheme 12.28
A similar approach in solid-phase chemistry uses a-cyanothioamides as start-

ing material for the formation of aminothiophenes. The a-cyanothioamides are
readily obtainable from isothiocyanates and acceptor-substituted acetonitriles. Both
of the synthons can be linked to the support. Treatment of the thioamides with a-
bromoketones results in S-alkylation. Under basic conditions (DBU in DMF), this
intermediate cyclizes with the nitrile and forms 3-aminothiophenes in good purity
(Scheme 12.29) [81, 83].
Scheme 12.29
Cyanopyridines are formed upon treatment of resin-bound chalcones with ace-

tonitrile and t-BuOK at rt using ultrasonic irradiation. The rst step is a Thorpe
reaction to yield 3-aminocrotononitriles which react in the subsequent step with
the chalcone [107].
12.4.2
Addition of Nitrogen Nucleophiles
Several additions of N-nucleophiles to nitriles were established on solid phase.

One of the earliest examples of this concept was the reaction of polymer-bound
phthalonitrile with ammonia and NaOMe to yield 1,3-diiminoisoindolines that
were further converted to phthalocyanines [108]. The reaction of b-oxo-nitriles with
hydrazines aorded 5-aminopyrazoles regioselectively (Scheme 12.30). Both poly-
mer-bound b-keto nitriles [109] and a-formyl nitriles [110] were used as substrates.
With the former, a preformed combination between a linker and the b-keto nitrile
Scheme 12.30
was attached to the support. a-Formyl nitriles are accessible by reaction of immo-
bilized benzylnitrile with Brederecks reagent [bis-(dimethylamino)-t-butyloxy-
methane]. Cyclization occurs upon treatment with hydrazines and heating at 70 C
in 10% AcOH/EtOH for 5 h. The 5-aminopyrazoles were obtained in high purity.
In a similar approach, a; b-unsaturated nitriles were cyclized with hydrazines
using NaOEt as a base to yield 3-amino-2-pyrazolines in high purity. Heating at 70

C in ethanol for 24 h was necessary for complete conversion [111].
Kaisers oxime resin was used for the introduction of a hydroxylamine group
to cyanouorobenzenes. Cleavage of the hydroxylamine and cyclization was per-
formed in a one-step procedure using TFA/5 N HCl to yield 3-aminobenzis-
oxazoles in high purity (Scheme 12.31) [112, 113]. An example with the in situ
generation of the hydroxylamine nucleophile is the reduction of a polymer-bound
2-nitro-benzylnitrile with tin(II) chloride dihydrate. Hydroxylamine, an intermedi-
ate of the reduction, is trapped by cyclization with the nitrile to aord 2-amino-1-
hydroxyindoles [114].
Scheme 12.31
Guanidines can also act as the attacking N-nucleophile. This feature has been
exploited for the solid-phase synthesis of 2,4-diaminoquinazolines. The guanidines
were synthesized using acylisothiocyanate resin and 2-aminobenzonitriles as
building blocks. Cleavage and cyclization occurs during heating with TFA/H2 O
(95:5) at 80 C for 16 h. The cleavage step is repeated once. Following this proce-
dure, diaminoquinazolines were obtained in high purity and good yield [115].
There are only a few examples of nucleophilic conversions of nitriles that occur
without cyclization. One example is the aminolysis of polymer-bound nitriles with
hydroxylamine hydrochloride and DIPEA in 2-methoxyethanol at 85 C for 16 h to
provide amide oximes with a quantitative yield (Scheme 12.32). The products ob-
tained were used in the synthesis of oxadiazoles [116]. Another example is the re-
action of a-(benzotriazol-1-yl)acetonitril with amines in 2-methoxyethanol at 7580

C. The formed amidines were not isolated but were directly treated with resin-
bound chalcones to yield aminopyridines that had high purity after cleavage.
Scheme 12.32
12.4.3
Addition of Sulfur Nucleophiles
Polymer-bound nitriles can be converted to thioamides using dithiophosphoric

acid O,O-diethylester in THF/H2 O at 70 C (Scheme 12.33) [117]. The thioamides
have been used for the synthesis of thiazoles (see Sect. 12.3.3) [94].
Scheme 12.33
References
1 M. M. Sim, A. Ganesan, J. Org. Chem. 12 V. Krchnak, A. S. Weichsel, D.

1997, 62, 32303235. Cabel, Z. Flegelova, M. Lebl, Mol.
2 A. K. Szardenings, T. S. Burkoth, Diversity 1995, 9, 149.
G. C. Look, D. A. Campbell, J. Org. 13 C. G. Boojamra, K. M. Burow, J. A.
Chem. 1996, 61, 67206722. Ellman, J. Org. Chem. 1995, 60, 5742
3 B. A. Kulkarni, A. Ganesan, J. 5743.
Chem. Soc., Chem. Commun. 1998, 14 H. Maehr, R. Yang, Tetrahedron Lett.
785786. 1996, 37, 54455448.
4 M. M. Sim, C. L. Lee, A. Ganesan, J. 15 A. R. Katritzky, L. H. Xie, G. F.
Org. Chem. 1997, 62, 93589360. Zhang, M. Griffith, K. Watson, J.
5 S. V. Ley, M. H. Bolli, B. Hinzen, S. Kiely, Tetrahedron Lett. 1997, 38,
A.-G. Gervois, B. J. Hall, J. Chem. 70117014.
Soc., Perkin Trans. 1 1998, 2239 16 N. M. Khan, V. Arumugam, S.
2241. Balasubramanian, Tetrahedron Lett.
6 J. Habermann, S. V. Ley, J. S. Scott, 1996, 37, 48194822.
J. Chem. Soc., Perkin Trans. 1 1998, 17 M. Gustafsson, R. Olsson, C. M.
31273130. Andersson, Tetrahedron Lett. 2001, 42,
7 K. Hemming, M. J. Bevan, C. 133136.
Loukou, S. D. Patel, D. Renaudeau, 18 M. W. Creswell, G. L. Bolton, J. C.
Synlett 2000, 15651568. Hodges, M. Meppen, Tetrahedron
8 S. W. Kaldor, M. G. Siegel, J. E. 1998, 54, 39833998.
Fritz, B. A. Dressman, P. J. Hahn, 19 H. Waldmann, M. Braun, J. Org.
Tetrahedron Lett. 1996, 37, 7193 Chem. 1992, 57, 4444.
7196. 20 S. Kobayashi, S. Nagayama, T.
9 S. W. Kim, S. Y. Ahn, J. S. Koh, J. H. Busujima, Tetrahedron Lett. 1996, 37,
Lee, S. Ro, H. Y. Cho, Tetrahedron 92219224.
Lett. 1997, 38, 46034606. 21 M. Shimizu, S. Itohara, Synlett 2000,
10 Y. Aoki, S. Kobayashi, J. Comb. 18281830.
Chem. 1999, 1, 371372. 22 A. Fujii, M. Sodeoka, Tetrahedron
11 J. Green, J. Org. Chem. 1995, 60, Lett. 1999, 40, 80118014.
42874290. 23 S. Kobayashi, I. Hachiya, S. Suzuki,
References 343
M. Moriwaki, Tetrahedron Lett. 1996, 43 C. X. Chen, I. A. McDonald, B.

37, 28092812. Munoz, Tetrahedron Lett. 1998, 39,
24 S. Kobayashi, M. Moriwaki, Tetra- 217220.
hedron Lett. 1997, 38, 42514254. 44 C. X. Chen, B. Munoz, Tetrahedron
25 S. Kobayashi, M. Moriwaki, R. Lett. 1998, 39, 67816784.
Akiyama, S. Suzuki, I. Hachiya, 45 C. X. Chen, B. Munoz, Tetrahedron
Tetrahedron Lett. 1996, 37, 77837786. Lett. 1999, 40, 34913494.
26 S. Kobayashi, Y. Aoki, Tetrahedron 46 S. Wendeborn, Synlett 2000, 4548.
Lett. 1998, 39, 73457348. 47 B. A. Lorsbach, R. B. Miller, M. J.
27 S. Kobayashi, R. Akiyama, H. Kurth, J. Org. Chem. 1996, 61, 8716
Kitagawa, J. Comb. Chem. 2000, 2, 8717.
438440. 48 B. A. Lorsbach, J. T. Bagdanoff, R.
28 S. Kobayashi, T. Furuta, K. Sugita, B. Miller, M. J. Kurth, J. Org. Chem.
O. Okitsu, H. Oyamada, Tetrahedron 1998, 63, 22442250.
Lett. 1999, 40, 13411344. 49 M. A. Youngman, S. L. Dax, Tetra-
29 Y. H. Wang, S. R. Wilson, Tetra- hedron Lett. 1997, 38, 63476350.
hedron Lett. 1997, 38, 40214024. 50 A. B. Dyatkin, R. A. Rivero, Tetra-
30 C. J. Creighton, C. W. Zapf, J. H. hedron Lett. 1998, 39, 36473650.
Bu, M. Goodman, Org. Lett. 1999, 1, 51 J. J. McNally, M. A. Youngman, S. L.
14071409. Dax, Tetrahedron Lett. 1998, 39, 967
31 D. Jonsson, H. Molin, A. Unden, 970.
Tetrahedron Lett. 1998, 39, 10591062. 52 L. H. Yang, L. Q. Guo, Tetrahedron
32 N. A. Petasis, Z. D. Patel, Tetrahedron Lett. 1996, 37, 50415044.
Lett. 2000, 41, 96079611. 53 H. A. Dondas, R. Grigg, W. S.
33 S. R. Klopfenstein, J. J. Chen, A. MacLachlan, D. T. MacPherson, J.
Golebiowski, M. Li, S. X. Peng, X. Markandu, V. Sridharan, S.
Shao, Tetrahedron Lett. 2000, 41, Suganthan, Tetrahedron Lett. 2000,
48354839. 41, 967970.
34 A. Golebiowski, S. R. Klopfenstein, 54 H. S. Wang, A. Ganesan, Org. Lett.
J. J. Chen, X. Shao, Tetrahedron Lett. 1999, 1, 16471649.
2000, 41, 48414844. 55 H. C. Zhang, K. K. Brumeld, L.
35 N. Schlienger, M. R. Bryce, T. K. Jaroskova, B. E. Maryanoff, Tetra-
Hansen, Tetrahedron 2000, 56, 10023 hedron Lett. 1998, 39, 44494452.
10030. 56 H. Miyabe, Y. Fujishima, T. Naito, J.
36 W. J. N. Meester, F. P. J. T. Rutjes, Org. Chem. 1999, 64, 21742175.
P. H. H. Hermkens, H. Hiemstra, 57 G. H. Jeon, J. Y. Yoon, S. Kim, S. S.
Tetrahedron Lett. 1999, 40, 16011604. Kim, Synlett 2000, 128130.
37 J. J. N. Veerman, F. P. J. T. Rutjes, J. 58 H. Miyabe, H. Tanaka, T. Naito,
H. van Maarseveen, H. Hiemstra, Tetrahedron Lett. 1999, 40, 83878390.
Tetrahedron Lett. 1999, 40, 60796082. 59 A. Paio, A. Zaramella, R. Ferritto,
38 R. C. D. Brown, M. Fisher, J. Chem. N. Conti, C. Marchioro, P. Seneci,
Soc. Chem. Commun. 1999, 1547 J. Comb. Chem. 1999, 1, 317325.
1548. 60 A. R. Katritzky, S. A. Belyakov, D.
39 B. Chenera, J. A. Finkelstein, D. F. O. Tymoshenko, J. Comb. Chem.
Veber, J. Am. Chem. Soc. 1995, 117, 1999, 1, 173176.
1199912000. 61 D. Tumelty, M. K. Schwarz, K. Cao,
40 M. Schuster, J. Pernerstorfer, S. M. C. Needels, Tetrahedron Lett. 1999,
Blechert, Angew. Chem. Int. Ed. 1996, 40, 61856188.
35, 19791980. 62 J. P. Mayer, G. S. Lewis, C. McGee,
41 S. Itsuno, A. A. El-Shehawy, M. Y. D. Bankaitis-Davis, Tetrahedron Lett.
Abdelaal, K. Ito, New J. Chem. 1998, 1998, 39, 66556658.
775777. 63 Z. M. Wu, P. Rea, G. Wickham,
42 C. X. Chen, B. Munoz, Tetrahedron Tetrahedron Lett. 2000, 41, 9871
Lett. 1998, 39, 34013404. 9874.
64 J. P. Mayer, G. S. Lewis, M. J. 86 H. P. Buchstaller, Tetrahedron 1998,

Curtis, J. W. Zhang, Tetrahedron Lett. 54, 34653470.
1997, 38, 84458448. 87 J. Y. Yoon, C. W. Cho, H. Han, K. D.
65 A. M. LaPointe, J. Comb. Chem. 1999, Janda, J. Chem. Soc. Chem. Commun.
1, 101104. 1998, 27032704.
66 D. Simoni, R. Rondanin, M. 88 C. Subramanyam, Tetrahedron Lett.
Morini, R. Baruchello, F. P. 2000, 41, 65376540.
Invidiata, Tetrahedron Lett. 2000, 41, 89 L. J. Fitzpatrick, R. A. Rivero,
67 C. Z. Zhang, A. M. M. Mjalli, 7482.
Tetrahedron Lett. 1996, 37, 54575460. 90 M. J. Soa, R. Hunter, T. Y. Chan,
68 E. A. Boyd, W. C. Chan, V. M. Loh, A. Vaughan, R. Dulina, H. M.
Tetrahedron Lett. 1996, 37, 16471650. Wang, D. Gange, J. Org. Chem. 1998,
69 N. J. Ede, A. M. Bray, Tetrahedron Lett. 63, 28022803.
1997, 38, 71197122. 91 C. M. Yeh, C. M. Sun, Tetrahedron
70 H. S. Oh, H. G. Hahn, S. H. Cheon, Lett. 1999, 40, 72477250.
D. C. Ha, Tetrahedron Lett. 2000, 41, 92 J. Lee, D. Gauthier, R. A. Rivero,
71 M. C. Munson, A. W. Cook, J. A. 93 S. Makino, N. Suzuki, E. Nakanishi,
Josey, C. Rao, Tetrahedron Lett. 1998, T. Tsuji, Tetrahedron Lett. 2000, 41,
39, 72237226. 83338337.
72 C. P. Holmes, J. P. Chinn, G. C. 94 D. Goff, J. Fernandez, Tetrahedron
Look, E. M. Gordon, M. A. Gallop, Lett. 1999, 40, 423426.
J. Org. Chem. 1995, 60, 73287333. 95 D. S. Dodd, O. B. Wallace, Tetrahe-
73 N. Schlienger, M. R. Bryce, T. K. dron Lett. 1998, 39, 57015704.
Hansen, Tetrahedron Lett. 2000, 41, 96 R. Y. Yang, A. Kaplan, Tetrahedron
51475150. Lett. 2000, 41, 70057008.
74 M. Patek, B. Drake, M. Lebl, 97 L. J. Wilson, S. R. Klopfenstein, M.
Tetrahedron Lett. 1996, 36, 22272230. Li, Tetrahedron Lett. 1999, 40, 3999
75 C. L. Lee, Y. L. Lam, S. Y. Lee, 4002.
Tetrahedron Lett. 2001, 42, 109111. 98 J. A. Josey, C. A. Tarlton, C. E.
76 F. J. Wang, J. R. Hauske, Tetrahedron Payne, Tetrahedron Lett. 1998, 39,
Lett. 1997, 38, 86518654. 58995902.
77 D. H. Drewry, S. W. Gerritz, J. A. 99 P. C. Kearney, M. Fernandez, J. A.
Linn, Tetrahedron Lett. 1997, 38, Flygare, Tetrahedron Lett. 1998, 39,
33773380. 26632666.
78 C. P. Lopez, P. Molina, E. Aller, A. 100 A. Gopalsamy, H. Yang, J. Comb.
Lorenzo, Synlett 2000, 14111414. Chem. 2000, 2, 378381.
79 D. H. Drewry, C. Ghiron, Tetrahe- 101 S. E. Schneider, P. A. Bishop, M. A.
dron Lett. 2000, 41, 69896992. Salazar, O. A. Bishop, E. V. Anslyn,
80 J. M. Villalgordo, D. Obrecht, A. Tetrahedron 1998, 54, 1506315086.
Chucholowsky, Synlett 1998, 1405 102 J. Chen, M. Pattarawarapan, A. J.
1407. Zhang, K. Burgess, J. Comb. Chem.
81 F. Zaragoza, Tetrahedron Lett. 1996, 2000, 2, 276281.
37, 62136216. 103 L. Gomez, F. Gellibert, A. Wagner,
82 F. Zaragoza, Tetrahedron Lett. 1997, C. Mioskowski, J. Comb. Chem. 2000,
38, 72917294. 2, 7579.
83 H. Stephensen, F. Zaragoza, J. Org. 104 R. Perez, O. Reyes, M. Suarez, H. E.
Chem. 1997, 62, 60966097. Garay, L. J. Cruz, H. Rodriguez, M.
84 P. Y. Chong, P. A. Petillo, D. Molero-Vilchez, C. Ochoa,
Tetrahedron Lett. 1999, 40, 45014504. Tetrahedron Lett. 2000, 41, 613616.
85 H. Shao, M. Colucci, S. J. Tong, H. 105 S. J. Shuttleworth, M. Quimpere,
S. Zhang, A. L. Castelhano, N. Lee, J. DeLuca, Mol. Diversity 1998,
Tetrahedron Lett. 1998, 39, 72357238. 4, 183185.
References 345
106 A. M. Shestopalov, V. P. Kislyi, E. Y. 112 S. D. Lepore, M. R. Wiley, J. Org.

Kruglova, K. G. Nikishin, V. V. Chem. 1999, 64, 45474550.
Semenov, A. C. Buchanan, A. A. 113 S. D. Lepore, M. R. Wiley, J. Org.
Gakh, J. Comb. Chem. 2000, 2, 2428. Chem. 2000, 65, 29242932.
107 A. L. Marzinzik, E. R. Felder, J. Org. 114 H. Stephensen, F. Zaragoza,
Chem. 1998, 63, 723727. Tetrahedron Lett. 1999, 40, 5799
108 C. C. Leznoff, P. I. Svirskaya, B. 5802.
Khouw, R. L. Cerny, P. Seymour, A. 115 L. J. Wilson, Org. Lett. 2001, 3, 585
B. P. Lever, J. Org. Chem. 1991, 56, 588.
8290. 116 N. Hebert, A. L. Hannah, S. C.
109 S. P. Watson, R. D. Wilson, D. B. Sutton, Tetrahedron Lett. 1999, 40,
Judd, S. A. Richards, Tetrahedron 85478550.
Lett. 1997, 38, 90659068. 117 R. J. Booth, J. C. Hodges, J. Am.
110 R. D. Wilson, S. P. Watson, S. A. Chem. Soc. 1998, 119, 48824883.
Richards, Tetrahedron Lett. 1998, 39, 118 M. Z. Hoemann, A. Mllikian-
28272830. Badalian, G. Kumaravel, J. R.
111 L. O. Lyngso, J. Nielsen, Tetrahedron Hauske, Tetrahedron Lett. 1998, 4749
Lett. 1998, 39, 58455848. 4752.
346
13
Chemistry of the Carbonyl Group
Tobias Wunberg
13.1
Introduction
The carbonyl group is one of the most important functional groups in organic
chemistry. It is found in various structural classes, each one having its own char-
acteristic and fascinating chemistry. The wealth of chemical transformations
involving carbonyl groups covers virtually all forms of organic reactions, thus
making the carbonyl group an unreplacable tool in synthetic organic chemistry.
Additionally, this structural unit is extremely important in medicinal chemistry.
Seventy per cent of known drugs (CMC database vers. 94.1) contain carbonyl
groups in various manifestations [1]. This chapter deals with the application of
carbonyl group chemistry to the generation of libraries. It will not include CaC
single bond-forming reactions, enolate chemistry, or reductions and oxidations in-
volving carbonyl groups. These reactions are dealt with in other chapters.
13.2
Chemistry of the Carbonyl Group and Combinatorial Chemistry
Since this chapter deals with mechanistically dierent chemical transformations, a

general statement about the application of carbonyl group chemistry for library
synthesis cannot be made. Some of the described reactions such as the formation
of amides or reductive aminations play a key role in combinatorial chemistry.
Others are frequently used, for example Wittig-type olenations, and some have
only rarely been used, e.g. Curtius degradation. Basically, they are all suited for
both solution-phase and solid-phase chemistry even though the choice between
these two formats has consequences for the reaction conditions. These aspects will
be discussed in more detail for each individual reaction.
For some reactions there is a standard procedure which is generally suited to a
rst test. But this does not guarantee a satisfactory result and does not suggest that
other methods may not give better yields and purities. Each reaction may have to
be optimized by parameters such as base, solvent, time, temperature, and reagents

ISBN: 3-527-30509-2
in order to determine reaction conditions that are applicable to as broad a range of

reactions as possible.
13.3
Chemistry of Carboxylic Acids
13.3.1
C(O)--X Bond-forming Reactions: General Remarks
From a mechanistic point of view, the transformation of carboxylic acids into

amides or esters might not be the most spectacular reaction, however nicely
they demonstrate the fundamental principles and mechanisms of carbonyl group
chemistry. For his pioneering work in solid-phase chemistry, Bruce Merrield
chose previously established procedures for the formation of amides (more pre-
cisely, peptides) [2]. Since then, the formation of amides has become one of the
best-elaborated reactions in solid-phase chemistry [3]. Since peptides usually have
pharmacokinetically unfavorable properties, the focus of combinatorial chemistry
in medicinal chemistry has recently shifted toward the synthesis of nonpeptidic,
more drug-like small molecules (see Chapter 22). Nevertheless, C(O)aN and
C(O)aO bond-forming reactions still play a key role in combinatorial chemistry
both in solution phase and on solid phase. The reliability and large number of
commercially available building blocks explain why this reaction type has main-
tained its importance.
13.3.1.1 Amides and Ureas
Formation of amides
There is a mechanistic requirement for the transformation of carboxylic acids into
amides: the introduction of a suitable leaving group instead of the OH group prior
to the reaction with a nucleophile (amine). Two principal ways of activation are
feasible: replacement of the OH group with better leaving groups (e.g. acid hal-
ides) or transformation of the OH moiety into a suitable leaving group (e.g. active
esters, anhydrides). While planning the synthesis of a library one should keep in
mind that the choice between solution and solid phase may cause limitations
which have their origin in the combination of the specic demands of resin-based
chemistry, the ecacy of coupling reagents, and the formation of acid chlorides.
A plethora of methods and conditions has been described for the formation of
acid chlorides in solution phase and most of them are applicable to parallel syn-
thesis and library production. Consequently, the reaction of acid chlorides with
aliphatic amines is a standard reaction and has been used in numerous pre-
parations of libraries in solution. In our hands, CH2 Cl2 or tetrahydrofuran (THF)
as solvent and NEt3 or DIEA as base are the standard methods. Even aromatic
amines can be smoothly converted into amides under these conditions. Further-
more, this protocol is also suitable for the formation of amides on solid phase with
348 13 Chemistry of the Carbonyl Group
immobilized aliphatic and aromatic amines. For resin-bound carboxylic acids,

however, there is an intrinsic problem with the formation of the corresponding
acid chloride. Acidic reagents such as SOCl2 or POCl3 are incompatible with acid-
sensitive linkers as well as with the resin itself. A few approaches promise a solu-
tion to this problem, e.g. Ghosezs reagent [4], Appels PPh3 /CCl 4 combination [5],
oxalyl chloride [6], or alternatively formation of acid uorides (Scheme 13.1) using
cyanuric uoride [7], DAST [8], or TFFH [9]. However, none of these methods has
so far been described for the synthesis of larger libraries.
Scheme 13.1. Transformation of aromatic carboxylic acids into acid uorides.
In addition to the use of acid chlorides, chemists have been successfully trans-
forming carboxylic acids into amides using coupling reagents. A large variety of
reagents has been developed which provide chemists with a tool-box for the syn-
thesis of large and complex structures [10]. Numerous examples demonstrate the
ecacy of these methods for library synthesis in solution phase as well as in solid
phase. In the latter case, both starting materials can be bound to the resin: activa-
tion of a polymer-bound acid followed by addition of the amine, or the addition of
an excess acid plus coupling reagent to a polymer-bound amine.
The reaction of active esters with aliphatic amines generally leads to the forma-
tion of the desired amide in high yield and purity. However, the formation of ani-
lides using active esters as acylating agents poses diculties and only the most re-
active coupling reagents may give satisfactory results (see Table 13.1). Therefore,
the use of acid chlorides is necessary when anilines are used as nucleophiles.
The best conditions for a particular acylation are highly dependent on the steric
and electronic nature of both the amine and carboxylic acid. There is no general
rule as to which reagent is the best for a particular reaction and each case has to be
optimized with respect to coupling reagent, base, solvent, etc. Nevertheless, there
are some general guidelines for the choice of an appropriate coupling reagent:
. Carbodiimide-mediated couplings without additional reagents (HOBt) are a

source for racemization. Therefore they are not recommended for uorenylmeth-
oxycarbonyl (Fmoc) amino acids [18].
. DIC/HONSu-mediated couplings occur under slightly acidic conditions, thus
avoiding formation of N-acyl ureas.
. HOBt-based active esters suppress racemization of amino acids. This type of
activation usually requires activating bases (usually DIEA or NMM).
. Pyrrolidino derivatives of both phosphonium and uronium salts derived from
HOBt are slightly more reactive and less toxic than the dimethylamino deriva-
tives (e.g. PyBOP vs. BOP).
Tab. 13.1. Coupling reagents for amide synthesis.
Building blocks Coupling reagent Comment Reference
Acids Amines
Aliphatic and Aliphatic DCC or DIC Potential racemization 11

aromatic (primary) during coupling of a-
(sterically amino acids. DIC is
undemanding) preferred for solid-phase
chemistry (soluble urea)
DIC/HONSu Slightly acidic conditions 12
suitable for strongly basic
amines (e.g. hydrazine)
Aliphatic and Aliphatic HOBt/DIC/DIEA Intermediate formation of 13
aromatic (primary) HOBt esters avoids
amino acids racemization
Aliphatic and Aliphatic HBTU or TBTU/ Preformed HOBt/DIC 14
aromatic (primary and DIEA combination (HBTU:
amino acids secondary) PF
6 salt; TBTU: BF4 salt)
PyBOP/DIEA Fast coupling makes it 15
suitable for base-sensitive
substrates
Aliphatic and Aliphatic and HOAt/DIC/DIEA Developed for cyclization of 16
aromatic aromatic peptides, useful for
amino acids coupling of hindered
amino acids.
HATU/DIEA Preformed HOAt/DIC 17
combination (PF 6 salt)
. Uronium salt-mediated couplings may cause side-reactions such as the transfor-

mation of the N-terminus into a guanidinium residue [19]. Phosphonium re-
agents do not take part in this reaction [20].
. HBTU and TBTU are very popular for peptide synthesis.
. HATU or HOAt/DIC most likely yield the best results for dicult couplings, e.g.
secondary amines [21], cyclizations, or anilines. Unfortunately, compared with
other reagents they are rather expensive.
In the early days of combinatorial chemistry, these methods were used for the
construction of peptide libraries on solid phase leading to potent, bioactive lead
structures or elucidation of binding motifs [22]. Today, the application of coupling
reagents for amide synthesis remains an essential part of combinatorial chemistry.
Amino acids have gained popularity as readily available, multifunctional templates
with a high degree of diversity and biological importance, and they are often used
as valuable building blocks for the library synthesis of small molecules [23].
For parallel amide synthesis in solution phase, polymer-bound variations of the
well-known coupling reagents have been shown to be powerful tools for avoiding
tedious work-up procedures. The rst report of modied DIC on a crosslinked

polystyrene (PS) resin appeared in the early 1970s [24]. More recently, an N 0 -
(3-dimethylaminopropyl)-N-ethylene carbodiimide (EDC)-based resin (P-EDC) was
developed that couples amines and carboxylic acids more eciently (Scheme 13.2)
[25].
Scheme 13.2. Use of P-EDC in amide bond formation.
Additionally, carboxylic acids can be activated by polymer-bound HOBt [26] or 4-

hydroxy-3-nitrobenzophenone. The latter reagent has been used for the synthesis
of a library of 8000 amides and esters from which a compound with considerable
herbicidal activity was identied (Scheme 13.3) [27].
Scheme 13.3. Synthesis of amides using polymer-bound 4-hydroxy-3-nitrobenzophenone.
Shortcomings of these methods include the limited scope of reactivity of N-

nucleophiles toward these reagents and problems in determining the absolute
loading of the activated resin. The use of polymer-supported tetrauorophenol
promises a solution to both of these problems [28]. In analogy to well-known
solution-phase transformations [29], carboxyl and sulfonyl activated esters can be
prepared that yield amides and sulfonamides, respectively, with a wide range of N-
nucleophiles (Scheme 13.4). Loading of the resin may be quantitatively determined
by 19 F-nuclear magnetic resonance (NMR) spectroscopy.
Scheme 13.4. Synthesis of amides using polymer-bound 4-hydroxy-3-nitrobenzophenone.

This methodology is routinely used for the synthesis of large libraries (10,000
members) for lead discovery or for targeted libraries, e.g. optimization of factor Xa
inhibitors [30].
Formation of ureas general aspects

There are two standard procedures that are used in the formation of ureas: The
classical reaction of isocyanates with amines, and the treatment of amines with
carbonyl insertion compounds such as p-NPCF [31] or CDI [32] followed by addi-
tion of another amine. Both procedures are suitable for library synthesis in solu-
tion phase or on solid support [33].
Formation of ureas using isocyanates. The solvent of choice for the reaction of
isocyanates with amines is CH2 Cl2 . The reaction usually is completed within 12
h (Scheme 13.5). Prolonged reaction times have been reported to lead to lower
product yields [34].
Scheme 13.5. Formation of ureas from amines and isocyanates.
In solid-phase chemistry, either amines or isocyanates can be immobilized.

The generation of resin-bound isocyanates may be achieved by treating amines
with phosgene or triphosgene [35]. Furthermore, the direct conversion of Fmoc-
protected amines into isocyanates has been described previously (Scheme 13.6) [36].
Scheme 13.6. Formation of isocyanates from Fmoc-protected amines on solid phase.
Trapping immobilized isocyanates with excess of amine proceeds rapidly (30

min). Using polymer-bound isocyanates as scavenging reagents, the time required
for the complete removal of amines (generally nucleophiles) from the reaction
mixture depends on the character of the amine (Scheme 13.7, Table 13.2) [37].
Scheme 13.7. Scavenging of amines using polymer-supported isocyanate.

Tab. 13.2. Comparative scavenging of nucleophiles in DCM (20 C) or DCE (60 C).a
Nucleophile PS-isocyanate (equiv.) T ( C) % Scavenged

(1% crosslinked)
1h 16 h
Piperidine 3.0 20 100

Benzyl amine 3.0 20 100
Aniline 2.0 20 19 89
Aniline 3.0 60 99
2-Aminobenzophenone 3.0 60 81
4-Methoxyphenyl-1-butanol 2.0 20 0 68
4-Methoxyphenyl-1-butanol 3.0 60 0 29
a Brochure by Argonaut Technologies: Polymer Reagents and
Scavengers.
Whereas aliphatic amines are completely removed within 1 h, aromatic amines

generally require longer reaction times and elevated temperatures.
Formation of ureas using carbonyl insertion compounds

Since a larger number of amines than isocyanates is commercially available, the
use of the carbonyl insertion method provides access to a larger and more diverse
number of compounds than the reaction of isocyanates (Scheme 13.8).
Scheme 13.8. p-NPCF-mediated formation of ureas.
This method is limited to the use of electron-rich and sterically undemanding

amines as nucleophiles. Even though anilines have also been used, ureas derived
from anilines are preferably prepared via transforming them into corresponding
isocyanates prior to coupling with the second amine.
The above-mentioned methods for the activation of amines proceed via in situ
formation of the corresponding isocyanate (Schemes 13.6 and 13.8). Therefore,
they are limited to primary amines. However, secondary amines may also be acti-
vated via formation of the corresponding carbamoyl chloride using phosgene or
triphosgene (Scheme 13.9) [38] or by the CDI analog 1,1 0 -carbonylbisbenzotriazole
[39].
Scheme 13.9. Activation of secondary amines with COCl2 for solid-phase synthesis of ureas.
In summary, the formation of ureas using either isocyanates or carbonyl inser-

tion compounds is a straightforward synthetic transformation suitable for library
synthesis both in solution and on solid phase.
Formation of ureas recent applications

Ureas have been used as precursors of the benzoxazine moiety. Anthranilic acids
were treated with isocyanates in solution and the obtained ureas were cyclized with
polymeric EDC (Scheme 13.10) [40]. Simultaneously, unreacted excess of an-
thranilic acid was bound to the carbodiimide and could be ltered o from the re-
action mixture yielding products in 8097% purity.
Scheme 13.10. Solution-phase library using ureas as precursors of benzoxazines.
13.3.1.2 Esters and Urethanes
General remarks
For both solution- and solid-phase chemistry, esters and urethanes commonly
serve as protecting groups for carboxylic acids and amines, respectively [41]. Addi-
tionally, they are one of the most common ways to attach a molecule to a poly-
meric support. In the context of library synthesis, esters and urethanes may of
course occur as part of the targeted molecule [42].
Formation of esters
A wealth of methods exist for the esterication of carboxylic acids. Almost all of
them are suitable for parallel synthesis. Among these methods, DIC/DMAP (Steg-
lich esterication) [43], 2,4,6-trichlorobenzoyl chloride (Yamaguchi esterication)
[44], or 2,6-dichlorobenzoyl chloride [45] and the reaction of alcohols with acid
chlorides or anhydrides are the most prominent ones in solution phase. In partic-
ular, the Steglich procedure seems to be suitable for automation and paralleliza-
tion since polymeric carbodiimides are readily available (Scheme 13.11) [46].
Conversion of polymer-bound alcohols using these methods is as ecient as
in solution phase. Owing to the lack of methods for acid chloride formation on
solid phase (see Section 13.3.1), esterication of immobilized carboxylic acids is
Scheme 13.11. Parallel esterication using polymeric carbodiimides: taxol analogs.
mostly realized using either the Steglich or the Yamaguchi procedure. Neverthe-
less, the condensation with primary or secondary alcohols using DIC/DMAP or
2,4,6-trichlorobenzoyl chloride has been well described. Additionally, the combina-
tion MSNT/NMI has been reported to be superior for the coupling of immobilized
aromatic carboxylic acids to primary and secondary alcohols compared with the
Steglich or Yamaguchi esterication (Scheme 13.12) [47].
Scheme 13.12. Esterication of aromatic carboxylic acids using MSNT/NMI.
Hydrolysis of esters
In solution, esters are normally hydrolyzed using hydroxides such as LiOH,
NaOH, or KOH in aqueous (50%) MeOH or THF [41]. These procedures are suit-
able for parallelization. Adaptation of these methods to solid phase sometimes re-
quires slight modication of experimental details. Because of the extremely poor
swelling properties of PS-based resins in water and alcohols, hydrolysis requires
addition of solvents with better swelling properties usually THF. NaOH or LiOH
in THF/H2 O (4:1 v/v) or THF/MeOH/H2 O (3:1:1 v/v) at room temperature (rt) or
at 50 C generally give good conversions (Scheme 13.13) [48].
Scheme 13.13. Saponication of esters during library synthesis on solid phase.
Formation of carbamates
There are two standard ways for the formation of carbamates: rst, from amines
and chloroformates (Scheme 13.13); second, from alcohols and isocyanates or car-
bonyl insertion compounds. In contrast to the reaction of amines with isocyanates,
the reaction of alcohols and isocyanates requires an activating base in order to

achieve fast conversion. Usually, NEt3 or DIEA is used (Scheme 13.14).
Scheme 13.14. Formation of carbamates from alcohols and isocyanates.
Besides this small modication, experimental details, scope, and limitations as

well as applications of this reaction in solution or on solid phase are analogous to
the formation of amides and ureas respectively (Section 13.3.1) [49].
13.3.2
Transformation of Carboxylic Acids into Other Functional Groups
The transformation of carboxylic acids into other functional groups is a powerful

tool for the generation of new functionality. However, the reactions covered in this
chapter have been described mostly as useful transformations but have not been
used for library synthesis. The synthesis of larger libraries using these concepts
has yet to be realized.
13.3.2.1 Formation of Ketones

Carboxylic acids are often used as precursors in the synthesis of aldehydes and ke-
tones. The standard way to transform a carboxylic acid into a ketone is the two-step
procedure of forming the corresponding Weinreb amide and subsequent addition
of metallorganic reagents (see Chapter 16). The transformation of a carboxylic acid
into the corresponding a-halomethyl ketone can be achieved by adding a diazo-
methane solution to the previously activated (via a mixed anhydride) carboxylic
acid. The resulting diazomethylketone can be transformed into the a-halo ketone
by treating it with tetrabutyl ammonium salts, (n-Bu 4 N X ) [50].
Using appropriately protected aspartic acid, this reaction sequence was used for
the solid-phase synthesis of a highly functionalized template bearing four dierent
functional groups (Scheme 13.15). Substitution of the chlorine followed by further
Scheme 13.15. Synthesis of amino acid-derived a-halomethyl ketones on solid phase.

derivatization completed the synthesis of (acyloxy)methylketones as irreversible

inhibitors of the cysteine protease ICE.
13.3.2.2 Formation of Amines: Curtius Degradation

The Curtius degradation transforms carboxylic acids via thermal degradation of
their corresponding azides into isocyanates. In the presence of alcohols, the reac-
tion yields carbamates, whereas in the presence of water the intermediate iso-
cyanate is directly degraded into an amino group. The standard procedure for
solution-phase conversion of the carboxylic acid into the rearranged isocyanate is
the two-step procedure forming the acid azide with DPPA in the presence of base
(usually NEt3 ) followed by heating the bound azide to 90 C in toluene or xylene
[51].
This well-established procedure has been adapted to solid-phase chemistry using
polymer-bound aromatic carboxylic acids (Scheme 13.16) [52]. In contrast to solu-
tion phase, the presence of water gave impure products, whereas in the presence
of alcohols the reaction cleanly yielded the carbamates. However, the use of 9-
uorenylmethanol (Fm-OH) yielded the Fmoc-protected amines from which the
unprotected amine can easily be obtained.
Scheme 13.16. Curtius degradation of carboxylic acids leading to Fmoc-protected amines.
13.3.2.3 Tebbe Olenation

The Tebbe olenation converts esters into the corresponding enol ethers that are
the starting points for a variety of chemical transformations leading to such dier-
ent structures as ketones, amines, thiazoles, and cyclohexanones (Scheme 13.17)
[53].
Scheme 13.17. Tebbe olenation of polymer-bound esters.

Despite its synthetic potential, the Tebbe olenation has only rarely been used
for parallel synthesis. The starting point for a library of thiazoles on solid phase
was the conversion of polymer-bound esters into the corresponding enol ethers
using Tebbe reagents in toluene/THF at room temperature. For the following on-
resin functionalization, the authors elegantly combined the principles of solid- and
solution-phase chemistry (Scheme 13.18): in a rst step, the enol ether is bromi-
nated on the resin, yielding an a-halo ketone equivalent. Formation of thiazoles via
Hantzsch synthesis then simultaneously led to cleavage of the heterocycles from
the resin. Removal of excess thiourea was accomplished by applying a polymeric a-
halo ketone as a scavenger resin.
Scheme 13.18. Modication of enol ethers yielding thiazoles.
13.3.2.4 Formation of Thioamides

Thioamides are valuable precursors for heterocycle synthesis, a prevalent struc-
tural element in marketed drugs. Formation of thioamides on solid support can be
achieved from readily synthesized primary amides of aliphatic and aromatic car-
boxylic acids by treatment with Lawesson reagent (Scheme 13.19) [54].
Scheme 13.19. Formation of thioamides on solid support.
13.4
Reactions of Aldehydes and Ketones
13.4.1
Reactions of Carbonyl Groups with CaH Acidic Compounds
13.4.1.1 Wittig and HornerEmmons Olenations
General aspects
The Wittig and the HornerEmmons olenations are well-established synthetic
transformations for the generation of double bonds. Parallelization of these ex-
tensively used reactions should be straightforward. However, in the literature there
are hardly any descriptions of libraries synthesized in solution. Probably, reactions
have been carried out in a parallel fashion but have not specically been reported
as libraries. Some reports deal with ways to simplify the work-up, e.g. by using
polymeric triphenylphosphine [55]. The situation is dierent for solid-phase syn-
thesis. The reaction of aldehydes or ketones with phosphonium ylides yielding
CaC double bonds was among the rst reactions to be used for the synthesis of
nonpeptidic molecules on solid phase [56]. Numerous examples prove the value of
Wittig and the HornerEmmons olenations for solid-phase synthesis.
Double bonds are versatile starting points for diversication and are, thus, inter-
esting building blocks for combinatorial chemistry. The double bonds obtained by
the Wittig reaction have been used for various purposes, e.g. in olen metathesis
reactions [57] or cycloadditions [58] (Scheme 13.20).
Scheme 13.20. Wittig reaction: diene formation as a precursor for a cycloaddition.
For solid-phase synthesis, two strategies have been pursued: generation of the
ylide in solution and adding it to a polymer-bound aldehyde, as well as the oppo-
site direction generation of the ylide on solid phase and subsequent addition of
the aldehyde to the resin. It is important to note that the choice between these two
possibilities has consequences for the reaction conditions. If the ylide is generated
on solid phase, KOtBu/THF has been reported to be better than NaHMDS/THF
for phosphonium salt-derived ylides [58a]. Additionally, the reaction time for the
generation of immobilized ylides is shorter (560 min) than in solution phase (up
to 3 h). Hydrolysis of these sensitive intermediates can be a signicant problem
unless the resin is rigorously dried prior to use, e.g. azeotroping it with benzene.
Owing to the highly basic conditions of the reaction, the choice of the linker is
also crucial. Even though the Wang linker has been employed previously [see 65],
most examples use more base-stable linkers, e.g. amide linkage [59], trityl-ethers
[56], and carbamates [60]. To avoid ester hydrolysis of substrates bound to Wang
resin, the following procedure has been recommended (Scheme 13.21): generation
of the phosphonate anion, removal of excess base under inert conditions, and ad-
dition of the aldehyde dissolved in 60% cyclohexane in THF [61].
Scheme 13.21. HornerEmmons reaction on Wang resin.

The reasoning behind the cyclohexane/THF mixture was that the less-polar
solvent mixture should suppress ester hydrolysis, while allowing the Horner
Emmons condensation to proceed. The authors successfully synthesized acrylic
acid derivatives from aldehydes containing aliphatic, aromatic, and basic function-
alities. The reaction generally was completed within 2 days.
The undesired cleavage from the resin during ylide generation can also be
avoided by attaching the ylide to the resin via the phosphonate moiety. In this case,
the HornerEmmons reaction has been used for cleaving the molecule from the
resin (Scheme 13.22) [62]. This approach was used for the library synthesis of cy-
clic ketones such as (dl)-muscone: a polymer-bound methylphosphonate was de-
protonated with n-BuLi and quenched with an alkenyl ester. The double bond was
used for subsequent introduction of an aldehyde moiety. The following intra-
molecular olenation (cyclorelease) led to the cyclic enones which were further
derivatized in solution phase.
Scheme 13.22. Intramolecular HornerEmmons reaction.
Recent examples
The use of commercially available polymer-bound PPh3 for Wittig reactions com-
bines ideas from solid-phase synthesis and the application of polymer-supported
reagents (Scheme 13.23) [63]. On the one hand (as a polymer-supported reagent) it
oers the advantage that the byproduct, triphenylphosphine oxide, remains at-
Scheme 13.23. Wittig reaction using polymer-supported triphenylphosphine.

tached to the resin. On the other hand (similar to the function of a linker in solid-
phase synthesis) it immobilizes benzyl halides.
Starting from 2-nitrobenzylbromide, after immobilization and chemical mod-
ications, the products may be cleaved o from the support by an intra- or inter-
molecular Wittig reaction. The intramolecular Wittig reaction yields indoles,
whereas the intermolecular pathway gives access to stilbenes [64].
Double bonds have also been used for the synthesis of peptidomimetics. In this
context, they serve as nonhydrolyzable rigid mimetics of the three-dimensional
structure of the amide bond. The HornerEmmons reaction has been employed as
part of a two-step procedure for solid-phase synthesis of b; g-unsaturated d-amino
acids that mimic dipeptides (Scheme 13.24) [65]. This concept combines both the
use of the double bond as an amide bond mimetic as well as the use of the double
bond for diversication.
Scheme 13.24. HornerEmmons reaction: solid-phase derivatization of the double bond.
13.4.2
Reductive Amination
13.4.2.1 General Aspects

Reductive amination is one of the most frequently used reactions for library gen-
eration in solution phase as well as on solid phase. Starting materials are diverse,
inexpensive, and readily available from commercial sources. Additionally, the sec-
ondary amines obtained may be widely applied to the generation of novel struc-
tures, e.g. heterocycles, sulfonamides, and amides [66]. Last but not least, the re-
action is well suited to automated synthesis. Not surprisingly, a large number of
methods has been elaborated for the multitude of electronic and steric demands of
the building blocks.
13.4.2.2 Formation of Imines

Imines are formed by the condensation of an amine with a ketone or an aldehyde.
Classical methods in solution phase shift the equilibrium toward the imine by re-
moving the water generated during the reaction, e.g. via azeotropic distillation or
applying drying reagents such as molecular sieves or inorganic sulfates. These
methods have also been used for solid-phase chemistry [67], but one should bear
in mind that the distribution of these reagents into a parallel array is not very
convenient. Therefore, trimethylorthoformate (TMOF) has gained popularity as a

universal and resin-compatible desiccant (Scheme 13.25) [68]. Additional methods
for imine formation include the simple use of a large excess of amine [69] or using
ultrasound in the presence of Na2 SO4 [70].
Scheme 13.25. Imine formation on solid support using TMOF as dehydrating reagent.
Imines formed in the presence of TMOF may be isolated and hence can be used
for various purposes besides reduction to amines, e.g. for cycloadditions [71].
In cases where the solubility of the amine component in neat TMOF is low,
cosolvents such as THF or dimethylformamide (DMF) can be used. As a rule of
thumb, the reaction is slower with polymer-bound aldehydes and the amine in so-
lution than with the opposite situation.
A given combination of building blocks has consequences for the reaction con-
ditions depending on the reactivity of the amine and carbonyl components (Table
13.3). The reaction of aliphatic amines and aromatic aldehydes reliably yields the
desired imine within short reaction times at room temperature. Other scenarios
may result in side-reactions or incomplete conversions. Aromatic amines also
form imines, but, depending on their electronic nature, this reaction may require
elevated temperatures and elongated reaction times. Imines derived from aliphatic
aldehydes tend to form the tautomeric enamines. The reactivity of ketones is
strongly inuenced by their structure. Cyclic ketones react nicely whereas acyclic
ketones often show hardly any conversion [72].
13.4.2.3 Reduction of Imines/Enamines

A number of reducing agents has been used for the reduction of imines to sec-
ondary amines. The most frequently used reagents on solid phase are: NaCNBH3
in 1% HOAc/DMF [73], freshly prepared NaBH(OAc)3 or (NBu 4 )BH(OAc)3 [74],
and BH3 py [69a, 75]. They all reduce imines and enamines (e.g. derived from
secondary amines and aldehydes) equally well. Generally, the reducing agent is
added in situ without isolation of the imines or the enamines.
Tab. 13.3. Imine formation depending on amine and carbonyl component.
Carbonyl Amine Comment
Aromatic aldehyde Aliphatic Clean reaction (3 h, rt)

Aliphatic aldehyde Aliphatic Equilibrium with the tautomeric enamine
Aromatic aldehyde Aromatic Requires elevated temperatures and
longer reaction times (e.g. 50 C, 16 h)
Cyclic ketone Aliphatic Mostly a clean reaction
Acyclic ketone Aliphatic Low conversion
Tab. 13.4. Optimized reaction conditions for reductive aminations using NaCNBH3 .
Aldehyde/Aminea Format Experimental detail
Aliphatic aldehyde/aliphatic Solution phase Simply requires NaCNBH3 in TMOF,

amine large excess of aldehyde, no
additional proton source
Aliphatic aldehyde/aliphatic Solid phase Simply requires NaCNBH3 in TMOF,
aminepb (resin) large excess of aldehyde, no
Sterically hindered aliphatic Solution phase Requires premixing (30 min) of
aldehydes/aliphatic amine and aldehyde prior to
amine addition of NaCNBH3 , no
Sterically hindered aliphatic Solid phase Requires premixing (30 min) of
aldehydes/aliphatic (resin) amine and aldehyde prior to
aminepb addition of NaCNBH3 , requires
additional proton source (MeOH
!!!, HOAc leads to overalkylation)
Aromatic aldehyde/ Solution phase Premixing with the amine in TMOF
aliphatic amine followed by the addition of
NaCNBH3 in the presence of 1%
HOAc
Aromatic aldehyde/ Solid phase Premixing with the amine in TMOF
aliphatic aminepb (resin) followed by the addition of
NaCNBH3 in the presence of 1%
HOAc
Aliphatic amine/ketonepb Solid phase pH 5 in MeOH (HOAc)
(pin)
Aromatic amine/ketonepb Solid phase pH 7 in MeOH (HOAc, NMM)
(pin)
a p.b., ( polymer bound) indicates which part is on solid phase.
Reaction conditions have been investigated for all reagents in order to achieve
maximum conversion and to suppress overalkylation. The classical reagent for re-
duction, NaCNBH3 [76], has been optimized with respect to aldehydes and amines
for both solution- and solid-phase chemistry (Table 13.4) [77].
13.4.2.4 Applications
Reductive aminations using polymeric reagents

Reductive aminations in solution phase sometimes require the tedious removal of
boron-containing by-products generated from the reduction step. Solid-supported
borohydrides circumvent this problem. For the synthesis of secondary amines
from primary aliphatic amines an excess of primary amines relative to the alde-
hyde component has been used. After reduction of the corresponding imine with
resin-bound borohydride, excess primary amine was removed by selective imine

formation using a polymer-supported aldehyde (Scheme 13.26) [78].
Scheme 13.26. Reductive amination in solution phase using polymeric borohydride.
Favorable relative kinetics of the competing reactions allowed simultaneous ad-

dition of both resins to the reaction mixture, thus simplifying the experimental
procedure.
Reductive aminations as a starting point for library synthesis

For library synthesis on solid phase, a major application of reductive aminations is
their use as a starting point for library synthesis. During the rst step, large diver-
sity has already been introduced from a multitude of commercially available
amines as building blocks. Subsequent acylation or sulfonylation of the generated
secondary amines is the next step during the synthesis of the desired compounds.
Most commonly, secondary amines are generated from a polymer-bound, elec-
tron-rich aromatic aldehyde (Scheme 13.27). The choice of the appropriate re-
ducing agent does not seem to be crucial, e.g. 2 equiv. RNH2 /NaBH(OAc)3 and 3
equiv. RNH2 /CH(OMe)3 /BH3 py have been successfully applied [79].
Scheme 13.27. Reductive amination as starting point for library synthesis.
Rinks amide linker has been used as a polymer-bound source of amines

(Scheme 13.28) [80]. It became obvious that clean conversion of the sterically
demanding benzhydrylamine was not straightforward and that the choice of the
Scheme 13.28. Reductive amination of Rinks amide linker.

reaction conditions for reducing the imine was crucial. Standard methods failed
(e.g. 110 equiv. R-CHO/NaCNBH3/1% HOAc in DMF). However, adjusting the
solvent system from anhydrous DMF to aqueous THF gave clean monoalkylation
with aliphatic and aromatic aldehydes as well as with ketones.
Reductive amination of ketones: benzopyran library

Even though reductive amination of ketones is often dicult, thorough opti-
mization of the reaction conditions can still lead to suitable synthetic protocols, as
demonstrated by the conversion of benzopyranones (Scheme 13.29). For the re-
duction of imines derived from these relatively unreactive ketones, combinations
of complex boron hydrides with standard proton sources such as HOAc or MeOH
(Table 13.4) failed. Furthermore, heating or sonication led to signicant cleavage
from the resin. However, the use of Ti(OiPr)4 in combination with NaBH(OAc)3
resulted in complete conversion to the desired amine.
Scheme 13.29. Reductive amination of ketones using Ti(OiPr)4 /NaBH(OAc)3 .
The presence of Ti(OiPr)4 requires that the reaction is carefully run under inert
conditions in order to avoid precipitation of TiO2 . The feasibility of this protocol
was demonstrated by the synthesis of a 8448-member library of benzopyrans [81].
Serendipitous reactions as an opportunity for anity breakthroughs

Neuropeptide Y is believed to be involved in the regulation of feeding, energy
metabolism, vascular tone, learning and memory, and the release of pituitary hor-
mones. Researchers have discovered that benzimidazoles act as potent antagonists
of the NPY-1 receptor. Further optimization of the side-chain has been addressed
by a solution-phase library. In order to optimize interaction with the receptor, the
distal piperidine has been modied via reductive amination using polymeric re-
agents and scavenger resins. Only one compound from this library appeared to be
more active than the lead for the library. However, upon resynthesis it became
clear that the anticipated product was not consistent with the spectroscopic data
and that the intermediate imine underwent a spontaneous PictetSpengler cycli-
zation, even in the absence of any reducing agent (Scheme 13.30) [82].
References 365
Scheme 13.30. Unexpected side-reaction yielding biologically active compound.
References
1 G. W. Bemis, M. A. Murcko, J. Med. 12 a) D. Sarantakis, J. Teichman, E. L.

Chem. 1999, 42, 50955099. Lien, R. L. Fenichel, Biochem.
2 B. Merrield, J. Am. Chem. Soc. Biophys. Res. Commun. 1976, 73, 336
1963, 85, 21492154. 342; b) G. B. Fields, C. G. Fields, J.
3 G. Jung, A. G. Beck-Sickinger, Petesh, H. E. van Wart, T. A.
Angew. Chem., Int. Ed. Engl. 1992, 31, Cross, Proc. Natl. Acad. Sci. USA
367383. 1988, 85, 13841388.
4 L. Ghosez, I. George-Koch, L. 13 W. Konig, R. Geiger, Chem. Ber.
Patiny, M. Houtekie, P. Bovie, P. 1970, 103, 788798.
Nshimyumukiza, T. Phan, Tetra- 14 R. Knorr, A. Treciak, W. Bann-
hedron 1998, 54, 92079222. warth, D. Gillessen, Tetrahedron Lett.
5 a) R. Appel, Angew. Chem. 1975, 87, 1989, 30, 19271930.
863874; b) J. B. Lee, J. Am. Chem. 15 a) J. Martinez, J. Bali, M.
Soc. 1966, 33, 3440. Rodriguez, B. Castro, M. Magous, J.
6 B. C. Hamper, S. A. Kolodzielj, A. Laur, M. F. Lignon, J. Med. Chem.
M. Scates, Tetrahedron Lett. 1998, 39, 1985, 28, 18741875; b) J. Coste, D.
20472050. Le-Nguyen, B. Castro, Tetrahedron
7 C. K. Sams, J. Lau, Tetrahedron Lett. Lett. 1990, 31, 205208; c) B. Castro,
1999, 40, 93599362. J. R. Dormoy, G. Evin, C. Selve,
8 C. Kaduk, H. Wenschuh, M. Tetrahedron Lett. 1975, 16, 1219
Beyermann, K. Forner, L. A. 1222.
Carpino, M. Bienert, Lett. Peptide 16 a) L. A. Carpino, J. Am. Chem. Soc.
Sci. 1996, 2, 285. 1993, 115, 43974398; b) L. A.
9 L. A. Carpino, A. El-Faham, J. Am. Carpino, A. El-Faham, Tetrahedron
Chem. Soc. 1995, 117, 54015402. 1999, 55, 68136830.
10 G. B. Fields, R. L. Noble, Int. J. Pept. 17 L. A. Carpino, A. El-Faham, C. A.
Protein Res. 1990, 35, 161214. Minor, F. Albericio, J. Chem. Soc.,
11 a) J. C. Sheehan, G. P. Hess, J. Am. Chem. Commun. 1994, 201203.
Chem. Soc. 1955, 77, 10671068; 18 a) E. Atherton, R. C. Sheppard, J.
b) J. C. Sheehan, M. Goodman, G. P. Chem. Soc. Chem. Commun. 1985,
Hess, J. Am. Chem. Soc. 1956, 78, 165166; b) H. Gross, L. Bilk,
19 a) H. Gausepohl, U. Pieles, R. W. 29 L. KisFaludy, I. Schon, O. Nyeki, M.

Frank, in: Proceedings of the 12th Low, Tetrahedron Lett. 1974, 39, 1785.
American Peptide Symposium. 30 Y. Gong, M. Becker, Y. M. Choi-
Smith, J. A., Rivier, J. E. (eds), Sledeski, R. S. Davis, J. M. Salvino,
ESCOM, Leiden 1992, pp. 523524; b) V. Chu, K. D. Brown, H. W. Pauls,
S. C. Story, J. V. Aldrich, Int. J. Pept. Bioorg. Med. Chem. Lett. 2000, 10,
Protein Res. 1994, 43, 292296. 10331036.
20 F. Albericio, M. Cases, J. Alsina, 31 a) S. M. Hutchins, K. T. Chapman,
S. A. Triolo, L. A. Carpino, S. A. Tetrahedron Lett. 1994, 35, 40554058;
Kates, Tetrahedron Lett. 1997, 38, b) S. M. Hutchins, K. T. Chapman,
21 a) A. A. Virgilio, J. A. Ellman, J. 2586.
Am. Chem. Soc. 1994, 116, 11580 32 H. A. Staab, Liebigs Ann. Chem. 1957,
11581; b) A. Nefzi, J. M. Ostresh, 609, 7583.
R. A. Houghten, Tetrahedron Lett. 33 a) S. W. Kaldor, J. E. Fritz, J. Tang,
1997, 38, 49434946. E. R. McKinney, Bioorg. Med. Chem.
22 a) C. P. Holmes, C. L. Adams, L. M. Lett. 1998, 8, 30413044; b) J. W.
Kochersperger, R. B. Mortensen, Nieuwenhuijzen, P. G. M. Conti,
L. A. Aldwin, Biopolymers 1995, 37, H. C. J. Ottenheijm, J. T. M.
199211; b) Z. M. Ruggeri, R. A. Linders, Tetrahedron Lett. 1998, 39,
Houghten, S. R. Russel, T. S. 78117814.
Zimmerman, Proc. Natl. Acad. Sci. 34 K. Burgess, J. Ibarzo, S. Linthicum,
USA 1986, 83, 57085712; c) A. G. D. H. Russel, H. Shin, A.
Beck-Sickinger, W. Gaida, G. Shitangkoon, R. R. Totani, A. J.
Schnorrenberg, R. Lang, G. Jung, Zhang, J. Am. Chem. Soc. 1997, 119,
Int. J. Pept. Protein Res. 1990, 36, 88 15561564.
94. 35 D. Limal, V. Semetey, P. Dalbon, M.
23 a) B. A. Bunin, J. A. Ellman, J. Am. Jolivet, J.-P. Briand, Tetrahedron Lett.
Chem. Soc. 1992, 114, 1099710998; b) 1999, 40, 27492752.
M. A. Marx, A.-L. Grillot, C. T. 36 P. Y. Chong, P. A. Petillo, Tetra-
Louer, K. A. Beaver, P. A. Bartlett, hedron Lett. 1999, 40, 45014504.
J. Am. Chem. Soc. 1997, 119, 6153 37 a) J. R. Booth, J. C. Hodges, J. Am.
6167; c) E. E. Swayze, Tetrahedron Lett. Chem. Soc. 1997, 119, 4882; b) M. W.
1997, 38, 86438636. Creswell, G. L. Bolton, J. C.
24 N. M. Weinshenker, C.-M. Shen, Hodges, M. Meppa, Tetrahedron 1998,
Tetrahedron Lett. 1972, 13, 3281 54, 3983.
3284. 38 G. T. Wang, Y. Chen, S. Wang, R.
25 M. C. Desai, L. M. S. Stramiello, Sciotti, T. Sowin, Tetrahedron Lett.
Tetrahedron Lett. 1993, 34, 76857688. 1997, 38, 18951898.
26 a) I. E. Pop, B. P. Deprez, A. L. 39 a) H. A. Staab, G. Seel, Liebigs Ann.
Tartar, J. Org. Chem. 1997, 62, 2594 Chem. 1958, 612, 187193; b) A. R.
2603; b) K. Dendrinos, J. Jeong, W. Katritzky, D. P. M. Pleynet, B.
Huang, A. G. Kalivrentenos, Chem. Yang, J. Org. Chem. 1997, 62, 4155
Commun. 1998, 449500. 4158.
27 J. J. Parlow, J. E. Normansell, Mol. 40 B. O. Buckman, M. M. Morissey, R.
Diversity 1995, 1, 266269. Mohan, Tetrahedron Lett. 1998, 39,
28 J. M. Salvino, N. V. Kumar, E. 14871488.
Orton, J. Airey, T. Kiesow, K. 41 a) P. J. Kocienski, Protecting Groups.
Crawford, R. Mathew, P. Thieme, Stuttgart 1994; b) T. W.
Krolikowski, M. Drew, D. Engers, Green, P. G. M. Wuts, Protective
D. Krolikowski, T. Heroin, M. Groups in Organic Synthesis, 2nd edn,
Gardyan, G. McGeehaan, R. Wiley, New York 1991.
Labaudiniere, J. Comb. Chem. 2000, 42 M. F. Gordeev, D. V. Patel, B. P.
2, 691697. England, S. Jonnalagadda, J. D.
References 367
Combs, E. M. Gordon, Bioorg. Med. P. Giannakakou, E. Hamel, Nature

Chem. Lett. 1998, 6, 883889. 1997, 387, 268272.
43 B. Neises, W. Steglich, Angew. Chem. 58 a) M. Crawshaw, N. W. Hird, K.
Int. Ed. Engl. 1978, 17, 522523. Irie, K. Nagai, Tetrahedron Lett. 1997,
44 J. Inanaga, K. Hirata, H. Saeki, T. 40, 71157118; b) N. W. Hird, K.
Katsuki, M. Yamaguchi, Bull. Chem. Irie, K. Nagai, Tetrahedron Lett. 1997,
Soc. Jpn. 1979, 52, 19891993. 38, 71117114; c) P. Grosche, A.
45 P. Sieber, Tetrahedron Lett. 1987, 28, Holtzel, T. B. Walk, A. W. Traut-
61476150. wein, G. Jung, Synthesis 1999, 11,
46 L. Bhat, Y. Liu, S. F. Victory, R. H. 19611970.
Himes, G. I. Georg, Bioorg. Med. 59 D. A. Campbell, J. C. Bermak, J. Org.
Chem. Lett. 1998, 8, 31813186. Chem. 1994, 59, 658660.
47 J. Nielsen, L. O. Lyngso, Tetrahedron 60 D. P. Rotella, J. Am. Chem. Soc. 1996,
Lett. 1996, 37, 84398442. 118, 1224612247.
48 N. Griebenow, T. Wunberg, 61 J. M. Salvino, T. J. Kiesow, S.
unpublished results. Darnbrough, R. Labaudiniere, J.
49 a) B. A. Dressman, L. A. Spangle, Comb. Chem. 1999, 1, 134139.
S. W. Kaldor, Tetrahedron Lett. 1996, 62 K. C. Nicolaou, J. Pastor, N.
37, 937940; b) H. P. Buchstaller, Winssinger, F. Murphy, J. Am.
Tetrahedron 1998, 54, 34653470; Chem. Soc. 1998, 120, 51325133.
c) D. P. Rotella, J. Am. Chem. Soc. 63 W. T. Ford, in: ACS Symposium
1996, 118, 1224612247; d) T. Series 308: Polymeric Reagents and
Wunberg, C. Kallus, T. Opatz, Catalysts. Ford, W. T. (ed.), ACS,
S. Henke, W. Schmidt, H. Kunz, Washington 1986, pp. 155185.
Angew. Chem. Int. Ed. 1998, 37, 2503 64 I. Hughes, Tetrahedron Lett. 1996, 37,
2505. 75957598.
50 M. T. Mujica, G. Jung, Synlett 1999, 65 P. Wipf, T. C. Henninger, J. Org.
19331935. Chem. 1997, 62, 15861597.
51 a) R. Bonjouklian, R. A. Ruden, J. 66 a) Heterocycle formation: P.-P. Kung,
Org. Chem. 1977, 42, 40954103; b) B. E. Swayze, Tetrahedron Lett. 1999,
Chantegrel, S. Gelin, Synthesis 40, 56515654; b) 684-membered
1981, 315316; c) H. Shao, M. library of MMP inhibitors: A. K.
Colucci, S. Tong, H. Zhang, A. L. Szardenings, D. Harris, S. Lam, L.
Castelhano, Tetrahedron Lett. 1998, Shi, D. Tien, Y. Wang, D. V. Patel,
39, 72357238. M. Navre, D. A. Campbell, J. Med.
52 L. S. Richter, S. Andersen, Chem. 1998, 41, 21942200; c) benzo-
Tetrahedron Lett. 1998, 39, 87478750. diazepinediones: C. G. Boojamra,
53 C. P. Ball, A. G. M. Barrett, A. K. M. Burow, J. A. Ellman, J. Org.
Commercon, D. Campere, Y. Kuhn, Chem. 1995, 60, 57425743.
R. S. Roberts, M. L. Smith, O. 67 C. P. Holmes, J. P. Chinn, G. C.
Venier, Chem. Commun. 1998, 2019 Look, E. M. Gordon, M. A. Gallop,
2020. J. Org. Chem. 1995, 60, 73287333.
54 J.-F. Pons, Q. Mishir, A. Nouvet, F. 68 G. C. Look, M. M. Murphy, D. A.
Brookeld, Tetrahedron Lett. 2000, Campbell, M. A. Gallop, Tetrahedron
41, 49654968. Lett. 1995, 36, 29372940.
55 D. H. Drewry, D. M. Coe, S. Poon, 69 a) N. M. Khan, V. Arumugam, S.
Med. Chem. Rev. 1999, 19, 97148. Balasubramanian, Tetrahedron Lett.
56 C. Chen, L. A. Ahlberg Randall, R. 1996, 37, 48194822; b) C. T. Bui,
B. Miller, A. J. Jones, M. J. Kurth, F. A. Rasoul, F. Ercole, Y. Pham,
J. Am. Chem. Soc. 1994, 116, 2661 N. J. Maeji, Tetrahedron Lett. 1998, 39,
2662. 92799282.
57 K. C. Nicolaou, N. Winssinger, J. 70 S. V. Ley, D. M. Mynett, W.-J. Koot,
Pastor, S. Ninkovic, F. Sarabia, Y. Synlett 1995, 10171019.
He, D. Vourloumis, Z. Yang, T. Li, 71 a) G. C. Look, J. R. Schullek, C. P.
Holmes, J. P. Chinn, E. M. Gordon, Bray, D. S. Chiefrai, R. M. Valerio,

M. A. Gallop, Bioorg. Med. Chem. Lett. N. J. Maeji, Tetrahedron Lett. 1995, 36,
1996, 6, 707712; b) R. Singh, J. M. 50815084.
Nuss, Tetrahedron Lett. 1999, 40, 1249 78 S. W. Kaldor, M. G. Siegel, J. E.
1252. Fritz, B. A. Dressman, P. J. Hahn,
72 C. Kallus, T. Wunberg, unpublished Tetrahedron Lett. 1996, 37, 71937196.
results. 79 a) E. E. Swayze, Tetrahedron Lett. 1997,
73 a) G. C. Look, M. M. Murphy, D. A. 38, 84658468; b) A. M. Fivush, T. M.
Campbell, M. A. Gallop, Tetrahedron Willson, Tetrahedron Lett. 1997, 38,
Lett. 1995, 36, 29372940; b) M. 71517154; c) commerical sources
Motokoff, K. Ren, L. K. Wong, J. with high loadings, e.g. Rapp
Med. Chem. 1992, 35, 46964703. Polymere or NovaBiochem.
74 a) A. F. Abdel-Magid, C. A. 80 E. G. Brown, J. M. Nuss, Tetrahedron
Maryanoff, K. G. Carson, Tetrahe- Lett. 1997, 38, 84578460.
dron Lett. 1990, 31, 55955598; b) D. 81 J. G. Breitanbacher, H. C. Hui,
W. Gordon, J. Steele, Bioorg. Med. Tetrahedron Lett. 1998, 39, 8207
Chem. Lett. 1995, 5, 4750. 8210.
75 E. E. Swayze, Tetrahedron Lett. 1997, 82 M. G. Siegel, M. O. Chaney, R. F.
38, 86438646. Bruns, M. P. Clay, D. A. Schober, A.
76 R. F. Borch, M. D. Bernstein, H. D. M. Abbema, D. W. Johnson, B. E.
Durst, J. Am. Chem. Soc. 1971, 93, Cantrell, P. J. Hahn, D. C.
28972904. Hunden, D. R. Gehlert, H.
77 a) A. K. Szardenings, T. S. Burkoth, Zarrinmayeh, P. L. Ornstein, D. M.
G. C. Look, D. A. Campbell, J. Org. Zimmermann, G. A. Koppel,
Chem. 1996, 61, 67206722; b) A. M. Tetrahedron 1999, 55, 1161911639.
369
14
Oxidation Except CC Double Bonds
Henning Steinhagen
14.1
Introduction
Oxidations belong to the very fundamental set of transformations in organic

chemistry. Comparing the rich repertoire of modern oxidation reactions in solu-
tion [1], relatively few reaction types and principles have been transferred to solid
phase and consequently to combinatorial chemistry. The main reason for this fact
is that oxidations usually do not add diversity in the construction of compound
libraries. Also, manipulations of the oxidation stage in combinatorial (multistep)
synthesis are often unwanted and can be avoided by choosing the right building
blocks of correct oxidation states. Nevertheless, oxidations on solid support are
sometimes very useful and reliable transformations. By far the most applied
transformation is the oxidation of primary and secondary alcohol functions to al-
dehydes and ketones. Another important class of oxidation reactions are the for-
mation of sulfoxides and sulfones from suldes. But also more complex oxidation
types such as heterocyclic synthesis and oxidative coupling reactions are becoming
more popular.
The aim of this chapter is to give an overview of useful oxidation reactions
on solid phase. The reactions can be principally divided into two classes: (1) poly-
mer-bound substrate and (2) polymer-bound oxidant. Being applied to combinato-
rial chemistry these two classes often correspond to solid-phase (class 1) and to
solution-phase (class 2) combinatorial chemistry. Since the eld of oxidation reac-
tions on solid support [2] and especially the use of polymer-bound reagents [3] has
been reviewed and published extensively, the focus of this chapter is more to pre-
sent some interesting examples rather than giving a complete literature survey of
all published procedures. Nevertheless, it has been an aim to supply the reader
with the most relevant literature in the references.
14.2
Oxidation of Alcohols to Aldehydes and Ketones
Conversion of alcohols are among the most used and reliable oxidation reac-
tions on solid phase. In general, many protocols from the classic repertoire

ISBN: 3-527-30509-2
370 14 Oxidation Except CC Double Bonds
of solution-phase oxidation reactions have been transferred successfully to solid

phase. By choosing the appropriate reagent, synthetic limitations of the sub-
strate (e.g. temperature instability, chemoselectivity, solvent) and also of the linker/
polymer support system should be carefully considered. The most common and
reliable reagents for oxidation of polymer-bound alcohols include SO3/pyridine
(Scheme 14.1) [4], Swern conditions (Scheme 14.2) [5], DessMartin periodinane
(DMP; Scheme 14.3) [6], perruthenate (TPAP) [7] and Cr reagents (PDC [8],
CrO2 Cl2 [9], CrO2 (Ot-Bu)2 [9b]; Scheme 14.4). Other published methods involve
NCS [10] and IBX [11] as oxidants. There have also been some reports for the
oxidation of polymer-bound phenols by various conditions mostly for coupling reac-
tions [12, see 57, 59, 60a] (Scheme 14.14). In comparison, there are many polymer-
Scheme 14.1. Oxidation step in the synthesis of peptide aldehydes of the (S)-MAPI type [4f ].
Scheme 14.2. Oxidation using the aldol strategy in the solid-phase synthesis of epothilone A [5].
Scheme 14.3. Domino oxidation/DielsAlder pathway to mniopetals [6e].

Scheme 14.4. Oxidationcyclization strategy for the solid-

phase synthesis of carboxypyrrolinones [9a].
bound oxidants available that are suitable for oxidation of alcohols in solution
to the corresponding aldehydes and ketones. Poly(vinyl pyridinium dichromate)
(PVPDC) is an inexpensive, easy-to-use, recyclable reagent for the oxidation of dif-
ferent alcohols, including primary, secondary and allylic alcohols [13]. The latter
can be also oxidized using polymer-supported ammonium perchromate, although
the reagent fails with saturated alcohols [14]. Silica-based chromium reagents have
also been reported as easy to prepare and use for the oxidation of several alcohols
[15]. Many other convenient-to-use reagents such as KMnO4 on kieselguhr [16] and
ammonium chlorochromate on silica [17] have been reported to oxidize a variety
of alcohols. Ammonium chlorochromate proved especially useful for the oxida-
tion of benzoins to benzils. Nevertheless, the main problems of chromium-based
reagents remain selectivity and toxicity issues and the mostly stoichiometric
use. This draw back could be overcome by a very useful reagent for the oxidation
of several alcohols, including primary, benzylic and secondary alcohols: polymer-
supported perruthenate (PSP) [18]. The reagent can be used stoichiometrically or
in catalytic amounts with molecular oxygen or an N-oxide as cooxidant. Using
molecular oxygen as a cooxidant also avoids the need for conventional work-up
(Scheme 14.5) [18b]. Another recently introduced useful oxidant is a TEMPO-
derived oxammonium resin [19]. This powerful oxidant cleanly converts primary
alcohols to aldehydes and also secondary alcohols to ketones (Scheme 14.6).
14.2.1
Examples of the Oxidation of Polymer-bound Primary Alcohols to Aldehydes
Bradley and coworkers [4f ] have described an interesting example using SO3/
pyridine for the oxidation of polymer-bound primary alcohols in the synthesis of
peptide aldehydes based on the human immunodeciency virus (HIV) protease
inhibitor (S)-MAPI. Peptide aldehydes are an important class of transition-state
analogs of dierent proteases and have been of considerable interest since their
initial discovery in natural products [20]. The eciency and reliability of the oxi-
dation step was dramatically improved by the incorporation of a small polyethylene
glycol (PEG) spacer between the linker and the solid support (polystyrene resin).
Scheme 14.5. Examples of oxidation using PSP [18].
In the course of the synthesis, the polymer-bound primary alcohol 1 was oxidized
by SO3/pyridine to the peptide aldehyde 2, which could be readily cleaved using
triuoroacetic acid (TFA).
An interesting example of the Swern oxidation of a primary alcohol in a multi-
step sequence on solid support (Merrield resin) was demonstrated by Nicolaou et
al. [5] in the synthesis of the anticancer agents epothilones A and B. In the course
of the synthesis, the TBS-protected alcohol 3 was deprotected with HF/pyridine
and subsequently oxidized to the aldehyde 4 (> 95% yield). The aldehyde was
essential for further conversion to 5 in a stereoselective aldol reaction. After three
additional steps [1, esterication; 2, metathesis upon cleavage; 3, epoxidation with
methyl-(triuoro-methyl)dioxirane], epothilone A was obtained.
14.2.2
Examples of the Oxidation of Polymer-bound Secondary Alcohols to Ketones
An interesting example using the oxidation of a secondary alcohol was demon-

strated in the synthesis of a building block for a library of analogs of mniopetal
[6e]. The DessMartin oxidation was used as an electronic activation of the di-
enophile 6 for the domino oxidation/inverse intramolecular DielsAlder reaction
attached to Wang resin. The nal product 7 was cleaved under oxidative conditions
using 2,3-dichloro-5,6-dicyanobenzoquinone (DDQ) [21].
Scheme 14.6. Examples of oxidation with oxammonium resin [19].
Miller at al. presented a simple and ecient way for the preparation of carboxy-
pyrrolinones on solid phase [9a]. The pyrrole system is an interesting potentially
bioactive motif for both agrochemicals and pharmaceutical drugs. In this ap-
proach, Wang resin-bound malonic acid [22] 8 was coupled with an amino alcohol
in the presence of 1-hydroxybenzotriazole hydrate (HOBt)/DIC, providing the hy-
droxyamide 9 in high yield. For the oxidation step to 10, several oxidizing reagents
were tested. Under Swern conditions the conversion was not complete because the
Swern reagent is unstable at temperatures above 10 C. SO3/pyridine is stable at
room temperature, but the reagent was not eective for all of the examples shown,
especially N-aryl-substituted compounds. The most broadly applicable reagent was
CrO2 (Ot-Bu)2 generated in situ according to Lezno et al. [9b]. The oxidation of
9 to 10 proceeded successfully for most substrates, and after ring closure with
lithium diisopropylamide (LDA)/ZnCl2 and subsequent cleavage with TFA, the
carboxypyrrolinones 11 could be obtained.
14.2.3
Examples of the Oxidation of Alcohols by Polymer-bound Reagents
Ley and Hinzen introduced polymer-supported perruthenate (PSP), which can be

easily prepared by washing an anion exchange resin with an aqueous solution of
potassium perruthenate [18]. The obtained reagent can be used stoichiometrically
or in catalytic amounts using molecular oxygen or N-oxides [N-methylmorpholine

N-oxide (NMO), TMAO] as cooxidant. Especially in the catalytic version (0.1 equiv.
PSP, O2 as cooxidant), this versatile reagent is very useful.
PSP cleanly oxidizes a,b-unsaturated (e.g. 12) and benzylic alcohols (e.g. 13) in 1
h to the corresponding ketones. Also nonactivated primary alcohols (e.g. 14) and
epoxy alcohols (e.g. 15) are converted, but reaction times are somewhat longer.
Secondary alcohols are unreactive, providing chemoselectivity with this reagent.
Another useful polymer-bound oxidant is the oxammonium TEMPO resin that
was introduced by Rademann and coworkers [19]. In contrast to PSP, this strong
oxidant reacts with both primary alcohols to aldehydes (e.g. 16, 18) and secondary
alcohols (e.g. 17) to the corresponding ketones.
In substrates such as 19, where the initial product is easy enolizable, further oxi-
dation directly leads to the 1,2-diketo compounds. The mechanism of oxidation
(Scheme 14.7) can be rationalized by the intermediate formation of an alkoxy-
TEMPO salt 22 that cleaves to 23 and the corresponding oxidized compound 24.
Prior to the oxidation, the TEMPO polystyrene 20 needs to be activated by NCS,
Br2 or Cl2 , yielding the oxammonium salt 21.
Scheme 14.7. Proposed mechanism for the oxidation of alcohols using oxammonium resin [19].
de Frutos and Curren presented a solution-phase synthesis of libraries of poly-

cyclic natural product analogs by cascade radical annulation (Scheme 14.8) [23].
The aim of the study was to explore the structureactivity relationship (SAR) of
mappicine ketone, which is an antiviral (HCMV, HSV) lead structure in the low
micromolar range [24]. A 48-member library was prepared from three building
blocks and the library was puried at the stage of the mappicine analogs. There-
fore, it was anticipated that a clean and easily removable oxidant would be obtained
with the goal of having suciently clean products for biological testing without
14.3 Oxidation of Polymer-bound Aldehydes to Carboxylic Acids 375
Scheme 14.8. Screening of polymer-bound oxidants in the

synthesis of mappicine ketone analogs [23].
further chromatography. From the screened oxidants, only the polymer-supported

perruthenate (PSP) and chromic acid proved to be useful, whereas other reagents
such as DessMartin periodinane (DMP), polymer-bound PDC, and permanganate
oxidation did not give good results.
14.3
Oxidation of Polymer-bound Aldehydes to Carboxylic Acids
Compared with the oxidation of alcohols to aldehydes and ketones, there are rela-
tively few reports of the direct oxidation of aldehydes to carboxylic acids under
solid-phase conditions. This is because the corresponding alcohols serve as more
stable and easily protectable functional groups in both solid and liquid phase.
Nevertheless, there have been some reports of the oxidation of polymer-bound al-
dehydes to carboxylic acids including the use of NaClO2 [25] and MCPBA [26] as
oxidants. An impressive example was demonstrated by Nicolaou et al. in the solid-
phase synthesis of a combinatorial library of sarcodictyins (Scheme 14.9) [25a]. Sar-
codictyins were discovered in 1987 in a Mediterranean coral [27a] and their potent
antitumor activity (Taxol-like mode of action) was recognized by Ciomei et al. in
1997 [27b]. In the example given, the tricyclic core system 25 was constructed
via multistep synthesis on Merrield resin. After deprotection of 25 using TBAF,
the primary alcohol was oxidized stepwise rst to the unsaturated aldehyde 26
with DMP. After subsequent oxidation to the corresponding carboxylic acid with
NaClO2 , esterication using MeOH/DCC led to the methyl ester 27. The stepwise
procedure gave optimal chemical yields (@95%).
Scheme 14.9. Oxidation sequence in the solid-phase synthesis of sarcodictyins [25a].
14.4
Oxidation of Sulfur-containing Compounds
Oxidation of sulfur-containing compounds on solid phase is a quite common and

usually high-yielding reaction. Most typically suldes are converted to their
corresponding sulfoxides or sulfones. Typical oxidants for polymer-bound sulfur-
containing compounds are MCPBA [28, 29] and H2 O2 [30, 31], but also less com-
mon reagents such as NaBrO2 [32], OsO4/NMO [33], and ozone [29e] have been
reported. In the case of MCPBA, the oxidation can usually be controlled by the
number of equivalents used (see Scheme 14.11) [28a]. Besides the oxidation of
suldes and sulfoxides, polymer-bound sulnamides have also been oxidized to
sulfonamides using dierent conditions [34].
Other oxidation procedures of polymer-bound sulfur-containing compounds
include thioacetals, which have been oxidatively cleaved from solid support using
PhI(Tfa)2 [35] or H5 IO6 [36].
14.4.1
Examples of the Oxidation of Polymer-bound Suldes to Sulfoxides and Sulfones
There are in general two reasons for the oxidation of a sulfur-containing com-
pound on solid phase. Either the oxidized form displays some interesting biologi-
cal or chemical activity, or the oxidation procedure is part of a cleavage strategy in
which, for example, the sulfoxide function is cleaved by elimination or the sulfone
is directly displaced with a nucleophile. A typical example of a cleavage procedure
using a sulfone was presented by Gayo and Suto in the synthesis of substituted
aminopyrimidines (Scheme 14.10) [29b]. The solid-supported (TG Thiol resin)
14.4 Oxidation of Sulfur-containing Compounds 377
Scheme 14.10. Oxidationcleavage strategy for the synthesis of aminopyrimidines [29b].
pyrimidine 28 was oxidized to the corresponding sulfone 29 with MCPBA and

subsequently cleaved through nucleophilic displacement by an amine, yielding the
substituted 2-amino pyrimidine 30.
An interesting example for the oxidation of suldes to either sulfoxides or sul-
fones with MCPBA was demonstrated by Mata in the synthetic approach to b-
lactams on solid support (Merrield and Wang resin) (Scheme 14.11) [28a]. The
carboxylic acid 31 was loaded onto Merrield resin yielding 32, and then either
oxidized to the sulfoxide 33 with 1.4 equiv. MCPBA at 0 C or to the sulfone 34
using a vefold excess of MCPBA at room temperature. Eventually, the b-lactams
could be cleaved using AlCl3 .
Scheme 14.11. Oxidation sequence of b-lactams to sulfoxides and sulfones [28a].
Grimstrup and Zaragoza presented an interesting synthetic route to highly func-

tionalized benzamides on solid phase (Wang resin) by a facile nucleophilic substi-
tution pathway (Scheme 14.12) [29c]. The thiol 35, which was derived from the
corresponding uoro compound and RSH, was rst oxidized to the sulfone 36.
This highly electron-decient aryl uoride was now easily substituted by a second-
ary amine R 0 R 00 NH, yielding 37, which could be readily cleaved to 38 from solid
support upon treatment with TFA. The order of the oxidation step and the
displacement step were in this case very important, since MCPBA also oxidizes
the anilide amine if the nucleophilic displacement with the amine was performed
directly on 35 followed by MCPBA oxidation.
Scheme 14.12. Nucleophilic substitution strategy to highly

functionalized benzamides on solid support [29c].
14.5
Oxidation of Selenium- and Phosphorus-containing Compounds
Compared with oxidations of sulfur-containing compounds on solid support, there

have been fewer examples of oxidation of selenium- or phosphorus-containing
compounds. Nevertheless, selenium compounds have attracted some attention
mainly because of their use as linker systems which can be easily cleaved under
oxidative conditions (see Chapter 4.3.7.3). Compared with nonpolymer-bound
selenium compounds [37], which are usually problematic because of their odor
and toxicity, the solid-phase-bound analogs are both totally odorless and conve-
nient to use. The oxidation of selenides to the corresponding selenoxides is usually
performed using H2 O2 [38], but also with other reagents such as NaIO4 [39], have
been reported. Oxidation of phosphorus-containing compounds is relatively rare
and often linked to the synthesis of oligonucleotides [40]. Phosphites have been
oxidized to phosphates using NMO [41] and iodine [42]. Phosphonates have also
been oxidized to phosphates using iodine [40].
14.5.1
Examples of the Oxidation (Cleavage) of Selenides to Selenoxides on Solid Support
A useful and versatile application of selenium-based solid-phase synthesis was

presented by Nicolaou et al. in the combinatorial synthesis of benzopyran-based
natural products (Scheme 14.13) [38c,d]. Various substituted ortho-prenylated phe-
nols 39 were directly loaded onto the selenium-based solid support (polystyrene)
leading to formation of the 2,2-dimethylbenzopyran system 40. This very mild and
selective procedure exhibited a broad tolerance toward a wide range of poly-
functionalized aromatic compounds. In all cases, the resin could be quantitatively
14.6 Oxidative Formation of Heterocycles on Solid Support 379
Scheme 14.13. Combinatorial synthesis of benzopyran-based

natural products using a selenium linker system [38c,d].
loaded using a threefold excess of 39. The further strategy in the course of con-
structing a combinatorial library contained various chemical manipulations (in
general transformation of R2 to R5). These transformations included annulations,
glycosidations, aldol condensations, and various coupling reactions, yielding the
products represented by formula 41. The selenium oxidation step readily cleaved
the products, yielding 42 in high purity and eciency with the introduction of a
double bond.
14.6
Oxidative Formation of Heterocycles on Solid Support
Solid-phase synthesis of heterocycles has become a central part of research in the

eld of combinatorial chemistry mainly because of the great structural variety and
potential biological activity. Familiar examples include quinolones, b-lactams and
dihydropyridines. There are many methods for the synthesis of heterocycles using
oxidations as important synthesis steps (compare Chapter 22). In general, the
main synthetic approaches can be divided into three categories represented by: A,
oxidative aromatization; B, oxidative cyclization or condensation; and C, formation
of heterocycles upon oxidative cleavage. Examples of A include the synthesis of
pyridines [43], quinazolinones [44] and isoquinolines [45]. Examples of B include
the synthesis of indolizines [46], pyrimidines [47], pyridazines [48], isoxazolines
[49], benzodiazepines [50], indazoles [51] and benzimidazoles [52]. Polymer-bound
quinolines have been activated for coupling by oxidation to the corresponding N-
oxides using MCPBA [53]. Examples of C include the synthesis of isoxazolines
[54], g-butyrolactones [55] and phenanthridines [56].
14.7
Oxidative Coupling and Cleavage Reactions on Solid Support
There are relatively few reports of oxidative coupling reactions on solid support.
Nevertheless, some quite complex reaction sequences have been successfully per-
formed. Phenols have been coupled to cyclic biarylethers using phenolic oxidation
employing thallium(III) salts [57]. Biaryls have been formed by oxidative coupling
using 1,3-dinitrobenzene (see Scheme 14.15) [58] and vanadium-based oxidants
[59]. Oxidative homocouplings of ortho-hydroxystyrenes yielding carpanones have
been performed using PhI(OAc)2 , as described in Scheme 14.14 [60a].
Scheme 14.14. Oxidative coupling strategy for the synthesis of carpanones [60].
In contrast to oxidative couplings, there have been many reports of cleavage re-
actions under oxidative conditions (compare Section 14.7.2). Most of these reports
directly refer to linker cleavage strategies (see Chapter 4.5). An interesting applica-
tion is the preparation of peptide aldehydes using the cleavage of amino alcohols
[61] and diols [62] with NaIO4 (see Scheme 14.16).
Other applications of oxidative cleavage procedures include arylethers which have
been cleaved using cerium ammonium nitrate (CAN) as an oxidant [63]. Benzyl-
ethers have been cleaved from solid support (Wang resin) using DDQ oxidation
[64] and benzylamines which have been cleaved from Merrield p-benzyloxy-
benzylamine (BOBA) resin by DDQ [65]. Aryl hydrazides have been used as linker
systems and can be oxidatively cleaved using dierent conditions including
Cu(OAc)2 and NBS [66].
14.7 Oxidative Coupling and Cleavage Reactions on Solid Support 381
14.7.1
Examples of Oxidative Coupling Reactions on Solid Support
Shair and coworkers presented a biomimetic approach to carpanone-like mole-

cules through oxidative heterocoupling on solid support (Scheme 14.14, PS-DES
resin, silyl and trityl linkers) [60a] based on the previous synthesis in solution
phase by Chapman et al. [67]. In a rst step, phenols 43 and 44 were oxidatively
coupled with PhI(OAc)2 and directly transformed to the DielsAlder adduct
45. The choice of the oxidant was crucial to this step, since the reacting phenols
had to be electronically dierentiated and coupled in the anticipated way. The
inverse electron demand DielsAlder reaction proceeded via an electronically
matched transition state. Cleavage from solid support with HF/pyridine yielded
the carpanone-like products 46. Experiments are under way to generate a split-and-
pool synthesis of a 100,000-member library and high-throughput biological screens
[60b]. Schreiber and coworkers presented a stereoselective synthesis of a biaryl-
containing medium ring system using the oxidation of biaryl cuprates on solid
support (polystyrene resin, silicon linker) (Scheme 14.15) [58a].
Scheme 14.15. Intramolecular biaryl synthesis using oxidation of cuprates [58a].
In the rst step, the attached biarylic compound 47 was converted to the inter-
mediary cyclic cuprate 48 using lithiation and treatment with copper cyanide. Sub-
sequently, the biaryl ten-membered ring 49 was formed upon exposure to the oxi-
dant 1,3-dinitrobenzene (1,3-DNB). After cleavage from solid support using HF/
pyridine the product 50 could be isolated in a diastereomeric ratio of 6:1 (P/M). A
disadvantage of the solid-phase approach was the decreased diastereomeric ratio,
which was better (20:1) in the analog reaction in solution phase.
14.7.2
Examples of Oxidative Cleavage Reactions on Solid Support
A useful route to the synthesis of C-terminal a-oxo aldehydes on solid support

was presented by Malnyk and coworkers [62]. As already described in Section 14.2.1,
peptide aldehydes are an important class of potentially bioactive compounds [20].
Since peptide aldehydes are prone to epimerization, considerable attention has
been focused on the construction of a new appropriate linker system to allow mild
reaction conditions. The strategy that was chosen (Scheme 14.16) contained a new
linker system as a key element that could be removed in a two-step procedure
using TFA and NaIO4 as oxidants. The peptide to be converted into the peptide
aldehyde was rst loaded onto the linker moiety 51 using standard solid-phase pep-
tide synthesis (SPPS), yielding 52, and then subsequently transferred to diol 53.
Mild cleavage of the diol using NaIO4 yielded the desired peptide aldehyde 54.
Scheme 14.16. Synthesis of a-oxo aldehydes using formyl transfer from the linker system [62].
References
1 a) R. C. Larock, Comprehensive in: Combinatorial Chemistry.

Organic Transformations, 2nd edn. Bannwarth, W. and Felder, E. (eds),
Wiley-VCH, New York 1999; b) M. Wiley-VCH, Weinheim 2000; d) B. A.
Hudlicky, Oxidations in Organic Bunin, The Combinatorial Index.
Chemistry, ACS Monograph 186, Academic Press, San Diego 1998;
Washington, DC 1990. e) D. Obrecht, J. M. Villalgordo,
2 a) F. Z. Dorwald, Organic Synthesis Solid-Supported Combinatorial and
on Solid Phase. Wiley-VCH, Parallel Synthesis of Small-Molecular-
Weinheim 2000; b) G. Jung in: Weight Compound Libraries.
Combinatorial Chemistry. Pergamon, Oxford 1998; dynamic
Bannwarth, W. and Felder, internet databases of references:
E. (eds), Wiley-VCH, Weinheim f ) http://www.combinatorial.com/;
1999; c) W. Bannwarth, E. Felder g) http://www.5z.com/divinfo/.
References 383
3 a) Key reference including literature Kim, J. Pfefferkorn, T. Li, J. Am.

coverage until 2000: S. V. Ley, Chem. Soc. 1998, 120, 10814; b) K. C.
I. R. Baxendale, R. N. Bream, Nicolaou, J. Pastor, N. Winssinger,
P. S. Jackson, A. G. Leach, D. A. F. Murphy, J. Am. Chem. Soc. 1998,
Longbottom, M. Nesi, J. S. Scott, R. 120, 5132; c) M. Reggelin, V.
I. Storer, S. J. Taylor, J. Chem. Soc., Brenig, R. Welcker, Tetrahedron Lett.
Perkin Trans 1 2000, 38154195; b) D. 1998, 39, 4801; d) secondary alcohol:
H. Drewry, D. M. Coe, S. Poon, L. A. Thompson, F. L. Moore, Y.-C.
Med. Res. Rev. 1999, 19, 97148; c) R. Moon, J. A. Ellmann, J. Org. Chem.
T. Taylor, Polymer-Bound Oxidizing 1998, 63, 2066; e) secondary alcohol:
Agents, ACS Symposium Series 1986, U. Reiser, J. Jauch, Synlett 2001, 1,
308, 42; d) Novabiochem-Catalogue, 90.
Polymer Supported Reagents 7 a) Benzylic alcohol: W. Li, B. Yan,
Handbook 2001; e) B. Hinzen in: J. Org. Chem. 1998, 63, 4092; b)
Combinatorial Chemistry. secondary benzylic alcohol: B. Yan,
Bannwarth, W. and Felder, E. (eds), Q. Sun, J. R. Wareing, C. F. Jewell,
Wiley-VCH, Weinheim 2000. J. Org. Chem. 1996, 61, 8765.
4 a) C. Chen, L. A. Ahlberg Randall, 8 a) A. M. Bray, D. S. Chiefari, R. M.
R. B. Miller, A. D. Jones, M. J. Valerio, N. Joe Maeji, Tetrahedron
Kurth, J. Am. Chem. Soc. 1994, 116, Lett. 1995, 28, 5081; b) J. A. Ellmann,
2661; b) B. Borhan, J. A. Wilson, M. Proceedings of the Solid-Phase Synthesis
J. Gasch, Y. Ko, D. M. Kurth, M. J. of Prostaglandins Conference. 209th
Kurth, J. Org. Chem. 1994, 60, 7375; ACS National Meeting, Anaheim, CA,
c) C. Chen, L. A. Ahlberg Randall, 1995.
R. B. Miller, A. D. Jones, M. J. 9 a) Secondary alcohol: P. C. Miller,
Kurth, Tetrahedron 1997, 53, 6595; T. J. Owen, J. M. Molyneaux, J. M.
d) M. Reggelin, V. Brenig, R. Curtis, C. R. Jones, J. Comb. Chem.
Welcker, Tetrahedron Lett. 1998, 39, 1999, 1, 223; b) C. C. Leznoff, T. M.
4801; e) D. P. Rotella, J. Am. Chem. Fyles, J. Weatherston, Can. J. Chem.
Soc. 1996, 118, 12246; f ) P. Page, 1977, 55, 1143.
M. Bradley, I. Walters, S. Teague, 10 a) K. C. Nicolaou, N. Winssinger,
J. Org. Chem. 1999, 64, 794; g) J. Pastor, F. Murphy, Angew. Chem.,
secondary alcohol: P. S. Furth, M. S. Int. Ed. Engl. 1998, 37, 2534.
Reitmann, A. F. Cook, Tetrahedron 11 a) W. H. Pearson, R. B. Clark,
Lett. 1997, 38, 5403; h) benzylic Tetrahedron Lett. 1997, 38, 7669;
alcohol: M. Fivush, T. M. Wilson, b) U. Reiser, J. Jauch, Synlett 2001,
Tetrahedron Lett. 1997, 38, 7151. 1, 90; c) secondary alcohol:
5 a) K. C. Nicolaou, N. Winssinger, J. T. L. Boehm, H. D. H. Showalter,
Pastor, S. Ninkovic, F. Sarabia, Y. J. Org. Chem. 1996, 61, 6498.
He, D. Vourloumis, Z. Yang, T. Li, 12 P. A. Tempest, R. W. Armstrong,
P. Giannakakou, E. Hamel, Nature J. Am. Chem. Soc. 1997, 119, 7607.
1997, 387, 268; b) K. C. Nicolaou, 13 J. M. J. Frechet, P. Darling, M. J.
D. Vourloumis, J. Pastor, N. Farrall, J. Org. Chem. 1981, 46,
Winssinger, Y. He, S. Ninkovic, 1728.
F. Sarabia, H. Vallberg, F. 14 H. Yang, B. Li, Synth. Comm. 1991,
Rohschangar, M. P. King, M. R. V. 21, 1521.
Finley, P. Giannakakou, P. 15 a) B. Khadilkar, A. Chitnavis, A.
Verdier-Pinard, E. Hamel, Angew. Khare, Synth. Comm. 1996, 26, 205;
Chem. Int. Ed. Engl. 1997, 36, 2097; c) b) J. G. Lee, J. A. Lee, S. Y. Sohn,
M. Marx, A. L. Grillot, C. T. Louer, Synth. Comm. 1996, 2, 543.
K. A. Beaver, P. A. Bartlett, J. Am. 16 L. D. Lou, W.-X. Lou, Synth. Comm.
Chem. Soc. 1997, 119, 6153. 1997, 27, 3697.
6 a) K. C. Nicolaou, N. Winssinger, 17 G. S. Zhang, Q.-Z. Shi, M.-F. Chem,
D. Vourloumis, T. Ohshima, S. K. Cai, Synth. Comm. 1997, 27, 3691.
18 a) B. Hinzen, S. V. Ley, J. Chem. Soc., 1995, 36, 2227; d) C. P. Holmes, J. P.

Perkin 1 1997, 1907; b) B. Hinzen, R. Chinn, G. C. Look, E. M. Gordon,
Lenz, S. V. Ley, Synthesis 1998, 977. M. A. Gallop, J. Org. Chem. 1995, 60,
19 S. Weik, G. Nicholson, G. Jung, 7328.
J. Rademann, Angew. Chem., Int. 29 Oxidation to sulfones: a) J. S. Patek,
Ed. Engl. 2001, 40, 1436. B. Zhu, Tetrahedron Lett. 1996, 37,
20 a) T. Aoyagi, T. Takeuchi, A. 8151; b) L. M. Gayo, M. J. Suto,
Matsuzaki, M. Kawamura, M. Tetrahedron Lett. 1997, 38, 211; c) M.
Kondo, M. Hamada, K. Maeda, H. Grimstrup, F. Zaragoza, Eur. J. Org.
Umezawa, J. Antibiot. 1969, 22, 283; Chem. 2001, 3233; d) U. Grabowska,
b) J. O. Westerik, R. Wolfenden, A. Rizzo, K. Farnell, M. Quibell, J.
J. Biol. Chem. 1972, 247, 8195. Comb. Chem. 2000, 2, 475; e) F. E. K.
21 a) S. Kobayashi, R. Akiyama, Kroll, R. Morphy, D. Rees, D. Gani,
Tetrahedron Lett. 1998, 39, 9211; Tetrahedron Lett. 1997, 38, 8573; f ) M.
b) T. L. Deegan, O. W. Gooding, Yamada, T. Miyajima, H. Horikawa,
S. Baudart, J. A. Proco, Tetrahedron Lett. 1998, 39, 289; g) B.
Tetrahedron Lett. 1997, 38, 4973. A. Kulkarni, A. Ganesan,
22 B. C. Hamper, S. A. Kolodziej, Tetrahedron Lett. 1999, 40, 5633; h) D.
A. M. Scates, Tetrahedron Lett. 1998, Obrecht, C. Abrecht, A. Grieder,
39, 2047. J. M. Villalgordo, Helv. Chim. Acta
23 O. de Frutos, D. P. Curran, J. Comb. 1997, 80, 65; i) C. Garcia-
Chem. 2000, 2, 639. Echeverria, Tetrahedron Lett. 1997,
24 a) T. R. Govindachari, K. R. 38, 8933; k) A. Barco, S. Benneti, C.
Ravidranath, N. Viswanathan, J. De Risi, P. Machetti, G. P. Pollini,
Chem. Soc., Perkin Trans 1 1974, 1215; V. Zanirato, Tetrahedron Lett. 1998,
b) I. Pendrak, R. Wittrock, W. D. 39, 7591; l) C. J. Burns, D. Robert,
Kingsbury, J. Org. Chem. 1995, 60, L. M. Salvino, G. McGeehan, S. M.
2912. Condon, R. Morris, M.
25 a) K. C. Nicolaou, N. Winssinger, Morrissette, R. Mathew, S.
D. Vourloumis, T. Ohshima, S. Darnbrough, K. Neuenschwander,
Kim, J. Pfefferkorn, T. Li, J. Am. A. Scotese, S. W. Djuric, J.
Chem. Soc. 1998, 120, 10814; b) J. C. Ullrich, R. Labaudiniere, Angew.
H. M. Wijkmans, A. J. Culshaw, A. Chem., Int. Ed. Engl. 1998, 37, 2848;
D. Baxter, Mol. Diversity 1998, 3, 117. m) F. Gosselin, M. Di Renzo, T. H.
26 a) X. Beebe, N. E. Schore, M. J. Ellis, W. B. Lubell, J. Org. Chem.
Kurth, J. Am. Chem. Soc. 1992, 114, 1996, 61, 7980; n) E. Flanigan, G. R.
10061; b) X. Beebe, C. L. Chiappari, Marshal, Tetrahedron Lett. 1970, 11,
M. J. Kurth, N. E. Schore, J. Org. 2403; PEG-bound thioethers: o) X. Y.
Chem. 1993, 58, 7320; c) J. T. Ayres, Zhao, K. W. Jung, K. D. Janda,
C. K. Mann, J. Polym. Sci., Polym. Tetrahedron Lett. 1997, 38, 977;
Lett. Ed. 1965, 3, 505. p) X. Y. Zhao, K. D. Janda, Tetra-
27 a) M. DAmbrosio, A. Guerriero, hedron Lett. 1997, 38, 5437. q) K. C.
F. Pietra, Helv. Chim. Acta 1987, Nicolaou, S. A. Snyder, A. Bigot,
70, 2019. b) M. Ciomei, C. Albanese, J. A. Pfefferkorn, Angew. Chem.
W. Pastori, M. Grandi, F. Pietra, 2000, 112, 1135. Angew Chem. Int. Ed.
M. DAmbrosio, A. Guerriero, C. Engl. 2000, 39, 1036.
Battistini, Proc. Am. Assoc. Cancer 30 Oxidation to sulfoxides: H. R. Russel,
Res. 1997, 38, 5, Abstract 30. R. W. A. Luke, M. Bradley,
28 Oxidation to sulfoxides: a) E. G. Mata, Tetrahedron Lett. 2000, 41, 5287.
Tetrahedron Lett. 1998, 39, 5287; b) T. 31 Oxidation to sulfones: D. L.
Masquelin, D. Sprenger, R. Baer, Marshall, I. E. Liener, J. Org. Chem.
F. Gerber, Y. Mercadal, Helv. Chim. 1970, 35, 867.
Acta 1998, 81, 646; c) M. Patek, 32 Oxidation to sulfoxides: D. M. R.
B. Drake, M. Lebl, Tetrahedron Lett. Cody, S. H. DeVitt, J. C. Hodges,
References 385
J. S. Kiely, W. H. Moss, M. R. Pavia, E. M. Gordon, Tetrahedron Lett. 1996,

B. D. Roth, M. C. Schroeder, C. J. 37, 4643; b) S. Tadasse, A. Bhandari,
Stankovic, US patent no. 5324483, M. A. Gallop, J. Comb. Chem. 1999,
1994. 1, 184.
33 Oxidation to sulfones: H. S. Han, 44 J. P. Mayer, G. S. Lewis, M. J.
K. D. Janda, Tetrahedron Lett. 1997, Curtis, J. W. Zhang, Tetrahedron
38, 1527. Lett. 1997, 38, 8445.
34 D. B. D. De Bont, W. J. Moree, R. M. 45 S. Berteina, A. De Maesmaeker,
J. Liskamp, Bioorg. Med. Chem. 1996, Tetrahedron Lett. 1998, 39, 5759.
4, 667. 46 D. A. Goff, Tetrahedron Lett. 1999, 40,
35 C. M. Huwe, H. Kunzer, Tetrahedron 8741.
Lett. 1999, 40, 683. 47 a) A. L. Marzinzik, E. R. Felder,
36 a) H. B. Lee, S. Balasubramanian, J. Org. Chem. 1998, 63, 723; b) B. C.
J. Org. Chem. 1999, 64, 3454; b) V. Hamper, K. Z. Gan, T. J. Owen,
Bertini, F. Lucchesini, M. Pocci, Tetrahedron Lett. 1999, 40, 4973.
A. De Munno, Tetrahedron Lett. 1998, 48 a) A. M. Boldi, C. R. Johnson, H. O.
39, 9263. Eissa, Tetrahedron Lett. 1999, 40, 619;
37 a) K. C. Nicolaou, N. A. Petasis, b) C. O. Ogbu, M. N. Qabar, P. D.
Selenium in Natural Product Synthesis. Boatman, J. Urban, J. P. Meara, M.
CIS, Philadelphia, PA 1984; b) D. D. Ferguson, J. Tulinsky, C. Lum,
Liotta, Organoselenium Chemistry. S. Babu, M. A. Blaskovich, H.
Wiley, New York 1986. Nakanishi, F. Q. Ruan, B. L. Cao,
38 a) K. C. Nicolaou, J. Pastor, S. R. Minarik, T. Little, S. Nelson,
Barluenga, N. Winssinger, Chem. M. Nguyen, A. Gall, M. Kahn,
Comm. 1998, 1974; b) T. Ruhland, Bioorg. Med. Chem. Lett. 1998, 8, 2321.
K. Anderson, H. Pedersen, J. Org. 49 a) R. C. Johnson, B. Zhang, PCT
Chem. 1998, 63, 9204; c) K. C. WO 0116116 A1; b) J.-F. Cheng, A.
Nicolaou, J. A. Pfefferkorn, G.-Q. M. M. Mjalli, Tetrahedron Lett. 1998,
Cao, Angew. Chem. 2000, 112, 750; 39, 939; c) B. B. Shankar, D. Y.
d) K. C. Nicolaou, G.-Q. Cao, J. A. Yang, S. Girton, A. K. Ganguly,
Pfefferkorn, Angew. Chem. 2000, Tetrahedron Lett. 1998, 39, 2447.
112, 755; e) R. Michels, M. Kato, 50 J. M. Berry, P. W. Howard, D. E.
W. Heitz, Makromol. Chem. 1976, Thurston, Tetrahedron Lett. 2000, 41,
177, 2311; f ) H. Russell, R. W. A. 6171.
Luke, M. Bradley, Tetrahedron Lett. 51 B. Yan, H. Gstach, Tetrahedron Lett.
2000, 41, 5287. 1996, 37, 8325.
39 M. J. Kurth, L. A. Ahlberg Randall, 52 D. Tumelty, M. K. Schwarz, K. Cao,
K. Takenouchi, J. Org. Chem. 1996, M. C. Needels, Tetrahedron Lett. 1999,
61, 8755. 40, 6185.
40 F. Eckstein, Oligonucleotides and 53 M. Z. Hoemann, A. Melikian-
Analogues; A Practical Approach. Badalian, G. Kumaravel, J. R. Hauske,
Oxford University Press, Oxford 1991. Tetrahedron Lett. 1998, 39, 4749.
41 C. A. Metcalf III, C. B. Vu, R. 54 S. Kobayashi, R. Akiyama,
Sundaramoorthi, V. A. Jacobsen, Tetrahedron Lett. 1998, 39, 9211.
E. A. Laborde, J. Green, Y. Green, 55 Y. Watanabe, S. Ishikawa, G. Takao,
K. J. Macek, T. J. Merry, S. G. T. Toru, Tetrahedron Lett. 1999, 40,
Pradeepan, M. Uesugi, V. M. 3411.
Varkhedkar, D. A. Holt, Tetrahedron 56 W.-R. Li, N.-M. Hsu, H.-H. Chou, S.
Lett. 1998, 39, 3435. T. Lin, Y.-S. Lin, Chem. Comm. 2000,
42 a) K. K. Ogelvie, M. J. Nemer, 401.
Tetrahedron Lett. 1980, 21, 4159; b) M. 57 a) K. Nakamura, H. Nishiya, S.
D. Matteucci, M. H. Caruthers, Nishiyama, Tetrahedron Lett. 2001, 42,
Tetrahedron Lett. 1980, 21, 3185. 6311; b) S. Yamamura, S. Nishiyama,
43 a) M. F. Gordeev, D. V. Patel, J. Wu, J. Synth. Org. Chem. Jpn. 1997, 55, 1029.
58 a) D. R. Spring, S. Krishnan, S. L. 63 a) A. Peyman, C. Weiser, E.

Schreiber, J. Am. Chem. Soc. 2000, Uhlmann, Bioorg. Med. Chem. Lett.
122, 5656; b) F. Ullmann, J. 1995, 5, 2469; b) K. Fukase, K.
Bielecki, Chem. Ber. 1901, 34, 2174. Egusa, Y. Nakai, S. Kusumoto, Mol.
59 J. W. ApSimon, D. M. Dixit, Can. J. Diversity 1997, 2, 182; c) H. P.
Chem. 1982, 60, 368. Nestler, P. A. Bartlett, W. C. Still,
60 a) C. W. Lindsey, L. K. Chan, B. C. J. Org. Chem. 1994, 59, 4723.
Goess, R. Joseph, M. D. Shair, J. 64 a) K. Fukase, Y. Nakai, K. Egusa, J.
Am. Chem. Soc. 2000, 122, 422; b) A. Porco, S. Kusumoto, Synlett 1999,
biological activity of carpanone-like 1074; b) Y. Ito, T. Ogawa, J. Am.
molecules: S. Maeda, H. Masuda, Chem. Soc. 1997, 119, 5562.
T. Tokoroyama, Chem. Pharm. Bull. 65 S. Kobayashi, Y. Aoki, Tetrahedron
1995, 43, 935. Lett. 1998, 39, 7345.
61 J. Rademann, M. Meldal, K. Bock, 66 a) C. Millington, R. Quarrell, G.
Chem. Eur. J. 1999, 5, 1218. Lowe, Tetrahedron Lett. 1998, 39, 7201;
62 a) O. Melnyk, J.-S. Fruchart, C. b) F. Stieber, U. Grether, H.
Grandjean, H. Gras-Masse, J. Org. Waldmann, Angew. Chem., Int. Ed.
Chem. 2001, 66, 4153; b) J.-S. Engl. 1999, 38, 1073.
Fruchart, H. Gras-Masse, O. 67 O. L. Chapman, M. R. Engel, J. P.
Melnyk, Tetrahedron Lett. 1999, 40, Springer, J. C. Clardy, J. Am. Chem.
6225. Soc. 1971, 93, 6696.
387
15
Reductions in Combinatorial Synthesis
Christopher P. Corrette and Conrad W. Hummel
15.1
Introduction
Reductions are one of the most fundamental and widely used transformations in
organic chemistry. The reduction of a wide variety of functional groups has been
exploited in both solid- and solution-phase combinatorial library synthesis. There
are a number of reviews that cover combinatorial chemistry, including reductions
[1]. This chapter is divided into two main sections. The rst section covers reduc-
tions where the substrate is support bound. The second section covers reductions
where the substrate remains in solution (resin-bound reagents and catalysts, catch-
and-release purication, and uorous chemistry). In general, the combinatorial
chemistry of peptides has been omitted in our coverage.
15.2
Solid-phase Reductions
15.2.1
Aldehyde Reductions
The reduction of solid-supported aldehydes to alcohols is a straightforward reac-

tion. As is the case with solution-phase chemistry, the popular borohydride reagent
NaBH4 chemoselectively reduces aldehydes in the presence of other reducible
functionalities, including esters [2], acetals [3], and nitro groups [4]. Typical con-
ditions use excess NaBH4 in tetrahydrofuran (THF) at ambient temperatures. The
use of an alcoholic co-solvent such as ethanol or methanol is often required. In
most cases, upon completion of the reaction, a dilute acid wash (AcOH or HCl)
is needed to completely remove the unreacted reagent. The progress of these
reactions, as well as other carbonyl reductions, can be followed by monitoring the
disappearance of the carbonyl band (about 1700 cm1 ) in the FTIR spectrum of
the resin [5].
Aldehyde reductions have been performed on a number of resins, including

ISBN: 3-527-30509-2
388 15 Reductions in Combinatorial Synthesis
the Merrield resin [2a], the Wang resin [2b], and an arylsulfonate ester resin [6].
They have also been used as a key step in the preparation of a variety of other
resins. The preparation of the acid-labile resins 2 [7] and 4 [8] each required
NaBH4 -mediated aldehyde reductions (Scheme 15.1). The improved synthesis of
SASRIN resin, described by Katritzky et al. [9], and the synthesis of a photolabile
6-nitrovanillin-based resin, described by Zehavi and Patchornik [4], also required
aldehyde reductions. The use of an acid wash to remove excess reagent is inappro-
priate in the case of the acid-labile resin preparations. In some of these cases, an
alcoholic solvent wash suces.
Scheme 15.1. Examples of aldehyde reductions in linker preparations.
15.2.2
Ketone Reductions
As with aldehyde reductions, the reagent of choice for simple ketone reductions on
a solid support is NaBH4 [10]. However, various other reducing agents have been
described in the literature to carry out this transformation. These include the
borohydride reducing agents diisoamylborane [11] and LiBH4 [12]. The latter was
used in the preparation of an acid-labile xanthone-based resin described by Sieber.
NaBH4 in combination with diethyl methoxyborane has also been used to reduce
the diketone 5 [13] to diol 6 (Scheme 15.2). Following boron oxidation and re-
moval, this diol was cyclized with dilute acid to d-lactone 7.
Scheme 15.2. Diketone reduction on solid phase.

Asymmetric reductions of ketones bound to resin are also possible. The silane re-
agents diphenylsilane and a-naphthylphenylsilane in the presence of the catalyst
prepared from m-dichlorotetraethylenedirhodium(I) and () or ()-DIOP asymmet-
rically reduced a polymer-bound ketone [14]. The resulting secondary alcohol, of
unknown optical purity, was part of a resin-bound asymmetric rhodium-containing
hydrogenation catalyst that was used to reduce the double bond of a-N-acylami-
noacrylic acids. However, the optical purities (@ 70% ee) of the resulting amino
acids were comparable to those obtained from the analogous homogeneous catalyst.
Diastereoselective ketone reductions can be achieved by a variety of methods. An
example of a diastereoselective ketone reduction is found in Patersons library syn-
thesis of polyketides [15]. To increase the degree of diversity in this library, the re-
duction of b-hydroxy ketone intermediates employed two dierent sets of condi-
tions, allowing access to both syn- and anti-1,3-diols. The former was obtained with
95% diastereoselectivity (ds). Treatment of the b-hydroxy ketone with (c-Hex)2 BCl
and triethylamine delivered a boron aldolate, which could be reduced with LiBH4
aording the syn derivative with 95% ds. The 1,3-anti-diol was generated with 97%
ds via the anti-selective EvansTishchenko reduction protocol, using stoichiometric
quantities of SmI2 and propanal, followed by a LiBH4 -mediated ester cleavage. Pat-
erson also points out that attempts to eect the anti reduction with Me4 NBH(OAc)3
resulted in lower diastereoselectivity (75%).
Other examples of both chelation- and nonchelation-controlled diastereoselec-
tive ketone reductions were described by Ellman in his synthesis of an aspartyl
protease inhibitor library [16]. To achieve chelation-controlled reduction, the a,b-
dialkoxy ketone 8 was treated with Zn(BH4 )2 in diethyl ether and THF at 20 C
(Scheme 15.3). Following deprotection and resin cleavage, the triol product was
peracetylated. Analysis by gas chromatography (GC) showed that the syn product
had been delivered in 6080% ds. Following separation of this mixture by prepa-
rative high-performance liquid chromatography (HPLC), the major diastereomer
was found to have a 90% ee, which demonstrated that only a small degree of race-
mization had occurred during an eight-step sequence that included reduction. The
anti compound was obtained with 74% ds, utilizing the nonchelation-controlled
conditions of l-selectride in THF at 75 C. In another example of substrate-
controlled reduction, Schlessinger was able to reduce ketone 10 stereoselectively
with NaBH4 (Scheme 15.4) [17].
Scheme 15.3. Diastereoselective reduction of an a,b-dialkoxy ketone.

Scheme 15.4. Diastereoselective reduction of an oxabicyclo ketone.
15.2.3
Ester Reductions
A number of hydride-based reagents can reduce solid-supported esters. For all

practical purposes, alcohols have been the usual targets of these reductions. De-
spite the ability to stop the reduction at the aldehyde oxidation state with the use of
stoichiometric reagents such as DIBAL in solution, this transformation has not
been reported for solid-phase-supported esters. The diculty of this transforma-
tion is not surprising, as chemists usually use excess reagents to drive reactions to
completion on solid phase and the use of stoichiometric reagents is very dicult to
achieve. The transformation from a carboxylic acid oxidation state to an aldehyde
has been successfully addressed on solid phase by utilizing Weinreb amides in-
stead of esters. These amides are known reliably to produce aldehydes upon re-
duction (see Section 15.2.6).
Of the reducing reagents used to carry out ester reductions to the corresponding
alcohol, DIBAL [2b, 18] and LAH [4, 13, 19] have been used most frequently.
An example of a solid-phase DIBAL reduction is shown in Scheme 15.5, where
the resin-bound a,b-unsaturated tert-butyl ester is reduced to the allylic alcohol
13. DIBAL reductions have been run in various solvents, including THF, Et2 O,
CH2 Cl2 , and toluene, from 78 C to ambient temperature, while LAH reductions
typically utilize THF or ether as the solvent at ambient to reux reaction temper-
atures. The quench of the excess reagent is usually carried out using ethyl acetate/
water or dilute aqueous HCl. Merrield, Wang, and trityl resins have all proven to
be stable to this strong reducing agent. Examples of LAH reductions are shown in
Scheme 15.6. Example 15.6A shows that an amide is concomitantly reduced with
an ester of a resin-bound amino acid to give the amino alcohol 15 [13]. LiBH4 has
also been used to reduce resin-bound esters, as shown in Scheme 15.7 [20]. A
Scheme 15.5. DIBAL-mediated ester reduction of resin-bound substrate.

Scheme 15.6. LAH reductions on solid support.
Scheme 15.7. Ester reduction on solid phase with LiBH4 .
NaBH4 -mediated ester reduction in ethanol and water has also been demon-
strated; however, this protocol may not be general as esters are typically inert to
this reagent.
Esters are common points of attachment for substrates to solid supports. Cleav-
age can be eected by saponication or by reduction, aording acids or alcohols,
respectively, as the nal products. For reductions, both DIBAL [21] and LAH [22]
have been described in the literature. Tietze and coworkers have demonstrated the
use of DIBAL in the two examples shown in Scheme 15.8, where concomitant re-
duction of a diester [21c] and a b-ketoester [21d] have led to diols 21 and 23, re-
spectively. Kurth and coworkers have also used this reagent to reduce the resin-
bound b-hydroxy ester 24, thus providing diol 25 [21a], which is a representative of
a 27-compound library (Scheme 15.9). Kuster and Scheeren have reductively cleaved
Scheme 15.8. Reductive cleavage of ester-linked substrates.

Scheme 15.9. Kurths DIBAL-mediated reduction of a b-hydroxy ester.
the a-amino ester 26 from Wang resin to obtain the primary amino alcohol 27
using LAH (Scheme 15.10) [22].
Scheme 15.10. Reductive cleavage of an amino ester with LAH.
Resin-bound acid chlorides have also been reduced to alcohols. Goldwasser and
Lezno have shown that diacid chlorides can be loaded onto 2% crosslinked poly-
styrene resin to give ester-linked acid chlorides. The resins can then be treated
with amines or hydride reducing agents to give amides or alcohols, respectively
[23]. In the latter case, the most successful reducing reagents were NaBH4 and
NaCNBH3 (4 equiv., in THF at ambient temperature), which delivered the desired
products in 67% and 65% yields, respectively. However, following basic cleavage
and esterication, it was found that these products were contaminated with the
dimethylester byproduct arising from incomplete reduction.
15.2.4
Mixed Anhydride Reductions
A mild method employed to obtain alcohols from carboxylic acids consists of using
a mixed anhydride intermediate. In their search for an optimized phosphomannose
isomerase inhibitor, researchers at Aymax coupled ten dierent symmetrical an-
hydrides and diacids to an immobilized 2-aminoindane-2-carboxamide to deliver
acids of the general structure 29 (Scheme 15.11). This set of acids was treated with
isobutylchloroformate and triethylamine in THF, followed by NaBH4 in water, to
deliver the primary alcohols 30 [24]. Further diversication led to a library of 600
analogs (60 pools of ten compounds). Chemists at Signal have also utilized this
reduction protocol to deliver pyrimidine 33 following Mitsunobu alkylation and sub-
sequent cleavage (Scheme 15.12) [25].
Scheme 15.11. Solid-phase reduction of acid via mixed anhydride.
Scheme 15.12. Pyrimidine synthesis using mixed anhydride reduction.
15.2.5
Thioester Reductions
In 1996, Kobayashi reported the rst synthesis of polymer-supported silyl enol

ethers (thioketene silyl acetals) [26]. These reactive intermediates were converted
to small libraries of b-amino alcohols [26a,c] and 1,3-diols [26b] according to
Scheme 15.13. Treatment of compound 34 with either an imine or an aldehyde in
the presence of catalytic amounts of Sc(OTf )3 gave the resin-bound b-amino thio-
ester 35 or b-hydroxy thioester 37, respectively. Following reductive cleavage of the
thioester with LiBH4 , the desired b-amino alcohols and 1,3-diols were obtained in
good yields. However, a chromatography step was required to obtain pure com-
pounds in both cases. The authors also demonstrated that the resin-bound b-
Scheme 15.13. Reductive cleavage of thioesters.

hydroxy thioester could be reduced to the b-hydroxy aldehyde 38 with DIBAL in

CH2 Cl2 , at 78 C [26b].
Thioester reduction on solid phase has also been successfully carried out using
LAH in THF. Scheme 15.14 shows the reduction of dithioester 40 to the propane-
1,3-dithiol derivative 41, which was used to produce ketones via dithiane chemistry
[27].
Scheme 15.14. LAH reduction of 1,3-dithioester.
In their Evans aldol approach to polyketide libraries, Reggelin et al. have also
utilized thioesters and their reduction as part of the synthetic strategy [28]. They
rst converted resin-bound oxazolidinones 42 to thioesters 43 via a three-step
protocol involving hydrolysis, thioester formation, and alcohol protection. They
next reduced the thioester with LiBH4 and reoxidized the resulting alcohol to
aldehyde 45 with DessMartin reagent (Scheme 15.15). This aldehyde could then
be used in a subsequent Evans aldol reaction. Unlike the examples given above,
this route was designed to leave the substrate on the resin following thioester
reduction.
Scheme 15.15. Resin-bound thioester reduction with LiBH4 .
15.2.6
Weinreb Amide Reductions
As mentioned in Section 15.2.3, the partial reduction of an ester to an aldehyde is

a dicult transformation on solid phase, since excess reagents are typically used to
drive reactions to completion. If reactions fail to go to completion and purications
are required, then one of the major advantages of solid-phase synthesis is forfeited.
In the case of ester reductions, alcohols are normally obtained owing to the use
of excess reagents. Reggelin et al. solved this problem in the solid phase by mak-
ing use of Weinreb amides, which deliver aldehydes upon reduction in standard
solution-phase chemistry. In their approach to polyketide libraries, they demon-
strated that the imides 46 can be converted to Weinreb amides under standard
conditions (Scheme 15.16). Following alcohol protection, these amides can be se-
lectively reduced with DIBAL to deliver the support-bound aldehydes 48 [29]. In
1998, Reggelin et al. replaced this sequence with another (see Section 15.2.5) that
goes through a thioester instead of the Weinreb amide. However, this change was
due to diculties arising from steps other than reduction [28].
Scheme 15.16. Weinreb amide approach to support-bound aldehyde.
Two other groups have developed Weinreb amide-based linkers that give alde-
hydes in solution upon reductive cleavage [30]. Salvino et al. modied a resin that
had been used for the synthesis of hydroxamic acids to give an O-linked Weinreb
amide linker [30d], whereas Martinez and coworkers synthesized an N-linked ver-
sion [30a]. The synthesis of C-terminal amino acid aldehydes has been successfully
demonstrated by both groups, providing clean products in low to moderate yields
using LAH as the reductant. Schemes 15.17 and 15.18 show the synthesis of Boc-
Phe-H using both linkers. In the case of the Martinez linker, this support has also
been applied to the synthesis of C-terminal peptide aldehydes [30b] and side-chain
aldehydes [30c]. The peptide analogs were produced without noticeable epimeri-
Scheme 15.17. Synthesis of C-terminal amino acid aldehyde

using an O-linked Weinreb amide resin.
Scheme 15.18. Synthesis of C-terminal amino acid aldehyde

using an N-linked Weinreb amide resin.
zation and the side-chains were reduced in high yield with LiAl(OtBu)3 H. The
O-linked resin was also employed to deliver ethyl ketones by treating inter-
mediate Weinreb amides with ethyl Grignard [30d]. Dinh and Armstrong also intro-
duced an N-linked Weinreb amide resin, which delivered ketones in low to
moderate yields upon treatment with Grignard reagents [31]. However, attempts to
reductively cleave these amides with LAH produced aldehydes in very low yields
(< 20%).
15.2.7
Sulfur Reductions
There have been a number of dierent solid-phase applications involving disul-

de and sulfone reductions. These include examples of simple functional group
manipulation, linker preparation, and traceless linker cleavage. Hummel and
Hindsgaul have shown that thio-oligosaccharides can be synthesized from polymer-
supported sugar derivatives functionalized with an anomeric disulde (Scheme
15.19) [32]. Reduction of the disulde with dithiothreitol (DTT) and subsequent
sodium thiolate formation leads to a thio-sugar capable of reacting with triated
glycosides. Following deprotection and resin cleavage, thio-oligosaccharides 57
were formed. In another example, Ellman and coworkers synthesized a series of
cyclic 9- and 10-member thioethers, utilizing a PBu3 -mediated reduction of a tert-
butyl-protected disulde as a key step [33]. They later modied this approach by
linking the substrate through a disulde bond, as shown in Scheme 15.20 [34].
In this case, the disulde bond was cleaved with tris-(2-carboxyethyl)phosphine
(TCEP), which gave the free thiol in solution along with excess TCEP and the phos-
phine oxide byproduct. The contaminants were of little consequence, as support-
bound N,N,N 0 ,N 0 -tetramethylguanidine (TMG) was not only able to induce cycli-
zation to the thioether, but was also able to scavenge these byproducts. In a recent
Scheme 15.19. Anomeric disulde reduction in the preparation of thio-oligosaccharides.
Scheme 15.20. TCEP-mediated disulde reduction leading to a b-turn mimetic library.

application, Lam and coworkers used NaBH4 to reduce a disulde bond in their
solid-phase approach to 1,4-benzothiazin-3(4H)-one derivatives [35].
In an example of linker preparation, Sucholeiki and coworkers have utilized
a b-mercaptoethanol-mediated reduction to synthesize the photolabile resin 62
(Scheme 15.21) [36]. Zhao and Janda also utilized a disulde reduction in the syn-
thesis of the thiol linker shown in Scheme 15.22 [37]. Treatment of a mixture of
disuldes generated in a previous alkylation step with DTT in water led to the de-
sired resin 64 in excellent yield. Following construction of the targeted substrate
on solid phase, oxidation of the thiol with KHSO5 in water gave a sulfone that was
cleaved with 5% Na/Hg in methanol and DMF to yield 66 [38]. The solvent mix-
ture of methanol and DMF (1:8) was crucial for this successful reductive cleavage
[39]. The use of additional methanol or THF as a replacement for DMF gave lower
yields and required the use of larger quantities of Na/Hg. Zhao and Janda have
also pointed out that, for reactions using soluble polyethylene glycol (PEG)-based
polymers, isopropanol is an excellent choice for polymer precipitation, and leading
to products of higher purity [38].
Scheme 15.21. Linker preparation utilizing b-mercaptoethanol-mediated disulde reduction.
Scheme 15.22. Preparation and use of Jandas soluble polymeric thiol linker.
15.2.8
Selenium Reductions
The ease with which selenium can be reduced and oxidized is well understood,
however the toxicity and odor of selenium compounds has limited their use. Nic-
olaou et al. recognized that by attaching selenium to a solid support these draw-
backs would be mitigated, and the positive attributes of selenium reagents and
substrates could then be exploited [40]. They have shown that supported selenium
reagents make excellent traceless linkers because loading of substrates and sub-
sequent cleavage to simple alkyl groups is carried out with equal ease. As shown in
Scheme 15.23, reduction of the selenium bromide 67 with LiBH4 delivers lithium
selenide 68, which then reacts with substrates containing an alkyl halide. Follow-
ing substrate modication (not shown), the carbonselenium bond can be reduced
with Bu3 SnH to give an alkyl group with no vestige of the linker remaining.
Alternatively, Nicolaou et al. have shown that these selenides can be treated with
oxidizing reagents to give an alkene.
Scheme 15.23. Preparation and use of Nicolaous selenium linker.
In another example of a selenium-based traceless linking strategy, Ruhland et al.

prepared and reacted PS-SeB(OEt)
3 Na with hydroxy-containing alkyl halides. The
resulting intermediates were then alkylated with phenols under Mitsunobu con-
ditions and cleaved with Bu3 SnH to give alkylated phenols [41].
In an example that does not involve selenium linkage to a solid support, Pearson
and Clark used a vinyl selenium reagent as an anionophile in a [3 2] cyclo-
addition with a solid-supported 2-azaallyl anion (Scheme 15.24) [42]. Following
condensation, the phenylselenide group was then reduced with Bu3 SnH giving
a 1,2-disubstituted pyrrolidine.
Scheme 15.24. Use of phenylvinylselenium as an anionophile

and selenium removal with n-Bu3 SnH.
15.2.9
Quinone Reductions
The redox chemistry of quinones has been used to prepare solid-phase linkers for
peptide synthesis [43]. The quinone can be easily reduced with NaBH4 or Na2 S2 O3
to provide the corresponding dihydroquinone. Treatment of the reduced product
with TBAF results in phenoxide displacement at the C-terminus of the attached
peptide, thus releasing the molecule from the resin. In initial eorts, the phenolic
oxygen forms a lactone and releases the peptide functionalized at the C-terminus
(Scheme 15.25A) [43a]. An improved approach is shown in Scheme 15.25B, in
which the peptide is provided without functionalization at the C-terminus via SN 2
displacement by the phenol [43b].
Scheme 15.25. Peptide release via quinone reduction and

phenol or phenoxide-mediated cleavage.
15.2.10
Amide Reductions
The reduction of amides to amines is a useful technique for the generation of di-
versity in combinatorial synthesis. Either separately, or in combination with the
complementary reductive amination techniques of aldehydes described in Section
15.2.12.4, an enormous number of amines and polyamines can be accessed from
the diverse set of amides and polyamides that can be generated via a combinatorial
approach. Further utility arises from the ability to increase diversity by modica-
tion of the product amines through any number of common approaches.
The reducing agents most routinely employed are BH3 THF [44], BH3 pyr [45],
or BH3 SMe 2 [46], although Red-Al [47] and LiBH4 [48] have also been used. Bor-
ane reductions are easily applied to resin-bound amides since any excess reducing
agent and resulting inorganic byproducts are easily washed away from the polymer
support. An important factor for such reductions is the cleavage of the borane
amine adducts. Acidic cleavage is incompatible with a variety of polymer supports,

therefore heating with piperidine has been used to remove boron from the desired
products [44b]. An iodine-mediated cleavage of the boraneamine adduct has
also been reported (Scheme 15.26) [45b, 49]. This method is compatible with acid-
sensitive solid supports such as Wang or Rink resins.
Scheme 15.26. Iodine work-up for borane reduction of amides on solid phase.
Several articles have been published on the use of amide reductions for the gen-
eration of combinatorial libraries [44, 45a,c]. Dipeptides are typically constructed
on resin, acylated at the N-terminus, and exhaustively reduced with BH3 THF or
BH3 pyr to give polyamines. This methodology has been used to generate hydan-
toins and cyclic ureas, thus generating libraries from libraries [44a]. This se-
quence has also been used to construct a 100,000-compound library of polyamines
and bicyclic guanidines (Scheme 15.27) [44b].
Scheme 15.27. Synthesis of polyamines and bicyclic

guanadines via borane reduction of dipeptides.
15.2.11
Carbamate Reductions
There are several examples of carbamate reductions wherein the carbonyl is ex-
haustively reduced to an N-methylamine. All of these examples use aluminum hy-
dride reagents. For example, Liu and Ellman used Red-Al-mediated carbamate re-
duction to prepare chiral N-methyl-2-pyrrolidinemethanol ligands [47]. Carbamate
linkers have been used as latent methylamines in solid-phase synthesis. Formation
of the carbamate on resin followed by LAH reduction generated the desired pri-
mary and secondary amines [50]. A carbamate linker has also been used to gen-
erate substituted N-methylpyrrolidines via reductive cleavage with LAH (Scheme
15.28) [51]. Xiao et al. used Na2 S2 O4 to reduce an O-piperidinyl carbamate linker,
thus revealing a secondary amine that underwent a cyclizative cleavage with a
pendant ester to release a desired alcohol [52].
Scheme 15.28. Synthesis of subsituted N-methylpyrrolidines via reductive cleavage.
15.2.12
Reductive Amination
15.2.12.1 General Considerations

Reductive amination is one of the most widely applied techniques in combinatorial
chemistry and is an excellent method for generating diversity (Scheme 15.29) [53].
Amines, aldehydes, and ketones as inputs for reductive amination are plentiful,
commercially available, and typically inexpensive. The technique has been well
established in routine organic chemistry [54], and has therefore provided a strong
foundation for explorations in both solid- and solution-phase library synthesis.
There is a wide variety of protocols for both imine formation and reduction, thus
providing a large set of choices for reaction conditions and reagents that can be
screened for a given set of inputs (e.g. primary vs. secondary amines).
Scheme 15.29. Diversity from secondary amines prepared by reductive amination.
Generally carbonyl reactivity follows the order aldehyde > cyclic ketone g acyclic
ketone. Steric considerations are important in reductive amination reactions, thus
hindered inputs may require forcing conditions for adequate results. For example,
hindered amino acid esters such as valine [53a] have been reported to be poor
inputs for reductive amination reactions as have methyl amines [55]. Secondary
amines can require repetitive cycles [56] of reductive amination, or very long reac-
tion times [56, 57] to obtain good conversion.
Electronic factors can also be important in reductive amination reactions, as evi-
denced by the higher reactivity of alkyl amines versus anilines. The more reactive
nature of alkyl amines and aldehydes can render them prone to bis-alkylation [44b,
58]. Reductive aminations can also be sensitive to solvent choice. Brown and co-
workers found that the use of aqueous THF was crucial for the successful reduc-
tive amination of a Rink amide resin [59].
Racemization of amino acid esters as amine inputs during reductive amina-
tion is another concern for library synthesis [60]. Racemization is expected to oc-
cur by equilibration during imine formation [61]. In order to suppress racemiza-
tion, imines can be formed in the presence of a reducing agent, thus avoiding
equilibration [58a, 61].
There are several methods for monitoring the progress of solid-phase reductive
amination. Qualitative nitrogen analyses such as a (Kaiser) ninhydrin test can
quickly and easily assess reaction progress [62]. Infrared spectroscopy can also be
used to detect consumption of the carbonyl and/or imine components in a reduc-
tive amination process by their characteristic CbO (17401720 cm1 ) and CbN
(@1650 cm1 ) stretches [63].
15.2.12.2 Imine Formation

Imines are formed by condensation of amines and aldehydes or ketones with loss
of water. Typically, aliphatic aldehyde-derived imines tautomerize to their corre-
sponding enamines. The classic methods for water removal such as azeotrope for-
mation or trapping with molecular sieves are neither practical nor economical for
application in a solid-phase library format [64]. A number of dierent approaches
have therefore been developed for imine formation in combinatorial chemistry to
supplant these techniques.
The most widely used reagent for imine formation in solid-phase organic syn-
thesis has been trimethylorthoformate (TMOF) [53b, 65]. TMOF is used as the
reaction solvent, or in conjunction with other solvents as solubility dictates, and
reacts with water as it is formed, thus driving the equilibrium toward imine for-
mation. TMOF is compatible with most resins and common reducing agents such
as NaBH3 CN, NaBH(OAc)3 , or BH3 pyridine (BAP).
The imine equilibrium is often shifted by using an excess of the input not
loaded on resin (anywhere from 2 to 20 equiv.). Imines can be formed in situ in the
presence of a reducing agent with or without added acids. The typical additive for
imine formation is 110% acetic acid (by volume) but p-TsOH [66] and PPTS [67]
have also been used to catalyze the condensation. Anhydrous inorganic salts such
as Na2 SO4 (with ultrasound) have been used to drive formation of imines in solid-
phase applications [68]. Titanium reagents such as Ti(OiPr)4 have been used to
facilitate reductive aminations via carbonyl activation and amine addition [69].
Use of Ti(OiPr)4 made possible the reductive amination of a relatively unreactive
ketone 97, as shown in Scheme 15.30 [69a].
Scheme 15.30. Reductive amination with Ti(OiPR)4 .
15.2.12.3 Reducing Agents for Reductive Amination

There is a myriad of reducing agents that can be used for reductive aminations in
solid-phase applications. The most common are NaBH3 CN (Borch reduction) [53,
56, 70], NaBH(OAc)3 [63a, 21b, 71], and BAP [57, 72], but Me4 NBH(OAc)3 [73],
NaBH4 [74], and LiBH4 [75] have also been used. Me4 NBH(OAc)3 and NaBH3 CN
have been used sequentially in a reductive amination protocol in which the indi-
vidual reductants provided incomplete or impure reaction products respectively
[76].
The borohydride reagents listed above typically reduce both imines and tau-
tomeric enamines (formed from aliphatic aldehydes) and can be used in large
excess as they are easily washed from the resin [77]. NaBH(OAc)3 has become a
favored reducing agent as it is not toxic and displays excellent chemoselectivity,
but NaBH3 CN is still frequently used. Borohydride reagents such as NaBH4 and
LiBH4 can be problematic as they may reduce starting aldehydes and ketones to
alcohols. The usual solution in such cases is to preform the imine before applica-
tion of the reductant in a two-step process.
15.2.12.4 Reductive Aminations as the Entry Point for Library Preparation

Frequently, reductive amination is used to load a variety of inputs onto a resin,
thus introducing diversity in the rst step of a library synthesis. A typical approach
is to react primary amines (e.g. amino acid esters) with electron-rich, resin-bound
aldehydes (Scheme 15.31) [63a, 78]. The acetophenone-containing resin 103 has
been loaded with amines via reductive amination for entry into parallel amide and
sulfonamide preparations (Scheme 15.32) [79].
Scheme 15.31. Loading of amino acid esters onto AMEBA-type resin.
Scheme 15.32. Reductive amination on an acetophenone-containing resin.

The combination of primary amines and electron-rich, resin-bound aldehydes

usually works well under a number of conditions, but hindered aldehydes have
occasionally been problematic. For example, a 3,5-dimethoxy-4-benzaldehyde-
containing resin was shown to be less reactive toward reductive amination than
the monomethoxy analog [80]. Schwarz et al. also observed that di-ortho (e.g.
dimethyl)-substituted aldehydes can be poor substrates for reductive amination
[81]. However, Ellman and coworkers reported reductive amination conditions that
work well with a polymer-supported 3,5-dimethoxy-4-benzaldehyde (Scheme 15.33)
[78a].
Scheme 15.33. Ellmans 1,4-benzodiazepine-2,5-dione synthesis.
Polymer-supported amines have also been used for reductive aminations with
aldehydes. There are several examples where Rink amide resin has been reduc-
tively alkylated [59b, 62b, 75a]. Katritzky et al. formed a variety of imines (both
electron-rich and -poor aromatic aldehydes) with TMOF and reduced them with
LiBH4 [75a]. Rivero and coworkers also used a two-step reductive amination pro-
cedure to prepare a library of 500 macrocycles (Scheme 15.34) [62b]. Benzyloxy-
Scheme 15.34. Macrocycle synthesis incorporating reductive amination as a diversity element.

Tab. 15.1. Recent libraries using reductive amination (since January 2000).
Library Reactantsa Reducing agent Method b Reference
Secondary amides Aniline/aldehydes NaBH4 B 74e

Macrolides Aldehyde/primary amines NaBH3 CN B 58b
Secondary amines/aldehydes
Tertiary amines Hydroxylamine/aldehydes BAP B 67
Tetrahydro- Aldehydes/amino alcohol NaBH(OAc)3 A 78f
quinoxalines
Peptide aldehydes Aldehydes/primary amines NaBH(OAc)3 A 83
Macrocycles Primary amine/aldehydes NaBH(OAc)3 B 62b, 85
3,4-Dihydro-1,4- Anilines/ketones NaBH3 CN A 84
benzothiazines (intramolecular)
Quinoxalinones Aldehydes/amino acid NaBH(OAc)3 A 86
Pyrrolidines Primary amine/aldehydes NaBH3 CN A 87
2-Carboxyindoles 5-Aminoindole/aldehydes NaBH3 CN A 88
b-Ketoamides/ Aldehydes/primary amines LiBH4 B 75b
imidazoles
Amines/amides Aldehydes/primary amines BAP B 72c
Tricyclics Primary amine/ NaBH(OAc)3 A 89
cinnamaldehydes
Piperidines Aldehydes/primary amines BAP B 72b
Tertiary Hydroxylamine/aldehydes NaBH(OAc)3 A 90
methylamines
Phenolic amino Primary amines/aldehydes NaBH(OAc)3 B 91
acids
Neoglycopeptides Amino acids/b-glycoside NaBH3 CN A 92
aldehydes
Lysine/glutamic Amino acids/aldehydes NaBH(OAc)3 B 93
acid derivatives
a First entry is resin-bound component.
b A, one-step procedure, in situ imine formation/reduction; B, two-
step procedure, imine formation then reduction.
aniline and p-benzyloxybenzylamine (BOBA) resins have also been reductively

alkylated with aldehydes and NaBH4 using two-step procedures [74c,e].
15.2.12.5 Recent Examples of Reductive Amination on Resin

There is a large number of libraries that have incorporated a reductive amination
step. This fact highlights the power and reliability of reductive amination for
library synthesis. Recently, a number of libraries have been prepared using re-
ductive amination chemistry. These library syntheses are listed in Table 15.1.
Specic examples include a diketopiperizine library eort at Aymax that relies
on reductive amination for a key diversity step (Scheme 15.35) [65a, 82]. Groth and
Meldal reported a combinatorial approach to N-terminal peptide aldehydes and di-
ketopiperazines using reductive amination [83]. They found that NaBH(OAc)3 in
dimethyl sulfoxide (DMSO)/CH2 Cl2 /AcOH (50:50:1) was optimal after an exten-
Scheme 15.35. Aymaxs solid-phase approach to diketopiperazines.
sive study of conditions, thus emphasizing the importance of varying reaction con-
ditions for successful reductive aminations. Barany and coworkers prepared a set
of 3,4-dihydro-1,4-benzothiazines using a one-pot alkylationintramolecular reduc-
tive amination to prepare the thiazine core [84]. A group at Abbott has prepared an
antibiotic screening library of 70,000 macrolides [58b]. The synthesis involved
three reductive amination steps (aldehydes with a primary amine and two second-
ary amines) to introduce diversity and began with a preconstructed macrolide core.
15.2.13
Azide Reductions

Reductions of aromatic azides provide anilines that are handles for diversication
and may be incorporated into benzo-fused heterocycles. Tin (SnCl2 ), phosphine, or
sulfur reagents are commonly used to carry out this transformation. Under some
tin reduction conditions, side-reactions, such as azide displacement or N-acetyla-
tion, can be problematic. In these cases, phosphine- or sulfur-mediated azide re-
ductions can be used as replacements.
15.2.13.2 Azide Reductions in Glycopeptide Preparations

Solid-phase azide reductions are heavily used in glycopeptide preparations. The
azide is frequently used as a point of attachment for the peptide, but may also be a
handle for diversication. The most commonly used reductants are sulfur based,
such as DTT or 1,3-propanedithiol, although phosphines have been used in several
examples.
Peters et al. [94] in an early example, and later Rademann and Schmidt [95], ob-
tained N-acetates from azide reductions using thioacetic acid and pyridine in solid-
phase glycopeptide preparations. Danishefsky and coworkers used both thiophenol
and 1,3-propanedithiol with Hunigs base in THF to eect azide reduction in solid-
supported trisaccharide- and disaccharide-containing glycopeptides, thus avoiding
N-acetate formation [96]. Glycopeptides have also been prepared on solid support
via azide reduction using DTT and 1,8-diazabicyclo[5.4.0]undecene-7 (DBU) in
DMF [97]. A modied Staudinger reaction has been applied to the preparation of
amides using a solid-supported glycoazide in a one-pot procedure (Scheme 15.36)
[98].
Scheme 15.36. Modied Staudinger reaction for the preparation of glycopeptides.
15.2.13.3 Small Molecule Libraries Incorporating Azide Reduction

A variety of small molecule libraries has been synthesized that incorporate azide
reductions using primarily SnCl2 and triarylphosphines. Ellmans group has pre-
pared several small molecule arrays by generating diversity at the amine prepared
by a tin-mediated azide reduction (Scheme 15.37) [16, 99]. Kim and coworkers have
also prepared a group of oligoureas using a tin-mediated azide reduction [100].
Scheme 15.37. Examples of small-molecule synthesis using azide reductions.
Another example from Chiron is the preparation of a small group of 1,4-benzo-

diazepine-2,5-diones by a PBu3 -mediated azide reduction [101]. Reaction of the
resulting aniline with a pendant ester formed the diazepine heterocycle. Triuoro-
acetic acid cleavage provided 21 benzodiazepines in good yields (Scheme 15.38).
Kahne and coworkers also used aqueous PMe3 to reduce azides on a TentaGel-
supported carbohydrate [102].
It has been reported by Zhou and coworkers that the reduction of a primary
azide with SnCl2 and thiophenol provided signicant amounts of an azide dis-
placement product (resulting from attack by thiophenol) [103]. To circumvent this
Scheme 15.38. Synthesis of 1,4-benzodiazepine-2,5-diones using an azide reduction.
problem, aqueous PPh3 provided the amine in good yield without any azide dis-
placement and allowed the synthesis of an array of hydroxybisamides. Nicolaou
et al. also used an aqueous PPh3 -mediated azide reduction methodology to provide
an amine for diversication in the preparation of a library of 50 sarcodictyins
[104].
15.2.13.4 Recent Examples of Azide Reduction on Resin

A variety of recent libraries has incorporated azide reductions in their synthetic
approach and are summarized in Table 15.2. For example, a library of phenolic ste-
roids has been prepared by Poirier and coworkers using both tin- and phosphine-
mediated azide reductions on various solid supports [105]. The phosphine reduc-
tion was employed when an o-nitrobenzyl ether linkage was used to avoid reduction
of the nitro group on the linker [105b]. A library of substituted oxazoles has been
prepared via derivatization of an amine generated from an azide reduction with
DTT and Hunigs base (Scheme 15.39) [106]. A small library of 1,3-oxazolidines
has been prepared using a tin-mediated azide reduction on solid support [107]. An
azide on solid support has also been reduced with TMSI. This acidic protocol was
used to avoid base-induced formation of a lactam side-product when using DTT/
DBU [108].
A library of 1300 disaccharides has been prepared on solid phase via azide re-
duction with aqueous PMe3 followed by amine derivatization with isocyanates and
Tab. 15.2. Recent libraries utilizing azide reduction (since January 1999).
Library Reducing agent Reference
Glycopeptides PhSH or 1,3-propanedithiol, DIEA 96b

DTT, DBU 97b
PBu3 98
DTT, DBU or TMSI 108
Hydroxybisamides Aqueous PPh3 103
Estradiols Aqueous PPh3 105a
SnCl2 , PhSH, TEA or aqueous PPh3 105b
Oxazoles DTT, DIEA 106
1,3-Oxazolidines SnCl2 , PhSH, TEA 107
Disaccharides Aqueous PMe3 109
1,3-Bis(acylamino)-2-butanones SnCl2 , PhSH, TEA 78e
Phenylglycinnamides Aqueous PMe3 110
Scheme 15.39. Synthesis of oxazoles incorporating an azide reduction.
acids (Scheme 15.40) [109]. An array of 18 1,3-bis-(acylamino)-2-butanones has

been prepared in which diversity was generated at an amine prepared by a SnCl2
azide reduction [78e]. Notably, a dimethyl ketal survived the conditions of this tin-
mediated reduction. A library of phenylglycinnamides has been prepared by gen-
erating a galactosylamine by means of an azide reduction with 1,3-propanedithiol
[110]. The galactosylamine was used in a series of Ugi reactions and cleaved from
the resin to generate eight dierent phenylglycinnamides.
Scheme 15.40. Disaccharide derivatization at an amine generated by an azide reduction.
15.2.14
Nitro Group Reductions

The reduction of aromatic nitro groups to anilines is an often-used transformation
in combinatorial chemistry. The aromatic nitro group serves two important func-
tions: it facilitates SN Ar reactions and provides an amine for further manipulation
following reduction. A frequent use of the resulting aniline in library synthesis has
been in the preparation of various benzo-fused heterocyclic compounds (Scheme
15.41) [111].
There are a variety of protocols that have been developed for the reduction of
nitro groups, and each oers dierent advantages and disadvantages. Some exper-
imentation may be required to nd suitable conditions for the system under study
since the most frequently used reducing reagent (SnCl2 ), while quite reliable, does
not always provide consistent results [112].
15.2.14.2 Tin-mediated Nitro Reductions

The reduction of aromatic nitro groups is often carried out using a tin reagent
(usually an aqueous solution of SnCl2 in DMF) [113, 114]. Acidic conditions typi-
Scheme 15.41. Synthesis of a benzimidazole library via tin-mediated nitro reduction.
cally accompany nitro reduction with SnCl2 , which presents a potential problem
with acid-sensitive polymer supports. Addition of a small amount of buer such
as sodium acetate often remedies this situation [35, 115]. DMF is the solvent of
choice for tin reductions, but N-formylation of o-diaminobenzenes generated from
2-amino-substituted nitrobenzenes and subsequent cyclization to benzimidazoles
has been observed as a side-reaction [116]. This result can be avoided by employ-
ing other solvents such as NMP or N-methylmorpholine (NMM). Tin reductions
often require heating and can benet from exclusion of oxygen [117].
Tin reductions have been used in a number of library syntheses. In an early ex-
ample, the tin-mediated reduction of solid-supported substituted nitrobenzenes led
to anilines that were derivatized to provide a small library of phenols following
cleavage (Scheme 15.42) [118]. The synthesis of a library of 3,4,5-substituted 1,5-
benzodiazepin-2-ones began with a tin-mediated nitro reduction on polymer
support (Scheme 15.43) [119]. Sequential hydrolysis and intramolecular amide
coupling provided the benzodiazepine core.
Scheme 15.42. Meyers approach to a phenolic library via a tin-mediated nitro reduction.
Scheme 15.43. Synthesis of a substituted benzodiazepin-2-one

library via a tin-mediated nitro reduction.
15.2.14.3 Nitro Reductions with Alternative Reagents

Tin-mediated reductions of nitro groups can occasionally give inconsistent results
or suer from incomplete reactions [112, 120], a serious problem in library syn-
thesis where reliability and purity are essential. Furthermore, tin impurities are
known to be problematic in many drug-screening assays, especially cellular assays
[121]. Therefore, a variety of reagents and conditions has been developed as alter-
natives to tin-mediated nitro reductions.
Sodium borohydride with Cu(acac)2 was used in the preparation of a benzimi-
dazole library in which SnCl2 gave inconsistent results (Scheme 15.44) [112]. A
comparative study of nitro reductions with Na2 S2 O4 versus SnCl2 on a set of 74
compounds has been performed [121]. The results show that Na2 S2 O4 is as eec-
tive as SnCl2 in nitro reductions, although resins compatible with aqueous solu-
tions must be used with Na2 S2 O4 . A set of sixteen dierent conditions for the solid-
phase reduction of a nitropyrimidine has also been explored [120]. In this study,
SnCl2 gave only 5065% conversion to the aminopyrimidine, while the best results
were obtained with LAH/AlCl3 , although the nal products were contaminated
with aluminum salts. Aromatic nitro groups have been successfully reduced with
CrCl2 at room temperature [122]. Other metal-mediated nitro reductions have also
been applied to library synthesis in both solid phase (Zn, NH4 Cl [123]) and solu-
tion phase (Fe, HCl [124]).
Scheme 15.44. Preparation of a benzimidazole library via a

NaBH4 -Cu(acac)2 -mediated nitro reduction.
15.2.14.4 Recent Examples of Nitro Reduction on Resin

A diverse set of structural motifs has been realized which incorporate a nitro re-
duction into the synthetic scheme of the library, typically mediated by tin. Table
15.3 lists recent libraries synthesized with incorporation of a nitro reduction. In-
cluded in this set are libraries of 1,4-benzoxa- and benzothiazin-3(4H)-ones as well
as benzimidazoles. A library of 56 1,4-benzoxa- and benzothiazin-3(4H)-ones was
prepared via a reduction, cyclization, and derivatization approach (Scheme 15.45)
[35]. A traceless solid-phase approach to a diverse group of substituted benzimida-
zoles incorporated a tin-mediated nitro reduction (Scheme 15.46) [125].
15.2.15
Imine Reductions (not Reductive Amination)
There are relatively few examples of imine reductions in combinatorial chemistry

that do not involve imines formed from carbonyls and amines. For the reduction
of imines generated from carbonyl compounds, see Sections 15.2.12 and 15.3.1.2
(reductive amination). For an example of imine formation via an aza-Wittig reac-
Tab. 15.3. Recent libraries utilizing nitro reduction (since January 1999).
Library Reducing agent Reference
2-Alkylthioimidazoles Zn, NH4 Cl, methanol 123b

Benzimidazoles SnCl2 , NMP 125
SnCl2 , NMP 126
SnCl2 , NMM 116b
Zn, NH4 Cl, methanol 123c
Benzimidazolones Zn, NH4 Cl, methanol 123a
Benzo[c]isoxazoles SnCl2 , DMF 127
1,5-Benzodiazepin-2-ones SnCl2 , DMF 119
1,4-Benzothiazepin-5-ones SnCl2 128
1,5-Benzothiazepin-4-ones SnCl2 , DMF 129
Benzothiazines SnCl2 , DMF 84
Benzothiazoles SnCl2 , DMF, NaOAc 115
1,4-Benzoxa/thiazin-3(4H)-ones SnCl2 , DMF, NaOAc 35
2-Carboxyindoles SnCl2 , DMF 88
Diaminobenzamides Fe, HCl 124
Dibenzo[b, f ]oxazocines SnCl2 , DMF 130
2,3-Dihydro-[1,5]-benzothiazepines SnCl2 , DMF, NaOAc 115
2,3-Dihydro-[1,5]-benzothiazepine-4(5H)-ones SnCl2 , DMF 81
3,4-Dihydro-2(1H)-quinazolinones SnCl2 , DMF 131
3,4-Dihydro-1H-quinazolin-2-thiones SnCl2 , DMF 131
1,2,3,4-Tetrahydroquinoxalin-2-ones SnCl2 , NMP 132
Scheme 15.45. Synthesis of 1,4-benzoxa- and thiazin-3(4H)-ones via a tin-mediated reduction.
Scheme 15.46. Synthesis of benzimidazoles via a traceless

linker and tin-mediated nitro reduction.
tion and subsequent reduction, see Section 15.3.1.2. Imine reductions have been
used in the synthesis of compounds on solid support as well as in linker activation
prior to cleavage (see below).
BischlerNapieralski cyclization products have been prepared on solid phase,
and the resulting cyclic imines were reduced with NaBH3 CN to provide tetrahy-
droisoquinolines (Scheme 15.47) [133]. When NaBH4 was used in this application,
the dihydroisoquinoline was cleaved at the esterresin linkage. An indolenine in-
termediate, generated via a Fischer indole reaction, was reduced with NaBH4 in the
synthesis of a small library of spiroindolines [134]. Resin-bound imines of amino
acids, prepared from transimination with N-H ketimines, have been reduced with
NaBH3 CN in an approach to a library of hydantoins [135]. In a new linker appli-
cation, a phenanthridine was reduced with NaBH4/BH3 THF [136]. The desired
acid was subsequently released via oxidative cleavage.
Scheme 15.47. Synthesis of tetrahydroisoquinolines involving an imine reduction.
15.2.16
Nitrile Reduction
Conti and coworkers have reported the reduction of a nitrile on solid support
[137]. An aromatic nitrile was reduced with BH3 SMe 2 in diglyme at 80 C to pro-
vide a benzylamine. The resulting molecule was then released from the resin
using an a-chloroethyl chloroformate methanol activation-cleavage strategy.
15.2.17
NN and NO Bond Reductions
Samarium diiodide has been used to cleave NaO bonds in a hydroxylamine trace-
less linker application [138]. Recently, a report was published that described both
nitrosamine and hydrazine reductions on solid phase for the preparation of an ar-
ray of a-substituted primary amines (Scheme 15.48) [139]. DIBAL reduction of the
nitrosamine to the corresponding hydrazine followed by addition of an aldehyde
gave the resin-bound hydrazone. Nucleophilic addition and subsequent borane re-
duction of the resulting derivatized hydrazine provided the target amines in mod-
Scheme 15.48. Preparation of a-substituted primary amines via hydrazine reductive cleavage.
est yields. This approach has also been used to prepare chiral hydrazones and the
corresponding chiral amine products with modest enantioselectivity (5086% ee)
[140].
15.2.18
Miscellaneous Reductions
There are a number of reductions performed on solid-supported functional groups

for which there are relatively few examples. These reductions can be categorized as
those in which the substrate remains attached to the resin, and those where it is
released. Wustrow and coworkers have used a reductive cleavage performed with
Pd(OAc)2 and formic acid to provide benzoate esters and benzamides from aryl sul-
fonates [141]. Reductions where substrates remain attached are listed in Table 15.4.
15.3
Solution-phase Reductions
15.3.1
Supported Reagents
15.3.1.1 Asymmetric Reagents

A number of dierent research groups have shown that polymer-bound amino al-
cohols can act as chiral ligands in asymmetric hydride reductions of various func-
Tab. 15.4. Miscellaneous reductions on solid-supported substrates.
Reduction Reducing agent Reference
Ozonide to alcohol NaBH4 , sonication 142

Ozonide to aldehyde PPh3 , sonication 142
Epoxide to alcohol LiBH4 143
Peroxide to alcohol (EtCO2 )3 P 144
Acetal to hydroxyether DIBAL 145
Lactone to diol LAH 43b
Alkyl chloride to alkane NaI then Bu3 SnH 146
Isoxazole to aldehyde LAH 147
Hydroxybenzotriazole to benzotriazole PCl3 or SmI2 148
Tin chloride to tin hydride LiBH4 149
Phosphine sulde to phosphine TfOMe then HMPT 150
Fig. 15.1. Itsunos asymmetric reduction ligands.
tional groups. Itsuno and coworkers attached optically active prolinol to polysty-
rene to give 152 and treated this product with BH3 THF to derive an enantio-
selective reducing agent (Figure 15.1) [151]. This reagent reduced prochiral ketones
to secondary alcohols in good optical purity. The highest optical yield (80%) was
obtained with a 1% crosslinked reagent (with 50% functionalization), which was
20% higher than that obtained by the solution-phase control. Following hydrolysis
of the reaction mixture with 2 M HCl, the polymer was collected via ltration.
Borane regeneration allowed this reagent to be used two more times. Itsuno and
coworkers also attached amino alcohols to a polymer through a pendant aromatic
group (Figure 15.1) [152]. An acetophenone oxime was reduced with the reagent
derived from this polymer-bound amino alcohol and NaBH4/ZrCl 4 or BH3 THF
[153]. The optical purity of the product was only 35% ee; however, the reagent
could be recycled.
Adjidjonou and Caze have also synthesized polymer-bound amino alcohols that
were combined with NaBH4 to reduce acetophenone [154]. These reagents deliv-
ered the product with modest enantioselectivity (up to 75% ee), which was much
more enantioselective than the product obtained from a solution-phase control ex-
periment (12% ee). Frechet et al. derived ligands from ephedrine and polystyrene
resin and utilized them in the LAH-mediated reduction of acetophenone [155].
The enantiomeric excess of the product was 79% when a lightly loaded insoluble
polymer species was utilized in the presence of an achiral phenol. The minimally
substituted resin allows the chiral amino alcohols to act independently from one
another and allows the hydride to access all of these units fully, thus providing
higher enantioselectivity.
15.3.1.2 Non-asymmetric Reagents
Borane-based reagents
In 1977, Gibson and Bailey introduced the rst solid-supported borohydride
exchange resin (BER) [156]. It should can be noted that, following use, this reagent
can be collected by ltration and regenerated. Early studies with this reagent
focused on carbonyl reductions and related chemoselectivities, which were found
to be better than those produced by NaBH4 in solution [157]. It was understood
that this dierence in selectivity was due in part to the slower reaction kinetics of
the support-bound reagent.
Fig. 15.2. Macroporous polystyrene-supported borohydride and cyanoborohydride.
Despite the recognized benets of BER, improvements have been continually

sought. As has been demonstrated with solution-phase NaBH4 reductions, the ad-
dition of catalytic quantities of transition metal salts (CuSO4 [158], Ni 2 B [159], and
Ni(OAc)2 [160]) enhances reactivity and provides the ability to reduce a broader
spectrum of functional groups. This area of research has also seen the introduc-
tion of zinc [161] and zirconium [162] borohydride polymers.
Reductive amination. Commercially available solid-supported reducing agents

such as BER and NaBH3 CN on exchange resin (PS-BH3 CN) are useful for solution-
phase reductive aminations [163]. Recently macroporous polystyrene versions of
NaBH4 (MP-BH4 ) and NaBH3 CN (MP-BH3 CN) have also become commercially
available (Figure 15.2) [164]. All of these reagents have the same advantage: they
are easily removed from the reaction mixture via ltration. PS-BH3 CN and MP-
BH3 CN have the added advantages of avoiding contamination of nal products
with cyanide and providing enhanced chemoselectivities (relative to BER and
MP-BH4 ).
Typically, reductive aminations with BER and MP-BH4 are two-step procedures,
usually performed in methanol (Scheme 15.49). The imine is preformed with 3-A
molecular sieves followed by addition of the reducing agent [165]. Any unreacted
amine can be scavenged with an appropriate polymer-supported scavenger (e.g.
Wang resin or PS-carboxaldehyde) [166].
Scheme 15.49. Two-step solution-phase reductive amination with BER.
Ley et al. have contributed a number of papers on the subject of polymer-

supported reagents, including reductive amination with BER [165c, 167] and PS-
BH3 CN in conjunction with scavenger resins [168]. Ley et al. recently described
the reductive amination of substituted bicyclo[2.2.2]octanes with BER and amine
scavenging with Wang resin (Scheme 15.50) [165c]. Kaldor et al. also reported the
use of BER and scavenger resins in the parallel preparation of small molecules
[166a]. They used PS-NCO, PS-CHO, and PS-COCl to scavenge excess primary
and secondary amines from crude reaction mixtures and isolated products with
purities exceeding 90% (HPLC).
Scheme 15.50. Ley s reductive amination/amine scavenging

approach to subsituted bicyclo[2.2.2]octanes.
Aldehyde and ketone reductions. In 1983, Yoon et al. studied the chemoselectivity
of carbonyl reductions in a series of competitive reduction experiments with
BER (no additives) [157a]. Their results showed that aldehydes were reduced in
preference to ketones. More interesting were their observations that there was se-
lectivity between aldehydes and between ketones. Aromatic aldehydes were prefer-
entially reduced in the presence of aliphatic aldehydes. Benzaldehydes with para-
substituted electron-withdrawing groups were reduced preferentially to those with
para electron-donating groups. It was also shown that unhindered ketones were
reduced in preference to hindered ketones. In a separate study by Yoon et al., it was
also shown that the addition of CuSO4 to BER increased the diastereoselectivity of
the reduction of norcamphor to norborneol (endo/exo 94:6 vs. 82:18) [158]. The
reduction of ketones and aldehydes has also been carried out using zinc [161]
and zirconium [162] borohydride reagents immobilized on polyvinylpyridine. The
zinc-based reagent is completely inert toward ketones; however, addition of FeCl3
gives low to moderate yields of ketone reduction products. The solid-supported
zirconium borohydride reduces both aldehydes and ketones in the absence of an
additive. Further, it has been shown that the BER-Ni(OAc)2 system fully reduces
aromatic aldehydes to toluene derivatives in high yield regardless of aromatic sub-
stitution [160b]. A hindered equivalent of BER, which diastereoselectively reduces
ketones to secondary alcohols, has recently been introduced by Smith et al. [169].
Studies on the reduction of a,b-unsaturated aldehydes and ketones have also
been carried out using these reducing agents. BER selectively adds hydride in a
1,2-fashion to these substrates, delivering allylic alcohols in high yield [157b]. The
same properties are exhibited by the zirconium reagent [162]; however, the zinc
reagent [161] shows chemoselectivity in that it reduces aldehydes without aecting
ketones. Sim and Yoon showed that addition of 0.1 equiv. of CuSO4 to BER under
standard conditions (5 equiv. BER, methanol, room temperature) fully reduced a,b-
unsaturated systems to saturated alcohols [158]. However, if the amount of BER
was reduced to 2 equiv., the saturated ketone was isolated [158]. Despite these re-
sults, Ley et al. recently published a report describing the isolation of the allylic
alcohol from a BER-CuSO4 -mediated a,b-unsaturated ketone reduction [167a]. In
their synthesis of (G)-epimaritidine, Ley et al. successfully utilized BER-CuSO4
and BER-NiCl2 to carry out the 1,2-reduction of an a,b-unsaturated ketone [167a].
It should be pointed out that the structural complexity of the substrate in the Ley
synthesis is much greater than that of Sim and Yoon. In the report of the synthesis
of (G)-epibatidine, Ley and coworkers also used the parent BER to carry out ketone
reductions in high yield [170].
Ester and acid chloride reductions. The reduction of fully oxidized carbons has
also been studied, but to a much lesser extent. Esters, for example, seem to be
inert to these exchange resins even when transition metal salts are employed. Acid
chlorides, on the other hand, have been reduced to both aldehydes and alcohols
depending on the resin used. Simple long-chain acid chlorides have been selec-
tively reduced to aldehydes in high yield by passage through a column of BER
[171]. Depending on the reaction conditions, Tamami and Goudarzian have shown
that polymeric Zn(BH4 )2 can deliver either the alcohol or the aldehyde, however
the products are not obtained cleanly [161b]. For example, if phenylacetyl chloride
is treated with Zn(BH4 )2 in hot THF, a 70:20 mixture of the alcohol and aldehyde
is recovered. If the reaction is run at room temperature in CH2 Cl2 , a 25:65 mixture
is obtained. Tamani and Lakouraj have also demonstrated that high yields of
clean alcohol can be obtained by using another polymeric zinc borohydride, poly-h-
(pyrazine)zinc borohydride, in THF at ambient temperature [172]. In Ley and
coworkers synthesis of (G)-epibatidine, the rst step involved an aromatic acid
chloride reduction to an alcohol mediated by BER [170].
Epoxide reductions. The reduction of epoxides has also been studied. BER with
CuSO4 does not react with aliphatic epoxides, yet cleanly reduces styrene oxide to
ethylbenzene [158]. Despite requiring additional quantities of reagents (10 equiv.
BER and 0.5 equiv. CuSO4 ), a-methylstyrene oxide and b-methylstyrene oxide
also gave the fully saturated alkylphenyl derivatives upon reduction. Supported
Zn(BH4 )2 was capable of reducing both aliphatic and styrenyl derivatives, how-
ever this reagent did not give fully reduced products. Instead, a mixture of the
more and less substituted alcohols was obtained, with the former predominating
[161b]. The poly-pyrazine zinc reagent was inert toward both types of epoxides
[172].
Halide reductions. Sim and Yoon looked at the reduction of alkyl and aryl halides
in detail. BER-CuSO4 was found to be inert toward simple alkyl and aryl chlorides,
while readily reducing primary and secondary alkyl bromides as well as aryl bro-
mides and iodides [158]. It should be noted that activated chlorides (benzylic or a
to an ester) can be reduced by this system. These chemoselectivities were demon-
strated by performing competition experiments. For instance, 1-bromo-4-chloro-
butane was readily reduced to 1-chlorobutane (95%) and p-bromochlorobenzene
was cleanly reduced to chlorobenzene (99%). Since aryl bromides required heat to
be eectively reduced, while aryl iodides did not, it was possible to selectively re-
duce p-bromoiodobenzene to bromobenzene at ambient temperature with a 97%
yield. Yoon et al. have also shown that BER-Ni(OAc)2 has nearly the same selectiv-
ity prole as BER-CuSO4 , and that this nickel-based system can be used to reduce
1-octyl tosylate to octane in 95% yield provided that NaI is present [160a].
Disulde reductions. Attempts to reduce disuldes with polymer-supported re-

agents has given variable results. BER-CuSO4 quantitatively reduces diphenyl di-
sulde, yet fails to convert n-butyl disulde to n-butylthiol [158]. On the other
hand, polymeric Zn(BH4 )2 has been successful in reducing both substrates (100%
and 40% respectively), as well as others [161b]. The parent BER quantitatively re-
duces diphenyl disulde [173].
Azide reductions. BERs and combinations with nickel or copper salts are eec-
tive at reducing alkyl and aryl azides [158, 174]. In an early application of BERs,
both aryl and arylsulfonyl azides were reduced in methanol to amines and sulfo-
namides [175]. BER-Ni(OAc)2 has been used to reduce a variety of azides [174].
Tamami and Lakourajs piperazine-based zinc reagent can reduce both aryl and
alkyl azides to amines [172]. Tamami and Goudarzians pyridine-based version re-
duces aryl and arylsulfonyl azides but does not react with alkyl azides [161b].
Nitro reductions. A number of support-bound borohydride reagents has been

used to reduce nitro groups [176]. BER-Ni(OAc)2 reduces aromatic and aliphatic
nitro groups and can be easily removed via ltration in a solution-phase approach
[177]. The BER-CuSO4 reagent couple also reduces aromatic and aliphatic nitro
groups [158]. BER-NiCl2 was used by Ley and coworkers to reduce a nitro group in
their synthesis of epibatidine [170].
Reductive cyclizations. The reductive addition of alkyl iodides to electron-decient

alkenes has been demonstrated utilizing the BER-Ni 2 B system [159a]. Examples of
radical additions to a,b-unsaturated esters, nitriles, and ketones have been shown
to occur in high yields. It has been demonstrated that the same reagent aects ali-
phatic alkene and vinyl ether reactions with a-bromo esters [159b].
Miscellaneous reductions. BER-Ni(OAc)2 also has been reported to reduce alde-

hyde oximes to amines [178].
Tin-based reagents
Polymeric tin hydrides are capable of reducing a number of functional groups, in-
cluding carbonyls, alkyl halides, and alcohols [179]. The last are reduced through
the intermediacy of a phenylthionocarbonate, according to the methodology set
forth by Barton [179b,c]. The main advantage of these reagents over tributyltin-
hydride (TBTH) is in the work-up. Separations to remove toxic tin byproducts are
avoided as the tin species can be easily removed by ltration.
In 1975, Crosby and coworkers introduced the rst of the supported tin re-
agents, a polystyrene-based n-butyldihydridotin species [179a]. This reagent
directly links a tin atom to the phenyl ring of the polystyrene backbone. In 1993,
Neumann and Petersheim published an optimized preparation for a polystyrene-
based monohydridotin reagent that utilizes a two-carbon linker between the tin
and aromatic backbone of the polymer [180]. Since aromatic tin bonds can be
labile, this aliphatic carbon-linked tin reagent was believed to be more stable
than Crosbys reagent. Dumartin et al. introduced tin reagents with 3- and 4-carbon
linkers that more closely resemble the structure and reactivity of TBTH [179d].
These tin reagents have been used to carry out carbonyl reductions in high yield,
including the reduction of both aliphatic and aromatic aldehydes and ketones. It
has also been shown that chemoselectivity can be achieved with these reagents, as
alkyl halides have been reduced in the presence of ketones [179a]. Neumann and
coworkers demonstrated the feasibility of alcohol deoxygenation by utilizing the
Barton protocol. This methodology required the conversion of an alcohol to a phe-
nylthionocarbonate, which was then reduced with a solid-supported tin reagent to
give the saturated alkyl compound [179b,c]. Neumann and coworkers have also
applied this reagent to the reductive cyclization of o-alkenyl halides [181].
Trialkylsilane-mediated reduction of carbonyls

A polymer-supported trialkylsilane has been used to hydrosilylate carbonyl alde-
hydes and ketones [182]. Treatment of the carbonyl compounds with the tri-
alkylsilane and Wilkinsons catalyst generated resin-bound alkoxysilanes (Scheme
15.51). Cleavage of the resulting alkoxysilane with HF provided the desired alco-
hols in fair to good yields.
Scheme 15.51. Reduction of aldehydes and ketones via hydrosilylation.
Polymer-supported dihydrolipoic acid-mediated reduction of disuldes

Disuldes of cystamine, cysteine, 2-hydroxyethyl disulde, and oxidized glutathione
have been reduced with polymer-bound dihydrolipoic acid [183]. The polymer is
prepared via NaBH4 reduction of lipoic acid on polymer (Scheme 15.52). The best
results for disulde reduction were obtained with a polyacrylamide solid support
in a pH range of 7.58.5.
Scheme 15.52. Preparation of polymer-supported dihydrolipoic acid.
Polymer-supported dihydropyridine-mediated reductions

Polymer-supported 1,4-dihydropyridines (PS-DHPs) have been used as NADH-type
reducing agents [184]. A divalent cation, typically magnesium, is required for re-
ducing activity and the reactions can be run in either organic or aqueous systems.
Bourguignon and coworkers used 1,4-dihydronicotinamide on Merrield resin

to reduce CbO, CbN, CbS, and CbC double bonds [184a]. Obika and coworkers
have developed a chiral sulnyl-containing DHP on Merrield resin that was used
to reduce methyl benzoylformate to the corresponding hydroxy ester (Scheme
15.53) [184c]. Quantitative chemical yields and high optical yields (96% ee) were
obtained when the reaction was run in acetonitrilebenzene (1:1) with 2.5 equiv. of
supported DHP and Mg(ClO4 )2 , respectively. The oxidized supported DHP could
be regenerated by treatment with propyl-1,4-dihydronicotinamide (PNAH).
Scheme 15.53. Polymer-supported chiral NADH model ketoester reduction.
Polymer-supported sulde reductions of ozonides

Ozonide reductions have been performed with solid-supported triphenylphosphine
[185] and suldes [186]. Appell and coworkers have prepared 3,3 0 -thiodipropionic
acid and its sodium salts as supported analogues of dimethylsulde for reductive
quenching of ozonides [186]. The best results were obtained in ozonolysis reac-
tions with the monosodium salt; as such, a polymer-supported version 172 was
prepared. The corresponding dialdehyde of ethyl 3-cyclopentenecarboxylate was
generated in a 92% yield after quenching the ozonide with this polymer-supported
reagent (Scheme 15.54).
Scheme 15.54. Polymer-supported sulde for reductive ozonolysis work-up.
Polymer-supported triphenylphosphines for the reduction of azides

Polymer-supported triphenylphosphine (PS-PPh2 ) is similar to unsupported
triphenylphosphine in solution-phase azide reductions. An added advantage of
PS-PPh2 is that the phosphine oxide generated is left on the polymer and is easily
removed from the product by ltration.
Polystyrene-supported triphenylphosphine has been used to reduce azides in a
series of azido nucleosides [187]. Yields were nearly quantitative and were similar
to those obtained with unsupported triphenylphosphine. Polyethylene glycol-
supported triphenylphosphine (PEG-PPh2 ) has been successfully applied to azide
reductions, providing amines in shorter reaction times than with PS-PPh2 [188].
Reaction of PS-PPh2 and azides provides iminophosphoranes that in turn can

react with aldehydes to provide imines (aza-Wittig reaction). This approach has
been used to generate a set of 20 imines which were reduced with PS-BH3 CN or
NaBH3 CN to give amines in good to excellent yields (Scheme 15.55) [189]. Imines
have also been prepared in a similar fashion using 1 equiv. of a noncrosslinked
polystyrene-supported triphenylphosphine [190]. This resin-bound phosphine has
a higher loading (1 mmol g1 ) than PEG-PPh2 (0.5 mmol g1 ) and can be used in
stoichiometric quantities (PS-PPh2 is typically used in excess).
Scheme 15.55. Synthesis of amines via aza-Wittig reaction and imine reduction.
15.3.2
Supported Catalysts
15.3.2.1 Asymmetric Catalysis

Homogeneous asymmetric catalysis has been widely studied in both academic and
industrial settings. A subset of this research involves the reduction of prochiral
ketones to chirally enriched secondary alcohols. Two of the more ecient methods
of carrying out this transformation have been described by the research groups of
Noyori [191] and Corey [192]. Despite the advantages of the catalyst systems in-
troduced by these groups, the cost of catalyst preparation is high, thereby making
reuse desirable. The recovery and purication can be a dicult process; therefore,
a number of research groups have pursued the preparation and use of heteroge-
neous analogs of these catalysts. By attaching these compounds to a solid support,
it is believed that the ease with which a catalyst could be recovered and reused
would be increased. However, catalyst-recycling improvements cannot come about
at the expense of catalyst activity and stereoselectivity. Polymeric catalyst design
has therefore taken into account the issues of active site symmetry, accessibility,
and exibility. The three major areas of research in this eld include hydro-
genations, transfer hydrogenations, and borane-mediated reductions.
Hydrogenations
Of the homogeneous asymmetric catalysts designed to carry out the reduction of
prochiral ketones with molecular hydrogen, perhaps none has garnered more
attention than the BINAP-Ru catalyst designed by Noyori [191b]. It should not
be surprising therefore that this catalyst system has been chosen for exploitation
by a number of research groups interested in heterogeneous catalysis. At least two
Fig. 15.3. Polymeric BINAP ligands.
dierent approaches have been used to incorporate the BINAP structure into a
polymer.
An approach chosen by a group from Oxford Asymmetry involved attaching
this C-2-symmetric ligand to an existing polymer with the attachment point distal
from the active site phosphine atoms [193]. This goal was accomplished by mono-
functionalizing the ligand at the 6-position with an alkyl carboxylic acid and then
coupling this group to aminomethyl polystyrene resin. The resulting non-C-2-
symmetric resin-bound ligand 179 (Figure 15.3) was then treated with a ruth-
enium(II) complex and methanolic HBr in acetone to give the active hydrogena-
tion catalyst. The catalyst (1.7 mol%) was added to a methanol/THF solution of the
substrate, which was then treated with 10 atm of hydrogen and heated to 70 C.
Reduction of the b-ketoester, methyl propionylacetate, was complete in 18 h with
an enantioselectivity of 97%. This heterogeneous catalyst was similar in activity
and selectivity to the parent homogeneous BINAP-Ru catalyst. Further, these data
show that the loss of C-2 symmetry is not detrimental to the parent catalysts se-
lectivity. Perhaps more important is that this catalyst was easily recovered and
reused two more times with only minimal losses in yield and enantioselectivity.
Another approach that has been used to incorporate BINAP into a polymer was
carried out by the Lemaire group [194]. This approach involved copolymerization
of a 6,6 0 -dimethylamine BINAP ligand with 2,6-tolylene diisocyanate to give a C-2-
symmetric BINAP polymer 180 (Figure 15.3). This noncrosslinked polymer was
soluble in DMF and DMSO, yet insoluble in the typical hydrogenation solvent
methanol. Utilizing conditions similar to those described above, Lemaire and co-
workers were able to completely reduce methyl propionylacetate in 14 h (0.1 mol%
catalyst, 40 atm., 50 C) to the desired b-hydroxyester in 98% ee. This catalyst was
also recovered and reused up to four times without any loss in activity or selectiv-
ity. Lemaire and coworkers utilized the same polymer in the presence of chiral
diamines [191c] to reduce simple ketones (lacking proximal heteroatoms),
such as substituted acetophenones to alcohols [195]. However, the enantiomeric
excesses of the products varied between 58% and 96%. It was also shown that
the absolute conguration of the added diamine is crucial to retain good enantio-
selectivity.
Chan and coworkers described another example of catalytic asymmetric hydro-

genation in 1999 [196]. Although the prepared catalyst was used in an olen
reduction, which is beyond the scope of this chapter, it is worthy of note. The
polymer formation was conceptually similar to that described by Lemaire, in
that the C-2 symmetry was retained by copolymerizing either enantiomer of a 5,5 0 -
difunctionalized BINAP with (2S,4S)-pentanediol and terephthaloyl chloride.
These polymers contained a polyester backbone, which imparted solubility in the
reaction solvent mixture of methanol and toluene (2:3, v/v). It was also possible
to precipitate these catalysts with excess methanol following reaction completion.
Utilization of either polymer to reduce 2-(6 0 -methoxy-2 0 -naphthyl)acrylic acid was
complete within 18 h, giving nearly equal and opposite enantiomeric excesses
(about 93% ee) of naproxen. These polymers were recycled up to ten times without
any loss of activity or selectivity.
Transfer hydrogenations
The replacement of molecular hydrogen by hydrogen donors is an issue of prac-
tical importance in the eld of catalytic asymmetric reduction (because of safety
concerns). As was the case for standard homogeneous hydrogenations, the Noyori
laboratory has made some of the most signicant contributions in this area.
Noyori and coworkers introduced the (1S,2S)- and (1R,2R)-N-( p-toluenesulfonyl)-
1,2-diphenylethylenediamine (TsDPEN) ligands, which carry out hydride transfer-
mediated ketone reductions in high yields and enantioselectivities when com-
plexed with ruthenium [191d].
Both the Oxford Asymmetry [197] and Lemaire [198] groups have incorporated
this ligand into polymers, using handles on the aromatic sulfonyl portion of the
ligand as the linkage point to the resin (Figure 15.4). Each group adopted a strat-
egy similar to the one they took in forming the BINAP polymers, described above.
The Oxford group attached the ligand via an amide bond to preformed polymers
(PS and PEG-PS) whereas the Lemaire group took a copolymerization approach.
The Lemaire group did not concern itself with producing a linear C-2-symmetric
polymer as they had previously, because the parent TsDPEN ligand is not C-2
symmetric. They copolymerized styrene and a TsDPEN ligand, equipped with a
vinyl group, in both the presence and absence of divinylbenzene, thus producing
both a crosslinked and a linear polymer.
Both groups studied the reduction of acetophenone; however, each group took
their own approach to optimize the reaction conditions. The Oxford group focused
on the variation of the hydride source, polymer, and solvent, while keeping the
Fig. 15.4. Polymeric TsDPEN ligands.

transition metal constant [197]. The Lemaire group varied the polymer and transi-
tion metal, while keeping the hydride source and solvent constant [198]. Regard-
less of which polymeric ligand (PS or PEG-PS) was used in the catalyst prep-
aration with [RuCl2 ( p-cymene)]2 , the Oxford group encountered diculties with
isopropanol as the hydrogen donor. In the case of ligand 181 (Figure 15.4), the
activity of the catalyst and the optical purity of the products were acceptable; how-
ever, catalyst recycling failed. In the case of ligand 182, both the conversion and the
enantioselectivity observed were low with the initial use of the catalyst. To circum-
vent these problems a switch was made from isopropanol to a mixture of formic
acid and triethylamine (5:2). This combination led to successful reductions using
either ligand. The catalyst formed from ligand 182, in neat HCO2 H:Et3 N, gave
product in 97% ee with 95% conversion in 28 h and could be reused once without
any loss in ee. The catalyst formed from ligand 181 required a cosolvent to deliver
favorable results. Addition of either DMF or CH2 Cl2 resulted in enantiomer ex-
cesses of 94% or better with a reasonable degree of conversion (> 60% at 18 h).
This catalyst was also successfully subjected to recycling.
Although the Lemaire group varied both the transition metal and the polymer
in their eorts to nd a heterogeneous transfer hydrogenation catalyst, there was
little dierence in activity and selectivity between their crosslinked and non-
crosslinked polymers. From these results, they chose to focus on the signicance of
the transition metal [198]. Both Ir(I) and Ru(II) complexes were used in the prep-
aration of the catalysts. The iridium catalyst was prepared by combination of the
polymeric TsDPEN ligand 183 and [Ir(I)(COD)Cl]2 in an isopropanolic solu-
tion of KOH, whereas the preparation of two ruthenium catalysts (from either
[Ru(benzene)Cl2 ]2 or [Ru( p-cymene)Cl2 ]2 ) required heat (70 C) and the replace-
ment of KOH with triethylamine. Of these, the best results were found utilizing
the iridium-based catalyst, which gave 96% conversion to the S-alcohol with 94%
ee after 72 h. Unfortunately, the reuse of this catalyst led to poor results in terms
of activity and selectivity. The ruthenium-based catalysts, on the other hand, were
much less selective (3164% ee), but were able to be reused up to four times.
For comparative purposes it is interesting to note that when both groups em-
ployed their ligand with [RuCl2 ( p-cymene)]2 , a crosslinked polymer, and isoprop-
anol (as solvent and hydride source), the optical purity of the alcohol produced was
similar (84% ee for Lemaire and 90.5% ee for Oxford); however, the activities were
quite dierent. After 48 h, the former group saw just 23% conversion while the
latter group saw 88% conversion after 18 h. It must be noted that the catalyst load
(2.5% vs. 1% respectively) and usage of KOH (presence vs. absence respectively)
were dierent.
In another eort to identify a heterogeneous catalyst system capable of carrying
out asymmetric reductions, the Lemaire group has copolymerized dialdimine
ligands 184, 185 (Figure 15.5) with varying amounts of polystyrene and/or DVB
[199]. The iridium-based catalysts formed from the resulting ligands were used in
the isopropanol-mediated transfer hydrogenation of acetophenone. Although the
level of activity for these catalysts was high, the enantiomeric excess of the prod-
ucts obtained were never greater than 70%. Catalyst recycling suered losses in
Fig. 15.5. Dialdimines and diamine used in the preparation of transfer hydrogenation catalysts.
both activity and selectivity. It is interesting to note that ruthenium and cobalt
failed to catalyze the reduction, and that a 71% crosslinked polymer gave higher
optical purity than both 15% and 100% crosslinked polymers. In another example
from the Lemaire group, diamine 186 (Figure 15.5) was copolymerized with both a
diacid chloride and a diisocyanate to give a poly(amide) and a poly(urea), respec-
tively [200]. Utilizing the rhodium-based catalysts prepared from these ligands, the
reduction results were less than optimal. The poly(amide) gave product in only
28% ee and the poly(urea) resulted in a product of only 60% ee. The latter catalyst
could be recycled at least twice.
Also worthy of mention are the Lemaire groups eorts directed toward catalyst
formation using molecular imprinting [201]. In an application of this method-
ology, this group copolymerized a preformed diaminerhodium complex with dii-
socyanate in the presence of the compound to be imprinted (the alcohol product)
optically pure 1-(S)-phenylethanol. Once the polymer was formed and the alcohol
was washed away, an imprint of the product was left in the catalytic site, which
allowed for binding of acetophenone (or a similar substrate) and biased reduc-
tion to the desired products. In practice, the imprinting eect was found to be
real, yet small. The enantiomeric excess of the product from acetophenone reduc-
tion increased modestly, from 33% to 43%, from the polymer catalyst formed in
the absence of the template to the one formed in the presence of the template.
Both of these optical purities were lower than those obtained using the diamine in
a homogeneous control reaction (55%). A drawback to this method is that it does
not allow for the reduction of a diverse set of ketones as the substrates must have a
similar structure to the imprinted molecule.
Borane-based reductions
A third major area of research directed at the heterogeneous asymmetric catalysis
of prochiral ketone reductions is focused on borane-based catalysts. Successful
solution-phase asymmetric reductions using chiral oxazaborolidines, described by
Itsuno et al. [151153] and Corey et al. [192], have prompted much of this re-
search.
Some of the early work carried out by Itsuno et al. involved covalent attachment
Fig. 15.6. Oxazaborolidine catalysts.
of an amino alcohol to a polystyrene backbone followed by carbonyl reduction with

the amino alcohol based-borane reagent to give products with moderate enantio-
selectivity [151153]. Although this work allowed for the recovery of the ligand, it
did not allow for the recovery of the intact boron catalyst for reuse. Some of the
more recent work has addressed this issue by covalently linking the boron atom of
the catalyst directly to the aromatic ring of polystyrene.
In an eort to capture some of the success of Corey and coworkers CBS catalyst
and apply it to the solid phase, a group from Sandoz derived a catalyst from (S)-
a,a-diphenyl-2-pyrrolidinemethanol and a crosslinked polystyrene boronic acid
[202]. Once in hand, this catalyst 187 was used to reduce acetophenone and cy-
clohexylmethyl ketone (Figure 15.6). In both cases, 10 mol% of the catalyst was
sucient when used in combination with a stoichiometric reductant in THF at 40

C. In the case of the reduction of the aromatic ketone acetophenone, an excellent
enantioselectivity of 98% was obtained for the product when BH3 SMe 2 was used
as the stoichiometric reductant and care was taken to add the ketone slowly. This
result was in line with that obtained when the monomeric catalyst was employed.
The reduction of cyclohexylmethyl ketone also gave product with the same selec-
tivity (about 80% ee) as was obtained by the monomer catalyst. This reduction
required the use of either BH3 SMe 2 or BH3 1,4-oxathiane as the stoichiometric
reductant. Following a methanol quench, it was shown that at least one round
of recycling was possible with this catalyst.
In a conceptually similar approach, Caze et al. have prepared catalysts from
(1R,2S)-()-norephedrine and two polystyrene boronic acids with diering degrees
of crosslinking [203]. The optimized reduction conditions involved premixing 30
mol% of BH3 SMe 2 (the stoichiometric reductant) with 30 mol% of the lesser
crosslinked catalyst 188 in THF at 20 C, and after 30 min gradually adding all of
the ketone and the remainder of the catalyst. This procedure delivered the product
of propiophenone reduction in 89% ee and in high yield. Recycling of this catalyst
was carried out up to three times. The more highly crosslinked catalyst, as well as
a thiophene-linked catalyst [204], gave inferior results to those obtained by the less
crosslinked polymer mentioned above.
More recently, Wandrey and coworkers attached a modied CBS ligand to a
siloxane-based copolymer via Pt-catalyzed hydrosilylation [205]. The resulting
soluble polymer is similar to the original Itsuno polymers in that the chiral amino
Fig. 15.7. Wandrey s oxazaborolidine catalyst.
alcohol, not the boron atom, acts as the point of attachment to the polymer.
The catalyst 189 is formed by combination of the polymer amino alcohol with
BH3 SMe 2 in THF (Figure 15.7). Aryl ketone reduction is then carried out by
treatment with the catalyst and stoichiometric quantities of BH3 SMe 2 in THF.
The resulting secondary alcohols are obtained in enantiomeric excesses ranging
from 89% to 98%, which compares favorably with nonpolymeric results. Un-
fortunately, the products still have to be puried by distillation or chromatography.
In early 2001, Zhao and coworkers reported the preparation of catalyst 190
(Figure 15.8) [206]. Unlike the amino alcohol described above, the nitrogen of this
ligand is attached to the resin via a sulfonamide bond. Product ee values were
good to excellent for the reduction of aromatic ketones and moderate for alkyl ke-
tones when this catalyst was employed. The combination of NaBH4 and Me3 SiCl
(or BF3 OEt2 ) was used as the stoichiometric reductant. Although the catalyst
could be reused up to three times, a regeneration step was required.
The asymmetric reduction of ketones has also been carried out using zinc com-
plexes of polynaphthyl ligands. These catalysts have been shown by the Pu group
to mediate the catecholborane reduction of prochiral ketones [207]. Although the
reduction of arylmethyl ketones gave products in good yield with ee values as high
as 80%, the reductions of alkyl and branched methyl ketones were much less suc-
cessful. After quenching the reaction, the homogeneous polymer was precipitated
by addition of methanol. Reuse of this catalyst also required a regeneration step.
15.3.2.2 Non-Asymmetric Catalysis

One of the main drawbacks of tributyltinhydride-mediated reductive dehalogena-
tions is the tin waste stream that is created. Utilization of polymeric tin reagents
reduces the diculties associated with their removal. A further improvement has
Fig. 15.8. Zhaos polymer-supported sulfonamide.

Fig. 15.9. Enholms tin catalyst.
been introduced which uses these tin reagents in catalytic quantities in the pres-
ence of stoichiometric amounts of sodium borohydride.
Enholm and Schulte developed a noncrosslinked polymer (191) that is soluble
in a number of organic solvents (Figure 15.9) [208]. This reagent can easily be
removed from a reaction mixture by precipitation with methanol. Alkyl and aryl
halide reductions have been carried out in N,N-dimethylacetamide (DMA) with 1.5
equiv. of NaBH4 , 0.1 equiv. of 191, and AIBN, as initiator. Because the reactions
are homogeneous, the reaction rates are faster than those found with insoluble
polymeric catalysts, with completion typically observed in just a few hours at
80 C.
Dumartin and coworkers demonstrated the utility of a polymeric tin iodide (192)
and compared it with the reducing capabilities of Neumanns tin chloride reagent
(193) (Figure 15.10, see Section 15.3.1.2) [181, 209]. In the comparative analysis of
1-bromoadamantane reduction, 0.050.9 equiv. of polymer 192 or 193 was combined
with NaBH4 (2.5 equiv.), AIBN (0.1 equiv.), and substrate in ethanol and heated to
65 C for 12 h. When 0.2 equiv. of the catalyst 192 was used, adamantane was ob-
tained in 93% GC yield, while 0.5 equiv. of Neumanns reagent gave only 40% of
the same product. Dumartins group also showed that catalyst 192 produces very
low levels of tin pollution and can be reused.
Bergbreiter and Walker introduced a catalytic tin halide polymer that reduced
alkyl and aryl bromides and iodides when combined with NaBH4 and catalytic
quantities of a crown ether [210]. Blanton and Salley extended this methodology by
attachment of both the crown ether and tin chloride to the same lightly crosslinked
polymer [211]. Although this polymeric co-catalyst showed lower activity than the
soluble catalyst controls, it showed a marked increase in activity (48%) over con-
trols with one catalyst supported and the other in solution. It appears that this
lightly crosslinked polymer was suciently mobile to allow the two catalysts to in-
teract. More recently, Deleuze and coworkers introduced an insoluble maleimide-
based polymer for catalytic tin reductions [212]. The reduction of 1-bromoadaman-
tane was successfully demonstrated, but the high reaction temperature required
(95 C) caused signicant leaching of tin.
Fig. 15.10. The tin catalysts of Dumartin and Neumann.

15.3.3
Unsupported Reagents Using Catch-and-release Purication
15.3.3.1 Reductive Amination

A catch-and-release approach has been used for purication of reductive amina-
tions on acid-containing products [213]. The reductive amination was performed
with NaBH4 and the crude reaction was mixed with DOWEX 1 8400 formate
resin. The solution was drained and the resin treated with TFA to provide the
clean product. A catch-and-release strategy has also been used to prepare small
groups of ureas and amides via solution-phase reductive amination with Ti(OiPr)4 /
NaBH4 (Scheme 15.56) [69c].
Scheme 15.56. Capture and release for rapid purication of a

solution-phase reductive amination reaction.
15.3.3.2 Amide Reductions

Bussolari and coworkers have also reported a resin quench-capture method for the
work-up of solution-phase amide reductions with BH3 THF [214]. Boraneamine
adducts were quenched by acidic AG 50W-X2 resin and boron-containing salts
were washed away while the desired amine was captured by the resin. Subsequent
treatment of the resin with ammonia released the desired amine products with
excellent purities (> 95% by LCMS). This approach was used to prepare a 300-
member library of 2-alkoxy- and 2-acyloxyphenylpropyl amines.
15.3.4
Fluorous Chemistry
All of the reductions described above required that either the substrate or the re-
agent be attached to a polymer support; however, a new method is emerging that
allows both reactants to remain in solution which takes advantage of the fact that
highly uorinated reagents are immiscible in both standard organic and aqueous
phases at ambient temperature, yet are miscible in organic solvents at elevated
temperatures. This solubility prole simplies product isolation and purication
by making it possible to separate products from byproducts by straightforward ex-
tractive work-ups. Curran and coworkers has shown that uorous chemistry is
ideally suited to carry out tin-based reductions [215]. They demonstrated that per-
uorinated tin reagents can reduce a number of functional groups including sele-
nides, alkyl halides, nitro groups, xanthates, and aldehydes. Alkyl halides have
been reduced with both stoichiometric and catalytic quantities of the tin hydride
reagent using NaCNBH3 as the stoichiometric reductant in the latter case. Curran
References 431
and coworkers also described reductive additions and cyclizations of alkyl and aryl
halides to alkenes.
15.4
Conclusions
Reductions have been of enormous synthetic utility in both supported and unsup-
ported combinatorial applications. While solid-phase organic synthesis has pro-
vided many examples of reductions over the last few decades, the area of solution-
phase combinatorial synthesis has emerged and has grown rapidly more recently.
As the introduction of new solid-supported reagents and catalysts continues, the
ability of those involved in the drug discovery process to both generate and opti-
mize lead compounds should increase.
References
1 a) P. H. H. Hermkens, H. C. J. 7 K. M. Brummond, J. Lu, J. Org.

Ottenheijm, D. Rees, Tetrahedron Chem. 1999, 64, 17231726.
1996, 52, 45274554; b) P. H. H. 8 C. T. Bui, N. J. Maeji, F. Rasoul,
Hermkens, H. C. J. Ottenheijm, A. M. Bray, Tetrahedron Lett. 1999,
D. Rees, Tetrahedron 1997, 53, 5643 40, 53835386.
5678; c) S. Booth, P. H. H. 9 A. R. Katritzky, D. Toader, K.
Hermkens, H. C. J. Ottenheijm, Watson, J. S. Kiely, Tetrahedron Lett.
D. Rees, Tetrahedron 1998, 54, 15385 1997, 38, 78497850.
15443; d) R. E. Dolle, K. H. Nelson, 10 a) P. F. Alewood, R. I. Brinkworth,
Jr, J. Comb. Chem. 1999, 1, 235282; R. J. Dancer, B. Garnham, A. Jones,
e) D. H. Drewry, D. M. Coe, S. Poon, S. B. H. Kent, Tetrahedron Lett. 1992,
Med. Res. Rev. 1999, 19, 97148; f ) R. 33, 977980; b) J. J. Burbaum, M. H.
G. Franzen, J. Comb. Chem. 2000, 2, J. Ohlmeyer, J. C. Reader, I.
195214; g) R. E. Dolle, J. Comb. Henderson, L. W. Dillard, G. Li, T.
Chem. 2000, 2, 383433; h) S. V. Ley, L. Randle, N. H. Sigal, D. Chelsky,
I. R. Baxendale, R. N. Bream, P. S. J. J. Baldwin, Proc. Natl. Acad. Sci.
Jackson, A. G. Leach, D. A. USA 1995, 92, 60276031; c) P. S.
Longbottom, M. Nesi, J. S. Scott, R. Furth, M. S. Reitman, A. F. Cook,
I. Storer, S. J. Taylor, J. Chem. Soc. Tetrahedron Lett. 1997, 38, 54035406;
Perkin 1 2000, 38154195. d) E. B. Akerblom, A. S. Nygren, K.
2 a) J.-U. Peters, S. Blechert, Synlett H. Agback, Mol. Diversity 1998, 3,
1997, 348350; b) S. Hanessian, F. Xie, 137148; e) A. V. Purandare, M. A.
Tetrahedron Lett. 1998, 39, 737740. Poss, Tetrahedron Lett. 1998, 39, 935
3 Q.-S. Ren, W.-Q. Huang, P.-L. Ho, 938.
Reactive Polymers 1989, 11, 237244. 11 M. R. Pavia, H. V. Meyers, G. Milot,
4 U. Zehavi, A. Patchornik, J. Am. M. E. Hediger, US Patent No. WO
Chem. Soc. 1973, 95, 56735677. 99/33431, July 8, 1999.
5 J. M. Frechet, C. Schuerch, J. Am. 12 P. Sieber, Tetrahedron Lett. 1987, 28,
Chem. Soc. 1971, 93, 492496. 21072110.
6 E. W. Baxter, J. K. Rueter, S. O. 13 D. R. Cody, S. H. H. DeWitt, J. C.
Nortey, A. B. Reitz, Tetrahedron Lett. Hodges, J. S. Kiely, W. H. Moos,
1998, 39, 979982. M. R. Pavia, B. D. Roth, M. C.
Schroeder, C. J. Stankovic, US Kobayashi, I. Hachiya, M. Yasuda,

Patent No. 5,324,483, June 28, 1994. Tetrahedron Lett. 1996, 37, 55695572;
14 T. Masuda, J. K. Stille, J. Am. Chem. c) S. Kobayashi, M. Moriwaki, R.
Soc. 1978, 100, 268272. Akiyama, S. Suzuki, I. Hachiya,
15 I. Paterson, M. Donghi, K. Tetrahedron Lett. 1996, 37, 7783
Gerlach, Angew. Chem. Int. Ed. Engl. 7786.
2000, 39, 33153319. 27 V. Bertini, F. Lucchesini, M. Pocci,
16 C. E. Lee, E. K. Kick, J. A. Ellman, J. A. De Munno, Tetrahedron Lett. 1998,
Am. Chem. Soc. 1998, 120, 97359747. 39, 92639266.
17 R. H. Schlessinger, C. P. 28 M. Reggelin, V. Brenig, R.
Bergstrom, Tetrahedron Lett. 1996, 37, Welcker, Tetrahedron Lett. 1998, 39,
21332136. 48014804.
18 a) S. Brase, D. Enders, J. 29 M. Reggelin, V. Brenig, Tetrahedron
Kobberling, F. Avemaria, Angew. Lett. 1996, 37, 68516852.
Chem. Int. Ed. Engl. 1998, 37, 3413 30 a) J.-A. Fehrentz, M. Paris, A.
3415; b) B. Furman, R. Thurmer, Heitz, J. Velek, C.-F. Liu, Tetrahedron
Z. Kaluza, R. Lysek, W. Voelter, Lett. 1995, 36, 78717874; b) J.-A.
M. Chmielewski, Angew. Chem. Int. Fehrentz, M. Paris, A. Heitz, J.
Ed. Engl. 1999, 38, 11211123. Velek, F. Winternitz, J. Martinez,
19 a) S.-S. Wang, J. Am. Chem. Soc. 1973, J. Org. Chem. 1997, 62, 67926796;
95, 13281333; b) E. Giralt, J. Rizo, c) M. Paris, C. Douat, A. Heitz, W.
E. Pedroso, Tetrahedron 1984, 40, Gibbons, J. Martinez, J.-A.
41414152; c) R. S. Garigipati, B. Fehrentz, Tetrahedron Lett. 1999, 40,
Adams, J. L. Adams, S. K. Sarkar, 51795182; d) J. M. Salvino, M.
J. Org. Chem. 1996, 61, 29112914; Mervic, H. J. Mason, T. Kiesow,
d) J. D. Winkler, W. McCoull, D. Teager, J. Airey, R. Labaudiniere,
Tetrahedron Lett. 1998, 39, 49354936. J. Org. Chem. 1999, 64, 18231830.
20 S. Kobayashi, R. Akiyama, 31 T. Q. Dinh, R. W. Armstrong,
21 a) M. J. Kurth, L. A. A. Randall, 32 G. Hummel, O. Hindsgaul, Angew.
C. Chen, C. Melander, R. B. Miller, Chem. Int. Ed. Engl. 1999, 38, 1782
K. McAlister, G. Reitz, R. Kang, 1784.
T. Nakatsu, C. Green, J. Org. Chem. 33 a) A. A. Virgilio, J. A. Ellman, J.
1994, 59, 58625864; b) S. V. Ley, Am. Chem. Soc. 1994, 116, 11580
D. M. Mynett, W.-J. Koot, Synlett 11581; b) A. A. Virgilio, S. C.
1995, 10171020; c) L. F. Tietze, A. Schurer, J. A. Ellman, Tetrahedron
Steinmetz, Angew. Chem. Int. Ed. Lett. 1996, 37, 69616964.
Engl. 1996, 35, 651652; d) L. F. 34 A. J. Souers, A. A. Virgilio, A.
Tietze, T. Hippe, A. Steinmetz, Rosenquist, W. Fenuik, J. A.
Chem. Commun. 1998, 793794. Ellman, J. Am. Chem. Soc. 1999, 121,
22 G. J. Kuster, H. W. Scheeren, 18171825.
Tetrahedron Lett. 2000, 41, 515519. 35 C. L. Lee, K. P. Chan, Y. Lam, S.-Y.
23 J. M. Goldwasser, C. C. Leznoff, Lee, Tetrahedron Lett. 2001, 42, 1167
Can. J. Chem. 1978, 56, 15621568. 1169.
24 A. Bhandari, D. G. Jones, J. R. 36 a) I. Sucholeiki, Tetrahedron Lett.
Schullek, K. Vo, C. A. Schunk, L. L. 1994, 35, 73077310; b) F. W.
Tamanaha, D. Chen, Z. Yuan, M. C. Forman, I. Sucholeicki, J. Org.
Needels, M. A. Gallop, Bioorg. Med. Chem. 1995, 60, 523528.
Chem. Lett. 1998, 8, 23032308. 37 X.-Y. Zhao, K. D. Janda, Tetrahedron
25 L. M. Gayo, M. J. Suto, Tetrahedron Lett. 1997, 38, 54375440.
Lett. 1997, 38, 211214. 38 X.-Y. Zhao, Tetrahedron Lett. 1998, 39,
26 a) S. Kobayashi, I. Hachiya, S. 84338436.
Suzuki, M. Moriwaki, Tetrahedron 39 X.-Y. Zhao, Bioorg. Med. Chem. Lett.
Lett. 1996, 37, 28092812; b) S. 1998, 8, 24392442.
References 433
40 K. C. Nicolaou, J. Pastor, S. 52 X.-Y. Xiao, M. P. Nova, A. W.

Barluenga, N. Wissinger, Chem. Czarnik, J. Comb. Chem. 1999, 1,
Commun. 1998, 19471948. 379382.
41 T. Ruhland, K. Andersen, H. 53 a) D. W. Gordon, J. Steele, Bioorg.
Pedersen, J. Org. Chem. 1998, 63, Med. Chem. Lett. 1995, 5, 4750;
92049211. b) G. C. Look, M. M. Murphy, D. A.
42 W. H. Pearson, R. B. Clark, Campbell, M. A. Gallop, Tetrahedron
Tetrahedron Lett. 1997, 38, 76697672. Lett. 1995, 36, 29372940.
43 a) A. Zheng, D. Shan, B. Wang, J. 54 a) S. Kim, C. H. Oh, J. S. Ko, K. H.
Org. Chem. 1999, 64, 156161; b) A. Ahn, Y. J. Kim, J. Org. Chem. 1985,
Zheng, D. Shan, X. Shi, B. Wang, 50, 19271932; b) M. D. Bomann, I.
J. Org. Chem. 1999, 64, 74597466. C. Guch, M. DiMare, J. Org. Chem.
44 a) A. Nefzi, J. M. Ostresh, J.-P. 1995, 60, 59955996; c) A. F. Abdel-
Meyer, R. A. Houghten, Tetrahedron Magid, K. G. Carson, B. D. Harris,
Lett. 1997, 38, 931934; b) P. J. C. A. Maryanoff, R. D. Shah, J. Org.
Brown, K. P. Hurley, L. W. Stuart, Chem. 1996, 61, 38493862.
T. M. Wilson, Synthesis 1997, 778 55 A. R. Brown, D. C. Rees, Z.
782; c) J. M. Ostresh, C. C. Schoner, Rankovic, J. R. Morphy, J. Am.
V. T. Hamashin, A. Nefzi, J.-P. Chem. Soc. 1997, 119, 32883295.
Meyer, R. A. Houghten, J. Org. 56 R. Devraj, M. Cushman, J. Org.
Chem. 1998, 63, 86228623; d) A. Chem. 1996, 61, 93689373.
Nefzi, J. M. Ostresh, R. A. 57 N. W. Kahn, V. Arumugam, S.
Houghten, Tetrahedron 1999, 55, Balasubramanian, Tetrahedron Lett.
335344; e) A. Nefzi, N. A. Ong, R. 1996, 37, 48194822.
A. Houghten, Tetrahedron Lett. 2000, 58 a) A. Nefzi, J. M. Ostresh, R. A.
41, 54415446; f ) B. Yan, N. Nguyen, Houghten, Tetrahedron Lett. 1997, 38,
L. Liu, G. Holland, B. Raju, J. Comb. 49434946; b) I. Akritopoulou-
Chem. 2000, 2, 6674; g) A. N. Zanze, T. J. Sowin, J. Comb. Chem.
Acharya, A. Nefzi, J. M. Ostresh, R. 2001, 3, 301311.
A. Houghten, J. Comb. Chem. 2001, 59 a) E. G. Brown, J. M. Nuss,
3, 189195. Tetrahedron Lett. 1997, 38, 84578460;
45 a) A. Nefzi, J. M. Ostresh, M. A. b) E. G. Brown, J. M. Nuss, US
Giulianotti, R. A. Houghten, Patent No. 5,861,532, January 19, 1999.
J. Comb. Chem. 1999, 1, 195198; 60 a) D. H. Coy, S. J. Hocart, Y. Sasaki,
b) S. Manku, C. Laplante, D. Kopac, Tetrahedron 1988, 44, 835841; b) P. T.
T. Chan, D. G. Hall, J. Org. Chem. Ho, D. Chang, J. W. X. Joyce, G. F.
2001, 66, 874885; c) A. Nefzi, Musso, Peptide Res. 1993, 6, 1012.
M. A. Giulianotti, R. A. Houghten, 61 C. G. Boojamra, K. M. Burow, L. A.
J. Comb. Chem. 2001, 3, 6870. Thompson, J. A. Ellman, J. Org.
46 S. Kobayashi, Y. Aoki, Tetrahedron Chem. 1997, 62, 12401256.
Lett. 1998, 39, 73457348. 62 a) J. Matthews, R. A. Rivero, J. Org.
47 G. Liu, J. A. Ellman, J. Org. Chem. Chem. 1997, 62, 60906092; b) C. L.
1995, 60, 77127713. Lanter, J. W. Guiles, R. A. Rivero,
48 K. Burgess, D. Lim, Chem. Commun. Mol. Diversity 1999, 4, 149153.
1997, 78586. 63 a) M. T. Bilodeau, A. M.
49 D. G. Hall, C. Laplante, S. Manku, Cunningham, J. Org. Chem. 1998, 63,
J. Nagendran, J. Org. Chem. 1999, 64, 28002801; b) L. Weber, P. Iaiza, G.
698699. Biringer, P. Barbier, Synlett 1998,
50 C. Y. Ho, M. J. Kukla, Tetrahedron 11561157; c) E. Farrant, S. S.
Lett. 1997, 38, 27992802. Rahman, Tetrahedron Lett. 2000, 41,
51 J. J. N. Veerman, F. P. J. T. Rutjes, 53835386.
J. H. vanMaarseveen, H. Hiemstra, 64 C. P. Holmes, J. P. Chinn, G. C.
Tetrahedron Lett. 1999, 40, 6079 Look, E. M. Gordon, M. A. Gallop,
6082. J. Org. Chem. 1995, 60, 73287333.
65 a) A. K. Szardenings, T. S. Burkoth, 75 a) A. R. Katritzky, L. Xie, G. Zhang,

G. C. Look, D. A. Campbell, J. Org. M. Griffith, K. Watson, J. S. Kiely,
Chem. 1996, 61, 67206722; b) E. M. Tetrahedron Lett. 1997, 38, 70117014;
Gordon, M. A. Gallop, D. V. Patel, b) H. B. Lee, S. Balasubramanian,
Acc. Chem. Res. 1996, 29, 144154. Org. Lett. 2000, 2, 323326.
66 A. R. Katritzky, S. A. Blyakov, D. O. 76 K. G. Estep, C. E. Neipp, L. M. S.
Tymoshenko, J. Comb. Chem. 1999, 1, Stramiello, M. D. Adam, M. P.
173176. Allen, S. Robinson, E. J. Roskamp,
67 M. Gustafsson, R. Olsson, C.-M. J. Org. Chem. 1998, 63, 53005301.
Andersson, Tetrahedron Lett. 2001, 42, 77 B. Barlaam, P. Koza, J. Berriot,
133136. Tetrahedron 1999, 55, 72217232.
68 F. Stieber, W. Grether, H. 78 a) C. G. Boojamra, K. M. Burow,
Waldmann, Angew. Chem. Int. Ed. J. A. Ellman, J. Org. Chem. 1995, 60,
Engl. 1999, 38, 10731077. 57425743; b) A. M. Fivush, T. M.
69 a) J. G. Breitenbucher, H. C. Hui, Wilson, Tetrahedron Lett. 1997, 38,
Tetrahedron Lett. 1998, 39, 82078210; 71517154; c) E. E. Swayze,
b) J. G. Breitenbucher, H. C. Hui, Tetrahedron Lett. 1997, 38, 84658468;
Figliozzi, World Patent Application d) K.-L. Yu, R. Civiello, D. G. M.
WO00003681, January 27, 2000; Roberts, S. M. Seiler, N. A.
c) S. Bhattacharyya, L. Fan, L. Vo, Meanwell, Bioorg. Med. Chem. Lett.
J. Labadie, Comb. Chem. High 1999, 9, 663666; e) D. S. Yamashita,
Throughput Screening 2000, 3, 117 X. Dong, H.-J. Oh, C. S. Brook, T. A.
124. Tomaszek, L. Szewczuk, D. G. Tew,
70 A. M. Bray, D. S. Chiefari, R. M. D. F. Veber, J. Comb. Chem. 1999, 1,
Valerio, N. J. Maeji, Tetrahedron Lett. 207215; f ) V. Krchnak, J. Smith,
1995, 36, 50815084. J. Vagner, Tetrahedron Lett. 2001, 42,
71 a) J. S. Koh, J. A. Ellman, J. Org. 24432446.
Chem. 1996, 61, 44944495; 79 C. T. Bui, A. M. Bray, F. Ercole,
b) V. Krchnak, A. S. Weichsel, Y. Pham, F. A. Rasoul, N. J. Maeji,
72 a) S. Carrington, J. Renault, S. 80 a) C. T. Bui, A. M. Bray, Y. Pham, R.
Tomasi, J.-C. Corbel, P. Uriac, I. S. Campbell, F. Ercole, F. A. Rasoul,
Blagbrough, Chem. Commun. 1999, N. J. Maeji, Tetrahedron Lett. 1998, 4,
13411342; b) E. A. Jefferson, K. G. 155163; b) C. T. Bui, F. A. Rasoul,
Sprankle, E. E. Swayze, J. Comb. F. Ercole, Y. Pham, N. J. Maeji,
Chem. 2000, 2, 441444; c) P. W. Tetrahedron Lett. 1998, 39, 92799282.
Davis, E. E. Swayze, Biotechnol. and 81 M. K. Schwarz, D. Tumelty, M. A.
Bioeng. (Comb. Chem.) 2000, 71, 19 Gallop, J. Org. Chem. 1999, 64, 2219
27. 2231.
73 a) S. Caddick, D. Hamza, S. N. 82 a) A. K. Szardenings, T. S. Burkoth,
Wadman, Tetrahedron Lett. 1999, Tetrahedron 1997, 53, 65736593; b) A.
40, 72857288; b) R. C. D. Brown, K. Szardenings, D. Harris, S. Lam,
M. Fisher, Chem. Commun. 1999, L. S. Shi, D. Tien, Y. Wang, D. V.
15471548. Patel, M. Navre, D. A. Campbell,
74 a) D. Sarantakis, J. J. Bicksler, J. Med. Chem. 1998, 41, 21942200;
Tetrahedron Lett. 1997, 38, 73257328; c) A. K. Szardenings, V. Antonenko,
b) P. C. Kearney, M. Fernandez, J. D. A. Campbell, N. DeFrancisco,
A. Flygare, J. Org. Chem. 1998, 63, S. Ida, L. Shi, N. Sharkov, D. Tien,
196200; c) Y. Aoki, S. Kobayashi, J. Y. Wang, M. Navre, J. Med. Chem.
Comb. Chem. 1999, 1, 371372; d) K. 1999, 42, 13481357.
Paulvannan, T. Chen, J. W. Jacobs, 83 T. Groth, M. Meldal, J. Comb. Chem.
Synlett 1999, 16091611; e) K. H. 2001, 3, 4563.
Gordon, S. Balasubramanian, Org. 84 T. S. Yokum, J. Alsina, G. Barany,
Lett. 2001, 3, 5356. J. Comb. Chem. 2000, 2, 282292.
References 435
85 C. L. Lanter, J. W. Guiles, R. A. 100 J. M. Kim, Y. Bi, S. J. Paikoff, P. G.

Rivero, US Patent No. 6,228,986, May Schultz, Tetrahedron Lett. 1996, 37,
8, 2001. 53055308.
86 V. Krchnak, L. Szabo, J. Vagner, 101 D. A. Goff, R. N. Zuckermann, J.
Tetrahedron Lett. 2000, 41, 28352838. Org. Chem. 1995, 60, 57445745.
87 J. M. Alvarez-Gutierrez, A. Nefzi, 102 R. Liang, L. Yan, J. Loebach, M. Ge,
R. A. Houghten, Tetrahedron Lett. Y. Uozumi, K. Sekanina, N. Horan,
2000, 41, 851854. J. Gildersleeve, C. Thompson, A.
88 J. Tois, R. Franzen, O. Aitio, K. Smith, K. Biswas, W. C. Still, D.
Huikko, J. Taskinen, Tetrahedron Kahne, Science 1996, 274, 1520
Lett. 2000, 41, 24432446. 1522.
89 S. Sun, I. J. Turchi, D. Xu, W. V. 103 J. Zhou, A. Termin, M. Wayland,
Murray, J. Org. Chem. 2000, 65, C. M. Tarby, Tetrahedron Lett. 1999,
25552559. 40, 27292732.
90 P. Blaney, R. Grigg, Z. Rankovic, 104 K. C. Nicolaou, N. Winssinger, D.
M. Thoroughgood, Tetrahedron Lett. Vourloumis, T. Ohshima, S. Kim,
2000, 41, 66356638. J. Pfefferhorn, J.-Y. Xu, T. Li, J. Am.
91 A. D. Morely, Tetrahedron Lett. 2000, Chem. Soc. 1998, 120, 1081410826.
41, 74057408. 105 a) M. R. Tremblay, J. Simard, D.
92 P. Arya, K. M. K. Kutterer, A. Poirier, Bioorg. Med. Chem. Lett.
Barkley, J. Comb. Chem. 2000, 2, 1999, 9, 28272832; b) M. R.
120126. Tremblay, D. Poirier, J. Comb.
93 P. J. Connolly, K. N. Beers, S. K. Chem. 2000, 2, 4865.
Wetter, W. V. Murray, Tetrahedron 106 U. Grabowska, A. Rizzo, K. Farnell,
Lett. 2000, 41, 51875191. M. Quibell, J. Comb. Chem. 2000, 2,
94 S. Peters, T. Bielfeldt, M. Meldal, 475490.
K. Bock, H. Paulsen, Tetrahedron Lett. 107 H. S. Oh, H.-G. Hahn, S. H. Cheon,
1992, 33, 64456448. D.-C. Ha, Tetrahedron Lett. 2000, 41,
95 J. Rademann, R. R. Schmidt, 50695072.
Carbohydrate Research 1995, 269, 217 108 K. M. Halkes, P. M. St. Hilaire,
225. A. M. Jansson, C. H. Gotfredsen,
96 a) J. Y. Roberge, X. Beebe, S. J. M. Meldal, J. Chem. Soc., Perkin Trans.
Danishefsky, Science 1995, 269, 202 1 2000, 21272133.
204; b) K. A. Savin, J. C. G. Woo, S. 109 a) M. J. Soa, N. Allanson, N. T.
J. Danishefsky, J. Org. Chem. 1999, Hatzenbuhler, R. Jain, R. Kakarla,
64, 41834186. N. Kogan, R. Liang, D. Liu, D. J.
97 a) E. Meinjohanns, M. Meldal, T. Silva, H. Wang, D. Gange, J.
Jensen, O. Werdelin, L. Galli- Anderson, A. Chen, F. Chi, R.
Stampino, S. Mouritsen, K. Bock, J. Dulian, B. Huang, M. Kamau, C.
Chem. Soc., Perkin Trans. 1 1997, 871 Wang, E. Baizman, A. Branstrom,
884; b) P. M. St. Hilaire, L. Cipolla, N. Bristol, R. Goldman, K. Han,
A. Franco, U. Tedebark, D. A. Tilly, C. Longley, S. Midha, H. R. Axelrod,
M. Meldal, J. Chem. Soc., Perkin J. Med. Chem. 1999, 42, 31933198;
Trans. 1 1999, 35593564. b) D. J. Silva, H. Wang, N. M.
98 J. P. Malkinson, R. A. Falconer, I. Allanson, R. K. Jain, M. J. Soa,
Toth, J. Org. Chem. 2000, 65, 5249 J. Org. Chem. 1999, 64, 59265929.
5252. 110 K. Oertel, G. Zech, H. Kunz, Angew.
99 a) E. K. Kick, J. A. Ellman, J. Med. Chem., Int. Ed. Engl. 2000, 39, 1431
Chem. 1995, 38, 14271430; b) F. X. 1433.
Woolard, J. Paetsch, J. A. Ellman, 111 J. P. Mayer, G. S. Lewis, C. McGee,
J. Org. Chem. 1997, 62, 61026103; D. Bankaitis-Davis, Tetrahedron Lett.
c) A. Lee, L. Huang, J. A. Ellman, J. 1998, 39, 66556658.
Am. Chem. Soc. 1998, 121, 9907 112 G. B. Phillips, G. P. Wei, Tetrahedron
9914. Lett. 1996, 37, 48874890.
113 For a non-combinatorial example, see: J. J. Parlow, Comb. Chem. High

M. Bartra, P. Romea, F. Urpi, J. Throughput Screening 2000, 3, 139
Vilarrasa, Tetrahedron 1990, 46, 587 151.
594. 125 D. Tumelty, K. Cao, C. P. Holmes,
114 a) J. P. Mayer, J. Zhang, K. Org. Lett. 2001, 3, 8386.
Biergarde, D. M. Lenz, J. J. 126 J. M. Smith, J. Gard, W. Cummings,
Gaudino, Tetrahedron Lett. 1996, 37, A. Kanizsai, V. Krchnak, J. Comb.
80818084; b) Y. Pei, R. A. Chem. 1999, 1, 368370.
Houghten, J. S. Kiely, Tetrahedron 127 H. Stephensen, F. Zaragoza,
Lett. 1997, 38, 33493352; c) J. Lee, Tetrahedron Lett. 1999, 40, 57995802.
W. V. Murray, R. A. Rivero, J. Org. 128 A. Nefzi, N. A. Ong, M. A.
Chem. 1997, 62, 38743879; d) A. S. Giulianotti, J. M. Ostresh, R. A.
Kiselyov, R. W. Armstrong, Houghten, Tetrahedron Lett. 1999, 40,
Tetrahedron Lett. 1997, 38, 61636166; 49394942.
e) J. P. Mayer, G. S. Lewis, M. J. 129 G. C. Morton, J. M. Salvino, R. F.
Curtis, J. Zhang, Tetrahedron Lett. Labaudiniere, T. F. Herpin,
1997, 38, 84458448; f ) A. S. Tetrahedron Lett. 2000, 41, 30293033.
Kiselyov, L. Smith II, R. W. 130 X. Ouyang, A. S. Kiselyov,
Armstrong, Tetrahedron 1998, 54, Tetrahedron 1999, 55, 82958302.
50895096. 131 Q. Sun, X. Zhou, D. J. Kyle,
115 C. L. Lee, Y. Lam, S.-Y. Lee, Tetrahedron Lett. 2001, 42, 41194121.
Tetrahedron Lett. 2001, 42, 109111. 132 F. Zaragoza, H. Stephensen, J. Org.
116 a) D. Tumelty, M. K. Schwarz, M. C. Chem. 1999, 64, 25552557.
Needles, Tetrahedron Lett. 1998, 39, 133 W. D. F. Meutermans, P. F.
74677470; b) A. Mazurov, Bioorg. Alewood, Tetrahedron Lett. 1995, 36,
Med. Chem. Lett. 2000, 10, 6770; c) Z. 77097712.
Wu, P. Rea, G. Wickham, Tetrahedron 134 Y. Cheng, K. T. Chapman,
117 G. A. Morales, J. W. Corbett, W. F. 135 S.-H. Lee, S.-H. Chung, Y.-S. Lee,
DeGrado, J. Org. Chem. 1998, 63, Tetrahedron Lett. 1998, 39, 94699472.
11721177. 136 W.-R. Li, N.-M. Hsu, H.-H. Chou, S.
118 H. V. Meyers, G. J. Dilley, T. L. T. Lin, Y.-S. Lin, Chem. Commun.
Durgin, T. S. Powers, N. A. 2000, 401402.
Winssinger, H. Zhu, M. R. Pavia, 137 P. Conti, D. Demont, J. Cals, H. C.
Mol. Diversity 1995, 1, 1320. J. Ottenheijm, D. Leysen, Tetrahedron
119 J. Lee, D. Gauthier, R. A. Rivero, Lett. 1997, 38, 29152918.
J. Org. Chem. 1999, 64, 30603065. 138 R. M. Myers, S. P. Langston, S. P.
120 R. Di Lucrezia, I. H. Gilbert, C. D. Conway, C. Abell, Org. Lett. 2000, 2,
Floyd, J. Comb. Chem. 2000, 2, 249 13491352.
253. 139 J. H. Kirchhoff, S. Brase, D. Enders,
121 R. A. Scheuerman, D. Tumelty, J. Comb. Chem. 2001, 3, 7177.
Tetrahedron Lett. 2000, 41, 65316535. 140 D. Enders, J. H. Kirchhoff, J.
122 a) A. Hari, B. L. Miller, Tetrahedron Kobberling, T. H. Peiffer, Org. Lett.
Lett. 1999, 40, 245248; b) A. Hari, B. 2001, 3, 12411244.
L. Miller, Angew. Chem., Int. Ed. Engl. 141 S. Jin, D. P. Holub, D. J. Wustrow,
1999, 38, 2777. Tetrahedron Lett. 1998, 39, 36513654.
123 a) P.-C. Pan, C.-M. Sun, Tetrahedron 142 C. Sylvain, A. Wagner, C.
Lett. 1999, 40, 64436446; b) C.-M. Mioskowski, Tetrahedron Lett. 1997,
Yeh, C.-M. Sun, Tetrahedron Lett. 38, 10431044.
1999, 40, 72477250; c) Y.-C. Chi, 143 D. P. Rotella, J. Am. Chem. Soc. 1996,
C.-M. Sun, Synlett 2000, 591594. 118, 1224612247.
124 M. S. South, B. L. Case, T. A. Dice, 144 D. Bonnet, C. Rommens, H. Gras-
G. W. Franklin, M. J. Hayes, D. E. Masse, O. Melnyk, Tetrahedron Lett.
Jones, R. J. Lindmark, Q. Zeng, 1999, 40, 73157318.
References 437
145 B. Furman, R. Thurmer, Z. Kaluza, 161 a) H. Firouszbadi, B. Tamami, N.

W. Voelter, M. Chmielewski, Goudarzian, Syn. Commun. 1991, 21,
Tetrahedron Lett. 1999, 40, 59095912. 22752285; b) B. Tamami, N.
146 a) C. R. McArthur, P. M. Worster, Goudarzian, Iran. J. Chem., Chem.
J. Jiang, C. C. Leznoff, Can. J. Chem. Eng. 1996, 15, 6371.
1982, 60, 18361841; b) P. M. 162 B. Tamami, N. Goudarzian, J. Chem.
Worster, C. R. McArthur, C. C. Soc., Chem. Commun. 1994, 1079.
Leznoff, Angew. Chem. Int. Ed. Engl. 163 a) R. O. Hutchins, N. R. Natale, I.
1979, 18, 221222. M. Taffer, J. Chem. Soc., Chem.
147 F. Gosselin, J. V. Betsbrugge, M. Commun. 1978, 10881089; b) N. M.
Hatam, W. D. Lubell, J. Org. Chem. Yoon, E. G. Kim, H. S. Son, J. Choi,
1999, 64, 24862493. Synth. Commun. 1993, 23, 15951599.
148 K. Schiemann, H. D. H. Showalter, 164 Commercially available from
J. Org. Chem. 1999, 64, 49724975. NovaBiochem and Argonaut
149 K. C. Nicolaou, N. Winssinger, J. Technologies. Both provide
Pastor, F. Murphy, Angew. Chem. Int. experimental details on their websites:
Ed. Engl. 1998, 37, 25342537. www.NovaBiochem.com and
150 S. R. Gilbertson, X. Wang, www.Argotech.com.
Tetrahedron Lett. 1996, 37, 64756478. 165 a) M. W. Creswell, G. L. Bolton, J.
151 S. Itsuno, K. Ito, A. Hirao, S. C. Hodges, M. Meppen, Tetrahedron
Nakahama, J. Chem. Soc., Perkin 1998, 54, 39833998; b) C. L. Nunns,
Trans. 1 1984, 28872893. L. A. Spence, M. J. Slater, D. J.
152 S. Itsuno, Y. Sakurai, K. Shimizu, Berrisford, Tetrahedron Lett. 1999,
K. Ito, J. Chem. Soc., Perkin Trans. 1 40, 93419345; c) S. V. Ley, A. Massi,
1990, 18591863. J. Chem. Soc., Perkin Trans. 1 2000,
153 S. Itsuno, M. Nakano, K. Ito, A. 36453654.
Hirao, M. Owa, N. Kanda, S. 166 a) S. W. Kaldor, M. G. Siegel, J. E.
Nakahama, J. Chem. Soc., Perkin Fritz, B. A. Dressman, P. J. Hahn,
Trans. 1 1985, 26152619. Tetrahedron Lett. 1996, 37, 71937196;
154 K. Adjidjonou, C. Caze, Eur. Polym. b) M. G. Siegel, M. O. Chaney, R. F.
J. 1995, 31, 749754. Bruns, M. P. Clay, D. A. Schober,
155 J. M. J. Frechet, E. Bald, P. A. M. V. Abbema, D. W. Johnson,
Lecavalier, J. Org. Chem. 1986, 51, B. E. Cantrell, P. J. Hahn, D. C.
34653467. Hunden, D. R. G. Zarrinmayeh,
156 H. W. Gibson, F. C. Bailey, J. Chem. P. L. Ornstein, D. M. Zimmerman,
Soc., Chem. Commun. 1977, 815. G. A. Koppel, Tetrahedron 1999, 55,
157 a) N. M. Yoon, K. B. Park, Y. S. 1161911639.
Gyoung, Tetrahedron Lett. 1983, 24, 167 a) S. V. Ley, O. Schucht, A. W.
53675370; b) A. R. Sande, M. H. Thomas, P. J. Murray, J. Chem. Soc.,
Jagadale, R. B. Mane, M. M. Perkin Trans. 1 1999, 12511252;
Salunkhe, Tetrahedron Lett. 1984, 25, b) S. V. Ley, A. Massi, J. Comb. Chem.
35013504. 2000, 2, 104107.
158 T. B. Sim, N. M. Yoon, Bull. Chem. 168 a) J. Habermann, S. V. Ley, J. S.
Soc. Jpn. 1997, 70, 11011107. Scott, J. Chem. Soc., Perkin Trans. 1
159 a) T. B. Sim, J. Choi, M. J. Joung, 1998, 31273130; b) S. V. Ley, M. H.
N. M. Yoon, J. Org. Chem. 1997, 62, Bolli, B. Hinzen, A.-G. Gervois, B.
23572361; b) M. J. Young, J. H. J. Hall, J. Chem. Soc., Perkin Trans. 1
Ahn, D. W. Lee, N. M. Yoon, J. Org. 1998, 22392241.
Chem. 1998, 63, 27552757. 169 K. Smith, G. E. El-Hiti, D. Hou,
160 a) N. M. Yoon, H. J. Lee, J. H. Ahn, G. A. DeBoos, J. Chem. Soc., Perkin
J. Choi, J. Org. Chem. 1994, 59, 4687 Trans. 1 1999, 28072812.
4688; b) B. P. Bandgar, S. H. 170 J. Habermann, S. V. Ley, J. S. Scott,
Kshirsagar, P. P. Wadgaonkar, Syn. J. Chem. Soc., Perkin Trans. 1 1999,
Commun. 1995, 25, 941945. 12531255.
171 K. Y. Gordeev, G. A. Serebren- 187 T. Holletz, D. Cech, Synthesis 1994,

nikova, R. P. Evstigneeva, J. Org. 789791.
Chem. 1986, 21, 26152616. 188 P. Wentworth, Jr, A. M.
172 B. Tamami, M. M. Lakouraj, Synth. Vandersteen, K. D. Janda, Chem.
Commun. 1995, 25, 30893096. Commun. 1997, 759760.
173 N. M. Yoon, J. Choi, J. H. Ahn, J. 189 K. Hemming, M. J. Bevan, C.
Am. Chem. Soc. 1994, 59, 34903493. Loukou, S. D. Patel, D. Renaudeau,
174 N. M. Yoon, J. Choi, Y. S. Shon, Synlett 2000, 15651568.
Synth. Commun. 1993, 23, 30473053. 190 A. B. Charette, A. A. Boezio, M. K.
175 G. W. Kabalka, P. P. Wadgaonkar, Janes, Org. Lett. 2000, 2, 37773779.
N. Chatla, Synth. Commun. 1990, 20, 191 a) R. Noyori, T. Ohkuma, M.
293299. Kitamura, J. Am. Chem. Soc. 1987,
176 For a comprehensive review of solid- 109, 58565858; b) R. Noyori in:
supported reagents, see [1h]. Asymmetric Catalysis in Organic
177 N. M. Yoon, J. Choi, Synlett 1993, Synthesis, Wiley-Interscience, New
135136. York 1994; c) T. Ohkuma, H. Ooka, S.
178 B. P. Bandgar, S. M. Nikat, P. P. Hashiguchi, T. Ikariya, R. Noyori,
Wadgaonkar, Synth. Commun. 1995, J. Am. Chem. Soc. 1995, 117, 2675
863869. 2676; d) S. Hashiguchi, A. Fujii, J.
179 a) N. M. Weinshenker, G. A. Takehara, T. Ikariya, R. Noyori, J.
Crosby, J. Y. Wong, J. Org. Chem. Am. Chem. Soc. 1995, 117, 75627563.
1975, 40, 19661971; b) M. Gerlach, 192 E. J. Corey, R. K. Bakshi, S. Shibata,
F. Jordens, H. Kuhn, W. P. J. Am. Chem. Soc. 1987, 109, 5551
Neumann, M. Peterseim, J. Org. 5553.
Chem. 1991, 56, 59715972; c) W. P. 193 D. J. Bayston, J. L. Fraser, M. R.
Neumann, M. Peterseim, Synlett, Ashton, A. D. Baxter, M. E. C.
1992, 801802; d) G. Dumartin, G. Polywka, E. Moses, J. Org. Chem.
Ruel, J. Kharboutli, B. Delmond, 1998, 63, 31373140.
M.-F. Connil, B. Jousseaume, M. 194 R. Halle, B. Colasson, E. Schulz,
Pereyre, Synlett, 1994, 952954. M. Spagnol, M. Lemaire, Tetrahedron
180 W. P. Neumann, M. Peterseim, React. Lett. 2000, 41, 643646.
Polym. 1993, 20, 198205. 195 R. Halle, E. Schulz, M. Spagnol,
181 U. Gerigk, M. Gerlach, W. P. M. Lemaire, Synlett 2000, 5, 680682.
Neumann, R. Vieler, V. Weintritt, 196 Q.-H. Fan, C.-Y. Ren, C.-H. Yeung,
Synthesis 1990, 448452. W.-H. Hu, A. S. C. Chan, J. Am.
182 Y. Hu, J. A. Porco, Jr, Tetrahedron Chem. Soc. 1999, 121, 74077408.
Lett. 1998, 39, 27112714. 197 D. J. Bayston, C. B. Tracers, M. E. C.
183 M. Gorecki, A. Patchornik, Biochim Polywka, Tetrahedron: Asym. 1998, 9,
Biophys Acta 1973, 303, 3643. 20152018.
184 a) G. Dupas, A. Decomeille, J. 198 R. Halle, E. Schulz, M. Lemaire,
Bourguignon, G. Queguiner, Synlett 1997, 12571258.
Tetrahedron 1989, 45, 25792590; b) F. 199 E. Breysse, C. Pinel, M. Lemaire,
M. Menger, C. A. West, J. Ding, J. Tetrahedron: Asym. 1998, 9, 897900.
Am. Chem. Soc. 1997, 633634; c) S. 200 P. Gamez, B. Dunjic, F. Fache, M.
Obika, T. Nishiyama, S. Tatematsu, Lemaire, J. Chem. Soc., Chem.
M. Nishimoto, K. Miyashita, T. Commun. 1994, 14171418.
Imanishi, Heterocycles 1998, 49, 261 201 a) P. Gamez, B. Dunjic, C. Pinel,
267. M. Lemaire, Tetrahedron Lett. 1995,
185 P. Ferraboschi, C. Gambero, M. N. 36, 87798782; b) F. Locatelli,
Azadani, E. Santaniello, Synth. P. Gamez, M. Lemaire, J. Mol. Cat.
Commun. 1986, 16, 667672. A. 1998, 135, 8998.
186 R. B. Appell, I. A. Tomlinson, I. 202 C. Franot, G. B. Stone, P. Engeli,
Hill, Synth. Commun. 1995, 25, 3589 C. Spondlin, E. Waldvogel,
3595. Tetrahedron: Asym. 1995, 6, 27552766.
References 439
203 C. Caze, N. E. Moualij, P. Hodge, 211 J. R. Blanton, J. M. Salley, J. Org.

C. J. Lock, J. Ma, J. Chem. Soc., Perkin Chem. 1991, 56, 490491.
Trans. 1 1995, 345349. 212 A. Chemin, H. Deleuze, B.
204 C. Caze, N. El Moualij, P. Hodge, Maillard, J. Chem. Soc., Perkin Trans.
C. J. Lock, Polymer 1995, 36, 621629. 1 1999, 137142.
205 M. Felder, G. Giffels, C. Wandrey, 213 B. C. Bookser, S. Zhu, J. Comb.
Tetrahedron: Asym. 1997, 8, 19751977. Chem. 2001, 3, 205215.
206 J.-B. Hu, G. Zhao, Z.-D. Ding, 214 J. C. Bussolari, D. C. Rehborn,
Angew. Chem. Int. Ed. Engl. 2001, 40, D. W. Combs, Tetrahedron Lett. 1999,
11091111. 40, 12411244.
207 a) L. Pu, Chem. Rev. 1998, 98, 2405 215 a) D. P. Curran, S. Hadida, J. Am.
2494; b) W.-S. Huang, Q.-S. Hu, L. Chem. Soc. 1996, 118, 25312532; b)
Pu, J. Org. Chem. 1999, 64, 7940 K. Olofsson, S.-Y. Kim, M. Larhed,
7956. D. P. Curran, A. Hallberg, J. Org.
208 E. J. Enholm, J. P. Schulte II, Org. Chem. 1999, 64, 45394541; c) D. P.
Lett. 1999, 8, 12751277. Curran, S. Hadida, M. Hoshino, A.
209 G. Dumartin, M. Pourcel, B. Studer, P. Wipf, P. Jeger, S.-Y. Kim,
Delmond, O. Donard, M. Pereyre, R. Ferritto, US Patent No. 4,859,247,
Tetrahedron Lett. 1998, 39, 46634666. January 12, 1999; d) D. P. Curran,
210 D. E. Bergbreiter, S. A. Walker, S. Hadida, S.-Y. Kim, Z. Luo, J. Am.
J. Org. Chem. 1989, 54, 51385141. Chem. Soc. 1999, 121, 66076615.
440
16
Cycloadditions in Combinatorial and
Markus Albers and Thorsten Meyer
16.1
Introduction
Cycloadditions are one of the most ecient reactions for the synthesis of isocyclic
and heterocyclic compounds in organic chemistry. The two most widespread are
the DielsAlder reaction ([4 2]) and the 1,3-dipolar cycloaddition ([3 2]). The
DielsAlder reaction is not only suitable for synthesis of carbocyclic but also for
N- or O-heterocyclic six-member rings (hetero-DielsAlder). The 1,3-dipolar cyclo-
additions are often used to synthesize ve-member aza- or azoxaheterocycles. In
addition to these, there is a whole string of other, less common cycloadditions
such as the [2 2] cycloaddition for the formation of four-member rings or the
[6 3] cycloaddition. The reactions usually proceed smoothly and only in some
cases is a moderate application of heat required. Owing to the pericyclic mecha-
nism two bonds are formed simultaneously in a usually stereo- and regiospecic
way, which can be promoted by Lewis acid catalysis [1]. Therefore, cycloadditions
are extremely valuable for the generation of stereogenic centers, especially during
natural product synthesis.
In this chapter the application of cycloadditions to combinatorial chemistry is
discussed. Almost all concepts and strategies are based on solid phase, with only a
few based on solution-phase chemistry. One reason behind this is the requirement
for full conversions. Transformations on solid support have signicant advantages
over those in solution. Most important is the simple removal of nonresin-bound
byproducts and excess of reagents, which is necessary to allow completion of the
cycloaddition within a reasonable time, by simply washing the resin with an appro-
priate solvent. In this way the products have high purity without a time-consuming
and expensive chromatographic purication. Solution-phase combinatorial chem-
istry is only applicable if the excess component is volatile, which allows its removal
in vacuo, or it carries an additional functional group, such as an amine, alcohol,
ketone, or aldehyde, so that scavengers can be used for its capture.
Many types of cycloadditions have been applied to solid phase, including the use
of a plethora of dierent dienes, dienophiles, dipoles, dipolarophiles, or olens.
These are either resin-bound or used as reagents, and are inter- or intramolecular

ISBN: 3-527-30509-2
16.2 [4 2] Cycloadditions 441
variants. Normal or inverse electron demand, and ordinary or hetero-DielsAlder

reactions, complete the set of combinatorial methods available to chemistry [2]. In
this chapter, the [4 2], [3 2], [2 2], and [6 3] cycloadditions are described in
more detail; additionally, sigmatropic rearrangements as pericyclic reactions are
described.
16.2
[4B2] Cycloadditions
The DielsAlder reaction is the most synthetically ecient method for the prepa-
ration of six-member rings and is a well-established reaction in combinatorial
chemistry. The typical [4 2] cycloaddition is a DielsAlder reaction with normal
electron demand between an electron-rich diene and an electron-poor dienophile.
There have been many examples of this reaction, especially in solid-phase synthe-
sis [2].
16.2.1
DielsAlder Reaction with Resin-bound Dienes
A variation on the typical reaction is to start with resin-bound dienes. One of

the most reactive, because it is electron rich, and well-known dienes is the Dani-
shefsky diene. Scheme 16.1 shows a direct route for the generation of a polymer-
supported version. For this purpose a polystyrene diethylsilane resin reacts rst
with triuoromethanesulfonic acid, forming a silyl triate resin. Subsequent treat-
ment with diverse a,b-unsaturated ketones and aldehydes produces silyl enol ether
dienes very easily. These reactive dienes are trapped with dienophiles such as N-
phenylmaleimide, yielding the bicyclic cycloadducts. Cleavage o the resin with
Scheme 16.1. DielsAlder reaction with resin-bound siloxy dienes.

442 16 Cycloadditions in Combinatorial and Solid-phase Synthesis
triuoroacetic acid forms the corresponding ketones and alcohols in 62100%

yield and 8198% purity [3].
Another possible route for the synthesis of cyclohexanone derivatives can be
realized by the attachment of a,b-unsaturated ketones to a piperazine resin as
enamines (Scheme 16.2) [4]. The electron-rich dienes react with electron-poor
E-nitrostyrene derivatives to the nitro-substituted cyclohexanones with moderate
yields but high purities. However, an almost equal mixture of diastereomers is ob-
tained, which may be explained by a nonconcerted cycloaddition mechanism re-
ecting the enamine character of the diene used. It is known from solution phase
that [4 2] cycloaddition with aminobutadienes can proceed via a step-wise pro-
cess [5]. This conclusion is supported by the observation of small amounts of an
open-chain enamine addition product.
Scheme 16.2. DielsAlder reaction with resin-bound amino

dienes. THF, tetrahydrofuran; TFA, triuoroacetic acid.
Using dierent substituted resin-bound cyclic dienamines, as depicted in

Scheme 16.3, the cycloaddition with a set of dienophiles (maleimides, nitro sty-
renes, diazo derivatives) occurs in a stereospecic way [6]. The endo but racemic
adduct is obtained by an a-face attack of phenylmaleimide giving 61% yield and
purity > 85%. The cyclic dienamine is built up by acylation of resin-bound 4-
hydroxypyridine followed by treatment with a Grignard reagent.
Scheme 16.3. Solid-phase-supported DielsAlder reaction with cyclic amino dienes.

Tebbe olenation of supported a,b-unsaturated esters is another elegant

method used to build up dienyl ethers (Scheme 16.4). The cycloaddition to di-
verse dienophiles in toluene produces cyclohexenes, which are converted to the
corresponding cyclohexanone library after cleavage with triuoroacetic acid. High
endoselectivity is observed at reaction temperatures of 80100 C, except for N-
methylmaleimide, for which room temperature is found to be sucient [7].
Scheme 16.4. Resin-bound oxydienes by Tebbe olenation. (dichloromethane (DCM))
An interesting intramolecular ruthenium-catalyzed olen/alkyne metathesis re-

action is used to produce dierent cyclic dienes suitable for DielsAlder reactions
on solid support (Scheme 16.5) [8]. The synthesis starts with resin-bound allylic
amides, which are deprotonated with lithium tert-butoxide, followed by reaction
with acetylene methanesulfonate derivatives in dimethylsulfoxide. The alkynylated
product obtained undergoes metathesis reaction with Grubbs ruthenium catalyst
and the diene thus formed is treated with maleimide in reuxing toluene to yield
the desired cycloadduct as a single diastereomer. The reaction sequence is used in
a split-and-mix fashion to prepare a 10 4 5 16-member isoindoline com-
binatorial library.
Scheme 16.5. Formation of resin-bound dienes by metathesis.
Scheme 16.6 gives a very attractive example of a completely stereoselective syn-

thesis of a tricyclic core starting from optically pure 3-bromo-3,5-cyclohexadiene-
1,2-diol linked to solid support via a ketal [9]. Subsequent epoxidation with dime-
thyldioxirane takes place with complete facial selectivity, and epoxide opening is
achieved with amines followed by acylation of the intermediate alcohol. The use of
Scheme 16.6. Stereoselective DielsAlder reaction via a chiral cyclic diene.
a Stille coupling with vinyl stannanes generates the diene for the DielsAlder
reaction with dierent dienophiles, which proceeds with complete facial selectivity
and endoselectivity. The high facial selectivity is rationalized by the sterically de-
manding ketal group which is eciently shielding the b-face of the molecule. In
sum, 16 cycloadducts are synthesized in high yields and purities.
Another example of an enantioselective cycloaddition is the reaction between
polymer-supported chiral amino furans and a variety of dienophiles, which can be
applied to the formation of sugar derivatives in natural product synthesis (Scheme
16.7) [10]. In order to generate the resin-bound furans, silylchloride resin [11] is
treated with the potassium enolate of the optically pure amino furanone. Reaction
with methyl acrylate provides the oxabicycloheptene adduct in a regio- and stereo-
selective way and, because of the steric demand of the pyrrolidine residue, the di-
enophile reacts at the less hampered a-face. Cleavage o the resin with tetrabutyl-
ammoniumuoride resumes the synthesis of a-substituted cyclohexenones.
Scheme 16.7. Enantioselective cycloaddition via optically pure furan as diene.
A synthetically interesting methodology is the DielsAlder/retro-DielsAlder re-

action as a safety-catch procedure. A resin-bound diene temporarily catches a di-
enophile by DielsAlder reaction, this is then modied further on solid support
[12]. Finally, a retro-DielsAlder reaction releases the transformed dienophiles

from the resin by regeneration of the resin-bound diene. Obviously, a major
advantage of this method lies in the high chemical and stereochemical purity of
the released compounds. Scheme 16.8 displays this procedure with a resin-bound
furan in a cycloaddition reaction to an electron-decient alkyne. The resulting
resin-bound bicyclic Michael system undergoes stereoselective addition of thio-
phenol, while the desired olenic product is released from the support by a retro-
DielsAlder reaction. It is noteworthy that the Michael addition carried out in
solution shows an E/Z ratio of 81:19.
Scheme 16.8. Solid-phase DielsAlder/retro-DielsAlder as a safety-catch procedure.
16.2.2
DielsAlder Reaction with Resin-bound Dienophiles
In contrast to the polymer-supported dienes, examples with resin-bound dieno-

philes are not so well represented. This may be due to the fact that more dieno-
philes than dienes are commercially available. Therefore, in solid-phase Diels
Alder reactions dienophiles are usually used as excess reagents. Nevertheless, few
reports with resin-bound dienophiles are published.
One of the rst DielsAlder cycloadditions applied to solid-phase combinatorial
chemistry is the reaction between polymer-supported acrylates and butadiene de-
rivatives (Scheme 16.9) [13]. Acrylic acids are rst attached to a polystyrene resin
via esterication, and the subsequent cycloaddition reactions take place in hot tol-
uene or xylene. After cleavage o the resin with tetrabutylammonium hydroxide
and esterication with diazomethane, mixtures of cis/trans isomers are obtained
Scheme 16.9. DielsAlder reaction with resin-bound acrylates.

with high regioselectivities. The observed ortho/meta ratio is in accordance with the
results obtained in solution phase. It is well documented that 1-substituted-1,3-
butadienes react with 1-substituted alkenes containing an electron-withdrawing
group, forming predominantly the ortho adduct.
Polymer-supported dehydroalanine derivatives are used as dienophiles in Diels
Alder reactions (Scheme 16.10) [14]. The dehydroalanines are generated by
coupling of N- and S-protected cysteines to the resin, oxidation of the suldes
to the sulfones, and elimination to the desired olens. After cycloaddition with
cyclopentadiene at 80 C and cleavage with 20% triuoroacetic acid in dichloro-
methane, mixtures of endo/exo isomers (1:2 to 1:4, 5181% yield) are detected
(determined by 1 H-NMR). The selectivities are similar to those reported in solu-
tion phase.
Scheme 16.10. DielsAlder reaction with resin-bound dehydroalanine derivatives.
The stereoselectivity of DielsAlder reactions can be increased by use of chiral

auxiliaries, as shown with Evans oxazolidinone. In order to introduce the stereo-
chemical information, enantiomerically pure Boc-l-tyrosine methylester is coupled
to hydroxymethyl Merrield resin using Mitsunobu methodology (Scheme 16.11)
[15]. Reduction of the ester and treatment with thionylchloride gives the chiral
oxazolidinone, which is then acylated with trans-crotonic anhydride, triethylamine,
and dimethylaminopyridine, thus forming the desired resin-bound dienophile. The
subsequent cycloaddition with cyclopentadiene is catalyzed by diethylaluminum
chloride as Lewis acid and the cycloadduct is cleaved from the resin by lithium
benzyloxide. The endo/exo ratio of 21:1 (86% ee) compares nicely with the results
obtained in solution phase.
Scheme 16.11. Optically pure oxazolidinones as chiral auxiliaries in cycloaddition.

Besides Lewis acids, the application of high pressure also facilitates the cy-
cloaddition reaction. Especially highly substituted and unreactive starting materi-
als, which show no reaction under normal conditions, can be forced to react. In a
microwave-assisted Knoevenagel reaction between resin-bound nitroalkenes and
aldehydes, E/Z mixtures of trisubstituted dienophiles are generated (Scheme
16.12) [16]. Treatment with 2,3-dimethylbutadiene under high pressure conditions
(15 kbar, 25 C) yields the cycloadducts, whereas stereoselective reduction with
lithium aluminumhydride gives the cyclic amines via a traceless linker strategy.
The stereoselective formation of one diastereomer from a diastereomeric mixture
of two cycloadducts (from a E/Z mixture of nitroalkenes) is rationalized by an
aci-nitro intermediate.
Scheme 16.12. DielsAlder reaction under high-pressure conditions.
During the synthesis of oligomers via tandem DielsAlder reactions, solid-phase

methodology is superior to solution-phase chemistry (Scheme 16.13) [17], whereas
under homogeneous reaction conditions, the reaction of an acrylate and a bisdiene
would lead to mixtures of oligomers and polymers. Oligomerization can be pre-
Scheme 16.13. Oligomerization via iterative DielsAlder reaction on solid support.

cisely controlled on solid support. Starting with a resin-bound acrylate derivative,

the DielsAlder reaction with an excess of bisdiene gives only one cycloadduct.
The second cycloaddition is performed with the bisdienophile divinyl ketone in the
presence of 15 equiv. of ZnCl2 and the nal cycloaddition is achieved by capping
the resin-bound dienophile with butadiene. Treatment with Triton B= and iodo-
methane then reveals the tricyclic ester. All cycloadditions reported proceed in a
regioselective way and, after aromatization with palladium/carbon in boiling di-
chlorobenzene, the desired acetophenones are obtained.
16.2.3
Intramolecular DielsAlder Reaction on Solid Support
In cycloaddition chemistry the intramolecular strategy is an elegant method of

reaction management. By tethering both components it is possible to bring the
reactive centers spatially together, so that the reaction proceeds under milder
conditions and the turnovers are also improved.
The intramolecular DielsAlder reaction (IMDA) with furan as the diene partner
has been widely used to prepare rigid oxygenated tricyclic compounds. A resin-
bound furan can easily be prepared through reductive alkylation of resin-bound
glycine and a set of furaldehydes (Scheme 16.14) [18]. Introduction of an activated
dienophile is then realized by acylation with dierent acrylic acids and cleavage
with triuoroacetic acid provides the tricyclic lactams in high yields and purities
(> 90%). Owing to the pericyclic and intramolecular reaction pathway just the exo
isomers are obtained. In order to overcome the limitation of the commercial avail-
ability of activated dienophiles, maleic anhydride is used, which can be hydrolyzed
and further reacted with amines.
Scheme 16.14. Intramolecular DielsAlder reaction with furan

derivatives. TMOF, trimethylorthoformate. (PFPTFA, triuoro-
acetic acid pentauorophenylester).
In order to increase the stereoselectivity, novel unsaturated amino acids are used
as dienophiles (Scheme 16.15) [19]. Phosphonoacetyl Wang resin [20] is hence
treated with an optically pure uorenylmethoxycarbonyl (Fmoc)-protected amino
acid aldehyde, forming the electron-decient dienophile with the intention of in-
Scheme 16.15. Enantioselective cycloaddition with unsaturated amino acid derivatives.
troducing the required stereochemical information into the cycloaddition process.

Deprotection of the amine allows the introduction of the diene component using
dierent methods. The rst example shows the acylation with 2,4-hexadionic acid
using isobutyl chloroformate as an activator. The following reductive alkylation
with benzaldehyde gives the benzylated precursor for the intramolecular Diels
Alder reaction, which is complete within 30 h at room temperature. Cleavage from
the resin provides a major diastereomer (> 90%) derived from the endo transition
state, which is inuenced by the 1,3-allylic interaction of the dienophile and steric
eect of the substituent R1.
An alternative transformation of the primary unsaturated amines is to connect
them directly to a diene by reductive alkylation with 2,4-hexadienal [19] (Scheme
16.16). Coupling to the resin-bound amine is realized by reductive alkylation of the
aldehyde or by acylation of the corresponding furanacrylic acids. Again, during the
cycloaddition only one stereoisomer is formed but after prolonged reaction times
of up to 2 days. The side-chain double bond of the vinylfuran acts as a part of the
diene participating in the DielsAlder reaction and the aromaticity of the furan
ring is restored through nal rearrangement.
Scheme 16.16. Formation of tricyclic products by intramolecular cycloaddition.

16.2.4
Hetero-DielsAlder Reaction on Solid Support
The hetero-DielsAlder reaction is a well-established method for the synthesis of

six-member heterocycles. An ecient way to access dihydropyrans lies in the reac-
tion of a,b-unsaturated ketones with enols. Starting with resin-bound acetoacetate,
the unsaturated ketones are formed by Knoevenagel reactions with dierent ali-
phatic aldehydes (Scheme 16.17) [21]. Treatment with a variety of enol ethers at 60

C for 3 days sets up a hetero-DielsAlder reaction with inverse electron demand.
Final cleavage with sodium methanolate provides the cycloadducts with excellent
purities of 90%. However, the diastereoselectivities are not very satisfying, display-
ing a ratio of 1:1 to 5:1 for the endo and exo products.
Scheme 16.17. Formation of dihydropyrans by hetero-DielsAlder reaction.
Diastereoselectivity can be increased by the use of chiral Lewis acids. Scheme

16.18 shows another cycloaddition to dihydropyrans with inverse electron demand.
The synthesis commences with resin-bound benzylidenepyruvic acid [22] and
the hetero-DielsAlder reactions with electron-rich enol ethers are catalyzed by
Eu(fod)3 . Cleavage o the resin is achieved by reduction with lithium alumi-
numhydride and the corresponding alcohols are formed in high yields with an
endo/exo selectivity of up to >97:3. The results are similar to those obtained under
homogeneous liquid-phase conditions.
Scheme 16.18. Chiral Lewis acids as catalyst in a hetero-DielsAlder reaction.
The aza-DielsAlder reaction allows one of the most convenient and versatile
approaches to nitrogen-containing six-member heterocycles. In a typical reaction
imines act as dienophiles and react with dienes to the precious cycloadducts. In
most cases the imines can be prepared in situ from amines and aldehydes, and
even simply mixing all three components (amine, aldehyde, and olen) together
gives good results using Lewis acids for catalysis. A very short synthesis is the one-
pot reaction between amino-methylated polystyrene resin, aldehydes, and diene
catalyzed by ytterbium triate (Scheme 16.19) [23]. The cycloaddition proceeds
smoothly at room temperature over 1248 h and yields and purities are >90%.
The cycloadducts are released from the resin utilizing a tertiary amine N-dealkyla-
tion method which involves chloroethyl chloroformate treatment and methanolic
decomposition of the resulting carbamates [24]. Only the desired [4 2] products
are released from the solid support, enabling a clean resin cleavage.
Scheme 16.19. Aza-DielsAlder reaction using Lewis acids for catalysis.
In order to generate triazolopyridazines, urazines as electron-poor diaza dieno-

philes are used in a hetero-DielsAlder reaction with dienes [25]. Therefore, di-
ethylphosphonoacetic acid is coupled to resin-bound amino acids and submitted to
HornerWadsworthEmmons reaction conditions with dierent a,b-unsaturated
aldehydes (Scheme 16.20) [26]. The dienes thus obtained then react with dierent
urazines, generated in situ from urazoles and iodobenzene diacetate.
Scheme 16.20. Hetero-DielsAlder reaction with in situ-

generated urazines. (PyBOP, benzotriazole-1-yl-oxy-tis-
pyrrolidino-phosphonium hexauorophosphate, NMM,
N-methylmorpholine).
16.2.5
DielsAlder Reaction in Solution Phase
It is true that transformations on solid support have some advantages over those in
solution, such as the use of an excess of reagents and the ease of removal of non-
resin-bound byproducts; in contrast, solution-phase chemistry often requires min-
imal investment of time during method development, has feasible scale-up, has
easy reaction monitoring, and no attachment points are required. A variety of imag-
inative techniques have been developed to rapidly purify the many reactions of a
solution-phase library in a parallel fashion. Some of these techniques include acid/
base extraction [27], uorous-phase extraction [28], polymer-supported reagents
[29] and catalysts [30], solid-phase extraction [31], or polymer-supported quench/
scavenging reagents [32].
The reaction with imines and dienes is well suited to solution-phase combinato-
rial chemistry using the scavenger methodology. Scheme 16.21 outlines the cyclo-
addition to 2,3-dihydro-4-pyridones under Lewis acid catalysis [33]. An equimolar
mixture of aldehydes and primary amines in trimethylorthoformate reacts to form
the imines. After evaporation of the solvent the cycloadducts are formed using an
excess of Danishefsky diene under ytterbium triate catalysis, which nally hydro-
lyzes both the cycloadducts to the desired pyridones and the excess of the diene to
the corresponding ketone. The diene decomposition product and, if the reaction
does not go to completion, any unreacted imine are removed with a polyamine
resin. After simple ltration followed by an acidic aqueous work-up dihydropyri-
done products are obtained with good yields (up to 90%) and high purities (80
90%). A variety of dierent imines, derived from alkyl, alkylaryl, pyridyl amines,
and from substituted anilines, undergo the cyclization.
Scheme 16.21. DielsAlder reaction using polymer-supported scavengers.
Even whole natural products are synthesized using an organized array of

polymer-supported reagents. Scheme 16.22 shows the synthesis of epibatidine with
a purity > 90%, avoiding the use of chromatographic purication steps [34]. A key
step in the synthesis is a cycloaddition reaction between a nitro alkene derivative
and an excess of a silyl-protected 2-oxadiene. Beginning with chloronicotinic acid,
chloride the dienophile is obtained by a reduction/oxidation sequence to the
aldehyde and addition of nitromethane with a subsequent elimination step. Treat-
ment with an excess of the volatile silyl-protected 2-oxadiene at 120 C provides the
cycloadduct in a quantitative yield. Hydrolysis to the corresponding ketone, reduc-
tion to the alcohol, mesylation, and reduction of the nitro group to the amine with
nal cyclization forms the endo isomer of epibatidine.
Scheme 16.22. Synthesis of epibatidine by DielsAlder reaction.
16.3
The most widely studied cycloadditions in solid-phase combinatorial synthesis are

[3 2] cycloadditions, which have been shown to comprise a wide range of dipoles
(nitrones, nitrile oxides, pyridinium salts, azomethine ylides, etc.) and dipolaro-
philes (alkenes, dienes, and alkynes). Depending on the nature of the 1,3-dipoles
employed in the transformations, various heterocycles such as isoxozazoles, iso-
xazolines, pyrrolidines, indolizines, and pyrrazoles are obtained [35]. These ve-
member ring systems represent a branch of unique pharmacophores and some are
also versatile synthetic intermediates in further functional group interconversions.
As mentioned in the introduction to this chapter, most applications of these
transformations are aimed at solid-phase combinatorial chemistry, while only one
solution-phase example has been reported to date [36].
16.3.1
Formation of Isoxazoles, Isoxazolines, and Isoxazolidines
Isoxazoles and isoxazolines are obtained by [3 2] cycloaddition of nitrile oxides to

alkynes or alkenes [37], while isoxazolidines are formed through reactions of
nitrones and olens (Scheme 16.23). As nitrile oxides often suer from decom-
position and dimerization in solution [38], these transformations should be carried
out on solid phase on which either the dipolarophile or the 1,3-dipole can be
immobilized.
Scheme 16.23. Synthesis strategies for the preparation of

isoxazoles, isoxazolines, and isoxazolidines.
In a representative example of the preparation of isoxazoles and oxazolines [39],

a polymer-bound olen or alkyne is treated with nitrile oxides (Scheme 16.24),
which are typically generated in situ either by using Mukaiyamas method utilizing
phenyl isocyanate and triethylamine [40] or by oxidizing oximes with sodium hy-
porchloride [41]. The conversions observed are generally high, although in some
cases the cycloaddition step has to be repeated up to three times when less stable
nitrile oxides are used.
Scheme 16.24. Formation of isoxazoles from resin-bound alkynes.
Intramolecular modications of the above-mentioned [3 2] process have also

been well established on solid-phase [42]. In a generic example, polymer-supported
nitro olens undergo 1,3-dipolar cycloadditions, giving three stereogenic centers in
the resulting tetrahydrofuroisoxazolines (Scheme 16.25). This highly stereoselec-

tive process proceeded after obtaining the nitro olens from Michael additions of
dienol alkoxides to b-nitrostyrene.
Scheme 16.25. Intramolecular addition of a polymer-bound nitrile oxide to an olen.
During the synthesis of a natural product-like library (see also Chapter 21), an
intramolecular cycloaddition is used as the key step in building up a polycyclic
template [43]. This product is formed by a Tamura tandem reaction [44] of a poly-
mer-bound epoxycyclohexanol and a set of nitrone carboxylic acids (Scheme 16.26).
After initial coupling of the 1,3-dipoles to a shikimic acid-derived alcohol, the sub-
sequent [3 2] cycloaddition proceeds with high stereo- and regioselectivity. A
variety of reagents and conditions have been screened for further manipula-
tions of the tetracyclic core thus formed and a split-and-mix library of more than 2
million compounds has been synthesized.
Scheme 16.26. Syntheses of tetracyclic cores by tandem

transesterication cycloadditions of epoxycyclohexanols and
nitrone carboxylic acids.
On the other hand, when nitrones are prepared in situ from 2-bromobenzalde-
hyde and methyl hydroxylamine and consequently reacted with polymer-bound
acrylates through a nontethered transition state (Scheme 16.27), they were found
to be less suitable for solid-phase combinatorial synthesis [45]. The yields recorded
are in the range of 2445% and even boosting the excess of reagent up to 40 equiv.
and extending the reaction times does not improve the results. In the latter case,
cleavage of the acids from the 2-chlorotrityl resin is observed owing to the pro-
longed exposure to heat.
Scheme 16.27. Syntheses of isoxazolidines by reactions of polymer-bound olens and nitrones.

More success is encountered by the same research group when polymer-bound

hydroxylamines are reacted with aldehydes and electron-decient olens such as
vinylsulfones and N-substituted maleimides (Scheme 16.28). Moreover, it is worth
mentioning that the electronic nature of the aldehydes employed has little impact
on the synthesis of isoxazolidines, whereas nitrones derived from ketones do not
react at all. The superiority of this alternative approach over the route involving
immobilized olens is demonstrated by the synthesis of a small split-and-mix
library comprising ten compounds.
Scheme 16.28. Syntheses of isoxazolidines by reactions of polymer-bound nitrones and olens.
In order to avoid elevated temperatures, ytterbium triate was successfully in-

troduced to [3 2] cycloaddition reactions, which were then found to proceed at
room temperature (Scheme 16.29) [46]. Acrylates of 1,3-oxazolin-2-ones are the
best olenic reaction partners, which can be attributed to their favorable electron-
ics. When other dipolarophiles such as methyl vinyl ketones or substituted acety-
lenes are used, reduced yields are observed, which can be attributed to the reduced
ability of Lewis acid coordination of the unsaturated systems screened.
Scheme 16.29. Yb(Otf )3 -catalyzed 1,3-dipolar cycloadditions of polymer-bound nitrones.
The isoxazolidines thus obtained are then derivatized further and consequently
converted to their corresponding isoxazolines by oxidative cleavage using 2,3-
dichloro-5,6-dicyanobenzoquinone (DDQ). During the initial work-up, ascorbic
acid is added in order to reduce the amount of remaining oxidant, but chromato-
graphy on silica gel is still found to be necessary.
Isoxazolidines can also be prepared from immobilized nitrile oxides, which are
easily generated through oxidation of polymer-bound aldoximes. In one case, N-
chlorosuccinimide (NCS) was used as the oxidant and the corresponding hydrox-
imoyl chlorides were converted to the reactive species by the dropwise addition of
triethylamine (Scheme 16.30) [47]. Immediate trapping with an excess of olens
gave the desired heterocycles with yields of 6080% and purities of >90%. Iso-
xazoles can also be prepared using this methodology.
Scheme 16.30. Syntheses of isoxazolines by oxidation of a

polymer-bound oxime with NCS and subsequent olenic
trapping.
In another example, the use of an additional amine base can be avoided when
a polymer-bound aldoxime is oxidized with commercially available household
bleach. After elimination of hydrogen chloride, the corresponding nitrile oxides are
obtained [48]. The generality and ease of this protocol is demonstrated when the
inverse strategy is pursued and resin-bound acrylates are successfully converted to
isoxazolines.
Solid-supported reagents can also be used for the in situ preparation of nitrones
with regard to the solution-phase synthesis of isoxazolidines (Scheme 16.31) [49].
This process has been carried out using polymer-supported perruthenate (PPS)
as the oxidant, but this procedure is limited to symmetrical hydroxylamines only.
In order to circumvent this limitation, aldehydes are normally condensed with
primary hydroxylamines in the presence of solid-supported acetate. After removal
of the polymer-bound reagent and transfer of the crude nitrone to a solution of
methyl acrylate, the desired cycloaddition product is isolated with an 81% yield.
Scheme 16.31. Synthesis of isoxazolidines using polymer-supported reagents.

16.3.2
Formation of Pyrrolidines
Pyrrolidines are typically formed by [3 2] cycloaddition reactions of stabilized

azomethine ylides and alkenes a well-documented process using solid support
(Scheme 16.32) [50]. Generation of the reactive dipoles can be achieved thermally
by Lewis acid activation or under basic conditions. The neighboring eects of a
stabilizing electron-withdrawing group are thereby required and, for that reason,
amino acids are the preferred building blocks as they are commercially available in
large numbers. Strategically, either the azomethine ylide or the dipolarophile can
be immobilized on solid support and both strategies have been used successfully.
Less commonly, ylides have been formed through transmetalation processes.
Scheme 16.32. Formation of pyrrolidines by [3 2]

cycloaddition of azomethine ylides to olens.
In a representative example of a heat-induced cycloaddition, a polymer-bound

amino acid was rst condensed with aldehydes and then reacted with N-substituted
maleimides (Scheme 16.33) [51]. The resulting prolines were obtained with high
diastereoselectivities and with satisfactory yields and purities of >72%.
Alternatively, the process can be carried out as a multicomponent procedure [52]
when amino acids and maleimides are reacted together with polymer-bound alde-
hydes.
Scheme 16.33. Solid-phase synthesis of substituted prolines.
Pursuing the inverse strategy, resin-bound dipolarophiles can also be reacted

with azomethine ylides [53], but the introduction of a base and a Lewis acid is vital
for the success of the transformations. After condensation of aromatic aldehydes
to 3-hydroxyacetophenone attached to Wang resin, the resulting a,b-unsaturated
ketones are treated with N-metalated azomethine ylides in the presence of 1,8-
diazabicyclo[5.4.0]undecene-7 (DBU) and LiBr (Scheme 16.34). Highly substituted
pyrrolidines are obtained with satisfying regio- and diastereoselectivities, but chal-
cones derived from sterically demanding aldehydes, for example 2,6-dichlorobenz-
Scheme 16.34. Formation of pyrrolidines from polymer-

supported chalcones. rt, room temperature.
aldehyde, do not yield any products. There has been no success using silver(I)
acetate as an additive the catalyst most often used in imine cycloaddition reac-
tions [54].
Other examples that make use of silver salts include the silver acetate-induced
cycloaddition of tryptophan-derived imines to polymer-bound acrylates (Scheme
16.35) [55] and synthetic eorts toward a split-and-mix library of mercaptoacyl
proline-based inhibitors of angiotensin-converting enzyme (ACE) [56]. Silver ni-
trate has also been used in the synthesis of fully substituted prolines derived from
histidine precursors [57], while intramolecular cycloadditions have yielded poly-
cyclic cores when both the imine and the enone are immobilized on solid support
[58]. It is worth mentioning that, during the syntheses of hydantoin-containing
Scheme 16.35. Silver(I) salt-induced formation of substituted prolines.

heterocycles, the insertion of 1,3-propanediol as a spacer moiety between the poly-

meric backbone and the glycinate generally facilitates the cycloaddition (Scheme
16.35). The desired tetracyclic cores are released from the resin after treatment
with isocyanates and base, whereas the latter reagent epimerizes the stereogenic
center at C7a. Another example of the tandem azomethine ylide cycloaddition and
carbanilide cyclization strategy uses zinc acetate and DBU as the catalytic system
[59].
Other conventionally used Lewis acids such as cesium uoride [60], silver triate
[61], or cobalt dichloride [62] have not yet been adapted to solid-phase combinato-
rial synthesis.
More reactive dipoles can be generated by transmetalation of 2-aza-allyl-
stannanes and butyl lithium (Scheme 16.36) [63], and the resulting unstabilized
anions are able to undergo [2 3] cycloadditions with electron-rich alkenes. Al-
though mixtures of regio- and stereoisomers are generally obtained, this protocol
complements the related azomethine ylide transformations which usually require
electron-poor olens.
Scheme 16.36. Synthesis of pyrrolidines via aza-allyl anion cycloadditions.
16.3.3
Formation of Furans
Ecient traceless solid-phase syntheses of furans derived from polymer-supported

isomunchnones have been reported [64]. The highly reactive 1,3-dipolar inter-
mediates which participate in the cycloaddition reactions with electron-decient
acetylenes are generated in situ by the decomposition of diazoesters with Rh(II)
catalysts. Upon heating, the intermediate bicyclic cycloadduct rearranges to the
desired furans and leaves polymer-supported isocyanate behind (Scheme 16.37).
Scheme 16.37. Traceless synthesis of furans via 1,3-dipolar

nchnones.
cycloaddition reactions of isomu
16.3.4
Formation of Imidazoles, Pyrroles, Pyrazoles, and Other Nitrogen-containing
Heterocycles
Imidazoles have also been synthesized on solid support utilizing a munchnone

[3 2] cycloaddition reaction with aryltosylimines as the key bond-forming step
(Scheme 16.38) [65]. This methodology has been successfully executed in solution
phase before, but the reaction yields are reduced by the tendency of munchnones
to undergo self-condensation [66]. This problem can be readily circumvented by
attaching the dipoles to AgroGel TM -MB-CHO.
nchnone intermediates.
Scheme 16.38. Formation of imidazoles via mu
Munchnones are prepared by reaction of an acylated polymer-bound amino

acid and N 0 -(3-dimethylaminopropyl)-N-ethylene carbodiimide (EDC) and should
immediately be reacted with tosylimines in one pot. It is dicult to cleave the im-
mobilized imidazoles thus obtained from the polymeric support but their release
can be achieved by boiling the resins in neat acetic acid, which takes advantage of
the robustness of the polymer-bound heterocycles, and unreacted starting mate-
rials or nonimidazole byproducts are removed through simple washing with tri-
uoroacetic acid (TFA) prior to the cleavage step. This new linking strategy has al-
lowed the preparation of an exploratory library containing 12 heterocycles (Scheme
16.38).
When munchnones are combined with electron-decient acetylenes, pyrroles
are obtained (Scheme 16.39) [67]. The precursors for the 1,3-dipolar cycloaddi-
tion are available through the Ugi four-component condensation (4UCC) (see
Chapter 23.7.5) and undergo an acid-catalyzed cycloelimination step. The resulting
nchnone intermediates.
Scheme 16.39. Formation of pyrroles via mu
1,3-oxazolinium-2-ones are then trapped with dimethyl acetylenedicarboxylate

(DMAD) or other electron-decient acetylenes [68] and yield pyrroles after aroma-
tization and loss of carbon dioxide.
In another example of a [2 3] cycloaddition reaction involving electron-
decient acetylenes, DMAD reacts with polymer-bound azomethine imines, form-
ing pyrazoles (Scheme 16.40) [69]. The 1,3-dipoles employed are generated from a-
silylnitrosoamides by a 1,4-silatropic shift and give heterocyclic Michael adducts in
up to 70% yield. The ratio of the regioisomers obtained is highly dependent on the
size of the adjacent substituents, whereas in the case of R H only one isomer
can be detected. Another interesting aspect of this strategy is the cyclization-
release methodology, avoiding the need for the cleavage operation. However, puri-
cation by silica gel chromatography was still found to be necessary.
Scheme 16.40. Traceless synthesis of pyrazoles.
Indolizines have also been synthesized on solid support by [3 2] cycloaddition

reactions of pyridinium ylides with electron-decient olens [70]. After alkylation
of polymer-bound isonicotinic acid with 2-bromoacetophenones, the resulting pyr-
idinium salts are treated with a,b-unsaturated ketones at elevated temperatures
(Scheme 16.41). However, the resulting tetrahydroindolizines rearrange upon
Scheme 16.41. Solid-phase synthesis of indolizines.

acidic cleavage with TFA, a phenomenon also observed during the transfer of the
Tsuge reaction to solid-phase chemistry [71].
The formation of the open-chain pyridinium salts is suppressed through oxi-
dation of the bicyclic core with the bimetallic complex TPCD [Co(pyridine)4 -
(HCrO4 )2 ]. After treatment with TFA, aromatic indolizines are obtained and an
exploratory library of nine members has been prepared.
16.4
The [2 2] cycloaddition reaction is one of the most synthetically ecient meth-

ods used for the preparation of four-member rings. However, only a limited num-
ber of protocols have been adapted to solid-phase combinatorial chemistry, while
particular focus has been turned toward the synthesis of mono-cyclic b-lactams
via the venerable Staudinger reaction [72]. In a representative example (Scheme
16.42), the cycloaddition reaction is initiated through the slow addition of acid
chlorides to a suspension of the imine resins in the presence of triethylamine [73].
Owing to the high reactivity and the accompanying tendency to undergo polymer-
ization reactions, the use of a multifold excess of the reagent is required. However,
even cycloadditions to imines derived from highly hindered amino acids usually
give satisfying results and the scope of the reaction can be extended to amino, O-
protected and vinyl ketenes.
Scheme 16.42. b-Lactams through [2 2] cycloaddition

reactions of ketenes to resin-bound imines.
The thus formed highly functionalized four-member ring heterocycles are also
valuable precursors for further chemical manipulations, particularly, when the b-
lactam strain is used to facilitate ring-opening reactions. A striking example of b-
lactams as versatile intermediates was given en route to a split-and-mix library of
4140 dihydroquinolinones (Scheme 16.43) [74]. Here, the nitro group of a [2 2]
cycloadduct is reduced and used as an internal nucleophile for the ring expansion
reactions.
Scheme 16.43. Dihydroquinolinones via polymer-supported b-lactam intermediates.

Another method for the solid-phase preparation of b-lactams from imines in-
volves titanium ester enolates derived from 2-pyridinethiols (Scheme 16.44) [75].
Scheme 16.44. Solid-phase synthesis of b-sultams.
Moreover, when sulfenes are used in the cycloaddition reactions to polymer-

supported imines, structurally analogous b-sultams are obtained [76]. Both reactive
species are generated in situ and smoothly react at 78 C. While the imines are
prepared by the condensation of aldehydes to immobilized amino acids, the sul-
fenes are formed by the addition of pyridine to methylchlorosulfonyl acetates.
In agreement with the solution-phase synthesis of sultams, two trans diaster-
eomers are obtained [77], but the success of the reaction is reduced when sterically
more demanding amino acids such as aspartic acid tert-butyl ester are used. On
the other hand, the utility of this method is indisputably high the entire reaction
sequence can be carried out with an acid-labile and a photolabile linker. It nicely
allows for the tiered release of compounds from polymeric beads onto live cells
during high-throughput screening (HTS). Further chemical modications of the
thiazetidine core also extend the scope of this strategy.
A [2 2] keteneiminium cycloaddition reaction has been used to prepare cy-
clobutanones on solid support (Scheme 16.45) [78]. The alkene resins are thereby
added to a vefold excess of the keteneiminium salts generated in situ from N,N-
dialkylamides according to the method of Ghosez and coworkers [79]. The result-
ing iminium salts are then hydrolyzed to the corresponding ketones with aqueous
sodium bicarbonate solution and further converted to g-lactams and g-lactones.
This solid-phase protocol is superior to the analogous chemistry carried out in
solution, as generally higher conversions are obtained and the purication of the
cyclobutanone iminium salts is facilitated by the immobilization on solid phase.
Scheme 16.45. Solid-phase synthesis of cyclobutanes.
16.5
[6B3] Cycloadditions on Solid Support
The [6 3] cycloaddition is an example of a more exotic reaction in combinatorial

solid-phase chemistry. One example of a [6 3] cycloaddition is the reaction be-
16.6 Rearrangements 465
tween fulvenes and benzoquinones forming heterosteroid frameworks (Scheme

16.46) [80]. In order to build up the resin-bound fulvene derivatives, dierent acids
are attached to polystyrene amino resin employing standard conditions (dicyclo-
hexyl carbodiimide (DCC), hydroxybenzotriazole (HOBt), dimethylaminopyridine
(DMAP)). Treatment with Meerwein salt and dierent sodium cyclopentadienides
provides the desired resin-bound fulvenes. Through cycloaddition with benzoqui-
nones the tricyclic adduct is released in a traceless fashion from the resin, which
can be recovered and used again. After purication by ltration through a short
pad of silica gel, the products are isolated in good yields and purity. In addition to
benzoquinones, iminobenzoquinones are also used in this type of cycloaddition.
Scheme 16.46. [6 3] cycloaddition on solid support.
16.6
Rearrangements
Among cycloadditions, sigmatropic rearrangements also belong to the group of

pericyclic reactions. New carboncarbon bonds are formed and, owing to the peri-
cyclic mechanism, there is the possibility of building up stereogenic centers in a
stereoselective fashion using chiral induction. Until now only Claisen rearrange-
ments have been applied to combinatorial chemistry. A typical example is the
polymer-supported IrelandClaisen rearrangement (Scheme 16.47) [81]. In this
solid-phase synthesis, a trialkylsilane linker is used that is rst converted to the
more reactive silyl triate. Treatment with dierent enolizable allylic esters pro-
vides the resin-bound silyl enol ethers as the reactive precursors for rearrange-
Scheme 16.47. Polymer-supported IrelandClaisen rearrangement.

ment. After completion of the reaction at 50 C in tetrahydrofuran, cleavage from

the resin is realized by methanolysis of the resin-bound silyl esters. The products
are isolated in good yields and high purity.
Not only polystyrene-based resins but also silica gel or mesoporous molecular
sieves have been used as solid support. Their thermal resistance at high temper-
atures and the opportunity of using polar solvents such as methanol or water
make these materials superior to traditional resins. Several dierent silica gels and
molecular sieves, which are capped with aminopropyltriethoxysilane and which
vary in their average mean pore size, are employed in a Claisen rearrangement
(Scheme 16.48) [82]. Attachment of hydroxymethylbenzoic acid with diisopro-
pylcarbodiimide gives the hydroxy-methylated support, which is coupled to further
acids bearing allylic side-chains. The Claisen rearrangement is then performed at
225 C without using any solvent and the products are cleaved as their methyl es-
ters after treatment with methanolic sodium methanolate. When silica gel is used
as the solid support, three major products have been isolated by column chroma-
tography that have been identied as two Claisen products (ratio 1.6:1) and a phe-
nol. In contrast, using the mesoporous molecular sieves gave only the desired
Claisen product. It is therefore concluded that higher selectivity correlates with the
greater distance between the molecules attached to the mesoporous molecular
sieves.
Scheme 16.48. Claisen rearrangement on silica gel and mesoporous molecular sieves.
References 467
References
1 a) J. Sauer, R. Sustmann, Angew. 14 B. A. Burkett, C. L. L. Chai,
Chem. 1980, 92, 773801; b) W. C. Tetrahedron Lett. 1999, 40, 70357038.
Herndon, Chem. Rev. 1972, 72, 157 15 J. D. Winkler, W. McCoull,
179; c) K. N. Houk, A. P. Marchand, Tetrahedron Lett. 1998, 39, 49354936.
R. E. Lehr, Pericyclic Reactions, Vol. 2, 16 G. J. Kuster, H. W. Scheeren,
Academic Press, New York 1977; d) P. Tetrahedron Lett. 2000, 41, 515519.
V. Alston, R. M. Ottenbrite, J. Org. 17 J. D. Winkler, Y.-S. Kwak, J. Org.
Chem. 1975, 40, 11111116; e) B. M. Chem. 1998, 63, 86348635.
Trost, J. Ippen, W. C. Vladuchik, J. 18 K. Paulvannan, T. Chen, J. W.
Am. Chem. Soc. 1977, 99, 81168118. Jacobs, Synlett, 1999, 10, 16091611.
2 a) R. E. Sammelson, M. J. Kurth, 19 a) S. Sun, W. V. Murray, J. Org.
Chem. Rev. 2001, 101, 137202; b) S. Chem. 1999, 64, 59415945; b) S. Sun,
Booth, Tetrahedron, 1998, 54, 15385 I. J. Turchi, D. Xu, W. V. Murray, J.
15443; c) B. A. Bunin, The Org. Chem. 2000, 65, 25552559.
Combinatorial Index, Academic Press, 20 P. Wipf, T. C. Henninger, J. Org.
New York 1998. Chem. 1997, 62, 15861588.
3 E. M. Smith, Tetrahedron Lett. 1999, 21 L. F. Tietze, T. Hippe, A. Steinmetz,
40, 32853288. Synlett, 1996, 10431044.
4 M. Crawshaw, N. W. Hird, K. Irie, 22 S. Leconte, G. Dujardin, E. Brown,
K. Nagai, Tetrahedron Lett. 1997, 40, Eur. J. Org. Chem. 2000, 65, 639
71157118. 643.
5 J. Barluenga, F. Aznar, M.-P. Cabal, 23 W. Zhang, W. Xie, J. Fang, P. G.
C. Valdes, J. Chem. Soc. Perkin Trans. Wang, Tetraderon Lett. 1999, 40, 7929
1 1990, 633. 7933.
6 C. Chen, B. Munoz, Tetrahedron Lett. 24 P. Conti, D. Demont, J. Cals, C. J.
1999, 40, 34913494. Ottenheijm, D. Leysen, Tetrahedron
7 C. P. Ball, A. G. M. Barrett, A. Lett. 1997, 38, 2915.
Commercon, D. Compere, C. Kuhn, 25 C. O. Ogbu, M. N. Quabar, P. D.
R. S. Roberts, M. L. Smith, O. Boatman, J. Urban, J. P. Meara,
Venier, Chem. Commun. 1998, 2019 M. D. Ferguson, J. Tulinsky, C. Lum,
2020. S. Babu, M. A. Blaskovich, Bioorg.
8 a) D. A. Heerding, D. T. Takata, C. Med. Chem. Lett. 1998, 8, 23212326.
Kwon, W. F. Huffman, J. Samanen, 26 A. M. Boldi, C. R. Johnson, H. O.
Tetrahedron Lett. 1998, 39, 68156818; Eissa, Tetrahedron Lett. 1999, 40, 619
b) S. C. Schurer, S. Blechert, 622.
Synlett, 1999, 12, 18791882. 27 a) D. L. Boger, W. Chai, R. S. Ozer,
9 S. Wendeborn, A. de Mesmaeker, C. Andersson, Bioorg. Med. Chem.
W. K.-D. Brill, Synlett, 1998, 865868. Lett. 1997, 7, 463466; b) D. L. Boger,
10 R. H. Schlessinger, C. P. C. Tarby, P. L. Myers, L. H.
Bergstrom, Tetrahedron Lett. 1996, 37, Caporale, J. Am. Chem. Soc. 1996,
21332136. 118, 21092112; c) S. Cheng, D. D.
11 a) M. J. Farrall, J. M. J. Frechet, Comer, J. P. Williams, P. L. Myers,
J. Org. Chem. 1976, 41, 3877; D. L. Boger, J. Am. Chem. Soc. 1996,
b) J. T. Randolf, K. F. McClure, 118, 25672570.
S. J. Danishefsky, J. Am. Chem. Soc. 28 a) A. Studer, D. P. Curran,
1995, 117, 5712. Tetrahedron 1997, 53, 66816688;
12 L. Blanco, R. Bloch, E. Bugnet, b) A. Studer, S. Hadid, R. Ferritto,
S. Deloisy, Tetrahedron Lett. 2000, 41, S. Kim, P. Jeger, P. Wipf, D. P.
78757878. Curran, Science 1997, 275, 823830.
13 V. Yedida, C. C. Leznoff, Can. J. 29 a) J. J. Parlow, Tetrahedron Lett. 1996,
Chem. 1980, 58, 11441150. 37, 52575261; b) J. J. Parlow, J. E.
Normansell, Mol. Diversity 1995, 1, 44 a) O. Tamura, T. Okabe, T.

266270; c) D. C. Sherrington, Yamaguchi, K. Gotanda, K. Noe,
P. Hodge, Synthesis and Separations M. Sakamoto, Tetrahedron 1995, 51,
Using Functional Polymers, Chichester, 107118; b) O. Tamura, T. Okabe, T.
Wiley 1988; d) A. Akelah, D. C. Yamaguchi, J. Kotani, K. Gotanda,
Sherrington, Chem. Rev. 1981, 81, M. Sakamoto, Tetrahedron 1995, 51,
557569. 119128.
30 a) S. Kobayashi, S. Nagayama. J. Am. 45 W. J. Haap, D. Kaiser, T. B. Walk,
Chem. Soc. 1996, 118, 89778978; G. Jung, Tetrahedron 1998, 54, 3705
b) S. B. Jang, Tetrahedron Lett. 1997, 3724.
38, 17931796. 46 S. Kobayashi, R. Akiyama,
31 a) M. G. Siegel, P. J. Hahn, B. A. Tetrahedron Lett. 1998, 39, 9211
Dressman, J. E. Fritz, J. R. 9214.
Grunwell, S. W. Kaldor, Tetrahedron 47 B. B. Shankar, D. Y. Yang, S.
Lett. 1997, 38, 33573360; b) L. M. Girton, A. K. Ganguly, Tetrahedron
Gayo, M. J. Suto, Tetrahedron Lett. Lett. 1998, 39, 24472448.
1997, 38, 513516. 48 J.-F. Cheng, A. M. M. Mjalli,
32 a) R. J. Booth, J. C. Hodges, J. Am. Tetrahedron Lett. 1998, 39, 939942.
Chem. Soc. 1997, 119, 48824883; 49 B. Hinzen, S. V. Ley, J. Chem. Soc.,
b) S. W. Kaldor, M. G. Siegel. B. A. Perkin Trans. 1, 1998, 12.
Dressman, P. J. Hahn, Tetrahedron 50 E. J. Kantorowski, M. J. Kurth, Mol.
Lett. 1996, 37, 71937195. Diversity 1996, 2, 207216.
33 M. W. Creswell, G. L. Bolton, J. C. 51 A. J. Bricknell, N. W. Hird, Bioorg.
Hodges, M. Meppen, Tetrahedron, Med. Chem. Lett. 1996, 6, 24412444.
1998, 54, 39833998. 52 B. C. Hamper, D. R. Dukesherer,
34 J. Habermann, S. V. Ley, J. S. Scott, M. S. South, Tetrahedron Lett. 1996,
J. Chem. Soc., Perkin Trans. 1, 1999, 37, 36713674.
12531255. 53 S. P. Hollinshead, Tetrahedron Lett.
35 E. J. Kantorowski, M. J. Kurth, Mol. 1996, 37, 91579160.
Diversity 1996, 2, 207216. 54 D. A. Barr, M. J. Dorrity, R. Grigg,
36 B. Hinzen, S. V. Ley, J. Chem. Soc., S. Hargreaves, J. F. Malone, J.
Perkin Trans. 1, 1998, 12. Montgomery, J. Redpath, P.
37 K. B. G. Torssel, Nitrile Oxides, Stevenson, M. Thornton-Pett,
Nitrones and Nitronates in Organic Tetrahedron 1995, 51, 273294.
Synthesis, VCH Publishers, Weinheim 55 H. A. Dondas, R. Grigg, W. S.
1988. MacLachlan, D. T. MacPherson,
38 R. A. Whitney, E. S. Nicholas, J. Markandu, V. Sridharan, S.
Tetrahedron Lett. 1981, 22, 33713374. Suganthan, Tetrahedron Lett. 2000,
39 Y. Pei, W. H. Moos, Tetrahedron Lett. 41, 967970.
1994, 35, 58255828. 56 M. M. Murphy, J. R. Schullek, E. M.
40 T. Mukaiyama, T. Hoshino J. Am. Gordon, M. A. Gallop, J. Am. Chem.
Chem. Soc. 1960, 62, 53395342. Soc. 1995, 117, 70297030.
41 a) P. N. Confalone, S. S. Ko, 57 B. Henkel, W. Stenzel, T. Schotten,
Tetrahedron Lett. 1984, 25, 947; b) A. P. Bioorg. Med. Chem. Lett. 2000, 10,
Kozikowski, J. G. Scripko, J. Am. 975977.
Chem. Soc. 1984, 106, 253. 58 Y.-D. Gong, S. Najdi, M. M.
42 X. Beebe, C. L. Chiappari, M. M. Olmstead, M. J. Kurth, J. Org. Chem.
Olmstead, M. J. Kurth, N. E. 1998, 63, 30813086.
Schore, J. Org. Chem. 1995, 60, 4204 59 G. Peng, A. Sohn, M. A. Gallop,
4212. J. Org. Chem. 1999, 64, 83428349.
43 D. S. Tan, M. A. Foley, B. R. 60 R. N. Butler, D. M. Farrell, J. Chem.
Stockwell, M. D. Shair, S. L. Res. Synop. 1998, 8283.
Schreiber, J. Am. Chem. Soc. 1999, 61 D. M. Cooper, R. Grigg, S.
121, 90739087. Hargreaves, P. Kennewell, J.
References 469
Redpath, Tetrahedron 1995, 51, 7791 Holmes, M. M. Murphy, B.

7808. Ruhland, J. W. Jacobs, E. M.
62 P. Allway, R. Grigg, Tetrahedron Lett. Gordon, M. A. Gallop, J. Med. Chem.
1991, 32, 58175820. 1996, 39, 16011608; c) R. Singh,
63 W. H. Pearson, R. B. Clark, J. M. Nuss, Tetrahedron Lett. 1999,
Tetrahedron Lett. 1997, 38, 76697672. 40, 12491252.
64 a) M. R. Gowravaram, M. A. Gallop, 73 B. Ruhland, A. Bhandari, E. M.
Tetrahedron Lett. 1997, 38, 69736976; Gordon, M. A. Gallop, J. Am. Chem.
b) D. L. Whitehouse, K. H. Nelson Soc. 1996, 118, 253254.
Jr, S. N. Savinov, D. J. Austin, 74 Y. Pei, R. A. Houghten, J. S. Kiely,
65 M. T. Bilodeau, A. M. Cunningham, 75 V. Molteni, R. Annunziata, M.
J. Org. Chem. 1998, 63, 28002801. Cijnquini, F. Cozzi, M. Benaglia,
66 R. Consonni, P. D. Croce, R. Tetrahedron Lett. 1998, 39, 12571260.
Ferraccioli, C. La Rosa, J. Chem. 76 M. F. Gordeev, E. M. Gordon, D. V.
Res. Synop. 1991, 188189. Patel, J. Org. Chem. 1997, 62, 8177
67 A. M. M. Mjalli, S. Sarshar, T. J. 8181.
Baiga, Tetrahedron Lett. 1996, 37, 77 M. J. Szymonifka, J. V. Heck,
68 A. M. Strocker, T. A. Keating, 78 R. C. D. Brown, J. Keily, R. Karim,
P. A. Tempest, R. W. Armstrong, Tetrahedron Lett. 2000, 41, 32473251.
Tetrahedron Lett. 1996, 37, 11491152. 79 J. B. Falmagne, C. Schmit, J.
69 K.-I. Washizuka, K. Nagai, S. Escudero, H. Vanlierde, L. Ghosez,
Minakata, I. Ryu, M. Komatsu, Org. Synth. 1990, 69, 199.
Tetrahedron Lett. 2000, 41, 691695. 80 B.-C. Hong, Z.-Y. Chen, W.-H.
70 D. A. Goff, Tetrahedron Lett. 1999, 40, Chen, Org. Lett. 2000, 17, 2647
87418745. 2648.
71 A. J. Bricknell, N. W. Hird, S. A. 81 Y. Hu, J. A. Porco Jr, Tetrahedron
Readshaw, Tetrahedron Lett. 1998, 39, Lett. 1999, 40, 32893292.
58695872. 82 I. Sucholeiki, M. P. Pavia, C. T.
72 a) B. Ruhland, A. Bombrun, M. A. Kresge, S. B. McCullen, A. Malek,
Gallop, J. Org. Chem. 1997, 62, 7820 S. Schramm, Mol. Diversity 1998, 3,
7826; b) Z.-J. Ni, D. Maclean, C. P. 161171.
470
17
Main Group Organometallics
Christopher Kallus
17.1
Introduction
Main group organometallics represent a class of powerful carbon nucleophiles that

allow the construction of CaC single bonds. Moreover, they can act as strong bases
and metalating agents, but also possess chelating and Lewis acid characteristics.
They are indispensable tools for the construction of organic molecular frameworks
which receive strong interest in classical syntheses of physiologically active sub-
stances. In contrast, the use of main group organometallics in combinatorial chem-
istry is underrepresented. This situation may be due to two major factors. First, the
number of commercially available compounds is limited, as is their diversity in
terms of structural variety. Second, the organometallic species are rather moisture-
sensitive and decompose rapidly in the presence of air. On the other hand, almost
no combinatorial equipment provides fully inert reaction conditions, making many
combinatorial syntheses involving organometallic reagents dicult to carry out.
Reagents carrying more sophisticated residues have to be freshly prepared, but not
every desirable chemical functionality is compatible with the high reactivity of this
reagent class. As a consequence, only robust anchoring groups such as Ellmans
tetrahydropyranyl linker or Wang ethers can be applied in solid-phase chemistry,
whereas standard linkers such as Wang esters or Rink amides are mostly excluded.
The resins used have to be dried carefully and the reactions need to be carried out
in dry glassware where deep cooling can be applied. In practice, batches of resins
for library synthesis have been prepared simultaneously prior to further diversi-
cation by easy reaction steps carried out in common parallel synthesis equipment.
Novel synthetic technologies such as Chemspeed TM or the Irori TM system may
lead to new trends.
All these factors in a very small number of combinatorial protocols in the area in
question. Moreover, not a single large library has been prepared with main group
organometallics, but only small collections of single compounds. In the context of
combinatorial chemistry, organometallic reagents have also been used for the
synthesis of novel resinanchor conjugates. Generally, the published protocols
describe solid-phase syntheses. However, an increasing number of interesting

ISBN: 3-527-30509-2
solutions to this enormously challenging eld have been presented and will be re-
viewed in this chapter.
CC bonds are formed by the attack of metalated carbon nucleophiles onto
electrophiles such as alkyl and aryl halides, carbonyl groups such as aldehydes,
ketones, and their heteroanalogs, as well as carbonic acid derivatives. Among meta-
lated species, organomagnesium and -lithium reagents are most commonly used
in combinatorial chemistry, whereas cuprates have drawn less attention. Only oc-
casionally and in special cases have organoaluminum, -boron, or -indium species
been employed.
Since the chemistry of the dierent metalated species is quite often similar, the
structure of this chapter is not guided by the various main group elements. In-
stead, it is organized by the type of chemical transformation, thus avoiding double
citations of the literature examples, where dierent organometallics are used for
the same transformation. Rather than dividing the subject into a strictly mecha-
nistic sense, the order is completely practical, following the synthetic intention
focused on a diversiable substrate (organonucleophile or electrophile) which can
be modied in a combinatorial sense. For instance, metalated aromatics are used
to make structurally diverse aromatic compounds by reaction with dierent types
of electrophiles while resin-bound ketones give diverse alcohols when reacted with
organometallics.
17.2
Reactions of Metalated Aromatics
Aryl lithium species are versatile precursors in the preparation of substituted

aromatics. Major applications include the syntheses of dierent functionalized
resins in polymer-assisted synthesis and of mini-libraries of substituted hetero-
cycles. Metalated aromatics are generally prepared from the corresponding aryl
halides with n-BuLi in tetrahydrofuran (THF) at low temperatures. Their reactions
with electrophiles are among the most frequently applied in combinatorial synthe-
sis owing to the fact that not only a broad range of electrophiles can be applied
under formation of dierent functional motifs, but also a large number of aryl
bromides as direct precursors of aryl lithiums are commercially available or can be
obtained by bromination during the combinatorial synthesis. Additionally, some
heterocyclic systems can be directly lithiated, which makes this type of reaction
even more interesting in a combinatorial sense. This feature represents an elegant
alternative to the functionalization of aromatics by Suzuki reactions, avoiding the
preparation of boronic acid building blocks.
Metalation of aromatic rings is one of the most fundamental reactions in solid-
phase synthesis. It has become the standard way of functionalizing simple poly-
styrene in order to couple handles, linkers, and reagents for further modications.
A typical reaction sequence consists of bromination of polystyrene in the presence
of Tl(OAc)3 or with ferric(III) chloride as a catalyst, and subsequent lithiation
using n-BuLi. Direct lithiation can be performed using n-BuLi and tetramethyl-
472 17 Main Group Organometallics
ethylene diamine or triethylene diamine. Lithiated polystyrene can serve as the

starting material for the preparation of polymer-bound carboxylic acids, thiols, sul-
des, boronic acids, amides, silyl chlorides, phosphines, alkyl bromides, aldehydes,
alcohols, or trityl functional groups for applications in polymer-assisted syntheses
using the corresponding electrophiles (Scheme 17.1) [16]. It also serves as the
starting material for sodium tris-ethoxyborane on selenylpolystyrene, one of the
rst selenium-based linker systems that allows a traceless cleavage [7]. The ex-
change was achieved by treating the lithiated polystyrene with selenium powder in
dry THF. This material also reacts with SO2 in THF to give polymer-bound lith-
ium phenyl sulnate, a well-established linker for the synthesis of trisubstituted
olens (see below) [8].
Scheme 17.1. Reactions of polymer-supported aryl lithiums.
A direct lithiation-substitution sequence on solid support has been described

with several ve-member ring heterocycles. Substituted hydroxyimidazoles are ob-
tained from O-imidazolyl-hydroxypolystyrene and n-BuLi followed by reactions
with various electrophiles such as alkyl halides, amides, aldehydes, carbon tetra-
chloride, disuldes, or acid chlorides (Scheme 17.2). Interestingly, in contrast to
the solution-phase procedure, solid-phase lithiation acylation occurs without any
formation of tertiary alcohols. The compounds thus synthesized have been puri-
ed by crystallization or chromatography [9]. In a similar manner, 2- and 2,5-
functionalizations of 3-polystyrenyl-O-trityl-hydroxymethylfurans and -thiophenes
can be achieved. The rst substitution takes place at the least hindered a-position,
presumably because of the steric bulk of the trityl linker. A subsequent lithiation
Scheme 17.2. Lithiation-substitution sequences of resin-bound heteroaromatics.
provides access to an attack on the position between the heteroatom and the hy-
droxymethyl group [10].
Solid-supported phenyl lithium and thiophenyl lithium serve as versatile pre-
cursors to the preparation of the corresponding resin-bound aryl isopropylsquarene
by reaction with diisopropyl squarate. The reactive intermediates provide a reaction
platform to generate several completely dierent cores, the so-called Multiple Core
Structure Libraries (MCSLs). From various possible compound shapes, quinones,
hydroquinones, and vinylogous amines derived from arylsquarenes have been re-
alized in small libraries. Further transformations at the squarene carbonyl group
are also possible (see below) [11].
In a similar fashion, the replacement of bromine with Grignard reagents leads
to magnesiated heterocycles as useful intermediates for further diversication.
This procedure has successfully been applied to the synthesis of several function-
alized thiophenes (Scheme 17.3). In contrast to reactions with the very polar orga-
nolithiums, the ester linkage and other functional groups are stable below 20 C
in the presence of an excess of Grignard reagent. Moreover, selective exchanges
on thiophene dibromides can be achieved at low temperatures. It should be men-
tioned that, in contrast to the alkoxymethyl thiophenyl lithium species, the rst
exchange and reaction with an electrophile takes place at the sterically more hin-
dered position between the heteroatom and the linking ester group. The direct-
ing eect of the anchoring group is based on a complexation between the magne-
sium and the ester group. The reaction is typically performed in the presence of
CuCN2LiCl in THF [12, 13].
Furthermore, organozinc bromides serve as building blocks for the solid-phase
synthesis of substituted aromatics. Since this reaction is catalyzed by Pd, it will be
discussed in Chapter 19.
Scheme 17.3. Halogen exchange with Grignard reagents and

subsequent reactions with electrophiles.
17.3
1,2-Additions to C X Groups
17.3.1
Reactions with Aldehydes
The reaction of resin-bound aldehydes with Grignard reagents is one of the

most commonly performed main group organometallic transformations on solid
support. The reaction has been applied to the synthesis of a uoride-labile linker
system which is suitable for immobilization of substrates such as esters, carba-
mates, and carbonates. Polystyrene methoxybenzaldehyde reacts smoothly with p-
TMSCH2 C6 H4 MgBr, forming the secondary diphenyl alcohol [14] (Scheme 17.4).
A Grignard reaction with an aldehyde has also been applied during the solid-
phase synthesis of (S)-zearalenone [15]. A stannane linker derived from polymer-
supported tin chloride in a reaction carries the aldehyde component which reacted
with a chiral TBS-protected organomagnesium alcohol leading to both diaster-
eomers of the secondary alcohol (Scheme 17.5).
In another example, polymer-supported uorenyl aminoaldehydes were treated
with various aryl magnesium reagents (Scheme 17.6). The norephedrines were
obtained after triuoroacetic acid (TFA)-induced cleavage of the uorenyl linker
[16].
One of the few examples dealing with resin-bound alkyl Grignard reagents is the
synthesis of 2,5-dihydrofurans and 1,3-dihydroisobenzofurans [17]. Hydroxy aryl
or alkenyl iodides were coupled on Wang resin as p-alkoxybenzyl ethers. The
Scheme 17.4. Solid-phase synthesis of a secondary alcohol as

uorine-labile linker via addition of a Grignard reagent to an
immobilized benzaldehyde derivative.
Scheme 17.5. Addition of a TBS-protected Grignard reagent to

a resin-bound aldehyde during synthesis of (S)-zearalenone.
Scheme 17.6. Formation of secondary alcohols from amino

acid derivatives in the synthesis of norephedrines.
subsequent iodinemagnesium exchange with i-PrMgBr gave the corresponding

Grignard reagent on beads, which reacts with several aldehydes to form secondary
alcohols (Scheme 17.7). Finally, cyclization during cleavage from the resin with
TFA occurs, yielding the desired furans.
Secondary alcohols can also be prepared by reacting organolithium species with
aldehydes. The reaction of polymer-supported m-alkoxy benzaldehyde with de-
protonated 2-phenyl-1,3-dithiane formed a dithiane-protected 3-alkoxy benzoin as
the key step in the synthesis of a photolabile safety-catch linker [18]. Since the di-
thiane group is easily removed by either bis-((triuoroacetoxy)iodo)benzene, mer-
cury(II) perchlorate, or periodic acid, this example may serve as a general protocol
for the preparation of a-hydroxy ketones. The success of the reaction is controlled
Scheme 17.7. Formation of resin-bound Grignard reagents and

addition of aldehydes providing secondary alcohols as
precursors to dihydrofurans.
13
by elemental analysis of sulfur and characteristic gel-phase C-NMR signals of the
dithiane methylenes (Scheme 17.8).
Scheme 17.8. a-Hydroxy ketones by reaction of polymer-bound

aldehydes with lithiated dithiane.
Similarly, secondary amines can be lithiated when immobilized as amidines and

transformed into secondary a-amino alcohols by reaction with aromatic aldehydes
[19]. Subsequent Williamson ether synthesis with benzyl halides and cleavage
from the resin by treatment with hydrazine/acetic acid provides a small library of
aminoethers (Scheme 17.9).
Allyl indium and allyl boronic acid pinacolates have been proven to be very mild
reagents for the nucleophilic attack of aldehydes. They are compatible even with
base and photolabile nitrobenzylic linker groups and are, in some cases, superior
to Grignard reagents or organolithiums [20]. In recent examples, resin-bound aryl
or amino acid aldehydes have been transformed into their homoallylic alcohols
(Scheme 17.10). The organoindium species have been prepared in situ from allyl
Scheme 17.9. Preparation of secondary amino alcohols from lithiated amidines.
Scheme 17.10. Formation of homoallylic alcohols on solid

support from allyl indium or allyl boronic acid pinacolate and
aldehydes.
bromide and indium powder in aqueous THF under ultrasonication. Alternatively,

the transformation can be carried out with boronic acid pinacolates in dichloro-
methane under anhydrous conditions. The reactions were successfully conducted
on both Tentagel= resin and polystyrene resins.
17.3.2
Reaction with Ketones
The reaction of ketones as electrophiles with organometallic reagents leads to

tertiary alcohols. As in the preceding chapters, the solid-phase application of this
reaction has been used in the synthesis of linkers and mini-libraries. In a repre-
sentative example, a novel acid-labile linker for solid-phase synthesis has been
prepared by the reaction of MeMgBr with resin-bound methyl phenylethyl ketone
[21]. Amines can then be immobilized on solid support by a functional group
equivalent to the Boc group, when coupled with p-nitrophenyl chloroformate onto
this resin (Scheme 17.11).
Scheme 17.11. Solid-phase synthesis of tertiary alcohols for the

preparation of t-alkyloxycarbonyl-linked amines.
3-Substituted 2-cyclohexenones can be synthesized by 1,2-addition of Grignard

reagents to polymer-bound alkoxy cyclohexenones, which were primarily prepared
from hydroxymethyl resin and 1,3-cyclohexandione [22]. During cleavage from
the resin with TFA, cyclohexenones were formed by elimination of water (Scheme
17.12). Organolithium compounds are also feasible but give somewhat lower
yields, while the reaction with more hindered carbon nucleophiles generally suf-
fers from low yields and unsatisfactory purities.
Scheme 17.12. Synthesis of substituted cyclohexenones.
For the preparation of tertiary alcohols from aryl squarenes in MCSLs, two
strategies using phenyl lithium reagents have been considered [23]. One involves
the use of a polymer-bound aryl lithium species, generated from an aryl bromide
with n-BuLi, which was reacted with alkyl 4-isopropoxysquarenes to yield benzo-
fused quinones after thermal cyclization and cleavage from the resin (Scheme
17.13, see also Section 17.2). The other pathway starts with a resin-bound squarene
which is then converted to a tertiary alcohol with phenyl lithium. If the hydroxyl
Scheme 17.13. MCSLs by addition of alkyl lithiums on squarenic acid derivatives.
group is protected, the subsequent cyclization aords aryl-substituted benzohy-

droquinones.
Treatment of resin-bound 2-substituted dihydropyridones with Grignard species
in the presence of CeCl3 led to 1,2-addition and the formation of tertiary alcohols
[24]. TFA-induced cleavage of the compounds from the resin produced 2,4-
disubstituted pyridines under oxidative conditions (O2 or air) or 2,4-disubstituted
tetrahydropyridines under reductive conditions (triethylsilane) (Scheme 17.14).
The starting material for this reaction sequence was obtained by the resin activa-
tion/capture strategy (REACAP, see below).
Scheme 17.14. Reaction of Grignard reagents with

piperidinones to tertiary alcohols during the preparation of
pyridines and tetrahydropyridines.
17.3.3
Reaction with Imines
The conversion of imines with organometallic reagents is slightly harder because

their reactivity is lower than the carbonyl groups. While organolithium compounds
undergo complete conversions at 78 C, Grignard reagents do react with imines
at elevated temperatures. The scope of the solid-phase version of this reaction has
been demonstrated on aldimines prepared from the amino group of Rink resin
and aldehydes making use of the tea-bag method [25] (Scheme 17.15). In prin-
ciple, aldimines derived from aromatic aldehydes work well, independent of their
electronic nature. The polymer support functions as a suitable NH-protecting
group, while other masked imines such as sulfenimines, sulfonimines, and TMS-
protected imines were not applicable in solid-phase chemistry. The cleavage of the
products thus formed from the resin yielded primary amines. Similarly, Schi
bases from polymer-bound benzaldehydes were reacted with allyl magnesium bro-
mide, providing secondary a-allyl amines [26].
Scheme 17.15. Substituted primary amines from solid-phase

synthesis of aldimines with organonucleophiles.
A convenient approach toward 2-substituted dihydropyridones that is an alter-

native to the tandem MannichMichael reaction with Danishefskys diene uses
4-methoxypyridine or 4-hydroxypyridine attached to polystyrene-hydroxymethyl
chloroformate resin [27, 28]. The activated resin reacts with 4-methoxypyridine
giving the acylpyridinium species, which is now accessible to a nucleophilic attack
by the Grignard reagent, a methodology which has been named resin activation/
capture approach (REACAP) by the authors. The reaction can principally be con-
sidered as an addition of a Grignard reagent to an activated CbN double bond. It
leads to the direct formation of the resin-bound dihydropyridinone, which can be
cleaved o with sodium hydroxide in methanol. The same reaction type was ap-
plied after linking 4-hydroxypyridine to hydroxymethyl polystyrene under Mitsu-
nobu conditions. Activation of the pyridine by acylation with acid chlorides allowed
the addition of Grignard reagents. The desired dihydropyridone was formed dur-
ing the cleavage with TFA from the resin (Scheme 17.16).
Scheme 17.16. 2-Substituted dihydropyridones formed by

attack of organometallics on acyl pyridinium species.
Any unreacted acylpyridinium intermediate remained on the solid support,

forming polymer-bound pyridine during the cleavage step. The carboxylic acid
thus released as a byproduct was removed by a scavenger resin.
The reactivity of terminal alkynes in the presence of catalytic amounts of
copper(I) chloride has been demonstrated by reaction of aldimines in Mannich
reactions [29]. The solid-phase three-component synthesis of a-substituted prop-
argylic amines is an application of this reaction type carried out with resin-bound
alkynes, with secondary amines, or with aldehydes in hot dioxane (Scheme 17.17).
In very recent examples, the milder and more exible Petasis variant of the solid-
supported Mannich reaction has been presented [3032]. Immobilized secondary
amines have been reacted with aldehydes and boronic acids to give the Mannich
products in a very simple manner.
Scheme 17.17. Solid-supported Mannich reactions with

metalated species. DMF, dimethylformamide.
17.3.4
Reaction with Enolates
a-Substituted ketones can be easily prepared by reaction of polymer-bound TMS

enolethers with triates after the addition of methyl lithium, as demonstrated dur-
ing the synthesis of prostaglandin E2 methyl esters on noncrosslinked polystyrene
(Scheme 17.18) [33]. Presumably, the organonucleophile cleaves the relatively
stable OaTMS bond, forming the highly reactive lithium enolate and tetramethyl-
silane. This reaction has not yet been applied to the synthesis of a series of
compounds or libraries.
Scheme 17.18. a-Alkylated ketones by reaction of TMS enolates with alkynyl lithium reagent.
17.4
Conjugate Addition to a,b-Unsaturated Carbonyls and Related Systems
Because of their particularly soft character, cuprates are the reagents of choice for
conjugate additions, but only a few examples of this reaction type in solid-phase
syntheses or combinatorial chemistry have yet been described. An application has
been demonstrated by the 1,4-addition to resin-bound dihydropyridones (obtained
from a Grignard reaction, see above) [27]. Cuprates have been prepared in a clas-
sical manner by the reaction of copper(I) iodide and Grignard reagents in the
presence of borontriuoride etherate (Scheme 17.19).
Scheme 17.19. Synthesis of 3-substituted piperinones by

reaction of cuprates with dihydropyridones.
Alkenyl-substituted ketones can be prepared by the reaction of a,b-unsaturated

ketones, as demonstrated during the synthesis of prostaglandins either by use of
solid or soluble supports (Scheme 17.20) [33, 34]. The vinyl cuprates employed in
Scheme 17.20. 1,4-Additions of unsaturated metalated species to cyclopentenones.

17.5 Nucleophilic Substitutions 483
this reaction can be prepared in situ from readily accessible terminal alkynes by
hydrozirconation or stannylation followed by transmetalation using Lipshutzs or
Babiaks protocol [35, 36].
The synthesis of b-substituted esters can be performed in a similar manner.
High enantioselectivities have been obtained in addition reactions of Me 2 CuLi or
Ph2 CuMgBr to chiral unsaturated esters immobilized on Wang Resin [37]. The
resulting trisubstituted hydroxy ester cyclizes upon cleavage from the resin form-
ing d-lactones in excellent yields and enantiopurities (Scheme 17.21).
Scheme 17.21. 1,4-Addition of cuprates on immobilized unsaturated esters.
17.5
Nucleophilic Substitutions
N-Nosylated alkenylaziridines are suitable substrates for SN 2 0 substitutions, where

the nosylate serves as a leaving group, expelled initially by the attack of cuprates on
the double bond [38]. Typical products are (E )-alkene amino acids, which are use-
ful isosteric nonhydrolyzable peptide bond replacements. In selected examples,
copper reagents prepared from organolithium or Grignard reagents were used for
the preparation of these a-substituted dipeptide isosteres on Wang resin (Scheme
17.22).
Scheme 17.22. Addition of cuprates to vinyl nosylate aziridines.
Grignard reagents can also serve as agents for functionalizing cleavage products
synthesized on the benzotriazole linker [39]. In an extremely short reaction se-
quence, consisting of resin capture of aldimines in a Mannich reaction and subse-
quent cleavage by nucleophilic substitution with Grignard reagents in reuxing

toluene, primary and secondary amines have been obtained in variable yields and
excellent purities. As in all similar cleavage reactions, an aqueous extraction step is
necessary (Scheme 17.23).
Scheme 17.23. Cleavage of highly substituted amines from

benzotriazole linker with Grignard reagents.
Finally, the application of cuprates as cleavage reagents has been demonstrated

in related solid-phase reactions [8]. Trisubstituted olens were synthesized by the
reaction of terminal allyl species immobilized on a phenylsulfone linker with cup-
rates prepared in situ from a range of Grignard reagents and copper(I) iodide
(Scheme 17.24). Purication by column chromatography of the products thus ob-
tained was found to be necessary.
Scheme 17.24. Trisubstituted olens from additions of cuprates on vinyl sulfones.
17.6
Reactions on Carboxylic Acid Derivatives and Related Systems
From a mechanistic point of view, reaction of Grignard compounds with carboxylic

acid derivatives is quite similar to the 1,2-additions mentioned previously. The
initial step is again the nucleophilic attack on the CbO double bond, leading to a
tetrahedral intermediate. The subsequent restitution of the carbonyl group is
accompanied by the simultaneous ejection of a leaving group.
17.6.1
Reaction with Esters
The solid-phase synthesis of a,a-dialkyl-substituted alcohols has been accom-

plished by the reaction of resin-bound esters with Grignard reagents. After two
successive additions, tertiary alcohols are obtained. In contrast to the previously
mentioned additions to ketones, only symmetrically disubstituted products are
accessible. This type of reaction has been carried out with methyl-2-hydroxy-3-
phenyl-propionate immobilized on Wang resin by an ether linkage giving the cor-
responding dimethyl alcohol [40]. It has also been used for the preparation of a
small library of N-alkyl-2-pyrrolidine-dialkyl-methanol ligands as potential catalysts

in diethylzinc additions from hydroxy proline, attached by the THP linker onto
solid support [41] (Scheme 17.25).
Scheme 17.25. Formation of a,a-distributed alcohols by the

addition of Grignard reagents to resin-bound esters.
In many examples, Grignard reagents have been applied for the release of prod-
ucts from the solid support. During the solid-phase synthesis of a PDE4 inhibitor,
MeMgBr was used to cleave the ester linkage leading to a dimethylphenyl alcohol
after treatment with ammonium chloride in ethyl acetate (Scheme 17.26) [42].
Scheme 17.26. Tertiary alcohols by cleavage of ester linkage with Grignard species.
17.6.2
Reactions with Weinreb Amides and Related Systems
One of the most popular transformations with main group organometallics on

solid supports is the reaction of Weinreb amides with kryptobases. These N-
methoxy-N-methylamides react with Grignard species to give ketones and with hy-
drides to give aldehydes, which contain desirable functional groups either for fur-
ther diversication (reductive amination) or as recognizing moieties in libraries of
serine/cysteine protease inhibitors. Little or no overalkylation occurs, presumably
because of the formation of a chelate of the metal ion with the carbonyl oxygen
and the N-methoxy oxygen. This stable intermediate decomposes readily to give a
carbonyl group upon treatment with acid (Scheme 17.27).
Scheme 17.27. Formation and breakdown of the tetrahedral

bidentate during reaction of Grignard reagents with Weinreb
amides.
For the synthesis of ketone or aldehyde libraries, the use of Weinreb amides as
anchoring groups is preferable. Although additional eorts during the work-up are
necessary, this strategy is advantageous because the reactive keto group is released
only at the stage of the cleavage step. In this context, the N-alkyoxyamide function
of b-alanin Weinreb amide on aminomethyl polystyrene has been used as a linker
group [43]. Since preformation of the linker conjugate with the substrate has to be
carried out in solution phase, this methodology appears to be somewhat laborious
(Scheme 17.28).
Scheme 17.28. Syntheses of ketones by cleavage of Weinreb-type linkers.
More conveniently, solid-supported Wang O-hydroxyl-N-alkyl amine, obtained by

reaction of N-hydroxyphthalimide with Wang resin and subsequent cleavage of the
phthalimide with methylamine, has been used in the immobilization of substrates
by a Weinreb amide linker [44]. The cleavage was carried out using EtMgBr to
provide ethyl ketones. Another successful method for the preparation of ketone
libraries on solid phase uses mercaptoacetylamide on polystyrene resin, which acts
in the same way as a Weinreb amide [45]. The starting carboxylic acid building
blocks were coupled as thioamides onto this linker. After treatment with Grignard
reagents, analytically pure products were released from the resin.
The combination of a Weinreb amide and an isonitrile functionality in one sin-
gle synthetic building block allows the preparation of a dipeptide methyl ketone
library by application of methyl Grignard reagent after the Ugi 4CC reaction
(Scheme 17.29). A 96-member library around a known anticonvulsant structure
has been synthesized according to this strategy [46].
Scheme 17.29. Synthesis of dipeptide alkyl ketones.
Another solid-phase protocol using the Weinreb methodology leads to a-hydroxy-

ketones, which have been shown to be ecient inhibitors of the aspartate pro-
tease renin [47]. Since the hydroxy group is the recognizing motif within this
enzyme family, uorenylmethoxycarbonyl (Fmoc)-hydroxy-b-amino acids are suit-
able templates for this purpose, preferably attached via the hydroxy group to the
solid support. The immobilized amino acids have been converted into ketones by
formation of the Weinreb amide with HClNH(OMe)Me and dropwise addition of
Grignard reagent in a one-pot procedure (Scheme 17.30). It is noteworthy that an
acetic acid/dichloromethane washing step is of crucial importance, presumably
because magnesium salts from the bisdentate complex have to be removed prior to
cleavage from the polystyrene resin. This method worked very well in the case of
primary unhindered Grignard reagents, while attempts with organolithium spe-
cies resulted in complex product mixtures.
Scheme 17.30. Solid-phase synthesis of an a-hydroxy ketone library.

A highly sophisticated application of the Weinreb amide transformation was part

of the synthesis of aspartyl protease inhibitor libraries targeting cathepsin D [48,
49]. 2,3-Dihydroxy propionic acid served as a suitable template, which was attached
to Wang resin via its a-hydroxy group, as in the previous example. The carboxylic
acid had to be transformed into a ketone for further chemical modications. The
standard Weinreb methodology that was chosen initially to accomplish this task
led to unwanted side-products for two reasons. First, overalkylation occurred to
a remarkable degree since the excess Grignard reagent was not completely de-
stroyed, while the breakdown of the tetrahedral intermediate had already delivered
the free ketone susceptible to further attack. Second, a competitive NaO bond
cleavage leads to N-methyl products in substantial amounts, depending on the
nature of the Grignard reagent used. While the problem of overalkylation has
been countered by addition of acetone to the reaction mixture to quench excess
Grignard, the problem of side-products occurring as a result of NaO bond cleavage
has remained unsolved. Therefore, the N-methoxy-N-methyl amide was replaced
by a simple pyrrolidine amide. The Grignard addition to this substrate provided
the desired ketones with no detectable overalkylation product (Scheme 17.31).
Herein, the a-alkoxy group serves as a Lewis base to stabilize the tetrahedral
intermediate instead of the N-methoxy group of the standard Weinreb amide.
For the library synthesis, a diverse set of commercially unavailable Grignard
reagents has been prepared from activated magnesium turnings (alkyl Grignards)
or Mg(anthracene)(THF)3 complex (activated benzyl-type Grignards). Using the
aforementioned chemistry, a library of more than 1000 compounds has been syn-
thesized, delivering several highly potent cathepsin D inhibitors. Later, the same
concept was applied to the synthesis of libraries targeting plasmepsin II, which
also yielded nanomolar inhibitors [50].
Scheme 17.31. Side-reactions of standard Weinreb amides and

synthesis of polymer-bound ketones from a-alkoxypyrrolidine
amides.
The solution-phase preparation of ketones from Weinreb amides is also feasible

using polymer-bound sulfonylhydrazide as a resin-capture reagent to isolate the
desired products [51]. In a short reaction sequence, this strategy was applied to
synthesize a small library of 1,2,3-thiadiazoles, released by treating the resin-bound
17.7 Aminolysis of Esters 489
hydrazones with SOCl2 . The tetrahedral intermediates from the Grignard reaction
were decomposed by addition of macroporous polystyrene-sulfonic acid resin (MP-
TsOH) and the ketones thus produced were captured by gentle heating with PS-
TsNHNH2 in acetic acid/THF (Scheme 17.32).
Scheme 17.32. Solution phase synthesis of ketones from

Weinreb amides during preparation of 1,2,3-thiadiazoles.
17.7
Aminolysis of Esters
Aminolysis of esters has been applied in combinatorial chemistry in order to gen-

erate the overwhelming diversity of amides in a single step. Organoaluminums
are the reagents of choice for inducing this reaction owing to their strong Lewis
acidity. This protocol has mostly been used for the derivatizing cleavage from hy-
droxyethyl polystyrene resin. Published examples include the synthesis of tetra-
hydrochinoline amides by PictetSpengler reaction [52] and the formation of 3-
hydroxypropionamides utilizing the BaylisHillman reaction [53] (Scheme 17.33).
Scheme 17.33. Aminolysis of ester bonds with organoaluminium reagents on solid support.
The ltrates must be carefully quenched and additional work-up was found to
be necessary. This reaction type has also been used for the simultaneous lactone
opening and amidation on solid support [37].
References
1 T. M. Fyles, C. C. Leznoff, Can. J. Balasubramanian, Tetrahedron Lett.

Chem. 1976, 54, 935. 1997, 38, 12271230.
2 F. Camps, J. Castells, M. J. 19 P. S. Furth, M. S. Reitman, R.
Ferrando, J. Font, Tetrahedron Lett. Gentles, A. F. Cook, Tetrahedron Lett.
1971, 17131714. 1997, 38, 66436646.
3 W. Heitz, R. Michels, Makromol. 20 C. L. Cavallaro, T. Herpin, B. F.
Chem. 1971, 148, 9. McGuiness, Y. C. Shimshock, R. E.
4 M. J. Farall, J. M. Frechet, J. Org. Dolle, Tetrahedron Lett. 1999, 40,
Chem. 1976, 41, 38773882. 27112714.
5 F. G. Bordwell, B. M. Pitt, J. Am. 21 R. Leger, R. Yen, M. W. She, V. J.
Chem. Soc. 1955, 77, 572577. Lee, S. C. Hecker, Tetrahedron Lett.
6 G. A. Crosby, N. M. Weinshenker, 1998, 39, 41714174.
H.-S. Uh, J. Am. Chem. Soc. 1975, 97, 22 M. E. Fraley, R. S. Rubino,
7 T. Ruhland, K. Andersen, H. 23 P. A. Tempest, R. W. Armstrong, J.
Pedersen, J. Org. Chem. 1998, 63, Am. Chem. Soc. 1997, 119, 76077608.
92049211. 24 C. Chen, B. Munoz, Tetrahedron Lett.
8 C. Halm, J. Evarts, M. J. Kurth, 1998, 39, 34013404.
Tetrahedron Lett. 1997, 38, 77097712. 25 A. R. Katritzky, L. Xie, G. Zhang,
9 S. Havez, M. Begtrup, K. Andersen, Tetrahedron Lett. 1997, 38, 70117014.
T. Ruhland, J. Org. Chem. 1998, 63, 26 B. Chenera, J. A. Finkelstein, D. F.
74187420. Veber, J. Am. Chem. Soc. 1995, 117,
10 Z. Li, A. Ganesan, Synlett 1998, 405 1199912000.
406. 27 C. Chen, I. A. McDonald, B. Munoz,
11 P. A. Tempest, R. W. Armstrong, J. Tetrahedron Lett. 1998, 39, 217220.
Am. Chem. Soc. 1997, 119, 76077608. 28 C. Chen, B. Munoz, Tetrahedron Lett.
12 L. Boymond, M. Rottlander, G. 1998, 39, 67816784.
Cahiez, P. Knochel, Angew. Chem. 29 J. J. McNally, M. A. Youngman, S. L.
Int. Ed. Engl. 1998, 37, 17011703. Dax, Tetrahedron Lett. 1998, 39, 967
13 M. Abarbi, J. Thibonnet, L. 970.
Berillon, F. Dehmel, M. 30 N. Schlienger, M. R. Bryce, T. K.
Rottlander, P. Knochel, J. Org. Hansen, Tetrahedron 2000, 56, 10023
Chem. 2000, 65, 46184634. 10030.
14 A. Routledge, H. T. Stock, S. L. 31 S. R. Klopfenstein, J. J. Chen,
Flitsch, N. J. Turner, Tetrahedron A. Golebiowski, M. Li, S. X. Peng,
Lett. 1997, 38, 82878290. X. Shao, Tetrahedron Lett. 2000, 41,
15 K. C. Nicolaou, N. Winssinger, J. 48354839.
Pastor, F. Murphy, Angew. Chem. Int. 32 A. Golebiowski, S. R. Klopfenstein,
Ed. Engl. 1998, 37, 25342537. J. J. Chen, X. Shao, Tetrahedron Lett.
16 F. Gosselin, J. v. Betsbrugge, M. 2000, 41, 48414844.
Hatam, W. D. Lubell, J. Org. Chem. 33 S. Chen, K. D. Janda, J. Am. Chem.
1999, 64, 24862493. Soc. 1997, 119, 87248725.
17 M. Rottlander, P. Knochel, J. 34 L. A. Thompson, F. L. Moore, Y.-C.
Comb. Chem. 1999, 1, 181183. Moon, J. A. Ellman, J. Org. Chem.
18 A. Routledge, C. Abell, S. 1998, 63, 20662067.
References 491
35 B. H. Lipshutz, E. L. Ellsworth, J. 45 I. Vlattas, J. Dellurecio, R. Dunn,

Am. Chem. Soc. 1990, 112, 7440. I. I. Sytwu, J. Stanton, Tetrahedron
36 K. A. Babiak, J. R. Behling, J. H. Lett. 1997, 38, 73217324.
Dygos, K. T. McLaughlin, J. S. Ng, 46 S. W. Kim, S. M. Bauer, R. W.
V. J. Kalish, S. W. Kramer, R. L. Armstrong, Tetrahedron Lett. 1998,
Shone, J. Am. Chem. Soc. 1990, 112, 39, 69936996.
7441. 47 O. B. Wallace, Tetrahedron Lett. 1997,
37 S. Hanessian, J. Ma, W. Wang, 49394942.
Tetrahedron Lett. 1999, 46314634. 48 E. K. Kick, D. C. Roe, A. G.
38 P. Wipf, T. C. Henninger, J. Org. Skillman, G. Liu, T. J. A. Ewing,
Chem. 1997, 62, 15861587. Y. Sun, I. D. Kuntz, J. A. Ellman,
39 K. Schiemann, H. D. H. Showalter, Chem. Biol. 1997, 4, 297307.
J. Org. Chem. 1999, 64, 49724975. 49 C. E. Lee, E. K. Kick, J. A. Ellman, J.
40 S. Hanessian, F. Xie, Tetrahedron Lett. Am. Chem. Soc. 1998, 120, 9735
1998, 39, 737740. 9747.
41 G. Liu, J. A. Ellman, J. Org. Chem. 50 T. S. Haque, A. G. Skillman, C. E.
1995, 60, 77127713. Lee, H. Habashita, I. Y. Gluzman,
42 Y. Han, A. Giroux, C. Lepine, F. T. J. A. Ewing, D. E. Goldberg, I. D.
Laliberte, Z. Huang, H. Perrier, Kuntz, J. A. Ellman, J. Med. Chem.
C. I. Bayly, R. N. Young, Tetrahedron 1999, 42, 14281440.
1999, 55, 1166911685. 51 Y. Hu, S. Baudart, J. A. Porco,
43 T. Q. Dinh, R. W. Armstrong, Jr. J. Org. Chem. 1999, 64, 1049
44 J. M. Salvino, M. Mervic, H. J. 52 K. Rolng, M. Thiel, H. Kunzer,
Mason, T. Kiesow, D. Teager, J. Synlett 1996, 10361038.
Airey, R. Labudiniere, J. Comb. 53 O. Prien, K. Rolng, M. Thiel,
Chem. 1999, 1, 134139. H. Kunzer, Synlett 1997, 325326.
492
18
Enolates and Related Species in Combinatorial
and Solid-phase Synthesis
Jochen Kruger
18.1
Introduction
The formation of carboncarbon bonds utilizing enolates and related species is

among the most prominent and useful processes in organic synthesis. Accord-
ingly, the extension of the established solution-phase repertoire to combinatorial
synthesis onto liquid phase and solid phase represents both an ambitious as well
as a rewarding goal.
Comprehensive compilations of the latest achievements in solid- and liquid-
phase enolate chemistry have been published recently [1].
In this chapter, we give a detailed account of the use of enolates and related spe-
cies in combinatorial chemistry. In addition to the available literature, we provide
an extensive comparison of solution- and solid-phase strategies in each section.
Moreover, we focus on the practical aspects and assess the suitability of a given
method for automation and library synthesis. We also discuss the scope and limi-
tations of each method, as well as its convenience for practical use.
18.2
Aldol Reactions
18.2.1
General Aspects
The aldol reaction between an aldehyde and an enolate or an enolate equivalent

delivers b-hydroxy carbonyls or, after dehydration, a,b-unsaturated carbonyls. Both
structural motifs represent valuable functionalities in natural product and hetero-
cycle synthesis. Thus, it seems conceivable that well-established methods for clas-
sical solution-phase aldol chemistry could be adapted to the requirements of com-
binatorial chemistry. However, the emphasis in this eld was clearly placed on
solid-phase strategies.

ISBN: 3-527-30509-2
The direct condensation between an aldehyde and a CaH acidic ketone was suc-
cessfully employed in solid-phase synthesis and library construction (see Section
18.2.2). In particular, Na and Zn enolates have played a dominant role in this eld.
Although the basic reaction conditions entail limitations arising from the base
sensitivity of some polymeric linkers or starting materials, this method presents a
powerful tool to perform aldol reactions on solid support.
For stereoselective aldol protocols, we discuss recent progress in the application
of boron enolates in solid-phase chemistry (see Section 18.2.3). In general, the
eciency of a boron aldol process on solid support is highly dependent on the
nature of the polymer, the polymeric linker, and the reactivity of the enolate. Thus,
for a given synthetic problem in solid-phase chemistry, the boron aldol protocol
has to be adjusted to the requirements of the desired transformation. To the best
of our knowledge, multicomponent library synthesis utilizing stereoselective boron
aldol reactions has not yet been reported.
In Section 18.2.4 we detail the latest achievements in the eld of liquid- and
solid-phase Mukaiyama aldol chemistry. This mild version of the aldol reaction can
serve as an attractive alternative for the direct aldol condensation employing eno-
lizable carbonyl compounds.
18.2.2
Li, Na, K, and Zn Enolates in Aldol Reactions
The synthesis of b-hydroxy carbonyls via a crossed aldol reaction between an alde-
hyde and an enolizable carbonyl compound has been adopted to solid phase,
whereas liquid-phase protocols in this eld are rather scarce.
Ruhland and Kunzer described the formation of aldol intermediates (2) upon
reaction of resin-bound aldehyde 1 with acetophenone in the presence of K2 CO3 at
elevated temperature (Scheme 18.1) [2]. Six aromatic and heteroaromatic methyl-
ketones were reported to be suitable substrates for this transformation, however,
yields and purities were not given. The intermediates (2) were used in the synthe-
sis of a diverse quinoline library of 12 products. Thereby, the eectiveness of the
aldol transformation as a key step in this sequence was demonstrated.
Scheme 18.1. Aldol reactions on solid phase employing K enolates.
A major obstacle in aldol chemistry on solid support is incomplete or sluggish

reactions due to variable extents of retro-aldol processes. In this regard, the use of
494 18 Enolates and Related Species in Combinatorial and Solid-phase Synthesis
Zn enolates has proved to be advantageous, since the amounts of retro-aldol prod-

ucts being formed during the process were minimized. As Kurth et al. [3] demon-
strated, immobilized Zn enolates react smoothly with aromatic aldehydes and give
the desired b-hydroxy ketones in good yields and purities. Accordingly, ester 3
loaded on Merrield resin was deprotonated at 78 C using an excess of lithium
diisopropylamide (LDA) followed by the addition of anhydrous ZnCl2 to trigger the
transmetalation to the corresponding Zn enolate. Finally, 27 aromatic aldehydes were
added and the aldol reaction proceeded smoothly at 0 C within 30 min (Scheme
18.2) [3]. Cleavage from the resin was accomplished by reduction of the ester link-
age with diisobutylaluminium-hydride (DIBAL-H) to yield the crude diols (4) as
mixtures of syn and anti products which were puried by preparative thin layer
chromatography (TLC). In the case of p-methoxybenzaldehyde as electrophile in
this reaction, an overall isolated yield of 26% was reported.
Scheme 18.2. Aldol reactions on solid phase employing Zn enolates.
A related strategy was applied by Nicolaou et al. for the synthesis of an epothi-
lone library [4]. A key step in this route leading to diversity with concomitant con-
struction of the CaC skeleton was an aldol reaction mediated by in situ-generated
Zn enolates (see Scheme 21.14). Both contributions demonstrate that even
more sophisticated reaction conditions including inert gas techniques and low-
temperature protocols are routinely applied in solid-phase synthesis today. The
only drawback in terms of manipulative convenience arose from the fact that the
products were puried by preparative TLC after cleavage. This aspect might be
dicult to realize in an automated library synthesis process.
The synthesis of a,b-unsaturated ketones using a crossed aldol strategy on solid
support is well established and has successfully been applied to solid-phase or-
ganic synthesis. Either the aldehyde moiety or the CaH acidic ketone can be linked
to the polymer via an ether or an amide linkage, whereas linkage via an ester
proved to be incompatible with the strongly basic reaction conditions.
In general, a solution of NaOMe as a solution in methanol is routinely used as a
standard base to promote the desired condensation event. A typical example of this
reaction is illustrated in Scheme 18.3. Here, the immobilized acetophenone (5) was
treated with 12 equiv. of NaOMe (0.5 M solution in MeOH) and 12 equiv. of aro-
matic aldehydes at room temperature to yield enones (6) (ve examples) [5]. The
reaction was conducted in tetrahydrofuran (THF) to eect sucient swelling of
the polymer. Alternatively, trimethylorthoformate (TMOF), which facilitates the
dehydration step, was used as the solvent instead [6]. This type of aldol condensa-
Scheme 18.3. Aldol condensations employing Na enolates.
tion of ketones has also been carried out employing Li enolates which were gen-
erated in situ using an excess of LiOHH2 O (20 equiv.) in dioxane [7] or dime-
thoxyethane (DME) [8] as solvent.
In conclusion, reliable aldol protocols for the solid-phase synthesis of a,b-unsat-
urated ketones are available; however, these processes are primarily restricted to
the condensation of methyl-arylketones with aromatic aldehydes, thus limiting the
options for diversication in library synthesis.
18.2.3
Boron Enolates in Aldol Reactions
The introduction of boron enolates has provided a signicant impetus in aldol

chemistry, especially with regard to stereoselective protocols. Therefore, the adap-
tation of solution-phase boron aldol strategies to solid-phase chemistry has been
an intense eld of investigation.
Gennari et al. reported an enantioselective aldol addition on solid support medi-
ated by a chiral boron enolate (Scheme 18.4) [9]. Accordingly, 4-(hydroxymethyl)-
benzaldehyde was bound to trityl resin and the resulting polymer (7) was treated
three times with an excess (@ 3 equiv.) of chiral boron enolate (8) in dichloro-
methane at 78 C. The resulting product was cleaved from the resin and puried
by chromatography to yield the corresponding b-hydroxythiolester (9) in 60% yield
with 88% ee.
Scheme 18.4. Enantioselective aldol reactions using chiral B enolates.
Paterson and coworkers demonstrated a powerful methodology that permits the

construction of polyketide libraries employing stereoselective propionate additions
to aldehydes (Scheme 18.5) [9, 10]. Thus, aldehyde 10 was reacted twice with an
excess of preformed (E )-propionate (11) in an argon atmosphere at low tempera-
ture to yield the corresponding aldol products on the polymer (Scheme 18.5, path
A). The resulting target molecules were cleaved from the resin using HF-pyridine
to yield the anti-congurated diols (12) after ash chromatography with high levels
of diastereoselectivity (ve examples: 9097% de) and good yields. Complementary
to this, the syn-congurated product (14) could be accessed using the (Z)-enolate
(13) (Scheme 18.5. path B). To achieve complete conversion in this reaction, alde-
hyde 10 was successively incubated three times, each time with an excess of eno-
late 13. The aldol product was cleaved from the resin and the resulting diol was
isolated after chromatography with 99% yield with 95% de in favor of the syn con-
guration.
Scheme 18.5. Stereoselective synthesis of anti and syn aldols using chiral B enolates.
Eventually, this concept of stereoregulated aldol chemistry was extended to the

construction of more complex polyketide sequences on solid support [10].
Evans oxazolidinone presumably represents the most prominent chiral auxiliary
in aldol chemistry. Accordingly, two strategies have been described to transfer this
concept to solid-phase chemistry. In the initial report by Reggelin and Brennig, al-
dehyde 16, immobilized on Wang resin, was reacted with preformed boron enolate
(15) (Scheme 18.6, path A) [11]. The aldol addition proceeded as expected and de-
livered the syn product 17 after cleavage from the resin (BCl3 ) in 74% de (the au-
thors could demonstrate that slight epimerization occurred under the harsh cleav-
age conditions; no yield was reported). However, further manipulations of the
resin-bound aldol product (e.g. OH protection) proved dicult. These problems
were attributed to the Wang linker present in 16.
Accordingly, a more exible Si-based linker was introduced for this reaction
(Scheme 18.6, path B) [12]. With 10 in place, the aldol reaction as well as further
manipulations proceeded without complications, even though lactone 18, which
Scheme 18.6. Stereoselective addition of chiral B enolates to resin-bound aldehydes.
formed upon cleavage from the resin was obtained in poor yield. Moreover, isola-
tion of the nal product required chromatography since the crude reaction mixture
was contaminated by oxazolidinone (19). Optimal results for the solid-supported
Evans aldol protocol were elaborated for soluble polyethylene glycol (PEG)-bound
aldehyde 20. This scenario comes closest to solution-like conditions having a
favorable impact on reaction kinetics (Scheme 18.6, path C) [13]. The polymeric
aldol adducts were precipitated from solution to obtain 21 (six examples, 5688%
yield) and 1 H-NMR measurements revealed that each product was formed as a
pure stereoisomer.
The three examples depicted in Scheme 18.6 clearly demonstrate that the choice
of the polymeric linker plays a crucial role in this solid-supported aldol process.
Furthermore, the scope of these reactions is limited to aldehydes bearing addi-
tional functional groups which allow the electrophile to be anchored to the poly-
mer. After cleavage, these functional groups reside as integral parts in the target
molecules.
An alternative strategy is based on resin-bound oxazolidinone 22, which was
synthesized on polymer support using l-tyrosine as the source of chirality [14]. As
depicted in Scheme 18.7 the (Z )-congurated boron enolate was generated by re-
action of 22 with an access of Bu2 BOTf in the presence of a tertiary amine such as
triethylamine using methylene chloride as the solvent of choice.
The excess of Bu2 BOTf had to be drained away prior to the addition of the alde-
hyde since deleterious eects with respect to the stereochemical outcome were re-
ported if additional Bu2 BOTf was present in the reaction mixture [15]. After com-
pletion of the aldol reaction, the resin was subjected to an aqueous LiOH solution
Scheme 18.7. Stereoselective addition of polymer-bound chiral B enolate 22 to benzaldehyde.
in THF to eect cleavage of carboxylic acid 23. Alternatively, NaOMe was used to
form the corresponding methyl ester instead. Finally, product 23 was obtained as
the optically pure syn diastereomer with a chemical purity of 94%, as concluded
from high-performance liquid chromatography (HPLC).
In summary, a number of solution-phase protocols for the addition of boron
enolates to aldehydes have been successfully adapted to solid-phase synthesis.
These reactions proceed with similar eciency to the well-established solution-
phase reactions. However, a relatively small number of examples have been
reported to date, rendering an assessment of the scope of solid-supported boron
aldol reactions exceedingly dicult. Moreover, product isolation is routinely
achieved by aqueous work-up in combination with chromatographic methods. This
aspect could certainly hamper the application of such a protocol for automated
synthesis and the construction of multicomponent libraries still remains a chal-
lenging goal.
18.2.4
The Mukaiyama Aldol Reaction
The Mukaiyama protocol describes the Lewis acid-mediated reaction between an

aldehyde and a silyl enol ether or ketene silyl acetal to yield aldol adducts. Much
eort has been expended in adapting this reaction to the needs of combinatorial
chemistry. The research activities in this area can be divided into two major cate-
gories: (1) the solution-phase approach employing immobilized catalysts and (2)
the solid-phase strategy comprising soluble catalysts and polymer-bound aldehydes
and silyl enol ethers.
18.2.4.1 Solution-phase Protocols Using Polymer-bound Reagents

As outlined in Table 18.1, a variety of polymeric catalysts have been reported to
eect the Mukaiyama aldol reaction in solution. For instance, immobilized trityl
cation 24 can function as a Lewis acid to activate dimethylacetals or benzaldehyde
toward addition of a range of silyl enol ethers (Table 18.1, entries 1 and 2). The
corresponding aldol products were isolated after aqueous work-up and prepara-
tive TLC in good yields.
Tab. 18.1. Polymer-supported reagents promoting the Mukaiyama reaction.
Entry Silyl enol ether Electrophile Catalyst Product Conditions and comments Reference
1 5 examples; 7295% yield; all 16

products puried by TLC
R4 aromatic
and aliphatic
2 PhaCHO 24 6 examples; 7296% yield; 16

products isolated by aqueous
work-up and preparative TLC
3 CH2 O Yb-Amberlyst 15 Reaction carried out in THF/H2 O 17

4:1; 82% yield; product
chromatographed
4 R3aCHO Al-Montmorillonite 11 examples; 6897% yield; 18

R3 aromatic products isolated by ltration
and aliphatic and Kugelrohr destillation
5 R4aCHO Montmorillonite K10 15 examples; 6287% yield; 19

R4 aromatic reactions carried out in water;
and aliphatic all products chromatographed
18.2 Aldol Reactions
499
500
Entry Silyl enol ether Electrophile Catalyst Product Conditions and comments Reference
6 R1aCHO Montmorillonite K10 5 examples; 5289% yield; water 19

R1 aromatic as solvent
and aliphatic
7 R3aCHO Neutral Al2 O3 13 examples; 7090% yield; 20

R3 aromatic sonication necessary; reagents
and aliphatic used neat; all products
chromatographed
8 R4aCHO Al2 O3 aZnCl2 19 examples; 7090% yield; 21

R4 aromatic sonication essential; products
and aliphatic isolated by aqueous work-up
and chromatography
9 PhaCHO 1 example; reaction in water; 22

98% yield
18 Enolates and Related Species in Combinatorial and Solid-phase Synthesis
10 R3aCHO 10 examples; CH2 Cl2 at 78 C; 23

R3 aromatic 885% yield; pure products
obtained by ltration
11 PhaCHO 1 example stoichiometric amount 24
of BH3 was used; at 78 C:
28% yield; 90% ee; at 10 C:
70% yield; 69% ee; best
solvent: THF; product
chromatographed
12 PhaCHO 1 example 32% conversion after 25
36 h, 26% ee; 2 mol% polymer
used; catalyst removed by
precipitation from pentane
product obtained by ltration
14 PhaCHO 1 example; 5 mol% catalyst in 26

DMF at rt; 94% yield; 74% ee
18.2 Aldol Reactions
501
Commercially available ion-exchange resins such as amberlysts or montmor-

illonite were shown to promote the Mukaiyama reaction in aqueous solvent mix-
tures (Table 18.1, entries 36). The products were obtained after ltration and dis-
tillation or chromatography. Neutral Al2 O3 or ZnCl2 -doped Al2 O3 (Table 18.1,
entries 7 and 8) have also been described as catalysts for the aldol addition, how-
ever, tedious reaction conditions, including sonication, render these methods less
attractive for automation and library synthesis. A polymeric Sc(OTf )3 (25) was
introduced by Kobayashi et al. [27] which cleanly eected the synthesis of aldol
adducts, especially in aqueous solution.
A major advantage of polymer-supported reagents consists in simplication of
the work-up procedure. Under optimal conditions, the product isolation is reduced
to a ltration and washing process, thus avoiding tedious chromatography. In this
regard, Ley and coworkers reported the formation of a,b-unsaturated ketones via a
Mukaiyama protocol (Table 18.1, entry 10). Accordingly, the reaction of aromatic
aldehydes and silyl enol ethers was catalyzed by immobilized trimethylsilyltriate
(TMSOTf ) (26) and the desired aldol products were isolated in excellent yields with
high purities by mere ltration.
Finally, enantioselective protocols were elaborated for the Mukaiyama reaction
(Table 18.1, entries 1114). The authors describe the synthesis of polymeric Lewis
acids and their application in asymmetric aldol reactions. In general, only benzal-
dehyde was used as a model system for these studies and moderate levels of
enantioselectivities with variable yields were observed.
18.2.4.2 Solid-phase Protocols

Kobayashi et al. [27] reported the synthesis of immobilized thioketene silyl acetals
and their use in Mukaiyama reactions mediated by rare earth metal salts. Thus,
silylated propionate 27 was reacted with benzaldehyde in the presence of 20 mol%
Sc(OTf )3 to eect conversion to the corresponding aldol adduct (Scheme 18.8)
[27]. The latter was cleaved from the resin upon reduction with LiBH4 to yield diol
28, which was isolated after aqueous work-up and preparative TLC in 82% yield.
Moreover, heteroaromatic and aliphatic aldehydes as well as dimethylacetals work
equally well as substrates for this sequence (in total, 12 examples). However, if
unsubstituted trimethylsilyl ketene acetals derived from acetic acid were employed,
the aldol adducts were isolated in poor yields. Better results were obtained if the
TMS group was replaced by t-butyldimethylsilyl (TBDMS). Accordingly, TBDMS
ketene silyl acetal (29) reacted smoothly with aldehyde 30 under BF3 catalysis
(Scheme 18.9) [28]. The resulting aldol intermediate was subjected to a tetrabutyl-
Scheme 18.8. Mukaiyama reactions on solid support using Sc(Otf )3 as catalyst.

ammonium-uoride (TBAF) solution in THF buered by acetic acid to eect re-

moval of the TBDMS group. The deprotected alcohol induced cyclative cleavage to
give lactone 31, which served as a precursor for the synthesis of 2-deoxy-l-glucose.
Scheme 18.9. Synthesis of 2-deoxy-l-glucose precursor using a solid-phase Mukaiyama reaction.
The Mukaiyama protocol has also been successfully conducted with immobi-
lized aldehydes. As depicted in Scheme 18.10, cyclic TMS enolether 33 was reacted
with aldehyde 32 mediated by Yb(OTf )3 to yield a,b-unsaturated ketone 34 after
cleavage in 91% yield [29]. The salient features of this process include the use of a
MeCN/H2 O mixture as the solvent for this reaction. Since conventional poly-
styrene resins were not compatible with these hydrophilic conditions, a resin
based on a polar polyoxyethylene/polyoxypropylene matrix was introduced for this
reaction.
Scheme 18.10. Solid-phase Mukaiyama reactions using immobilized aldehydes.
In summary, a broad range of liquid- and solution-phase strategies are available

for the Mukaiyama aldol reaction in a parallel fashion. However, the limited com-
mercial availability of silyl enol ethers or ketene silyl acetals should be taken into
account for library design. Additionally, for both solution- and solid-phase strat-
egies, it has to be evaluated whether the work-up and purication protocols suit
the individual requirements for automation and library synthesis.
18.3
1,4-Addition of Enolates to Michael Acceptors
The 1,4-addition of enolates to Michael acceptors can be eected by base catalysis.

Consequently, method development for solution-phase parallel synthesis focused
on the use of immobilized bases to promote the addition step and simplify catalyst
separation and product isolation. As early as 1958, Bergmann and Corett reported
the use of basic exchange resins as catalysts for the Michael addition of enolates to
a,b-unsaturated carbonyls and acrylonitriles (Scheme 18.11) [30]. The reaction

conditions were elaborated for a variety of Michael donors such as ketones and
a-branched aldehydes (15 examples in total). To date, a range of novel polymeric
catalysts has been introduced. Of particular interest are immobilized quaternary
ammonium salts that proved to be eective for the addition of soft enolate nucleo-
philes to Michael acceptors [31]. Along these lines, asymmetric Michael additions
have been reported based on immobilized optically active alkaloids [32]. However,
applications of these methods for the synthesis of versatile libraries in solution
phase have not yet been demonstrated.
Scheme 18.11. Enolate additions to Michael acceptors mediated by a basic exchange resin.
More recently, Ley and Massi reported a tandem Michael protocol for solution-
phase combinatorial synthesis leading to the bicyclo[2.2.2]octanone skeleton 40
that was further elaborated in subsequent amination reactions [33]. The bicyclic
scaold was constructed upon reaction of 2 equiv. of conjugated dianions (39) with
tert-butyl acrylates (38). As outlined in Scheme 18.12, the reaction mixture was
quenched with Amberlyst 15 (path A) and a simple ltration process provided
pure endo products (40) (with R2 OEt or OiBu), whereas the crude product
(with R2 methyl) was contaminated by hydrolyzed 3-methyl-2-cyclohexen-1-one.
Therefore, this mixture was treated with polymer-supported thiophenol and diiso-
propylethylamine (DIPEA) to scavenge the excess of hydrolyzed starting material
(39c) followed by neutralization of ammonium salts using MP carbonate (path B).
After ltration the desired products (40) were nally isolated in pure form. These
carefully orchestrated reaction and work-up conditions formed the basis for a rapid
Scheme 18.12. Tandem Michael reactions using polymer-supported reagents.

synthesis of a larger library, since the reaction protocol can easily be automated
and avoids tedious chromatography.
The synthesis of the bicyclo[2.2.2]octanone framework via a tandem Michael re-
action has also been adapted to solid phase [34].
The 1,4-addition of enolates to Michael acceptors in solid-phase chemistry has
been examined by Domnguez et al. [35]. These authors investigated the addition
of resin-bound glycinates (41) to various a,b-unsaturated acceptors (Scheme 18.13).
The standard conditions for typical Michael acceptors such as acrylates, include 3
equiv. of Schwesinger-type base BEMP and 5 equiv. of acceptor 42 in NMP at room
temperature (rt) for 16 h to yield the Michael adducts 43 in high purity. For more
reactive acceptors (e.g. acrylonitriles) only 1.5 equiv. of 42 were used to avoid dou-
ble addition, while less reactive electrophiles 42 (e.g. substituted acrylates) required
additional base and acceptor 42 (each 10 equiv.). In total, 15 examples are given
composing a diverse set of enolate additions to a,b-unsaturated Michael acceptors.
Additionally, the resin-bound intermediates 42 were further modied on the poly-
mer, including deprotection of the imine, acylation of the amino group with qui-
naldic acid, and cleavage using triuoroacetic acid (TFA). The nal products were
obtained in good yields (6188%) and purities (7487%), indicating that the
Michael addition as depicted in Scheme 18.13 proceeded on the resin without
incident and with high eciency.
Scheme 18.13. 1,4-Addition of resin-bound glycinates.
Enantioselective Michael additions on solid phase utilizing immobilized Evans

oxazolidinone has also been reported; however, only one model system was de-
scribed, lacking options for diversity in library synthesis [14b].
In contrast, the addition of silyl enol ethers and silyl ketene acetals to a,b-
unsaturated carbonyls has attracted more attention in solid-phase chemistry.
As depicted in Scheme 18.14, solid-supported thiosilyl ketene acetal 44 reacted
smoothly with a,b-unsaturated ketones in the presence of 20 mol% Sc(OTf )3 to
yield the corresponding adducts on solid phase. The products were cleaved by the
Scheme 18.14. 1,4-Additions of silyl ketene acetals on solid phase.

action of NaOMe and were subjected to chromatography to yield 1,5-dicarbonyls

(46) in good to excellent yields (4891%, nine examples) [17a].
An alternative approach was based on resin-bound Michael acceptors which
were reacted with soluble silyl enol ethers. This concept was realized by Ellingboe
and coworkers, who reported the synthesis of immobilized 1,5-diketones employ-
ing polymeric enone 47 and 4 equiv. of TMS enol ether (48). The Michael addition
was eected by CsF in dimethyl sulfoxide (DMSO) to yield 49. The best results
were obtained if R1 was an aromatic or nonenolizable aliphatic residue, while R2
should preferably be aromatic or heteroaromatic. The target molecules 49 repre-
sented important intermediates for the construction of a pyridine library (Scheme
18.15) [36].
Scheme 18.15. Michael addition of silyl enol ether to polymer-

supported a,b-unsaturated ketones.
In summary, a diverse repertoire of combinatorial methods for Michael addi-

tions is available. The application of these methods to library synthesis has dem-
onstrated that 1,4-additions of enolates are useful transformations for creating
diversity with concomitant formation of CaC bonds.
18.4
Alkylation of Enolates
The alkylation of CaH acidic carbonyls represents a valuable transformation to

gain an additional diversity step for a given library. Thus, extensive eorts have been
devoted to optimizing alkylation protocols especially for solid-phase synthesis.
18.4.1
a-Alkylation of Carbonyl Compounds
The alkylation of ketone-derived enolates has been realized in solution-phase

chemistry employing solid-supported reagents. In this regard, Montanari and
coworkers reported the reaction of benzylbromide with benzylmethylketone using
an immobilized quaternary phosphonium salt as a phase transfer catalyst [37]. The
product could be obtained in excellent yield (95%) after ltration and extraction.
However, the scope of this reaction has not yet been extended to additional exam-
ples or library synthesis.
Silyl enol ethers have also been described to function as suitable substrates for
the alkylation process. Accordingly, 56 was reacted with prenylbromide (51) in the
presence of ZnCl2 -doped acidic alumina to give ketone 52 in 72% yield (Scheme
18.16) [38]. This reaction worked well with allylic, benzylic, and tertiary halides,
leading to the alkylated products after a simple extraction step with CH2 Cl2 in
good yields (6072%).
Scheme 18.16. Alkylation of silyl enol ethers using ZnCl2 -doped alumina.
The elegant studies of Ellman and coworkers toward the synthesis of arylacetic
acid libraries represented classical solid-phase synthesis [39, 40]. This concept
called for a reliable enolate-alkylation protocol that proved to be feasible for the
construction of a diverse set of target molecules (Scheme 18.17). Accordingly,
Kenner et al.s sulfonamide linker [41] was chosen to bind the aryl acetic acid pre-
cursor to solid phase to yield polymer 53. The resin was subsequently treated with
15 equiv. of LDA to generate the corresponding trianion, which was trapped by
quenching with an excess of alkylhalide to selectively yield the monoalkylated
product 54. This alkylation reaction works equally well for a range of halides, in-
cluding benzylic and aliphatic halides (ve examples). The intermediates 54 were
further manipulated to give a diverse set of arylacetic acids which were isolated in
excellent yields (88100%) and high purities after cleavage. From these results, it
could be concluded that the alkylation event further upstream in this sequence
proceeded smoothly and with high eciency.
Scheme 18.17. a-Alkylation on solid support using Kenners sulfonamide linker.
The alkylation of amide and ester enolates derived from deprotonation of the
corresponding a-acidic precursor has been reported in solid-phase synthesis using
LiHMDS [42] and KHMDS [43], respectively.
18.4.2
a- and g-Alkylation of 1,3-Dicarbonyl Compounds
The 1,3-dicarbonyl moiety represents a versatile template for the synthesis of het-
erocycle libraries, especially if alkylation protocols can provide an additional an-
chor for diversity. Accordingly, the development of methods which selectively tar-
get the mono- or dialkylation of a,b-dicarbonyls has attracted recent attention.
In this context, a variety of solution-phase strategies has been elaborated. Most
strategies are based on the use of polymer-supported bases such as Amberlite
anion-exchange resins [44] or immobilized uoride sources [45]. A typical example
is illustrated in Scheme 18.18 [46]. Celite coated with KF cleanly eected the
monoalkylation of acetylacetone to yield 56 in 96% yield. In contrast, the system
Al2 O3 aKF predominantly delivered the corresponding disubstituted product under
otherwise identical conditions.
Scheme 18.18. Alkylation of b-dicarbonyls using immobilized KF.
In general, the scope of the solution-phase strategies is limited to a small num-

ber of examples, and to the best of our knowledge no application in library syn-
thesis has been published to date.
In contrast, methods that were developed for the alkylation of 1,3-dicarbonyls on
solid support have had a signicant impact on library synthesis.
The optimal conditions for the a-alkylation of b-diketones and b-ketoesters
include the use of excess TBAF and alkyl halide in THF at rt (Table 18.2, entries
1 and 2). Under these conditions, the oxygen atoms in 57 and 58 are shielded by
complexation with the sterically demanding tetrabutylammonium counterion,
thereby preventing O-alkylations with concomitant nucleophilic activation toward
a-alkylation. Importantly, this protocol required strictly anhydrous conditions, oth-
erwise the yields were poor. This methodology has successfully been applied in the
synthesis of pyrazole and isoxazole libraries. However, a major drawback arises
from the incompatibility of this process with the presence of N-heteroaryl or furyl-
functionalities, and, furthermore, the use of benzylbromide as alkylating agent
gave only sluggish results. As an alternative to TBAF, other bases such as 1,8-
diazabicyclo[5.4.0]undecene-7 (DBU) were used to eect the desired a-alkylation of
CaH acidic b-dicarbonyl compounds (Table 18.2, entry 3). The latter example also
illustrates that electrophiles bound to solid phase can be eciently employed in
these alkylation reactions.
Similar processes involved the use of Merrield resin or the more reactive
(bromo-methyl)-polystyrene/divinylbenzene (PS/DVB) resin as polymeric electro-
phile to covalently bind 1,3-dicarbonyls. The requisite enolates were generated in
solution by utilizing NaH [51], Na in ethanol [52], or KOH under phase transfer
conditions as base [53]. Contributions in this eld mainly focused on the develop-
ment of new linkers and will not be discussed in detail.
A slightly dierent concept relies on the well-established Pd-catalyzed allylic
alkylation of CaH acidic 1,3-dicarbonyls with allylic acetates and carbonates. This
Tab. 18.2. Alkylation of resin-bound b-dicarbonyls.
Entry b-Dicarbonyl R 0 X/electrophile Product Conditions Comment Reference
1 R 0 aliphatic 20 equiv. TBAF 6 examples 47

X Br, I 36 equiv. R 0 X no g- or O-
THF, 3 h, rt alkylation
observed
2 R 0 allyl, Et, CH2 Z 10 equiv. TBAF 5 examples 48

R 0 0 benzyl 44 equiv. R 0 X conditions 49
X Br, I THF, 2 h, rt incompati-
ble with R
N-heteroaryl
or furyl
3 10% DBU/DMF 3 examples 50

20 C, 16 h
Z electron-withdrawing group.
18.4 Alkylation of Enolates
509
chemistry has been adapted to solid phase and it has been shown that resin-bound
malonates could be cleanly a-dialkylated by this method [54].
An important modication of 1,3-dicarbonyls is the g-alkylation. This has
been accomplished on solid phase commencing from resin-bound b-ketoester (63),
which was deprotonated with an excess of LDA to generate the corresponding di-
enolate (Scheme 18.19) [55].
Scheme 18.19. g-Alkylation of resin-bound b-ketoesters.
Subsequently, the excess LDA was drained away and 25 equiv. of alkyl halide
(R1X) were added to eect mono-g-alkylation. The resulting monoenolate could
serve as starting material for a second alkylation step. Thus, treatment of the eno-
late intermediate with n-BuLi regenerated the dianion which was quenched with
R2X to yield dialkylated products (64) in good yields. The g-alkylation worked well
with aliphatic, benzylic, and allylic halides (X Br or I; nine examples).
18.4.3
Stereoselective Alkylations of Enolates
The diastereoselective alkylation of enolates controlled by chiral auxiliaries is one

of the most reliable processes in asymmetric solution-phase chemistry. The trans-
fer of this concept to solid phase would oer manipulative convenience since ex-
cess reagents could be removed by simple washing procedures, and, nally, the
auxiliary could be recovered by ltration.
Table 18.3 summarizes the progress in this eld that has been achieved to date.
Lezno and coworkers [56, 57] reported the application of immobilized amino al-
cohols as chiral auxiliaries to eect stereoselective alkylation of ketones (Table 18.3,
entry 1).
The levels of asymmetric induction were found to be in the same range as in
solution. The stereoselective alkylation of resin-bound amide 67 was described by
Kurth and coworkers (Table 18.3, entry 2) [58, 59]. The alkylation occurred with
good diastereomeric excess and cleavage from the resin was accomplished by an
iodo-lactonization protocol. The adoption of the Meyers oxazoline methodology to
solid phase (Table 18.3, entry 3) was accompanied by drawbacks, mainly arising
from low chemical yields due to incomplete hydrolysis of the nal product. Allin
[61] and Burgess [62] independently reported their endeavors toward a solid-phase
version of an Evans oxazolidinone auxiliary (Table 18.3, entry 4). Both groups
could demonstrate that strong electrophilic halides react readily with pregenerated
oxazolidinone enolates to yield the corresponding alkylated products with medium
to high levels of optical purity. Cleavage from the resin was accomplished by hy-
Tab. 18.3. Stereoselective enolate alkylations on solid phase.
Entry Resin R 0X Product Conditions Remarks Reference
1 Mel, iPrl 1. LDA, THF, 0 C 2 examples; 56

2. R 0 X, rt 6095% ee; 57
3. Cleavage (H ) 8087% yield
2 Mel, allyl-l 1. 2 equiv. LDA, 0 C 2 examples; 58

2. 3 equiv. R 0 X, 0 C ! rt 24 h >87% de 59
3 BnCl 1. n-BuLi THF 1 example; 60

2. 650 equiv. BnCl 56% ee;
3. Cleavage (H2 SO4 , EtOH) 4345% yield
4 BnBr 1. 23 equiv. LDA, THF, 0 C 4 examples; 61

BnOCH2 Cl 2. 25 equiv. BnBr 7696% ee; 62
allyl-Br 3. LiOH or LiBH4 (cleavage) 2066% yield
18.4 Alkylation of Enolates
511
drolysis (LiOH) to liberate the carboxylic acid or, alternatively, by reduction (LiBH4 )
leading to the corresponding alcohols.
For all examples depicted in Table 18.3, convenient recycling of the chiral auxil-
iary has been demonstrated and the polymers could be reused for further applica-
tions. However, the majority of protocols required rather drastic reaction con-
ditions for the cleavage of the nal product, which implies tedious work-up and
purication procedures rendering this chemistry less amenable for automation.
Diastereoselective alkylations have also been successfully applied in the synthe-
sis of more complex molecules on solid support. For instance, Hanessian et al.
showed that polymeric ester 73 could be deprotonated by the action of KHMDS
followed by the addition of reactive electrophiles such as allylic iodides (three ex-
amples) to yield the corresponding a-alkylated product on solid support (Scheme
18.20) [63].
Scheme 18.20. Diastereoselective alkylation of esters on solid support.
This resin was treated with TFA to eect cleavage and lactonization leading to
enantiopure lactones (74) which were isolated in 75% yield (using two steps). The
stereochemical outcome of this reaction was rationalized via a Felkin-type transi-
tion state model.
In Chen and Jandas elegant studies toward a resin-supported synthesis of pros-
taglandin F2a , the a-alkylation of the central cyclopentanone core represented a key
step [64].
As depicted in Scheme 18.21, the requisite enolate was generated by lithiation of
the TMS enol ether (75) using excess methyl lithium. Upon addition of triate 76
the desired product 77 was isolated in pure form. For these studies a soluble non-
crosslinked polystyrene was selected as polymer support, since this choice guaran-
teed solution-like kinetics for each step of this sequence. Additionally, the soluble
Scheme 18.21. Enolate alkylation as a key step in solid-phase synthesis of prostaglandin F2a .
polymer allowed the monitoring of reaction intermediates by nuclear magnetic

resonance (NMR).
18.4.4
Alkylation of Protected Glycines
Suitably protected glycine esters are readily alkylated to yield protected a-amino
acids. Accordingly, this route oers convenient access to tailor-made unnatural
amino acids which are valuable templates in organic synthesis.
Benzophenone imines derived from glycine esters serve as the starting materials
of choice for the alkylation of glycine. This is the result of the convenient protocols
that are available for imine formation as well as the high selectivity of these imines
toward monoalkylation.
Polymer-supported reagents have been developed to produce the above-
mentioned transformation. For instance, Palacios et al. reported the use of immo-
bilized P-ylides as strong non-nucleophilic bases [65]. Moreover, a stereoselective
alkylation procedure has been elaborated previously [66].
As depicted in Scheme 18.22, protected glycine 78 was reacted with an excess of
reactive halides, such as benzyl or allylic bromide under phase transfer conditions
(seven examples). As chiral catalyst, the immobilized tertiary ammonium salt 80
was used, and for a range of products medium to good levels of induction were
observed. The products 79 were isolated after ltration and extraction into the or-
ganic layer without the need for chromatographic purication.
Scheme 18.22. Stereoselective alkylation of glycine imine 78.
The alkylation of glycine Schi bases has also been established in solid-phase
chemistry (Table 18.4). The most frequently reported conditions include the use of
Schwesinger-type bases in combination with an excess of alkyl halides in polar
solvents. For instance, imine 81 immobilized on Wang resin was treated with
BEMP and alkyl halide to selectively yield the monoalkylated products 82 (Table
18.4, entry 1). These products were further modied on solid support by cleavage
of the benzophenone imine followed by acylation of the amino group. Finally, the
resulting peptides were cleaved from the resin with TFA to deliver the corre-
Tab. 18.4. Alkylation of glycine derivatives on solid support.
Entry Polymer R 0X Product Conditions Remarks Reference

514
1 R 0 aliphtic, 210 equiv. R 0 X 10 examples; 67

benzylic 20 equiv. BEMP exclusively 68
X Br, I NMP, rt, 24 h mono-
alkylation
2 R 0 benzyl, allyl, MeCN, excess K2 CO3 5 examples; 69

aliphatic 1.5 equiv. R 0 X, products
X Br reux obtained by
precipitation
from Et2 O
3 R 0 benzylic, 2 equiv. BEMP 36 examples; for 70
allylic 3 equiv. R 0 X R iPr no
X Br complete
reaction
4 R 0 benzyl, 1. 5 equiv. BEMP, 17 examples; 71

allyl, aliphatic 5 equiv. R 0 X, DCM 61100%
X Br, I 1 equiv. yield; 51
18 Enolates and Related Species in Combinatorial and Solid-phase Synthesis
89% ee
2. NH2 OH
3. TFA
18.5 Claisen-type Condensations 515
sponding products in excellent yields (77100%). These results indicate that the
alkylation event at the outset of the sequence must have proceeded with high e-
ciency.
A related process was described for PEG-bound glycine 83 (Table 18.4, entry 2).
The authors showed that the PEG polymer not only simplied product isolation,
but also accelerated the reaction signicantly. This catalytic eect was attributed
to the close relationship of the PEG polymers with crown ethers, which are well
known to be benecial in phase transfer reactions.
Dialkylated amino acids were accessed starting from natural a-amino acids
which were transformed to aldimines of type 85, and subsequent alkylation with
halides (Table 18.4, entry 3) led to the expected products 86. This concept has been
validated for a broad range of amino acids (36 examples).
Finally, a stereoselective alkylation of protected glycine on polymer support has
been reported by ODonnell et al. (Table 18.4, entry 4) [71]. Optimal results were
obtained if Coreys quaternary ammonium catalyst 89 was used as the source of
chirality. The immobilized intermediates were deprotected (NH4 OH) and cleaved
from the resin (TFA) to yield the free amino acids (88) in good chemical and opti-
cal purity.
18.5
Claisen-type Condensations
The reactions between enolates and esters deliver 1,3-dicarbonyl compounds

which are valuable intermediates in heterocyclic chemistry. An early study by Co-
hen et al. demonstrated that this kind of transformation could be realized utilizing
polymer reagents. Accordingly, benzophenone was deprotonated with immobilized
trityl lithium (91) and the resulting enolate was trapped with polymeric o-nitro-
phenyl benzoate (90) to yield b-diketone (92) with a 96% yield after ltration
(Scheme 18.23) [72]. The yield by far exceeded the results obtained for the corre-
sponding reaction in solution phase (a 50%). This result is due to the fact that
immobilized trityl lithium could be used in great excess to drive the enolate addition
to completion. More importantly, the presence of the alkyl lithium base proved to
be compatible with the o-nitrophenyl benzoate (90) since both reactive sites were
shielded by a polymeric matrix, thus avoiding deleterious interactions. This wolf
lamb strategy has clearly shown that polymer reagents not only simplify work-up
but can also provide an innovative eect in optimizing reaction conditions.
Scheme 18.23. Wolflamb reaction for the synthesis of b-ketoesters.

The synthesis of b-diketones has also been reported in solid-phase chemistry. In

a standard protocol NaH is used as the base of choice to generate the requisite ke-
tone enolate, which reacts with an excess of ester to yield the desired products. A
typical example is illustrated in Scheme 18.24. Here, methylketone (93) was at-
tached to the polymer by a Rink amide linker which proved stable toward the
strongly basic reaction conditions. Upon reaction with aromatic esters in the pres-
ence of NaH, the b-diketones (95) were obtained in excellent yields [48, 49, 73].
However, the scope of the reaction was limited to a narrow set of aromatic and
heteroaromatic esters.
Scheme 18.24. 1,3-b-Diketone synthesis on solid support.
A more recent contribution in this eld reported a novel selenium linker which
was used to immobilize methylketone (96). Enolate generation was eected by
LiHMDS followed by addition of acylcyanides as electrophiles to produce 1,3-
diketones (97) in good yields (Scheme 18.25) [74]. Alternatively, the use of Weinreb
amides [75] or b-ketoester [76] as electrophiles in this Claisen-type reaction have
been described.
Scheme 18.25. Solid-phase synthesis of 1,3-diketones using acylcyanides.
In conclusion, the construction of b-dicarbonyls, especially in solid-phase syn-

thesis, is a well-established process. However, the scope of this reaction is primar-
ily restricted to nonenolizable electrophiles such as aromatic esters, acylcyanides,
or Weinreb amides.
18.6
Dieckmann Condensations
The Dieckmann reaction as an intramolecular version of the Claisen condensation

oers a valuable means of construction of ring systems with the concomitant for-
18.6 Dieckmann Condensations 517
mation of a CaC bond. If nonsymmetric dicarbonyl precursors are used in this

reaction, ne-tuning of the conditions is often needed to selectively obtain the de-
sired product. For instance, amino acid derivatives (98) have been used in solution-
phase chemistry as open-chain cyclization precursors. Chemoselective deproto-
nation of the CaH acidic amide was achieved by preferably allowing electron
withdrawing groups for R3 (Scheme 18.26) [77, 78]. Amberlyst A26 (OH form)
was selected as base for this reaction and the resulting tetramic acids (99) were
rst obtained as salts immobilized on the basic exchange resin. Subsequently, the
resin was washed to remove byproducts and excess reagents followed by incuba-
tion with TFA to liberate the nal products (99) as free acids. In total, this concept
of solid-phase resin capture delivered a range of tetramic acids in good yields and
high purities (ten examples), including a convenient work-up protocol which
should be suitable for automation.
Scheme 18.26. Parallel synthesis of tetramic acids in solution phase.
Following the seminal contributions of Rapoport in the eld of solid-phase-

supported unidirectional Dieckmann reactions [79], the vast majority of more recent
communications have dealt with the solid-phase synthesis of tetramic acids. Ac-
cordingly, OH-functionalized polymers such as Wang resin loaded with amino acid
derivatives were exposed to basic reaction conditions, as outlined in Scheme 18.27.
A variety of bases were employed for this reaction, including NaOEt [80], KOH
[81], DIPEA [82], or Bu 4 NOH [83]. The cyclization occurred as expected with con-
comitant release of the anionic form of the tetramic acid into solution. The free
acid (101) was nally isolated by treatment with a strong acid or acidic ion-
exchange resin. More importantly, the cyclative cleavage strategy employed in
these examples guaranteed high purities for the products since the latter were only
released into solution if the desired cyclization event took place rst.
Scheme 18.27. Solid-phase synthesis of tetramic acids.

Owing to the convenient reaction protocols both the liquid- and solid-phase syn-
thesis of tetramic acids appears to be an attractive tool for multicomponent library
synthesis.
18.7
Knoevenagel Condensations
The condensation of aldehydes with carbonyl compounds bearing an additional

electron withdrawing group (e.g. b-ketoesters or malonates) is usually designated
as a Knoevenagel condensation. The resulting alkylidene products serve as ideal
precursors for the synthesis of a range of heterocycles such as dihydropyrimidines,
pyrimidines, pyrimidinones, dihydropyridines, pyrazoles, dihydropyranes, or cou-
marines. Libraries prepared in solution phase as well as on solid phase with a
broad range of templates underscore the value of this reaction for combinatorial
purposes.
Owing to the high acidity of the activated carbonyl moiety, weak bases such as
ammonia, ammonium salts, primary or secondary amines, and salts thereof suf-
ce to promote the condensation. Hence, polymer-supported Bronsted bases have
been applied in solution-phase Knoevenagel reactions. A typical example is shown
in Scheme 18.28. A range of malonates, malonitriles, cyanoacetates, and oxoesters
(102) were condensed with nonenolizable aromatic aldehydes in the presence of
polymeric amine (103) under continuous ow conditions. The alkylidene products
(104) were isolated after removal of the solvent and purication by chromatogra-
phy or recrystallization in acceptable to excellent yields (2998%) [84]. Other poly-
meric reagents reported for the Knoevenagel process include the use of ion-
exchange resins [85], immobilized tetraalkylammonium hydroxides [86], Al2 O3
[87], Al2 O3 aKF [88], or molecular sieves [89]. However, these solution-phase
methods have not yet been applied in library synthesis.
Scheme 18.28. Knoevenagel condensations using polymer reagents.
In contrast, solid-phase protocols have been far more popular for Knoevenagel
reactions since the condensation products are often important intermediates in
multistep sequences which are best supported by solid-phase chemistry. Depend-
ing on the nature of the linker, the CaH acidity of the substrate, and the structure
of the aldehyde, dierent conditions have been employed. Piperidine or piperidine
acetate have been successfully used as catalysts for the Knoevenagel reaction and
18.7 Knoevenagel Condensations 519
seem to be the methods of choice. For instance, Gallop, Bhandari, and coworkers
reported that malonate (105) immobilized on TentaGel resin cleanly reacts with
aromatic aldehydes (eight examples) under the conditions depicted in Scheme
18.29 [90, 91]. The Knoevenagel products (106) were further transformed to pyrro-
lopyridines utilizing a Hantzsch protocol for construction of the pyridine hetero-
cycle. The nal products in this sequence were obtained in decent yields (2050%)
with excellent purities (> 90%), reecting almost quantitative conversion for each
step of the synthesis. Additionally, this methodology was extended to a library syn-
thesis of 4800 compounds, thereby demonstrating the broad scope of the Knoeve-
nagel reaction. Instead of TMOF, molecular sieves were also used to remove water
from the reaction mixture [92]. Under similar reaction conditions, salicylaldehydes
were eectively condensed with resin-bound malonates to yield the coumarin
skeleton on solid support [93].
Scheme 18.29. Knoevenagel condensations on solid support.
If the basic piperidine is buered by acetic acid, even milder conditions for the
Knoevenagel condensation are obtained. As illustrated in Scheme 18.30, malonates
(107) loaded onto Wang resin were reacted with a range of aromatic and aliphatic
aldehydes to yield the corresponding Knoevenagel products on solid support. After
cleavage, the carboxylic acids (108) were obtained as mixtures of E and Z isomers
in good yields (4598%) and high purities (conversion 9298%). This protocol was
further applied in a library synthesis comprising 96 products of type 108 and the
majority of products were obtained with purities > 75% as determined by HPLC
[94]. Moreover, this procedure was especially suited for the use of enolizable ali-
phatic aldehydes in the Knoevenagel condensation on solid support [95]. In this
context, it was also reported that ethylenediamine diacetate (EDDA) very eectively
catalyzed the condensation of both aromatic and aliphatic aldehydes with resin-
bound malonates [5c].
Scheme 18.30. Knoevenagel condensations on solid support.

18.8
Addition of Enolates to Imines
18.8.1
Synthesis of b-Amino Esters and Alcohols via Enolate Addition to Imines
Mannich-type reactions include the addition of enolates to imines and deliver val-
uable b-amino acid derivatives. Mild reaction conditions were reported employing
silyl enol ether or ketene silyl acetals which add to preformed or in situ-gen-
erated aldimines in the presence of catalytic amounts of Lewis acids. In this re-
gard, a variety of polymeric rare earth metal salts were reported to promote the
aforementioned process eciently [96]. For instance, Kobayashi et al. introduced a
microencapsulated scandium triate which exhibited high catalytic activity in the
Mannich reaction [22a]. As outlined in Scheme 18.31, the imino-aldol reaction be-
tween aldimine 109 and propiophenone-derived silyl enol ether 110 proceeded
smoothly to produce b-aminoketone 111 in excellent yield. Furthermore, the cata-
lyst was recycled and reused up to seven times in the Mannich process without
there being any deleterious eects on the yield. These reactions work best with al-
dimines originating from aromatic or heteroaromatic aldehydes.
Scheme 18.31. Mannich-type reactions promoted by microencapsulated Sc(Otf )3 .
Complementary, polymer-supported catalysts such as p-acidic dicyanoketeneace-

tals [97] or optically active palladiumBINAP complexes [26] have also been used
to eect the addition of silyl enol ethers to imines.
The use of polymeric catalysts for the Mannich reaction has dramatically sim-
plied the isolation and recycling of the catalysts by mere ltration and washing
operations, however, the isolation of the reaction products, such as 111, was rou-
tinely achieved by aqueous work-up procedures followed by chromatography.
Therefore, the application of this methodology to the synthesis of libraries would
require the work-up and purication protocols to be adapted to automation.
An interesting multicomponent Mannich reaction has been recently reported
by Prabhakaran and Iqbal (Scheme 18.32) [98]. Ketones or b-ketoesters (112)
were condensed with aromatic aldehydes (113) and acetylchloride in acetonitrile
in the presence of a polyaniline-supported cobalt catalyst. The resulting N-acetyl-
b-amino acid derivatives (114) (eight examples given) were isolated by a simple
work-up protocol comprising a ltration and a washing step to deliver 114 in
acceptable yields (4668%) and excellent HPLC purities (95100%). Here, the anti-
18.8 Addition of Enolates to Imines 521
congurated products were formed predominantly. The mechanism of this reac-

tion presumably involves the addition of in situ-generated cobalt enolates to a cati-
onic iminium species [99].
Scheme 18.32. Multicomponent Mannich reactions using a polymer-supported cobalt catalyst.
Mannich reactions have also been established in solid-phase chemistry. Kobaya-

shi et al. introduced resin-bound thiosilyl ketene acetal 115 and elaborated an e-
cient Mannich protocol on solid support (Scheme 18.33) [100]. Thus, reaction of
115 with imines 116 in the presence of 10 mol% Sc(OTf )3 delivered the corre-
sponding b-amino thioesters which were subsequently cleaved from the resin
upon reduction with LiBH4 to yield the b-amino alcohols 117 in good yields (42
78%; 19 examples) after aqueous work-up and preparative TLC. A broad range of
substrates were used in this reaction with R1 being hydrogen, methyl, or benzy-
loxy, and R2 and R3 preferably being aromatic or heteroaromatic groups. This re-
action can also be conducted as a one-pot, three-component condensation starting
from amine, aldehyde, and silyl enol ether comprising in situ generation of the
requisite aldimine [101]. Furthermore, the scope of this methodology has been ex-
tended by using the Sc(OTf )3 -mediated Mannich reaction as a key step in the
solid-phase synthesis of amino sugar derivatives [28].
Scheme 18.33. Mannich reactions on solid support to yield b-amino alcohols.
The solid-phase synthesis of novel a-amino acid derivatives (119) has also been
elaborated for soluble silyl enol ethers in combination with immobilized imines
[102]. A recent report described the use of polymer-supported imino acetates (118)
as suitable substrates for the Mannich reaction (Scheme 18.34) [103]. Accordingly,
the Sc(OTf )3 -catalyzed process delivered a set of unnatural aspartic acid derivatives
(119) which were cleaved from the resin by transesterication using NaOMe.
Under similar conditions polymer-supported acylhydrazones reacted with ketene
silyl acetals and the corresponding adducts underwent cyclative cleavage upon
treatment with NaOMe to yield substituted pyrazolones [104].
Scheme 18.34. Solid-phase synthesis of aspartic acid derivatives.
18.8.2
Solid-phase Synthesis of b-Lactams via Enolate Additions to Imines
The synthesis of b-lactams is conveniently achieved by [2 2] cycloaddition of

ketenes with imines [105], or, alternatively, by addition of enolates to imines with
subsequent ring closure [106]. The latter strategy has been adapted to solid-phase
synthesis by Enders and coworkers, who utilized the T1-triazene linker system
[107]. The resin was loaded with alanine methylester to give 120 (Scheme 18.35)
[108]. The precursor 120 was then transferred into its dianion using an excess of
LiHMDS and subsequently treated with imines derived from aniline and aromatic
aldehydes. Traceless cleavage of the resulting b-lactams was accomplished in a two-
step process including formation of the diazonium salt followed by decomposition
of the diazonium intermediate to yield the target molecules 121. With R aryl or
heteroaryl, a range of products (eight examples) was obtained in good yields (53
71%) with high purities (8898%) and excellent diastereoselectivity in favor of the
trans-congurated product (90 to b96% de).
Scheme 18.35. Solid-phase synthesis of b-lactams employing a traceless linker strategy.
A related process was reported involving in situ-generated Ti enolates and imines

immobilized on soluble PEG resins [109].
18.9
Nitro-aldol Reactions
The nitro-aldol reaction (Henry reaction) represents a useful tool for the introduc-
tion of a nitrogen functionality onto an organic scaold. The base-promoted addi-
18.9 Nitro-aldol Reactions 523
tion of CaH acidic nitroalkanes to aldehydes has been realized in solution phase
by utilizing polymer-supported reagents. For instance, immobilized 1,5,7-triaza-
bizyclo[4.4.0]dec-1-ene (TBD) has been reported to catalyze the aforementioned
process [110]. The use of polymeric TBD dramatically simplied work-up, and
product isolation was reduced to a simple ltration process. However, only a lim-
ited number of examples were reported that lacked data on experimental details
and product purity.
Other polymeric bases which catalyze the Henry reaction are polymeric ylides
[65], ion-exchange resins such as Amberlyst A21 [111], or basic La 3 polymers
[112]. Again, the scope of these methods is rather limited to a small set of exam-
ples, and an assessment regarding the suitability of these reagents for library syn-
thesis is therefore exceedingly dicult.
Polymer-supported reagents were also successfully used to promote the 1,4-
addition of nitroalkanes to Michael acceptors. Accordingly, KF on basic alumina
was found to catalyze the addition of CaH acidic nitro-compounds to a range of
a,b-unsaturated ketones and esters (Scheme 18.36) [113, 114]. The reactions were
driven to completion by using a large excess of the nitroalkane. Finally, the adducts
124 were isolated after ltration and evaporation of the excess nitroalkane in good
yields (39100% for 14 examples). The best results were obtained if the Michael
acceptors were unsubstituted in the b-position.
Scheme 18.36. Michael addition of nitroalkanes mediated by KF on alumina.
Other groups introduced basic alumina [115] or Amberlyst ion-exchange resins

[116] as catalysts for the Michael addition of nitroalkanes.
In solid-phase chemistry the addition of nitromethane to immobilized aromatic
aldehydes belongs to a standard procedure.
A typical example of the Henry reaction on solid support is illustrated in
Scheme 18.37 [117]. The isoxazole aldehyde 125 loaded onto the polystyrene resin
via a Cl-trityl linker was treated with a large excess of nitromethane and triethyl-
amine in a THF/EtOH solvent mixture. The addition proceeded at rt within 3 h
Scheme 18.37. Henry reaction on solid support.

and the resulting Henry adduct was cleaved from the resin to produce phenol
126 with a 96% yield and with 95% purity. Practically identical conditions were re-
ported for other polymeric substrates [118].
18.10
The BaylisHillman Reaction
The BaylisHillman reaction comprises the addition of aldehydes to activated al-

kenes mediated by tertiary amines such as 1,4-diazabicyclo[2.2.2]octane (DABCO)
or 3-quinuclidinol (3-QDL). The resulting allylic alcohols display a dense array of
functional groups and thereby serve as versatile templates for further modica-
tions.
Several protocols for the BaylisHillman reaction on solid phase have been de-
scribed. In a typical example reported by Jung and coworkers, acryloin-loaded Cl-
trityl resin was treated with a large excess of p-triuoromethylbenzaldehyde and 10
equiv. DABCO in a 1:1 mixture of DMSO/CHCl3 (Scheme 18.38) [119].
Scheme 18.38. BaylisHillman reaction on solid support.
The mixture was maintained at rt for 2 days and the procedure was repeated to
achieve complete conversion. After acidolysis with TFA, the BaylisHillman prod-
uct 128 was obtained with a crude purity of 97% and with an 85% yield after prepa-
rative HPLC. Similar protocols have been disclosed by other groups. Kunzer and
coworkers used dimethylformamide (DMF) as solvent and 3-QDL as base to pro-
mote the BaylisHillman addition [120], while Kulkarni and Ganesan reported
that a 3:1 DMF/MeCN solvent mixture in combination with DABCO and catalytic
amounts of La(OTf )3 were benecial to the process [121]. The major limitations
for the solid-phase versions of the BaylisHillman transformation arise from in-
complete reactions and a narrow range of aldehydes that are able to react smoothly
under the aforementioned conditions. Large excesses of the reagents or prolonged
reaction times with repeated incubations did not dramatically improve the situa-
tion.
Preferably, aromatic aldehydes with electron-withdrawing substituents work well
in these reactions while less reactive aromatic or aliphatic aldehydes gave sluggish
reactions. A slightly dierent protocol for the polymer-supported BaylisHillman
reaction was described by Reiser and coworkers [122]. Herein, acrolein immobi-
lized on a soluble PEG resin via an ester linkage was reacted with a range of alde-
18.11 Miscellaneous 525
hydes using ethanol as solvent and 3-QDL as base. The reaction with a diverse
set of aldehydes (six examples), including aliphatic aldehydes, could be driven to
completion since the soluble polymer guaranteed solution-like kinetics. However,
it was also reported that the ester linkage to the PEG polymer was partly cleaved
under the reaction conditions, leading to a lower yield of the desired product.
In conclusion, the BaylisHillman reaction on solid phase is an established pro-
cess; however, owing to the inherent limitations, a careful selection of the poly-
meric linker as well as the aldehyde set used in this reaction should be addressed
prior to multicomponent library synthesis.
Finally, an interesting three-component version of the BaylisHillman reaction
was reported on solid support. Thus, resin 127 was treated with aldehydes and
sulfonamides in the presence of DABCO in dioxane at 70 C. This cocktail gave
rise to the formation of functionalized sulfonamides 129 which represent useful
intermediates for further manipulations (Scheme 18.39) [123]. The versatility of
this chemistry has been shown for aromatic and heteroaromatic aldehydes in
combination with arylsulfonamides. The best results were obtained if electron-
decient aldehydes were employed in this process.
Scheme 18.39. Three-component BaylisHillman reaction on solid support.
18.11
Miscellaneous
A solid-phase version of the IrelandClaisen rearrangement has been reported. A

key feature of this concept was the formation of silyl ketene acetals on solid sup-
port employing polymeric silyl triate 132 (Scheme 18.40) [124]. The resulting
enolate intermediate (133) cleanly underwent an IrelandClaisen rearrangement
Scheme 18.40. IrelandClaisen rearrangement on solid support.

in THF at 50 C to yield the corresponding silyl esters which were cleaved from the
resin by transesterication. The reaction worked well for a range of allylic esters,
however, esters derived from acetic acid failed to give the desired rearrangement
product (134). This result is presumably due to a large extent to C-silylation in
the enolizationimmobilization event.
An elegant approach to substituted phenols via a cyclative cleavage strategy was
reported by Katritzky and coworkers (Scheme 18.41) [125]. Merrield resin loaded
with 3-hydroxypyridine was alkylated with bromoacetone to give pyridinium salt
(135). The latter was reacted with a,b-unsaturated ketones under basic conditions
to yield Robinson anellation product 136, which aromatized with concomitant
cleavage from the resin. A range of chalcones (12 examples) were successfully uti-
lized in this reaction and the phenols 137 were isolated after aqueous work-up and
column chromatography in good yields with high purities.
Scheme 18.41. Solid-phase synthesis of substituted phenols.
Another example demonstrates that functionalized organometallics can con-

veniently be handled under anhydrous conditions in solid-phase organic synthesis
(Scheme 18.42) [126]. The amino acid derivative 138 loaded on Wang resin was
treated with an excess of LDA under a nitrogen atmosphere to generate the corre-
sponding lithium enolate. Subsequent transmetalation with ZnBr2 resulted in the
formation of the Zn enolate, which underwent intramolecular carbozincation to
yield organozinc intermediate 139. The latter was quenched with reactive electro-
philes (I2 or H ) and cleavage from the resin led to the formation of proline de-
rivatives (140). As concluded from liquid chromatography/mass spectrometry (LC/
MS), the desired products have been formed virtually quantitatively (no yields were
reported) as single diastereomers.
Scheme 18.42. Solid-phase synthesis of substituted proline derivatives.

References 527
This carbozincation protocol (depicted in Scheme 18.42) oers an innovative

approach to substituted proline derivatives; however, the scope of this process is
limited with respect to diversication. Thus, the extension of this methodology to a
broader range of substrates as well as the adaptation of the reaction protocol to
automation clearly remains a challenge.
References
1 a) For solid phase, see: R. E. Gerlach, Angew. Chem. Int. Ed. 2000,
Sammelson, M. J. Kurth, Chem. Rev. 112, 34533457.
2001, 101, 137202; b) for polymer- 11 M. Reggelin, V. Brenig, Tetrahedron
supported reagents, see: S. V. Ley, Lett. 1996, 37, 68516852.
I. R. Baxendale, R. N. Bream, P. S. 12 M. Reggelin, V. Brenig, R.
Jackson, A. G. Leach, D. A. Welcker, Tetrahedron Lett. 1998, 39,
Longbottom, M. Nesi, J. S. Scott, 48014804.
R. I. Storer, S. Taylor, J. Chem. Soc., 13 M. Reggelin, V. Brenig, C. Zur,
Perkin Trnas. 1, 2000, 38154195. Org. Lett. 2000, 2, 531533.
2 T. Ruhland, H. Kunzer, Tetrahedron 14 a) A. V. Purandare, S. Natarajan,
Lett. 1996, 37, 27572760. Tetrahedron Lett. 1997, 38, 87778780;
3 M. J. Kurth, L. A. Ahlberg Randall, b) C. W. Phoon, C. Abell, Tetrahedon
C. Chen, C. Melander, R. B. Miller, Lett. 1998, 39, 26552658.
J. Org. Chem. 1994, 59, 5862. 15 H. Danda, M. M. Hansen, C. H.
4 a) K. C. Nicolaou, D. Vourloumis, Heatchcock, J. Org. Chem. 1990, 55,
T. Li, J. Pastor, N. Winssinger, Y. 173181.
He, S. Ninkovic, F. Sarabia, H. 16 T. Mukaiyama, H. Iwakiri, Chem.
Vallberg, F. Roschangar, N. P. Lett. 1985, 13631366.
King, M. R. V. Finlay, P. 17 a) S. Kobayashi, R. Akiyama, T.
Giannakakou, P. Verdier-Pinard, E. Furuta, M. Moriwaki, Molecules
Hamel, Angew. Chem. 1997, 109, Online 1998, 2, 3539; b) L. Yu, D.
21812187; b) K. C. Nicolaou, N. Chen, J. Li, P. G. Wang, J. Org.
Winssinger, J. Pastor, S. Ninkovic, Chem. 1997, 62, 35753581.
F. Sarabia, Y. He, D. Vourloumis, Z. 18 M. Kawai, M. Onaka, Y. Izumi, Bull.
Yang, T. Li, P. Giannakakou, E. Chem. Soc. Jpn. 1988, 61, 12371245.
Hamel, Nature, 1997, 387, 268272. 19 T. P. Loh, X.-R. Li, Tetrahedron 1999,
5 a) S. P. Hollinshead, Tetrahedron 55, 1078910802.
Lett. 1996, 37, 91579160; b) S. P. 20 B. C. Ranu, R. Chakraborty,
Hollinshead, WO 98/08813; c) for Tetrahedron 1993, 49, 53335338.
additional examples, see: P. Grosche, 21 B. C. Ranu, M. Saha, S. Bhar,
A. Holtzel, T. B. Walk, A. W. Synthetic Commun. 1997, 27, 3065
Trautwein, G. Jung, Synthesis 1999, 3077.
11, 19611970. 22 a) S. Kobayashi, S. Nagayama, J. Am.
6 C. Chiu, T. Tang, J. W. Ellingboe, J. Chem. Soc. 1998, 120, 29852986; b) S.
Comb. Chem. 1999, 1, 7377. Kobayashi, S. Nagayama, J. Am.
7 A. L. Marzinzik, WO 98/155532. Chem. Soc. 1998, 120, 4554; c) S.
8 A. L. Marzinzik, E. R. Felder, J. Org. Nagayama S. Kobayashi, Angew.
Chem. 1998, 63, 723727. Chem. Int. Ed. 2000, 39, 567569.
9 C. Gennari, S. Ceccarelli, U. 23 F. Haunert, M. H. Bolli, B. Hinzen,
Piarulli, K. Aboutayab, M. Donghi, S. V. Ley, J. Chem. Soc., Perkin Trans. 1
I. Paterson, Tetrahedron 1998, 54, 1998, 22352237.
1499915016. 24 S. Kiyooka, Y. Kido, Y. Kaneko,
10 I. Paterson, M. Donghi, K. Tetrahedron Lett. 1994, 35, 52435246.
25 A. Mandoli, D. Pini, S. Orlandi, F. P. Wright, Mol. Diversity 1996, 2,

Mazzini, P. Salvadori, Tetrahedron 197206.
Asymmetry 1998, 9, 14791482. 41 G. W. Kenner, J. R. McDermott, R.
26 A. Fujii, M. Sodeoka, Tetrahedron C. Sheppard, J. Chem. Soc., Chem.
Lett. 1999, 40, 80118014. Commun. 1971, 636637.
27 S. Kobayashi, I. Hachiya, M. 42 Z. Zhu, B. Mckittrick, Tetrahedron
Yasuda, Tetrahedron Lett. 1996, 37, Lett. 1998, 39, 7479.
55695572. 43 S. Hanessian, F. Xie, Tetrahedron Lett.
28 S. Kobayashi, T. Wakabayashi, M. 1998, 39, 737740.
Yasuda, J. Org. Chem. 1998, 63, 4868 44 a) G. Gelbard, Synthesis 1977, 113
4869. 116; b) K. Shimo, S. Wakamatsu, J.
29 A. Graven, M. Grtli, M. Meldal, J. Org. Chem. 1963, 28, 504506.
Chem. Soc., Perkin Trans. 1, 2000, 955 45 J. M. Miller, K.-H. So, J. Chem. Soc.,
962. Chem. Comm. 1978, 466467.
30 E. D. Bergmann, R. Corett, J. Org. 46 J. Yamawaki, T. Ando, Chem Lett.
Chem. 1958, 23, 15071510. 1979, 755758.
31 I. Rodriguez, S. Iborra, A. Corma, 47 L. T. Tietze, A. Steinmetz, F.
F. Rey, J. Jorda, Chem. Commun. Balkenhohl, Bioorg. Med. Chem. Lett.
1999, 593594. 1997, 7, 13031306.
32 a) P. Hodge, E. Khoshdel, J. 48 A. L. Marzinik, E. R. Felder,
Waterhouse, J. Chem. Soc., Perkin Tetrahedron Lett. 1996, 37, 10031006.
Trans I, 1983, 22052209; b) M. 49 A. L. Marzinik, E. R. Felder,
Inagaki, J. Hiratake, Y. Yamamoto, Molecules, 1997, 2, 1730.
J. Oda, Bull. Chem. Soc. Jpn., 1987, 60, 50 H. Stephensen, F. Zaragoza,
41214126; c) R. Alvarez, M. A. Tetrahedron Lett. 1999, 40, 57995802.
Hourdin, C. Cave, J. dAngelo, P. 51 a) O. W. Gooding, S. Baudart, T. L.
Chaminade, Tetrahedron Lett. 1999, Deegan, K. Heisler, J. W. Labadie,
40, 70917094. W. S. Newcomb, J. A. Porco Jr, P.
33 S. V. Ley, A. Massi, J. Comb. Chem. van Eikeren, J. Comb. Chem. 1999, 1,
2000, 2, 104107. 113122; b) T. Redemann, H.
34 a) S. V. Ley, D. M. Mynett, W.-J. Bandel, G. Jung, Mol. Diversity 1998,
Koot, Synlett, 1995, 10171020; 4, 191197.
b) H.-J. Gutke, D. Spitzner, 52 E. T. M. Wolters, G. I. Tesser, R. J.
Tetrahedron, 1999, 55, 3931 F. Nivard, J. Org. Chem. 1974, 39,
3936. 33883392.
35 E. Dominguez, M. J. ODonnell, W. 53 J. M. J. Frechet, M. D. de Smet, M. J.
L. Scott, Tetrahedron Lett. 1998, 39, Farrall, J. Org. Chem. 1979, 44,
21672170. 17741778.
36 C. Chiu, Z. Tang, J. W. Ellingboe, J. 54 L. F. Tietze, T. Hippe, A. Steinmetz,
Comb. Chem. 1999, 1, 7377. Chem. Commun. 1998, 793794.
37 H. Molinari, F. Montanari, S. 55 L. F. Tietze, A. Steinmetz, Synlett
Quici, P. Tundo, J. Am. Chem. Soc. 1996, 667668.
1979, 101, 39203927. 56 P. M. Worster, C. R. McArthur, C.
38 G. L. Kad, V. Singh, A. Khurana, S. C. Leznoff, Angew. Chem. 1979, 91,
Chaudhary, J. Singh, Synth. 255.
Commun. 1999, 29, 34393442. 57 C. R. McArthur, P. M. Worster,
39 a) B. J. Backes, J. A. Ellman, J. Am. J.-L. Jiang, C. C. Leznoff, Can. J.
Chem. Soc. 1994, 116, 1117111172; b) Chem. 1982, 60, 18371841.
J. A. Ellman, Acc. Chem. Res. 1996, 58 H.-S. Moon, N. E. Schore, M. J.
29, 132143. Kurth, J. Org. Chem. 1992, 57, 6088
40 J. A. Porco Jr, T. Geegan, W. 6089.
Devonport, O. W. Gooding, K. 59 H.-S. Moon, N. E. Schore, M. J.
Heisler, J. W. Labadie, B. Newcomb, Kurth, Tetrahedron Lett. 1994, 35,
C. Nguyen, P. van Eikeren, J. Wong, 89158918.
References 529
60 A. R. Colwell, L. R. Duckwall, R. quinolin-2-(1H)-ones, see: B. A.

Brooks, S. P. McManus, J. Org. Kulkarni, A. Ganesan, Chem.
Chem. 1981, 46, 30973102. Commun. 1998, 785786.
61 S. M. Allin, S. Shuttelworth, 79 a) J. I. Crowley, H. Rapoport, J. Am.
Tetrahedron Lett. 1996, 37, 80238026. Chem. Soc. 1970, 92, 63636365; b) J.
62 K. Burgess, D. Lim, Chem. Commun. I. Crowley, H. Rapoport, J. Org.
1997, 785786. Chem. 1980, 45, 32153227.
63 S. Hanessian, J. Ma, W. Wang, 80 J. Matthews, R. A. Rivero, J. Org.
Tetrahedron Lett. 1999, 40, 46314634. Chem. 1998, 63, 48084810.
64 S. Chen, K. D. Janda, Tetrahedron 81 T. T. Romoff, L. Ma, Y. Wang, Synlett
Lett. 1998, 39, 39433946. 1998, 13411342.
65 F. Palacios, D. Aparicio, J. M. de los 82 L. Weber, P. Iaiza, G. Biringer, P.
Santos, A. Baceiredo, G. Bertrand, Barbier, Synlett 1998, 11561158.
Tetrahedron 2000, 56, 663669. 83 B. A. Kulkarni, A. Ganesan,
66 R. Chinchilla, P. Mazon, C. Najera, Tetrahedron Lett. 1998, 39, 43694372.
Tetrahedron Asymmetry, 2000, 11, 84 E. Angeletti, C. Canepa, G.
32773281. Martinetti, P. Venturello, J. Chem.
67 M. J. ODonnell, C. W. Lugar, R. S. Soc., Perkin Trans. I 1989, 105107.
Pottorf, C. Zhou, Tetrahedron Lett. 85 R. W. Hein, M. J. Astle, J. R. Shelton,
1997, 38, 71637166. J. Org. Chem. 1961, 26, 48744878.
68 M. J. ODonnell, C. Zhou, W. L. 86 I. Rodriguez, S. Iborra, A. Corma,
Scott, J. Am. Chem. Soc. 1996, 118, F. Rey, J. Jorda, Chem. Commun.
60706071. 1999, 593594.
69 B. Sauvagnat, F. Lamaty, R. Lazaro, 87 a) J. A. Cabello, J. M. Campelo, A.
J. Martinez, Tetrahedron Lett. 1998, Garcia, D. Luna, J. M. Marinas, J.
39, 821824. Org. Chem. 1984, 49, 5195; b) S.
70 W. L. Scott, C. Zhou, Z. Fang, M. Chalais, P. Laszlo, A. Mathy,
ODonnell, Tetrahedron Lett. 1997, 38, Tetrahedron Lett. 1982, 23, 4927.
36953698. 88 a) D. Villemin, Chem. Commun. 1983,
71 M. J. ODonnell, F. Delgado, R. S. 10921093; b) J. Yamawaki, T.
Pottorf, Tetrahedron 1999, 55, 6347 Kawate, T. Ando, T. Hanafusa, Bull.
6362. Chem. Soc. Jpn. 1983, 56, 18851886.
72 a) B. J. Cohen, M. A. Kraus, A. 89 G. A. Taylor, J. Chem. Soc., Perkin
Patchornik J. Am. Chem. Soc. 1977, Trans. I 1981, 3132.
99, 41654167; b) B. J. Cohen, M. A. 90 S. Tadesse, A. Bhandari, M. A.
Kraus, A. Patchornik, J. Am. Chem. Gallop, J. Comb. Chem. 1999, 1, 184
Soc. 1981, 103, 76207629. 187.
73 K. H. Bleicher, J. R. Wareing, 91 A. Bhandari, B. Li, M. A. Gallop,
Tetrahedron Lett. 1998, 39, 45874590. Synthesis 1999, 19511960.
74 K. C. Nicolaou, G.-Q. Cao, J. A. 92 M. F. Gordeev, D. V. Patel, J. Wu, E.
Pfefferkorn, Angew. Chem. Int. Ed. M. Gordon, Tetrahedron Lett. 1996,
2000, 39, 739743. 37, 46434646.
75 F. Balkenhohl, C. von dem 93 a) B. T. Watson, G. E. Christiansen,
Bussche-Hunnefeld, A. Lansky, C. Tetrahedron Lett. 1998, 39, 60876090;
Zechel, Angew. Chem. 1996, 108, b) A. Svensson, K.-E. Bergquist, T.
24362488. Fex, J. Kihlberg, Tetrahedron Lett.
76 D. R. Cody, S. H. DeWitt, J. C. 1998, 39, 71939196; c) Y. Xia, Z.-Y.
Hodges, B. D. Roth, M. C. Yang, A. Brossi, K.-H. Lee, Org. Lett.
Schroeder, C. J. Stankovic, W. H. 1999, 1, 21132115.
Moos, M. R. Pavia, F. S. Kiely, WO 94 B. C. Hamper, D. M. Snyderman, T.
94/08711. J. Owen, A. M. Scates, D. C. Owsley,
77 B. A. Kulkarni, A. Ganesan, Angew. A. S. Kesselring, R. C. Chott, J.
Chem. 1997, 109, 25652566. Comb. Chem. 1999, 1, 140150.
78 For the synthesis of 4-hydroxy- 95 a) L. F. Tietze, A. Steinmetz, Angew.
Chem., Int. Ed. 1996, 35, 651652; b) 110 D. Simoni, R. Rondanin, M.

L. F. Tietze, T. Hippe, A. Steinmetz, Morini, R. Baruchello, F. P.
Synlett 1996, 10431044; c) B. C. Invidiata, Tetrahedron Lett. 2000, 41,
Hamper, K. Z. Gan, T. J. Owen, 16071610.
Tetrahedron Lett. 1999, 40, 49734976. 111 G. Rosini, R. Ballini, M. Petrini,
96 a) S. Kobayashi, S. Nagayama, J. Org. Synthesis 1986, 4648.
Chem. 1996, 61, 2256; b) S. 112 T. Saiki, Y. Aoyama, Chem. Lett. 1999,
Kobayashi, S. Nagayama, J. Am. 197798.
Chem. Soc. 1996, 118, 8977; c) S. 113 D. E. Bergbreiter, J. J. Lalonde, J.
Kobayashi, S. Nagayama, Synlett Org. Chem. 1987, 52, 16011603.
1997, 653654; d) L. Yu, D. Chen, J. 114 J. H. Clark, G. Cork, J. Chem. Soc.,
Li, P. G. Wang, J. Org. Chem. 1997, Perkin Trans. I 1983, 22532258.
62, 35753581. 115 B. C. Ranu, S. Bhar, Tetrahedron
97 N. Tanaka, Y. Masaki, Synlett 2000, 1992, 48, 13271332.
406408. 116 a) R. Ballini, M. Petrini, G. Rosini,
98 E. N. Prabhakaran, J. Iqbal, J. Org. Synthesis 1987, 711713; b) R.
Chem. 1999, 64, 33393341. Ballini, P. Marzialia, A.
99 B. Bhatia, M. M. Reddy, J. Iqbal, J. Mozzicafreddo, J. Org. Chem. 1996,
Chem. Soc., Chem. Commun. 1994, 61, 32093211.
713714. 117 S. Batra, S. K. Rastogi, B. Kundu, A.
100 a) S. Kobayashi, I. Hachiya, S. Patra, A. P. Bhaduri, Tetrahedron
Suzuki, M. Moriwaki, Tetrahedron Lett. 2000, 41, 5971.
Lett. 1996, 37, 28092812; b) S. 118 a) X. Beebe, N. E. Schore, M. J.
Kobayashi, M. Moriwaki, Tetrahedron Kurth, J. Am. Chem. Soc. 1992, 114,
Lett. 1997, 38, 42514254. 1006110062; b) X. Beebe, N. E.
101 S. Kobayashi, M. Moriwaki, R. Schore, M. J. Kurth, J. Org. Chem.
Akiyama, S. Suzuki, I. Hachiya, 1995, 60, 41964203; c) X. Beebe, C.
Tetrahedron Lett. 1996, 37, 77837786. L. Chiappari, M. M. Olmstead, M. J.
102 S. Kobayashi, Y. Aoki, Tetrahedron Kurth, J. Org. Chem. 1995, 60, 4204
Lett. 1998, 39, 73457348. 4212; d) J. Rademann, M. Meldal, K.
103 S. Kobayashi, R. Akiyama, H. Kita- Bock, Chem. Eur. J. 1999, 5, 1218
gawa, J. Comb. Chem. 2000, 2, 438440. 1225.
104 a) S. Kobayashi, T. Furuta, K. 119 a) H. Richter, G. Jung, Mol. Diversity
Sugita, O. Okitsu, H. Oyamada, 1998, 3, 191194; b) H. Richter, T.
Tetrahedron Lett. 1999, 40, 13411344; Walk, A. Holtzel, G. Jung, J. Org.
b) S. Kobayashi, H. Oyamada, WO Chem. 1999, 64, 13621365.
99/46238. 120 O. Prien, K. Rolng, M. Thiel, H.
105 G. I. Georg, V. T. Ravikumar in: The Kunzer, Synlett 1997, 325326.
Organic Chemistry of b-Lactams, 121 B. A. Kulkarni, A. Ganesan, J.
VCH, New York 1993, pp. 295368. Comb. Chem. 1999, 1, 373378.
106 D. J. Hart, D. C. Ha, Chem. Rev. 1989, 122 R. Racker, K. Doring, O. Reiser, J.
89, 14471465. Org. Chem. 2000, 65, 69326939.
107 S. Brase, D. Enders, J. Kobberling, 123 H. Richter, G. Jung, Tetrahedron Lett.
F. Avemaria, Angew. Chem. 1998, 110, 1998, 39, 27292730.
36143616; Angew. Chem., Int. Ed. 124 Y. Hu, J. A. Porco Jr, Tetrahedron Lett.
1998, 37, 34133415. 1999, 40, 32893292.
108 S. Schunk, D. Enders, Org. Lett. 125 A. R. Katritzky, S. A. Belyakov, Y.
2000, 2, 907910. Fang, J. S. Kiely, Tetrahedron Lett.
109 a) V. Molteni, R. Annunziata, M. 1998, 39, 80518054.
Cinquini, F. Cozzi, M. Benaglia, 126 P. Karoyan, A. Triolo, R.
Tetrahedron Lett. 1998, 39, 1257; b) R. Nannicini, D. Giannotti, M.
Annunziata, M. Benaglia, M. Altamura, G. Chassaing, E.
Cinquini, F. Cozzi, Chem. Eur. J. Perrotta, Tetrahedron Lett. 1999, 40,
2000, 6, 133138. 7174.
531
19
Solid-phase Palladium Catalysis for High-
throughput Organic Synthesis
Yasuhiro Uozumi and Tamio Hayashi
19.1
Introduction
Palladium-mediated organic transformations have emerged as a powerful tool in

the domain of synthetic organic chemistry [1]. Recently, high-throughput organic
synthesis by solid-phase chemistry has been gaining in popularity owing to the
ease of purication of the products [2]. Palladium-catalyzed reactions have also
found widespread utility in the preparation of small molecule libraries, especially
for medicinal screening purposes. This chapter surveys solid-phase synthetic re-
actions [3] by palladium catalysis.
19.2
CarbonCarbon and CarbonNitrogen Bond-forming Reactions of Aryl and Alkenyl
Halides
19.2.1
Cross-coupling Reactions
Palladium complexes catalyze the reaction of organometallic reagents (R-m) with

aryl or alkenyl halides and related compounds (R 0 X) to give cross-coupling prod-
ucts (RR 0 ) (Scheme 19.1). It is generally accepted that the catalytic cycle of the
reaction proceeds via oxidative addition of R 0 X to palladium(0) and subsequent
ligand exchange of the resulting LnPd(R 0 )X with R-m to give, as the key interme-
diate, the unsymmetrical diorganometal LnPd(II)(R)R 0 . From this intermediate,
the product RR 0 is released by reductive elimination to leave a LnPd(0) spe-
cies that undergoes the next catalytic cycle. Transfer of an alkyl group from R-m
to LnPd(R 0 )X, the so-called transmetalation step, takes place with organometallic
compounds of Mg, Zn, B, Al, Sn, Si, Zr, etc.
Among the many organometallic reagents used for cross-coupling, organoboron
reagents and organotin reagents have been extensively examined for solid-phase
applications. Palladium-catalyzed coupling of aryl halides with a terminal alkyne in
the presence of a copper salt has also been studied on solid phase.

ISBN: 3-527-30509-2
532 19 Solid-phase Palladium Catalysis for High-throughput Organic Synthesis
Scheme 19.1. Reaction pathway of cross-coupling reactions.
19.2.1.1 Reactions of Aryl and Alkenyl Halides with Organoboron Reagents

The palladium-catalyzed cross-coupling of aryl halides with organoboron reagents
(the so-called SuzukiMiyaura coupling) has become an indispensable carbon
carbon bond-forming reaction in ne organic synthesis [4]. One of the earliest
examples of its solid-phase application was using the aryl bromide 1 supported
on polystyrene resin with a sulfonamide linker (Scheme 19.2) [5]. The Suzuki
Miyaura coupling of the bromide 1 with aryl boronic acids or alkyl 9-BBN in
aqueous tetrahydrofuran (THF) took place in the presence of Pd(Ph3 P)4 with
Na2 CO3 as the base at 65 C. Nucleophilic cleavage of the resulting resin-bound
products 2 and 3 gave the corresponding coupling products in excellent yields.
Couplings of various halogenobenzoates (49), the m-iodobenzyl ester 10, and
the p-, m-, o-bromobenzaldehyde acetals 1214 bound to the polystyrene (PS) ma-
trix resin are summarized in Tables 19.1, 19.2, and 19.3, respectively. Reactions of
the resin-supported p-iodobenzoate 4 with arylboronic acids were catalyzed by
Pd2 (dba)3 (dba dibenzylideneacetone) at room temperature in aqueous dime-
thylformamide (DMF) to give good to excellent yields of the corresponding biaryl
carboxylic acids after hydrolysis (Table 19.1, entries 13). The iodobenzoate 4 also
reacted with pinacol alkenylborates and tributylborane in the presence of
Pd(Ph3 P)4 (Table 19.1, entries 4 and 5) [6]. Coupling of the p-bromobenzoate 5
with various electron-rich as well as electron-decient arylboronic acids was exam-
ined with Pd(Ph3 P)4 in aqueous dimethoxyethane (DME) (Table 19.1, entries 6
10) [7]. Base-mediated methanolysis of the resulting resin gave methyl 4-(4 0 -
19.2 Carbon--Carbon and Carbon--Nitrogen Bond-forming Reactions of Aryl and Alkenyl Halides 533
Scheme 19.2. Solid-phase SuzukiMiyaura coupling:

preparation of substituted arylacetic acid derivatives.
substituted aryl)benzoates in excellent yields. The bromobenzoates 79 having

ortho substituents underwent the SuzukiMiyaura coupling under the same reac-
tion conditions (Table 19.1, entries 1214).
The iodobenzene 10 connected to the PS resin by benzyl benzoate linkage re-
acted with a wide variety of arylboronic acids, including heteroaromatic reagents
in aqueous dioxane at 100 C (Table 19.2) [8]. Palladium acetate catalyzed the cou-
pling to give the m-arylbenzyl alcohols (11) after methanolysis in satisfactory yields.
Palladium-catalyzed cross-coupling of the cyclic acetals of o-, m-, and p-bromo-
benzaldehydes bound to the PS resin (1214) was also examined with various
arylboron reagents in aqueous DME in the presence of Na2 CO3 to produce various
biaryl carboxaldehydes after acid hydrolysis of the acetal linker (Table 19.3) [9].
It is worth noting that the biaryl coupling products having substituents at their
2,6- as well as 2,2 0 -positions were readily obtained despite their steric hindrance
(Table 19.3, entries 3 and 12). Thus, the coupling of mesitylboronic acid with
the p-bromobenzene 12 and o-carbamoylphenylboronic acid with the o-bromo-
benzene 14 gave 4-mesitylbenzaldehyde and 2-(2-carbamoylphenyl)benzaldehyde,
respectively.
Tab. 19.1. Coupling of resin-bound aryl iodide with boron reagents.
Entry Aryl halide Boron reagent Product Yield (%)

Entries 15, ref. 6; entries 614, ref. 7. Conditions: Pd2 (dba)3

(510 mol%), K2 CO3 (2 equiv.), DMF, rt, then CF3 COOH/CH2 Cl2
(for entries 13); Pd(Ph3 P)4 (510 mol%), K2 CO3 (2 equiv.), DMF,
rt, then CF3 COOH/CH2 Cl2 (for entries 4 and 5); Pd(Ph3 P)4
(5 mol%), 2 M Na2 CO3 , DME, reux, then NaOMe, MeOH (for
entries 614).
Tab. 19.2. Solid-phase SuzukiMiyaura coupling with base labile linker.
Entry ArB(OH)2 Conditions Yield (%)

Entry ArB(OH)2 Conditions Yield (%)
Ref. 8: conditions: A, AraB(OH)2 (4 equiv.), K2 CO3 (9 equiv.),

Pd(OAc)2 (10 mol%), dioxane/H2 O 6/1, 100 C, 24 h; B,
AraB(OH)2 (8 equiv.), K2 CO3 (18 equiv.), Pd(OAc)2 (20 mol%),
dioxane/H2 O 6/1, 100 C, 24 h.
Tab. 19.3. Coupling of resin-bound aryl iodide with boron reagents.

Ref. 9: conditions: boron reagent (3 equiv.), Pd(Ph3 P)4 (5 mol%),

2 M Na2 CO3 (8 equiv.), DME, reux, 24 h; then dioxane, 3 M HCl,
80 C, 24 h.
Scheme 19.3. Sequential transformation of polymer-supported

haloamides into boronates and biaryls by use of Miyauras
arylboronate formation and SuzukiMiyaura coupling.
The SuzukiMiyaura coupling using resin-supported boron reagents has also

been investigated (Scheme 19.3 and Table 19.4) [10]. The resin-supported aryl-
boron reagents (17) were prepared by palladium-catalyzed introduction of pinacol
borate on solid support. Thus, p-, m-, and o-iodobenzene Rink amide resins (16)
were treated with 2 equiv. of bis-(pinacolato)diboron in DMF in the presence of
PdCl2 (dppf ) to give 17 in high yields. The coupling reactions of the resulting
borates with an excess of aryl halides (ArX in Table 19.4) were catalyzed by
Pd(Ph3 P)4 in DMF upon heating to give excellent yields of the corresponding
biaryl carboxamides 18, which were readily converted to 19 (Table 19.4).
One advantage of solid-phase coupling was demonstrated in the preparation of
tetrasubstituted alkenes (Scheme 19.4) [11]. The Z-bisborate 20 prepared by palla-
dium-catalyzed diboration was treated with an alkyl halide R 0 X in the presence of
catalytic PdCl2 (Ph3 P)2 and KOH as base in aqueous DMF to give a mixture of the
mono- and dialkylated olens (21 and 22). The reaction mixture was then taken
onto the coupling with a Rink p-iodobenzamide without further addition of the
palladium catalyst. The monoalkylated intermediate bearing the unreacted borate
group underwent solid-phase coupling to form 23, leaving the dialkylated alkene
22 in the solution phase. After removal of the dialkylated alkene 22 by ltration,
the resulting resin-bound tetrasubstituted alkene 23 was detached from the resin
to give the p-alkenylbenzamide 24 in excellent purity.
Solid-phase cross-coupling of the alkyl 9-BBN was used to introduce the silyl
traceless linker on solid support (Scheme 19.5) [12]. Palladium-catalyzed solid-
phase coupling of the alkyl 9-BBN 26 having an anisyl-(dimethyl)silyl group gave
the PS-alkyl-(anisyl)dimethylsilane 27, which was readily converted into the chlo-
rosilane 28 by treatment with HCl. The alkylchlorosilane resin reacted with the
lithiated pyridine 29 to give 30, the intermediate for the pyridine-fused benzaze-
pines 31 being released in traceless fashion on subsequent treatment with a uo-
ride reagent.
Tab. 19.4. Transformation of haloamides into polymer-supported boronates and biaryls.
Starting Boronate Yield (%) ArX Product Yield (%)

haloamide
Ref. 10: yields are based on incorporation of halobenzoyl group on the resin.
Scheme 19.4. Synthesis of tetrasubstituted ethylenes on solid support via resin capture.
Scheme 19.5. Introduction of a traceless silicon linker onto

polymer support using SuzukiMiyaura coupling.
The solid-phase synthesis of the prostaglandin E (PGE) and prostaglandin F

(PGF) families was carried out via palladium-catalyzed coupling of alkyl 9-BBN as
the key step (Scheme 19.6) [13]. The solid-supported bromocyclopentene 34 and
the (bromopropenyl)cyclopentene 38 were substituted with alkyl groups by cou-
pling with butyl or pentyl 9-BBN to give the key intermediates of PGE and PGF
derivatives (for example 36), respectively.
Scheme 19.6. Solid-phase synthesis of PGE and -F series.
Another interesting application of the SuzukiMiyaura coupling is the solid-

supported pinacolate boron linker (Scheme 19.7) [14]. The boron pinacolate
prepared from the arylboronic acid 39 and the pinacol carboxylic acid 40 was con-
nected to polystyrene-poly(ethylene glycol) resin (TentaGel) to give 41. After con-
densation with 42, the resulting aryl iodidearyl borate 43 underwent intramo-
lecular cross-coupling to release the biaryl macrocyclic peptide 44.
19.2.1.2 Reactions of Aryl and Alkenyl Halides with Organotin Reagents

In addition to the SuzukiMiyaura coupling, another widely investigated coupling
reaction is palladium-catalyzed cross-coupling of aryl and alkenyl halides with or-
ganotin reagents (the so-called Stille coupling) [15]. Scope and limitation studies
on the coupling of halogenoaryl carboxylic amides supported on Rink, Wang, and
PS resin are summarized in Table 19.5 [16, 17]. The Stille coupling of o-, m-, and
p-halogenobenzamides with alkenyl and aryl-(tributyl)stannanes (including heter-
oaromatics) was carried out in aprotic solvents using palladium complexes of
triarylphosphine or arsenic ligands to give good to excellent yields of the corre-
sponding cross-coupling products (Table 19.5).
Scheme 19.7. Solid-phase synthesis of macrocyclic b-turn mimics with boronate linker.
The resin-supported arylstannane 45 was also examined for Stille coupling with
bromobenzenes (Table 19.6) [18]. Thus, the reaction of the PS resin-supported p-
tributylstannylbenzoate 45 with 3 equiv. of aryl bromide took place in 1-methyl-2-
pyrrolidinone (NMP) at 90 C to give the coupling products on solid support. A
palladacycle catalyst 46 was used for the coupling in the presence of LiCl to pro-
mote the reaction more eciently. Methanolysis of the resulting resin gave the
corresponding methyl p-arylbenzoates in 8095% yields.
The solid-phase synthesis of the library of the highly functionalized fused ring
system shown in Scheme 19.8 was achieved via the Stille coupling of an alkenyl
bromide with a series of alkenylstannanes, resulting in conjugate dienes and a
subsequent DielsAlder reaction (Scheme 19.8) [19].
19.2.1.3 Reactions of Aryl Halides with Terminal Alkynes

The palladium-catalyzed coupling of an aryl halide with a terminal alkyne pro-
moted by CuI and base, the so-called Sonogashira reaction [20], is recognized as
the most powerful method for the preparation of aryl acetylene derivatives. The
solid-phase Sonogashira reaction was examined for the coupling of the resin-
supported m-iodobenzylbenzoate 54 and (m-iodobenzyloxy)acetamide 55 with vari-
ous terminal alkynes, as shown in Table 19.7 [21]. The coupling was carried out
with an excess of alkynes using a PdCl2 (Ph3 P)2 /CuI/Et3 N system to give the corre-
Tab. 19.5. Coupling of polymer-supported aryl iodides with vinyl/aryl stannanes.

AraX (alkyl)3 SnR (R vinyl or aryl) ! AraR (R vinyl or aryl)
Entry Aryl iodide Stannane Product a Yield (%)b

Entry Aryl iodide Stannane Producta Yield (%)b
Conditions: entries 17 (ref. 16): Pd2 (dba)3 (5 mol%), Ph3 As (20

mol%), NMP, 45 C; entries 8, 9, 1115, 1724, and 26 (ref. 17):
stannane (3 equiv.), Pd(Ph3 P)4 (5 mol%), DMF, 60 C, 24 h;
entries 10, 16, 25, and 27: Pd2 (dba)3 (5 mol% Pd), (2-furyl)3 P,
DMF, 60 C, 48 h.
a Entries 15: product cleaved from the resin with 5% TFA/DCM
(entries 15), 90% TFA (entries 67), or aq. LiOH THF-MeOH-
H2 O (entries 827). Ar 1 4-H2 NCOC6 H4 , Ar 2 4-
HOCOCH(CH3 )NH-COC6 H4 , Ar 3 2-HOCOC6 H4 , Ar 4 3-
HOCOC6 H4 , Ar 5 4-HOCOC6 H4 , Ar 6 (3-hydroxycarbonyl)-5-
pyridyl, Ar 7 (2-hydroxycarbonyl)-5-furyl.
b Entries 124: isolated yield; entries 2527: determined by HPLC
and 1 H NMR.
Tab. 19.6. Coupling of polymer-supported aryl stannane with aryl halides.
Entry Aryl halide Yield (%)
Ref. 18
sponding ethynylbenzenes in nearly quantitative yields. The ethynylbenzyl alco-

hols 56 or the (ethynylbenzyloxy)acetamide 57 were released from the resulting
resin by methanolysis of the benzoate linker or acid hydrolysis of the Rink acet-
amide linker, respectively.
The Sonogashira reaction has often been used as a key step for the solid-phase
preparation of indole derivatives. Thus, for example, the solid-phase coupling of
o-iodoacetanilide 58 with phenylacetylene using PdCl2 (Ph3 P)2 , CuI, and base, fol-
lowed by alkaline hydrolysis of the ester linkage, gave the indole 5-carboxylic acid
Scheme 19.8. Solid-phase synthesis of highly functionalized fused ring systems.
59 in 72% yield in one pot, thereby showing that the Sonogashira coupling and
subsequent intramolecular cyclization to form the indole ring proceeds on solid
phase (Scheme 19.9) [22].
The Rink resin-supported o-iodo(N-methanesulfonyl)anilide 60 gave the 2-
substituted indoles 61 which underwent, after deprotection of the N-mesyl group,
a solid-phase Mannich reaction to aord the (2-alkyl-3-aminomethyl)indole 5-
carboxamides 64 (Scheme 19.10) [23].
Tab. 19.7. Palladium-catalyzed coupling of solid-supported aryl iodides with terminal

acetylenes.
Entry Aryl iodide Acetylene Conditions Yield (%)

Entry Aryl iodide Acetylene Conditions Yield (%)
Ref. 21 conditions: A, acetylene (4.0 equiv.), PdCl2 (Ph3 P)2

(10 mol%), Cul (20 mol%), Et3 N/dioxane 1/2, rt, 24 h; B,
acetylene (8.0 equiv.), PdCl2 (Ph3 P)2 (20 mol%), Cul (40 mol%),
Et3 N/dioxane 1/2, rt, 24 h; C, acetylene (4.0 equiv.),
PdCl2 (Ph3 P)2 (10 mol%), Cul (20 mol%), Et3 N/dioxane 1/2,
50 C, 24 h.
Scheme 19.9. Solid-phase synthesis of indoles using Pd-catalyzed acetylene coupling.

Scheme 19.10. Solid-phase Mannich substitution of indoles.
Similarly, the benzofurans 66 as well as the (2,3,6-substituted)indoles 70 were

also synthesized on solid phase (Schemes 19.11 and 19.12) [24, 25].
Scheme 19.11. Solid-phase synthesis of benzofurans using Pd-catalyzed acetylene coupling.
An unsubstituted terminal acetylene group was introduced on a resin-supported

aromatic ring by Sonogashira coupling of (trimethylsilyl)acetylene followed by
carbonsilicon bond cleavage with tetrabutylammonium uoride (Scheme 19.13)
[26]. The resulting arylacetylene 73 was subjected to the copper-mediated Mannich
reaction on solid support with various aldehydes and piperazines to aord a library
of arylpropynylamines 74 in excellent chemical yields and purities.
Scheme 19.12. Solid-phase synthesis of trisubstituted indoles.
Scheme 19.13. Combination of Sonogashira and Mannich reactions.

A solid-supported terminal alkyne was also examined for the Sonogashira cou-
pling (Scheme 19.14) [27]. Thus, propiolic acid was connected to PS oxyamino
resin prepared from the phthalimide 75 via the Gabriel synthesis to give the solid-
supported propiolic amide 76. The palladium-catalyzed coupling of the supported
propiolic amide 76 with the halogenonucleoside 77 proceeded under the standard
Sonogashira conditions to give the nucleoside hydroxamic acid 79.
Scheme 19.14. Solid-phase synthesis of nucleoside hydroxamic acids.
19.2.1.4 Solid-phase Palladium-catalyzed Cross-coupling Using Aryl and Benzylzinc

Reagents
It has been well established that cross-coupling of aryl halides (pseudo-halides)
with aryl and benzylzinc reagents are also catalyzed by palladiumphosphine com-
plexes, as are those with organoboron and organostannane reagents. Solid-phase
cross-coupling of arylzinc reagents with supported aryl halides was catalyzed by a
palladium complex of bis-(diphenylphosphino)ferrocene (dppf ) in THF to give
biaryls in good to excellent yields. Representative results are summarized in Table
19.8 [28]. Reactions of supported p-bromobenzoate with 2 equiv. of o-, m-, and p-
substituted arylzinc reagents bearing an electron-withdrawing or electron-donating
group took place at room temperature to give the corresponding biaryls in good
chemical yields (Table 19.8, entries 17). Meta- and o-bromobenzoate also under-
went coupling on resin support under the same reaction conditions to give the
Tab. 19.8. Coupling of polymer-supported aryl bromides with arylzinc reagents.
Entry Aryl halide Aryl zinc Product Yield (%)
Ref. 28
biaryl 2-carboxylic ester and the 3-carboxylic ester, respectively (Table 19.8, entries
9 and 10). Heteroaromatic biaryl derivatives were obtained from solid-supported
bromopyridine or thiophenylzinc (Table 19.8, entries 8 and 11).
It is noteworthy that zinc-mediated cross-coupling was used for the prepara-
tion of diarylmethanes (Scheme 19.15) [29]. Thus, the coupling of the Rink amide
of the o-, m-, and p-iodobenzoyl substrates with 10 equiv. of 4-cyanobenzylzinc
and 2,6-dichlorobenzylzinc reagents was catalyzed by a catalyst generated from
Pd2 (dba)3 and tri(2-furyl)phosphine to give the corresponding benzylphenylcar-
boxamides 80 and 81 in high yields. The synthetic sequences shown in Scheme
19.16, where the zinc-mediated arylaryl and arylbenzyl couplings were per-
formed on resin support, gave AraAraCH2 aAr products in high purity.
Scheme 19.15. Solid-phase coupling of aryl iodides with benzylzinc reagents.
19.2.2
Palladium-catalyzed Arylation and Alkenylation of Olens
Palladium-catalyzed arylation and alkenylation of olens (the so-called Heck reac-

tion) [30] are versatile means for making a carboncarbon bond. Aryl and alkenyl
halides (pseudo-halides) (RX) are employed for the Heck reaction as alkylation
agents for the olenic substrates.
Scheme 19.16. Multiple coupling process of aryl- and

benzylzinc reagents with supported aryl halides.
The Heck reaction is generally thought to proceed via the reaction pathway
shown in Scheme 19.17. Oxidative addition of RX to palladium(0) gives LnPd(R)X.
Coordination of an olen substrate to LnPd(R)X gives Pd(II) (h 2 -olen)R. Insertion
of the h 2 -olen ligand into the PdR bond gives a s-alkylpalladium intermediate
which subsequently undergoes b-hydride elimination to give the Heck product and
LnPd(H)X.
The intermolecular Heck reaction of resin-supported aryl iodides with olen
substrates was examined on various polymer supports. Representative results are
Scheme 19.17. Pathway of Heck reaction.
summarized in Table 19.9, where conjugated olens were used to exhibit high re-
activity [31, 32]. The Heck reaction of the Wang resin-supported 4-iodobenzoate
with ethyl acrylate was catalyzed by Pd(OAc)2 in DMF to give the ethyl cinnamate
product in 91% yield (Table 19.9, entry 1). The unsymmetrical stilbene was ob-
tained from methoxystyrene in 90% yield (Table 19.9, entry 2). Alkenylation of io-
dobenzoates supported on PSpolyethylene glycol (PEG) resin and peptide amide
linker (PAL) resin took place at 37 C in the presence of Pd(OAc)2 -PPh3 in aque-
ous DMF (Table 19.9, entries 47).
The Heck reaction of a supported styrene with solution-phase aryl iodides was
also examined under essentially the same conditions (Table 19.10). Thus, the Wang
resin-supported styrene carboxylate reacted with iodobenzene, bromonaphthalene,
bromothiophene, and bromopyridine in DMF on heating to give the corresponding
b-arylstyrene-4-carboxylic acids upon release from the resin support. A palladium
complex generated in situ by mixing Pd2 (dba)3 and tri-(2-furyl)phosphine (Table
19.9, conditions B) exhibited high catalytic activity for the reaction with aryl bro-
mides (Table 19.9, entries 2, 4, and 5).
Aryl halides having allylamine or acrylamide substituents at their ortho posi-
tions have been well documented to undergo an intramolecular Heck reaction to
form indole ring systems. The intramolecular indole ring construction has been
applied to the solid-phase synthesis of libraries of indole derivatives. Thus, the 2-
bromoaniline 85, which was connected at its 5-position to PSPEG resin by a
Wang-type linker, was converted to the N-acyl-N-allylanilines 86 using the standard
uorenylmethoxycarbonyl (Fmoc) method. The supported substrates 86 were sub-
Tab. 19.9. Solid-phase Heck reaction of supported aryl halides.
Entry ArX Alkene (alkyne) Product Yield (%)
Entries 13, ref. 31; entries 47, ref. 32. Conditions: entries 1 and
3, Pd(OAc)2 , Et3 N, Bu 4 NCl, DMF, 8090 C, 16 h; entry 2,
Pd2 (dba)3 , (o-tol)3 P, DMF, 100 C, 20 h; entries 47, Pd(OAc)2 ,
PPh3 , Et3 N, Bu 4 NCl, DMF/H2 O (9:1), 37 C, 4 h.
jected to the palladium-catalyzed Heck reaction. The resulting resin was treated
with CF3 COOH to give N-acyl-3-alkyl-6-hydroxyindoles (87) in good to excellent
yields and purities (Scheme 19.18) [33]. An acrylamide group showed good reac-
tivity for the intramolecular Heck reaction (Scheme 19.19) [34]. Thus, cyclization
of Rink resin-supported (2-iodo)acrylanilides (90) was catalyzed by Pd(OAc)2 -PPh3
Tab. 19.10. Solid-phase Heck reaction of supported styrene with aryl halides.
Entry ArX Conditions Product Yield (%)
Ref. 31: condition A, Pd(OAc)2 , Et3 N, Bu 4 NCl, DMF, 8090 C,

16 h; B, Pd2 (dba)3 , (o-tol)3 P, DMF, 100 C, 20 h.
Scheme 19.18. Solid-phase synthesis of indoles.

Scheme 19.19. Solid-phase synthesis of oxindoles.
in DMF to give the oxindoles 91. N-Allyl-2-iodoanilines (94) which were supported
on Rink amide resin by their N-alkyl side-chains also underwent Heck cyclization
in the presence of Pd-PPh3 species in aqueous DMF at 80 C to aord 3-(resin-
connected alkyl)indoles (95) (Scheme 19.20) [35]. Cleavage of the resin support
under acidic conditions gave high yields of the indoles 96, which bear 3-(amino-
carbonyl)methyl and N-benzyl groups. Preparation of an oligopeptide library at the
5-position of the indole skeleton was achieved by use of resin-supported 5-carboxy
indole 95 as a scaold (Scheme 19.20, bottom).
A macrocyclic peptide was synthesized on solid support via Heck cyclization
(Scheme 19.21) [36]. An oligopeptide chain (98) bearing aryl iodide and acrylamide
groups was prepared by the standard Fmoc method on PS resin. Heck reaction of
the oligopeptide 98 took place at 37 C in aqueous DMF in the presence of the
Pd(OAc)2 -PPh3 catalyst to give, after deprotection and release from resin support,
Scheme 19.20. Solid-phase synthesis of indoles (2).
the macrocyclic peptide 100 in 30% overall yield based on the loading of the start-
ing resin. A benzazepine skeleton was constructed on solid support by intramo-
lecular Heck reaction (Scheme 19.22) [37]. The Wang resin-supported (N-butenyl)-
2-iodobenzamides 101 (R CH3 or CH2 Ph) underwent Heck cyclization with
Pd(OAc)2 -PPh3 to give 102. Acidic cleavage of the Wang ester, followed by treat-
ment with diazomethane, gave the benzazepines 103 in high yields.
19.2.3
Amination of Aryl Halides
Palladium-catalyzed amination of aromatic halides [38] has become a powerful

tool in solid-phase organic synthesis. Thus, various Rink resin-supported aryl
bromides were coupled with aniline derivatives to give N-aryl anilines in quan-
titative yields, as seen in Table 19.11, entries 1, 2, 4, and 5 [39]. The aromatic ami-
Scheme 19.21. Palladium-catalyzed formation of macrocyclic peptide on solid support.
Scheme 19.22. Solid-phase synthesis of benzazepines via intermolecular Heck reaction.

Tab. 19.11. Palladium-catalyzed amination of resin-bound aryl bromide.
Entry Aryl halide Amine Condition Product Yield (%)

Entry Aryl halide Amine Condition Product Yield (%)
Entries 15, ref. 39; entries 610, ref. 40. Conditions: A, amine
(3 equiv.), Pd2 (dba)3 (5 mol%), (o-tol)3 P, NaOBu-t (1020 equiv.),
toluene, 100 C; B, amine (10 equiv.), Pd2 (dba)3 (20 mol%),
(o-tol)3 P (80 mol%), NaOt-Bu (1020 equiv.), toluene, 100 C; C,
amine (10 equiv.), Pd2 (dba)3 (20 mol%), BINAP (80 mol% P),
NaOBu-t (1020 equiv.), toluene, 100 C
nations were carried out with the Pd2 (dba)3 /tri-(o-tolyl)phosphine catalyst system
and NaOt-Bu in toluene at 100 C to give complete conversion of the substrates.
Resin-bound o-bromides showed little activity, presumably owing to their steric
hindrance (Table 19.11, entry 3). PSPEG Rink amide (TG RAM) resin-bound p-
bromobenzamide was also examined for coupling with piperidine and pyrrolidine
to give the N-arylpiperidine and N-arylpyrrolidine in 81% and 49% yields, respec-
tively, under essentially the same conditions (Table 19.11, entries 6 and 7) [40]. It
has been documented that primary and secondary aliphatic amines result in sig-
nicant reduction of the bromide using (o-tol)3 P and that the improved conditions
with 2,2 0 -bis(diphenylphosphino)-1,1 0 -binaphthyl (BINAP) (Table 19.11, conditions
C) decrease this side reaction. The yield of N-arylpyrrolidine (49%) increased to
93% with BINAP (Table 19.11, compare entry 7 with 8). The use of BINAP as a
ligand also allowed for the successful coupling of primary amines. Thus, benzyl-
amine reacted with the TG RAM-supported p- and m-bromobenzamide with
the Pd/BINAP catalyst to give 99% and 89% yields, respectively, of the p- and m-
(benzylamino)benzamide (Table 19.11, entries 9 and 10).
19.2.4
Miscellaneous Reactions [41]
19.2.4.1 Heteroannulation
It has been reported that annulation of a 2-iodoaniline with an internal alkyne
takes place in the presence of a palladium catalyst to give a 2,3-disubstituted indole
in one step (Larock annulation) [42]. The annulation of 4-carboxamide-2-iodoani-
lines (104) supported on Rink resin with an excess amount of disubstituted al-
kynes was catalyzed by Pd(OAc)2 -PPh3 to give the indoles 105 (Table 19.12, route
A) [43]. Cleavage of the resin moiety from 105 by triuoroacetic acid gave the
2,3,5-trisubstituted indoles 108 in excellent yields (Table 19.12, entries 15). The 2-
iodoaniline 106 bound to the resin support at its N1 position by the THP linker
reacted with alkynes under palladium-catalyzed conditions to give N-resin-bound
indole 107 (Table 19.12, route B). Acidic cleavage of the NTHP linkage gave high
Tab. 19.12. Solid-phase Larock heteroannulation.
Entry Route Condition X R R1 R2 Yield (%)
1 A i CONH2 H Pr Pr 91
2 A i CONH2 H Me t-Bu 87
3 A i CONH2 H Me Ph 86
4 A ii CONH2 COCH3 Pr Pr 95
5 A i CONH2 COCH(CH3 )2 Me t-Bu 75
6 B iii H H Ph SiMe3 73
7 B iii H H Me t-Bu 55
Entries 15, ref. 41; entries 67, ref. 42. Condition i, alkyne
(1015 equiv.), Pd(OAc)2 (10 mol%), Ph3 P (20 mol%), LiCl
(1 equiv.), K2 CO3 (5 equiv.), DMF, 80 C; ii, alkyne (1015 equiv.),
Pd(OAc)2 (10 mol%), Ph3 P (20 mol%), Bu 4 NCl (1 equiv.), KOAc
(5 equiv.), DMF, 80 C; iii, alkyne (excess), PdCl2 (Ph3 P)2
(20 mol%), tetramethylguanidine (10 equiv.), DMF, 110 C.
Scheme 19.23. Solid-phase synthesis of tropane derivatives via

palladium-mediated three-component coupling.
yields of the 2,3-disubstituted indole 108 (X H) (Table 19.12, entries 6 and 7)

[44].
19.2.4.2 Insertion Cross-coupling Sequence (Dialkylation of Tropene)

Three-component couplings of the resin-supported tropene 109, an aryl bromide,
and an arylboronic acid or phenylacetylene were promoted by palladium(0) to give
vicinal disubstituted tropanes (111) (Scheme 19.23) [45]. Thus, the reaction of 109
with an aryl bromide took place in THF with palladium(0) to give the s-alkylpalla-
dium intermediate 110, which coupled with an arylboronic acid or phenylacetylene
successively to give 111 (R Ar or CCPh). Tropane 112 or 113 was obtained from
111 through deprotection, reductive N-alkylation, and acidic cleavage of resin. The
monosubstituted tropane 114 was obtained similarly by reductive cleavage of the s-
alkylpalladium bond of the intermediate 110 with formic acid.
19.2.4.3 Coupling Reactions on Various Solid Supports

The Heck reaction, the SuzukiMiyaura, Sonogashira, and Stille couplings with
aryl iodide were examined on various resin supports (Table 19.13) [46]. Thus, aryl
Tab. 19.13. Palladium-catalyzed various coupling with a traceless linker.
Resin Substrate Coupling conditions Cleavage Product Yield (%)

conditions
TentaGel Substrate (6 equiv.) A 83

Pd(OAc)2 (20 mol%)
Polystyrene NaOAc (3 equiv.) B 85
Bu 4 NBr (1 equiv.)
ArgoPore DMA, 100 C, 24 h B 96
TentaGel Substrate (10 equiv.) A 74
Pd(Ph3 P)4 (2 mol%)
TentaGel K3 PO4 (2 equiv.) B 86
aq. DMA, 80 C, 24 h
TentaGel C 93
Polystyrene C 67
ArgoPore A 60
TentaGel Substrate (6 equiv.) C 50
PdCl2 (Ph3 P)2 (10 mol%)
Polystyrene Cul (20 mol%) C 92
Dioxane, Et3 N, rt, 24 h
ArgoPore C 86
TentaGel Substrate (5 equiv.) C 90
Pd2 (dba)3 (10 mol%)
Polystyrene Ph3 As (40 mol%) C 79
Dioxane, 60 C, 24 h
ArgoPore C 80
Ref. 46: conditions A, Cu(OAc)2 (0.5 equiv.), MeOH, pyridine

(10 equiv.), rt, 2 h; B, Cu(OAc)2 (0.5 equiv.), n-propylamine, rt,
2 h; C, NBS (2 equiv.), CH2 Cl2 , rt, 45 min.
iodide was connected to PSPEG resin (TentaGel), standard PS resin, and macro-
porous PS resin (ArgoPore) with a hydrazine linker. The supported aryl iodides
(115) were subjected to the coupling reactions under the conditions listed in Table
19.13 to give 116. The resulting resins (116) were subsequently subjected to linker
cleavage conditions A, B, or C (see Table 19.13) to give the substituted aromatics in
a traceless fashion.
19.3
Solid-phase Reactions by Way of p-Allylpalladium Intermediates
Substitution reactions of allylic substrates with nucleophiles have been shown to

be catalyzed by certain palladium complexes. The catalytic cycle of the reactions
involves p-allylpalladium as the key intermediate (Scheme 19.24). Oxidative addi-
tion of the allylic substrate to a palladium(0) species forms a p-allylpalladium(II)
complex, which undergoes attack of a nucleophile on the p-allyl moiety to give an
allylic substitution product.
Scheme 19.24. Reaction pathway of allylic substitution via a p-allylpalladium intermediate.
19.3.1
Cleavage of Allyl Ester Linkers
A carboxylic acid moiety connected to a polymer resin by an allyl ester linker was
released under palladium-catalyzed allylic substitution conditions. Thus, an allyl
ester group of the PS resin-supported tripeptide 117 was cleaved reductively by tin
hydride in the presence of a palladium-PPh3 catalyst to release the peptide in high
yield. Carbonoxygen bonds of supported allyl esters 118120 were also readily
cleaved by morpholine by way of p-allylpalladium intermediates (Scheme 19.25) [47].
Scheme 19.25. Palladium-catalyzed cleavage of allylic anchoring groups.
An allyl ester of a resin-bound carboxylic acid was activated with palladium(0) to

form the Pd(h 3 -allyl)(OC(O)-resin) species 124 which readily undergoes attack by a
nucleophile to provide functionalization and release of the allyl moiety 123 in one
step (Table 19.14) [48]. Thus, the resin carboxylate ester 122 bearing a conjugated
diene moiety prepared by solid-phase ruthenium-mediated metathesis reacted with
an active methylene compound (Table 19.14, entries 14) or morpholine (Table
Tab. 19.14. Preparation of conjugated dienes via Ru-catalyzed cross-metathesis and Pd-
catalyzed allylic substitution on solid support.
Entry NuH or NuNa Product Yield (%)
Ref. 48.
19.14, entry 5) in the presence of a palladium-phosphine catalyst to give the diene

123 in high yield.
Treatment of compound 125 bearing an amino group at the homoallylic position
with palladium-dppe catalyst gave the exo-methylenepyrrole 126 via formation of a
p-allylpalladium intermediate and subsequent intramolecular nucleophilic attack
of an amino group (Scheme 19.26) [49].
Scheme 19.26. Solid-phase synthesis of pyrrolidines via

palladium-catalyzed cyclization cleavage.
19.3.2
N-Allylation via p-Allylpalladium Intermediates
The reaction of an allyl ester with a nitrogen nucleophile bound to the PSPEG
resin gave the N-allylation product (Scheme 19.27) [50]. Thus, the reaction of 2-
methoxycarbonylmethyl-2-propen-1-ol (128) with the TentaGel-bound benzylamine
127 in the presence of Pd(PPh3 )4 gave the N-allylation product 129. After ester-
ication of the allylic alcohol of 129, the resulting allyl acetate 130 was subjected
to palladium-catalyzed allylic substitution, again with various nitrogen nucleo-
philes. A resin-supported p-allylpalladium intermediate generated in situ under-
went nucleophilic attack by primary, secondary, tertiary, and cyclic amines to give
the corresponding allylic amines (131) on solid support. The N-(2-aminomethyl-2-
propenyl)-N-benzylglycine derivatives 132 were released from the resin 131 by al-
kaline hydrolysis in moderate to high yields.
19.3.3
Insertionp-Allylic Substitution System
Solid-phase synthesis of the (2-alkenyl)indoline derivatives 134 has been achieved

in one pot by the reaction of the immobilized aryl halides 133 and conjugated di-
enes which proceeded through a palladium-catalyzed insertionp-allylic substitu-
tion sequence (Scheme 19.28) [51]. Thus, the Rink resin-supported aryl iodide 133
was added to palladium(0) oxidatively to form the arylpalladium intermediate 135.
The arylpalladium intermediate 135 reacted with the diene to give the p-allylpalla-
Scheme 19.27. Solid-phase preparation of N-benzylglycine derivatives.
Scheme 19.28. Synthesis of indoles via palladium-catalyzed annulation.

dium 137 via the alkylpalladium 136. The p-allylpalladium should readily undergo
intramolecular nucleophilic attack of nitrogen atom at the ortho position to form
the 2-(alkenyl)indoline 134.
Three-component coupling of an aryl halide, 1,5-hexadiene, and the Rink-sup-
ported piperidine 138 was catalyzed by palladium to give the N-(6-aryl-2-hexenyl)-
piperidine 141 via the insertionp-allylic substitution pathway (Scheme 19.29) [52].
The alkylpalladium intermediate 140 generated in solution phase underwent a b-
eliminationinsertion process which was terminated by the formation of thermo-
dynamically stable p-allylpalladium 143. The resulting p-allylpalladium complex
143 reacted with piperidine on the resin supports to give the N-alkylated piper-
idines 139 in high yield.
Scheme 19.29. Palladium-catalyzed three-component coupling.
19.4
Palladium Catalysis with Solid-supported Complexes
Homogeneous transition metal catalysts are widely used for a variety of organic
transformations. High-throughput synthesis by solution-phase catalysis has also
been recognized as a useful methodology with the advent of ecient methods

for compound purication. One approach employs supported catalysts that can
be readily removed by ltration. Several reviews have covered the synthetic use of
solid-supported reagents, including transition metal complexes [53]. A number
of support-bound palladium complexes, in particular palladiumphosphine com-
plexes, have been designed and prepared to combine the advantages of both ho-
mogeneous and heterogeneous catalysts in one system [54]. This class of resin-
bound palladium catalysts would solve the basic problems of homogeneous
catalysts, namely the separation and recycling of the catalysts. These palladium
complex catalysts are also advantageous in that contamination of the ligand resi-
due in the products is avoided.
19.4.1
Preparation of Solid-supported Palladium Complexes and Their Use in Palladium
Catalysis
Standard procedures for the preparation of polymer-supported catalysts usually

entail surface modication of commercially available polymer resins, e.g. polysty-
renedivinylbenzene (PSDVB) or chloromethylated PSDVB resin. Thus, the re-
action of chloromethylated polystyrene with an excess of lithium diphenylphos-
phide gave the (diphenylphosphino)methylated polystyrene 145 in quantitative
yield (Scheme 19.30). The palladium(0) complex 146 was obtained by the treat-
ment of 145 with Pd(PPh3 )4 . The reaction of 145 with PdCl2 (or PdCl2 (cod)) gave
the resin-bound palladium(II) complex 147 which was readily converted to 146 by
reduction with hydrazine in the presence of PPh3 . The physical properties of the
resin matrix and the loading value of the phosphine residue are dependent on the
crosslinking value (DVB, %) and the yield of the chloromethylation step, respec-
Scheme 19.30. Preparation of phosphinylated polystyrenepalladium complexes.

tively. The resin-bound palladiumphosphine complex 146 catalyzed nucleophilic

allylic substitution via p-allylpalladium intermediates [55], telomerization of dienes
[56], the Heck reaction [57], the SuzukiMiyaura coupling [58], etc.
The bisphosphines 148 and 150 bearing alkyl substituents on their phosphorus
atoms were supported on PS resin by the nucleophilic substitution of the chloro-
methyl groups on the resin to give 149 and 151, respectively (Scheme 19.31) [59].
A palladium complex of 149 showed moderate catalytic activity to promote the
Heck reaction of iodobenzene with methyl acrylate.
Scheme 19.31. Various ligands bound to polystyrene support.
The biarylphosphines 152 also reacted with the chloromethylated PS resin under
basic conditions to give the PS-supported biarylphosphines 153 (Scheme 19.32)
[60]. The resin-bound biaryl-(dialkyl)phosphines 153 were the ligands designed for
use in the palladium-catalyzed amination and SuzukiMiyaura coupling of aryl
halides, especially those of aryl chlorides, whereas the use of electron-rich phos-
phine ligands allowed for an increase in the scope of the aryl halide substrate [61].
Scheme 19.32. Various ligands bound to polystyrene support (2).
The polymer-supported carbene complexes of palladium 155 were prepared by

the nucleophilic substitution of the bromomethylated Wang resin with 154 under
basic reaction conditions (Scheme 19.33) [62]. The catalytic activity of 155 for the
Heck reaction of aryl bromides with acrylates or styrene was found to exhibit high
turnover numbers (TON) up to 5000. The supported carbene complexes 155 were
air-stable and recyclable catalysts.
Scheme 19.33. Various ligands bound to polystyrene support (3).
Polymerization of ligand monomers is a useful tool for preparing polymer-

supported ligands. The crosslinked polystyrene-bound ferrocenyl bisphosphine
ligand 157 was prepared by the copolymerization of styrene, divinylbenzene, and
1,1 0 -bis-(diphenylphosphino)-2-vinylferrocene (156) (Scheme 19.34) [63]. The load-
ing density of the catalyst on the support was readily controlled by the ratio of the
monomers used.
Scheme 19.34. Preparation of polymer-bound ferrocenylphosphine.
Carbonylative intramolecular Stille coupling to form macrocyclic molecules was

investigated with a palladium complex of the polymer-bound ferrocenyl phosphine
157 (Scheme 19.35). One of the major problems encountered in the intramolecu-
lar macrocyclization is the formation of linear oligomers via an intermolecular
pathway. Site isolation of the catalytic sites on a polymer backbone has been
achieved with relatively low loading density of the catalyst to suppress the in-
termolecular reactions. Thus, ester 158 bearing an alkenylstannane and an alkenyl

triate gave high yields of the corresponding keto lactone 159 with the Pd(0)/157
complex and LiCl under carbon monoxide, whereas only moderate yields of the
macrocycles were obtained under homogeneous conditions using Pd(PPh3 )4 or
PdCl2 (dppf ).
Scheme 19.35. Palladium-catalyzed macrocyclization.
The polypyrrole-bound mono- and bisphosphines 162 and 163 were prepared
as their P-borane complexes from the corresponding monomers 160 and 161 via
FeCl3 -induced or electrochemical polymerization conditions (Scheme 19.36) [64].
These phosphineborane complexes reacted with palladium(II) without prede-
complexation to give the polypyrrole-bound palladium(0)phosphine complexes,
where the borane on the phosphorus atom served as a reducing agent of palladiu-
m(II). The resulting immobilized polypyrrole palladium(0)phosphine complexes
catalyzed the Heck reaction and the p-allylic substitution of allyl acetates.
Scheme 19.36. Preparation of polypyrrole-bound phosphineborane.
Ring-opening methathesis polymerization of the norbornene monomer 164 hav-

ing a 2-endo-N,N-di-(2-pyridyl)carbamide group was carried out via a living poly-
merization using the Schrock catalyst (Scheme 19.37) [65]. The resulting living
polymer chains were crosslinked using 1,4,4a,5,8,8a-hexahydro-1,4,5,8-exo-endo-
dimethanonaphthalene (165) to give the bispyridyl ligand 166. Its palladium com-
plex 167 generated by treatment of 166 with H2 PdCl 4 catalyzed the Heck reaction
of aryl bromides and even aryl chlorides. Thus, the reaction of chlorobenzene with
styrene in the presence of 0.003 mol% of the palladium species 167 and tetrabuty-
lammonium bromide in dimethylacetamide at 140 C gave an 89% isolated yield
of trans-stilbene where the TON observed reached 23,600.
Scheme 19.37. Ring-opening metathesis polymerization (ROMP) of monomer ligands.
Polyaminoamide (PAMAM) dendrimers of generation 04 on silica [66] and

carbosilane dendrimers [67] were used as solid support for immobilization of the
palladium catalysts. Thus, for example, (diphenylphosphino)methyl groups were
introduced on the terminal nitrogen of PAMAM chains by treatment of 168 with
paraformaldehyde and diphenylphosphine (Scheme 19.38). Treatment of the re-
sulting dendrimer bearing diphenylphosphino groups with PdMe 2 (tmeda) gave
the chelate complex 169, which showed good catalytic activity in the Heck reaction.
The triarylphosphine moiety was incorporated into the PSPEG resin by a solid-
phase amide-forming reaction (Scheme 19.39) [68]. Thus, a mixture of the PEG
PS amino resin, 2 equiv. of 4-(diphenylphosphino)benzoic acid, 1-(3-dimethylami-
nopropyl)-3-ethylcarbodiimide hydrochloride (EDCI), and 1-hydroxybenzotriazole
hydrate (HOBt) in DMF was agitated to give the PSPEG resin-supported phos-
phine 171. The complete consumption of the amino residue of the PEG chain was
conveniently monitored by the Kaiser test. Formation of the palladiumphosphine
complex 172 on the resin was performed by mixing [PdCl(p-C3 H5 )]2 and 171 in an
appropriate organic solvent at ambient temperature for 10 min. The PSPEG
resin-supported complex 172 exhibited high catalytic activity in water due to its
amphiphilic property. Allylic substitution [68], Heck reaction [69], carbonylation
[70], and SuzukiMiyaura [70] coupling took place in a single aqueous medium at
room temperature by use of 172.
Scheme 19.38. Dendrimer-bound palladiumphosphine complex.
Amphiphilic polymer-supported phosphine ligands were also prepared on

poly(N-isopropyl)acrylamide (PNIPAM) resin (Scheme 19.40) [71]. The palladium
complex of the PNIPAMphosphine, formed from reaction of 174 or 175 with
Pd(dba)2 , showed high catalytic activity both in organic solvents and in water to
promote p-allylic substitution of allyl carbonates and the Sonogashira reaction of
aryl iodides.
19.4.2
Solid-supported Chiral Palladium Catalysts
Asymmetric reactions catalyzed by transition metal complexes containing optically

active ligands have attracted great interest because of their synthetic utility. A vast
Scheme 19.39. PSPEG resin-supported amphiphilic palladiumphosphine complexes.
Scheme 19.40. PNIPAM-supported amphiphilic phosphine ligands.
amount of research has been reported to date on asymmetric reactions using homo-
geneous catalyst systems in which activity and stereoselectivity can be tuned by vary-
ing the ligand structure. Recently, immobilization of the enantioselective catalysts
has been recognized as one of the most promising strategies for achieving highly
stereoselective catalysis under heterogeneous conditions [72]. Several examples of
chiral ligands supported on polymer resin, which have found utility in asymmetric
palladium catalysis, are shown in Scheme 19.41. Palladium complexes of the resin-
supported 2-diphenylphosphino-2 0 -substituted-1,1 0 -binaphthyl (MOP) ligand 176
[73] and pyridinoxazoline 179 [74] catalyzed allylic substitution with good to high
stereoselectivity. The PS-supported BINAP 177 [75] was applied to a palladium(II)-
catalyzed aldol reaction of a silyl enolate [76]. A novel chiral ligand, (3R,9aS)-(2-
aryl-3-(2-diphenylphosphino)-phenyl)-tetrahydro-1H-imidazo[1,5-a]indole-1-one was
designed, prepared, and immobilized on an amphiphilic polystyrene-poly(ethylene
References 581
glycol) graft copolymer (PSPEG) resin (178) [77]. A palladium complex of the PS
PEG resin-supported ligand 178 catalyzed the allylic substitution of both cyclic and
acyclic allylic esters in water with high enantioselectivity (up to 98% ee). The PS
PEG-supported Pd complex was readily recovered by simple ltration and reused
without loss of catalytic activity or enantioselectivity.
Scheme 19.41. Resin-supported chiral ligands.
References
1 For reviews, see: a) J. Tsuji, Palladium 5 B. J. Backes, J. A. Ellman, J. Am.

Reagents and Catalysts. John Wiley and Chem. Soc. 1994, 116, 1117111172.
Sons, Chichester 1995; b) R. F. Heck, 6 J. W. Guiles, S. G. Johnson, W. V.
Palladium Reagents in Organic Synthe- Murray, J. Org. Chem. 1996, 61,
sis. Academic Press, New York 1985. 51695171.
2 For recent reviews, see: a) B. A. 7 R. Frenette, R. W. Friesen, Tetra-
Bunin, Combinatorial Index. hedron Lett. 1994, 35, 91779180.
Academic Press, London 1998; b) D. 8 S. Wendeborn, S. Berteina, W. K.-D.
Obrecht, J. M. Villalgordo, Solid- Brill, A. D. Mesmaeker, Synlett 1998,
Supported Combinatorial and Parallel 671675.
Synthesis of Small-Molecular-Weight 9 S. Chamoin, S. Houldsworth, C. G.
Compound Libraries, Tetrahedron Kruse, W. I. Bakker, V. Snieckus,
Organic Chemistry Series Vol. 17. Tetrahedron Lett. 1998, 39, 41794182.
Elsevier, Oxford 1998. 10 S. R. Piettre, S. Baltzer, Tetrahedron
3 For a recent review, see: F. Z. Lett. 1997, 38, 11971200.
Dorwald, Organic Synthesis on 11 a) S. D. Brown, R. W. Armstrong, J.
Solid Phase, Wiley-VCH, Weinheim Am. Chem. Soc. 1996, 118, 63316332;
2000. b) S. D. Brown, R. W. Armstrong, J.
4 a) A. Suzuki, Pure Appl. Chem. 1985, Org. Chem. 1997, 62, 70767077.
57, 1749; b) N. Miyaura, A. Suzuki, 12 a) F. X. Woolard, J. Paetsch, J. A.
Chem. Rev. 1995, 95, 2457. Ellman, J. Org. Chem. 1997, 62, 6102
6103; b) C. Vanier, A. Wagner, C. Zhou, Tetrahedron Lett. 1995, 36,

Mioskowski, Tetrahedron Lett. 1999, 45674570.
40, 43354338. 33 W. Yun, R. Mohan, Tetrahedron Lett.
13 L. A. Thompson, F. L. Moore, Y.-C. 1996, 37, 71897192.
Moon, J. A. Ellman, J. Org. Chem. 34 V. Arumugam, A. Routledge, C.
1998, 63, 20662067. Abell, S. Balasubramanian,
14 W. Li, K. Burgess, Tetrahedron Lett. Tetrahedron Lett. 1997, 38, 64736476.
1999, 40, 65276530. 35 a) H.-C. Zhang, B. E. Maryanoff, J.
15 J. K. Stille, Angew. Chem. Int. Ed. Org. Chem. 1997, 62, 18041809.
Engl. 1986, 25, 508524. 36 K. Akaji, Y. Kiso, Tetrahedron Lett.
16 M. S. Deshpande, Tetrahedron Lett. 1997, 38, 51855188.
1994, 35, 56135614. 37 G. L. Bolton, J. C. Hodges, J. Comb.
17 S. Chamoin, S. Houdsworth, V. Chem. 1999, 1, 130133.
Snieckus, Tetrahedron Lett. 1998, 39, 38 a) S. L. Buchwald, A. S. Guram, R.
4175418. A. Rennels, Angew. Chem. Int. Ed.
18 M. S. Brody, M. G. Finn, Tetrahedron Engl. 1995, 34, 13481350; b) J. F.
Lett. 1999, 40, 415418. Hartwig, J. Louie, Tetrahedron Lett.
19 S. Wendeborn, A. D. Mesmaeker, 1995, 36, 3609.
Synlett 1998, 865867. 39 Y. D. Ward, V. Farina, Tetrahedron
20 K. Sonogashira, Y. Tohda, Tetra- Lett. 1996, 37, 69936996.
hedron Lett. 1975, 44674470. 40 C. A. Willoughby, K. T. Chapman,
21 S. Berteina, S. Wendeborn, W. K.-D. Tetrahedron Lett. 1996, 37, 7181
Brill, A. D. Mesmaeker, Synlett 1998, 7184.
676678. 41 For examples of miscellaneous
22 M. C. Fagnola, I. Candiani, G. synthetic applications of palladium-
Visentin, W. Cabri, F. Zarini, N. catalyzed coupling reactions, see:
Mongelli, A. Bedeschi, Tetrahedron a) P. A. Tempest, R. W. Armstrong,
Lett. 1997, 38, 23072310. J. Am. Chem. Soc., 1997, 119, 7607
23 H.-C. Zhang, K. K. Brumeld, L. 7608 (SuzukiMiyaura coupling,
Jaroskova, B. E. Maryanoff, Stille coupling); b) M. A. Lago, T. T.
Tetrahedron Lett. 1998, 39, 44494452. Nguyen, P. Bhatnagar, Tetrahedron
24 D. Fancelli, M. C. Fagnola, D. Lett. 1998, 39, 38853888 (Suzuki
Severino, A. Bedeschi, Tetrahedron Miyaura coupling); c) Y. Han, A.
Lett. 1997, 38, 23112314. Giroux, C. Lepine, F. Laliberte, Z.
25 M. D. Collini, J. W. Ellingboe, Huang, H. Perrier, C. I. Bayly, R.
Tetrahedron Lett. 1997, 38, 79637966. N. Young, Tetrahedron, 1999, 55,
26 A. B. Dyatkin, R. A. Rivero, 1166911685 (SuzukiMiyaura
Tetrahedron Lett. 1998, 39, 36473650. coupling); d) M. Larhed, G.
27 S. I. Khan, M. W. Grinstaff, Lindeberg, A. Hallberg, Tetrahedron
Tetrahedron Lett. 1998, 39, 80318034. Lett. 1996, 37, 82198222 (Stille
28 S. Marquais, M. Arlt, Tetrahedron coupling); e) F. W. Forman, I.
Lett. 1996, 37, 54915494. Sucholeiki, J. Org. Chem 1995, 60,
29 M. Rottlander, P. Knochel, Synlett 523528 (Stille coupling); f ) P. R. L.
1997, 10841086. Malenfant, J. M. J. Frechet, Chem.
30 a) R. F. Heck, Org. React. 1982, 27, Commun. 1998, 26572568 (Stille
345; b) R. F. Heck in: Comprehensive coupling); g) J. C. Nelson, J. K.
Organic Synthesis, Vol. 4. Trost, B. Young, J. S. Moore, J. Org. Chem
M., Fleming, I. (eds), Pergamon 1996, 61, 81608168 (Sonogashira
Press, New York 1991, 833. reaction); h) S. I. Khan, M. W.
31 K.-L. Yu, M. S. Deshpande, D. M. Grinstaff, J. Am. Chem. Soc. 1999,
Vyas, Tetrahedron Lett. 1994, 35, 8919 121, 47044705 (Sonogashira
8922. reaction); i) S. Huang, J. M. Tour, J.
32 M. Hiroshige, J. R. Hauske, P. Am. Chem. Soc. 1999, 121, 49084909
References 583
(Sonogashira reaction); j) F. Homsi, K. D. Nasturica, Synthesis 2000, 1035

Nozaki, T. Hiyama, Tetrahedron Lett. 1074.
2000, 41, 58695872 (Si-mediated 54 Development of nano-particles of
coupling); k) Y. Han, A. Roy, A. palladium crystallites encapsulated
Giroux, Tetrahedron Lett. 2000, 41, inside polymer resin have become a
54475451 (Zn-mediated coupling); major challenge; their synthetic use is,
l) H. A. Dondas, R. Grigg, W. S. however, still limited to hydrogenation
MacLachlan, D. T. MacPherson, J. of unsaturated compounds. For
Markandu, V. Sridharan, S. examples, see: a) D. E. Bergbreiter,
Suganthan, Tetrahedron Lett. 2000, B. Chen, T. J. Lynch, J. Org. Chem.
41, 967970 (Heck reaction); m) S. 1983, 48, 41794186; b) M. Zecca, R.
Ma, D. Duan, Z. Shi, Org. Lett. 2000, Fisera, G. Palma, S. Lora, M.
2, 14191422 (Heck-type reaction). Hronec, M. Kralik, Chem. Eur. J.
42 R. C. Larock, E. K. Yum, J. Am. 2000, 6, 19801986.
Chem. Soc. 1991, 113, 66896690. 55 B. M. Trost, E. Keinan, J. Am. Chem.
43 H.-C. Zhang, K. K. Brumeld, B. E. Soc. 1978, 100, 77797781.
Maryanoff, Tetrahedron Lett. 1997, 38, 56 K. Kaneda, H. Kurosaki, M.
24392442. Terasawa, T. Imanaka, S. Teranishi,
44 A. L. Smith, G. I. Stevenson, C. J. J. Org. Chem. 1981, 46, 23562362.
Swain, J. L. Castro, Tetrahedron Lett. 57 C.-M. Andersson, K. Karabelas, A.
1998, 39, 83178320. Hallberg, J. Org. Chem. 1985, 50,
45 J. S. Koh, J. A. Ellman, J. Org. Chem. 38913895.
1996, 61, 44944495. 58 a) S.-B. Jang, Tetrahedron Lett. 1997,
46 F. Stieber, U. Grether, H. 38, 17931796; b) I. Fenger, C. L.
Waldmann, Angew. Chem. Int. Ed. Drian, Tetrahedron Lett. 1998, 39,
1999, 38, 10731077. 42874290; c) K. Inada, N. Miyaura,
47 a) F. Guibe, O. Dangles, G. Tetrahedron 2000, 56, 86618664.
Balavoine, Tetrahedron Lett. 1989, 30, 59 a) M. A. Fox, D. A. Chandler, P.-W.
26412644; b) H. Kunz, B. Dombo, Wang, Macromolecules 1991, 24, 4626
Angew. Chem. Int. Ed. Engl. 1988, 27, 4636; b) P.-W. Wang, M. A. Fox, J.
711713; c) P. L.-Williams, G. Jou, F. Org. Chem. 1994, 59, 53585364.
Albericio, E. Giralt, Tetrahedron Lett. 60 C. A. Parrish, S. L. Buchwald, J.
1991, 32, 42074210; d) O. Seitz, H. Org. Chem. 2001, 66, 38203827.
Kunz, J. Org. Chem. 1997, 62, 813 61 A. F. Littke, C. Dai, G. C. Fu, J. Am.
826. Chem. Soc. 2000, 122, 4020.
48 S. C. Schurer, S. Blechert, Synlett. 62 J. Schwarz, V. P. W. Bohm, M. G.
1997, 166168. Gardiner, M. Grosche, W. A.
49 R. C. D. Brown, M. Fisher, Chem. Herrmann, W. Hieringer, G.
Commun. 1999, 15471548. Raudaschl-Sieber, Chem. Eur. J.
50 Z. Flegelova, M. Patek, J. Org. 2000, 6, 17731780.
Chem. 1996, 61, 67356738. 63 J. K. Stille, H. Su, D. H. Hill, P.
51 Y. Wang, T.-N. Huang, Tetrahedron Schneider, M. Tanaka, D. L.
Lett. 1998, 39, 96059608. Morrison, L. S. Hegedus,
52 Y. Wang, T.-N. Huang, Tetrahedron Organometallics 1991, 10, 19932000.
Lett. 1999, 40, 58375840. 64 N. Riegel, C. Darcel, O. Stephan, S.
53 For reviews, see: a) D. C. Bailey, S. H. Juge, J. Organomet. Chem. 1998, 567,
Langer, Chem. Rev. 1981, 81, 109 219233.
148; b) S. J. Shuttleworth, S. M. 65 M. R. Buchmeiser, K. Wurst, J. Am.
Allin, P. K. Sharma, Synthesis 1997, Chem. Soc. 1999, 121, 1110111107.
12171239; c) K. Burgess, A. M. 66 a) H. Alper, P. Arya, S. C. Bourque,
Porte, Advance Catalytic Processes G. R. Jefferson, L. E. Manzer, Can.
1997, 2, 6982; d) S. J. Shuttle- J. Chem. 2000, 78, 920924; b) similar
worth, S. M. Allin, R. D. Wilson, dendrimer-bound phosphine ligands
anchored on PS resin have been Vankelecom, P. A. Jacobs (eds)

prepared for rhodium-catalyzed Chiral Catalyst Immobilization and
reactions, see: P. Arya, G. Panda, N. Recycling. Wiley-VCH, Weinheim
V. Rao, H. Alper, S. C. Bourque, L. 2000.
E. Manzer, J. Am. Chem. Soc. 2001, 73 Y. Uozumi, H. Danjo, T. Hayashi,
123, 28892890. Tetrahedron Lett. 1998, 39, 8303.
67 E. B. Eggeling, N. J. Hovestad, J. T. 74 K. Hallman, E. Macedo, K.
B. H. Jastrzebski, D. Vog, G. V. Nordstrom, C. Moberg, Tetrahedron
Koten, J. Org. Chem. 2000, 65, 8857 Asymmetry 1999, 10, 40374046.
8865. 75 a) D. J. Bayston, J. L. Fraser, M. R.
68 a) Y. Uozumi, H. Danjo, T. Hayashi, Ashton, A. D. Baxter, M. E.
Tetrahedron Lett. 1997, 38, 3557; b) H. Polywka, E. Moses, J. Org. Chem.
Danjo, D. Tanaka, T. Hayashi, Y. 1998, 63, 31373140; b) D. J. Bayston,
Uozumi, Tetrahedron 1999, 55, 14341. J. L. Fraser, M. R. Ashton, A. D.
69 Y. Uozumi, T. Watanabe, J. Org. Baxter, M. E. Polywka, E. Moses,
Chem. 1999, 64, 6921. Speciality Chemicals 1998, 18, 224
70 Y. Uozumi, H. Danjo, T. Hayashi, J. 226.
Org. Chem. 1999, 64, 3384. 76 A. Fujii, M. Sodeoka, Tetrahedron
71 D. E. Bergbreiter, Y.-S. Liu, Lett. 1999, 40, 80118014.
Tetrahedron Lett. 1997, 38, 7843. 77 Y. Uozumi, K. Shibatomi, J. Am.
72 For a review, see: D. E. De Vos, I. F. J. Chem. Soc. 2001, 123, 29192920.
585
20
Olen Metathesis and Related Processes for CC
Multiple Bond Formation
Florencio Zaragoza
20.1
Introduction
Olen metathesis refers to a reaction in which two alkenes exchange their alkyli-
dene fragments (Scheme 20.1) [15]. This reaction has been applied to the prepa-
ration of compound libraries in solution and has also been used for solid-phase
synthesis, thus enabling its application to automated parallel synthesis. Examples
of metathesis on solid phase include the chemical transformation of resin-bound
intermediates as well as the cleavage of nal products from the support.
Scheme 20.1. The mechanism of olen metathesis,

dissociative mechanism for ruthenacyclobutane formation [27],
and some useful ruthenium-based catalysts.

ISBN: 3-527-30509-2
586 20 Olefin Metathesis and Related Processes for CC Multiple Bond Formation
Olen metathesis can be catalyzed both by heterogeneous catalysts (mainly sup-

ported transition metal oxides) and by soluble transition metal complexes (mainly
tungsten, molybdenum, or ruthenium carbene complexes); the process has been
known and exploited industrially since the early 1960s [6, 7]. However, it was not
until soluble and highly eective catalysts were discovered by Schrock, Grubbs,
and others that this reaction could be performed under suciently mild conditions
to enable its systematic application to organic synthesis. Ruthenium carbene com-
plex 1 [8], and the newer, more eective complexes 2 [912] and 3 [1318] (Scheme
20.1) are particularly well suited for organic synthesis because of their high stabil-
ity and chemoselectivity. These and related complexes tolerate a broad selection of
functional groups and mediate olen metathesis even in the presence of air and
protic solvents, including water [1921]. New catalysts with improved properties
are continuously being developed [2226].
The mechanism by which carbene complexes catalyze olen metathesis is
shown in Scheme 20.1. A reversible 2 2 cycloaddition of the carbene complex to
the alkene yields a metallacyclobutane, which upon cycloreversion can yield either
the products of olen metathesis or the starting materials. Because all of these
transformations are reversible, equilibrium toward the desired products must be
shifted either by continuous removal of one of the products (e.g. ethylene) or by
using substrates for which olen metathesis cannot be reversed (e.g. strained cy-
cloalkenes).
In the case of ruthenium carbene complexes such as 1, one of the phosphine li-
gands dissociates from the complex during catalysis [27]. It is still being debated
whether this dissociation takes place before or after coordination to the alkene. In
the case of complex 3, it has been shown that olen metathesis is initiated by a
dissociative mechanism, as shown in Scheme 20.1 [27].
Although the currently available catalysts are exceedingly useful for many appli-
cations, a series of drawbacks still limits their scope, and there is ample room for
improvement. Hopefully, some of these weaknesses will be overcome as our un-
derstanding of the precise mechanism of carbene complex-mediated olen meta-
thesis deepens and new types of catalysts emerge. One of the problems of current
metathesis catalysts is that they generally yield internal alkenes as mixtures of E-
and Z-isomers. Moreover, because the required carbene complexes can also react
with soft nucleophiles other than alkenes, care must be taken to remove all traces
of amines, pyridines, imidazoles, or other potential ligands from the solvent and
the reactants in order to avoid deactivation of the catalyst. For the same rea-
son, olen metathesis proceeds best in solvents of low nucleophilicity [CH2 Cl2 >
toluene > tetrahydrofuran (THF)]. Electron-rich alkenes (enamines, enol ethers)
do not usually undergo metathesis because donor-substituted carbene com-
plexes are formed as intermediates, which are no longer electrophilic enough to
act as metathesis catalysts. With some of the most recently developed catalysts
(such as 3, Scheme 20.1), however, even enol ethers may undergo metathesis [17].
The reaction rate of olen metathesis sharply decreases in the series terminal
alkene > internal, disubstituted alkene > trisubstituted alkene [2, 14], and 1,2-
disubstituted cis-alkenes are usually more reactive than the corresponding trans-
alkenes.
Most of the currently used catalysts (e.g. 1, 2, and 3) are ruthenium benzylidene
complexes. One of the reasons for choosing the benzylidene ligand is that styrene
does not generally undergo cross-metathesis eciently when using ruthenium
carbene complexes as catalysts [28]. For this reason, only small amounts of prod-
uct resulting from a cross-metathesis with styrene will result, even if large amounts
of catalyst are used (see, for example, Scheme 20.20).
Olen metathesis reactions have been grouped into dierent categories (Scheme
20.2). These include self-metathesis (reaction of one alkene with itself ), cross-
metathesis (reaction of two dierent alkenes with each other), ring-opening meta-
thesis polymerization (ROMP, polymerization of a strained, cyclic alkene), and
ring-closing metathesis (RCM, cyclization of a diene). All these types of olen
metathesis can be conducted on insoluble supports, and can thus be adapted to
automated, parallel solid-phase synthesis. For combinatorial chemistry in solution,
mainly cross-metathesis and ROMP have been used.
Scheme 20.2. Categories of olen metathesis reactions [2].
Alkynes are also suitable substrates for catalytic olen metathesis (Scheme 20.3).
Treatment of a mixture of an alkene and an alkyne with a metathesis catalyst can
lead to the clean formation of dienes [29, 30]. Because alkynes usually react faster
than alkenes with carbene complexes, the formation of dienes from alkenes and
alkynes is assumed to proceed via the initial addition of the catalyst to the alkyne,
followed by cycloreversion and reaction of the resulting vinylcarbene complex with
the alkene (Scheme 20.3). Treatment of alkynes with carbyne complexes can bring
about alkyne metathesis [1, 31], which presumably also proceeds via reversible
2 2 cycloadditions (Scheme 20.3). Some of these intriguing transformations have
also been performed on insoluble supports, and might be suitable for parallel syn-
thesis.
Scheme 20.3. Metathesis of alkynes.
20.2
Olen Metathesis in Solution
For the preparation of compound libraries in solution using olen metathesis,

mainly two strategies have been employed. These are the cross-metathesis of mix-
tures of terminal alkenes, to yield mixtures of internal, disubstituted alkenes, and
the oligomerization by ring-opening metathesis of strained, cyclic alkenes (Scheme
20.4). Ring-closing metathesis in solution has been used mainly for the prepara-
tion of small arrays of compounds or of single compounds.
Scheme 20.4. Strategies for the preparation of compound mixtures using olen metathesis.
20.2.1
Scope and Limitations of Olen Metathesis in Solution
Cross-metathesis of two dierent terminal alkenes in solution only rarely gives

high yields of one product (for recent advances in selective cross-metathesis, see
20.2 Olefin Metathesis in Solution 589
[14, 28, 3234]). Usually, mixtures of the products of cross-metathesis and of self-
metathesis are obtained, each of them as mixtures of E- and Z-isomers. Unfor-
tunately, some alkenes show a high tendency to undergo self-metathesis (to form
symmetric dimers; see, for example, [35, 36]), whereas other alkenes (acryloni-
trile, styrenes) undergo self-metathesis only slowly or not at all. For this reason,
cross-metathesis of mixtures of dierent olens will not always yield the statisti-
cally expected amounts of internal olens. This feature can cause problems during
the deconvolution of such compound libraries because potent ligands formed only
in low quantities are usually dicult to identify by deconvolution.
A further problem of cross-metathesis in solution is that a purication step will
usually be required to remove the catalyst. With the recent development of immo-
bilized catalysts (e.g. 46) [3741], however, this problem has been reduced. Un-
fortunately, all of the immobilized ruthenium carbene complexes described so far
(Scheme 20.5) lose activity rather quickly; this fact might be due to the inherent
instability of these complexes and to the fact that during catalysis detachment of
the metal from the support can readily occur.
Scheme 20.5. Support-bound ruthenium carbene complexes,

useful as insoluble metathesis catalysts [24, 3841]. PS,
crosslinked polystyrene; PEG, poly(ethylene glycol).
All known metathesis catalysts, being essentially electrophilic reagents, react

with nucleophiles such as amines, nitrogen-containing heterocycles, and thiols.
Accordingly, alkenes containing these functional groups (which are often impor-
tant for the interaction of small molecules with proteins) cannot be used as build-
ing blocks for library preparation, unless these functional groups are eectively
masked.
20.2.2
Examples of Library Preparation by Cross-metathesis in Solution
One of the rst examples of the preparation of compound libraries by cross-

metathesis was reported by Boger and coworkers [4244], who dimerized mixtures
of alkenoyl iminodiacetamides by cross-metathesis in solution (Scheme 20.6). The
aim of this work was to identify new agonists or antagonists for biochemical signal
transduction processes which involve the dimerization or oligomerization of pro-
Scheme 20.6. Preparation of libraries of iminodiacetamides by cross-metathesis.
teins [e.g. tyrosin/serine/threonine kinase receptors, cytokine receptors, tumor ne-

crosis factor (TNF) receptors].
During optimization of the chemistry they found that 3-butenamides (n 1;
Scheme 20.6) did not undergo metathesis at all, and 4-pentenamides n 2 only
reacted sluggishly under the conditions of cross-metathesis. Longer o-alkenoyl
amides, however, cleanly yielded the expected internal alkenes [44]. The libraries
were usually puried by column chromatography.
Similarly, Benner and coworkers [45] prepared mixtures of internal alkenes by
cross-metathesis of mixtures of terminal olens. The resulting libraries of alkenes
were oxidized to the corresponding diols or epoxides. The mixtures of diols were
the starting monomers for receptor-assisted combinatorial synthesis, in which
these diols were to be dimerized reversibly to borate esters in the presence of a re-
ceptor. Under conditions of dynamic equilibrium, enhanced concentrations of
those borate esters with highest anity to the receptor are to be expected [45].
The authors observed during the optimization of the metathesis reaction that
certain alkenes (Scheme 20.7) failed to undergo cross-metathesis and others only
reacted sluggishly, depending on the functional groups present in these alkenes.
In particular, nitrogen-containing alkenes did not undergo metathesis this might
be due to complexation with the catalyst.
A further example of target-accelerated combinatorial synthesis has been re-
ported by Nicolaou et al. [46]. With the aim of nding new vancomycin dimers
with improved antibiotic activity, various alkenylated derivatives of vancomycin
were subjected to conditions of olen metathesis in the presence of derivatives of
l-Lys-d-Ala-d-Ala, the peptide to which vancomycin strongly binds and thereby in-
hibits the cell wall growth of bacteria (Scheme 20.8). Cross-metathesis was per-
formed in aqueous solution at 23 C in the presence of a phase-transfer catalyst
(C12 H25 NMe3 Br) and with (Cy3 P)2 Cl2 RubCHPh (0.2 equiv.) (1) as metathesis cata-
lyst. In this instance, it was observed that addition of the target peptide in fact led
to increased concentrations of those dimers which were also the more potent anti-
biotics.
Scheme 20.7. Suitability of alkenes for cross-metathesis [45].
Brandli and Ward [47] prepared mixtures of internal, disubstituted alkenes by

equilibration of internal olens (oleic acid derivatives). Their synthesis was per-
formed either in dichloromethane or without any solvent, and proceeded satisfac-
torily with as little as 0.1% of (Cy3 P)2 Cl2 RubCHPh (1) if no solvent was used. With
gas chromatographymass spectrometry (GC/MS) and 13 C-NMR (nuclear mag-
netic resonance) spectroscopy the authors were able to identify all ten expected
products (each as E/Z mixture) of the equilibration of two dierent, unsymmet-
rical alkenes (Scheme 20.9).
Scheme 20.8. Vancomycin dimers prepared by cross-

metathesis (m 1, 2, 3, 7; R H, b-Ala, l-Asn, d-LeuNMe, g-
Abu, l-Arg, l-Phe [46]).
Scheme 20.9. Equilibration of internal alkenes by cross-metathesis [47].
20.2.3
Examples of Library Preparation by Ring-closing Metathesis in Solution
Ring-closing metathesis is increasingly being used for the preparation of confor-

mationally constrained analogs of peptides. Most of the examples reported, how-
ever, only describe the synthesis of single compounds or of small arrays of com-
pounds. These syntheses are only rarely based on easily available dienes, and are
therefore not always suitable for the preparation of large compound libraries.
Moreover, unlike cross-metathesis, ring-closing metathesis is an intramolecular
reaction which does not increase the number of products or their diversity. Hence,
ring-closing metathesis only allows the conversion of one library into another,
without changing the total number of products within this library.
Cyclic peptides are an important tool for the identication of turns within a
peptide which are critical for its biological activity. In analogy to the Ala-scan, in
which all the amino acids of a peptide are sequentially replaced by alanine to
identify those amino acids which are crucial for biological activity, a loop scan
(Scheme 20.10 [48]) may be used to locate possible turns within a peptide and to
identify conformationally constrained analogs (710) of the original peptide (11).
Scheme 20.10. Illustrative example of loop scan. Four cyclic

analogs (710) of the original peptide are prepared and their
biological activity is compared with the activity of the original
peptide (11). X variable spacer.
Some new strategies for the preparation of cyclic peptides by ring-closing meta-
thesis are presented below to illustrate the scope of these cyclizations.
Liskamp and coworkers have investigated the cyclization of N-alkenylated pep-
tides (12) by ring-closing metathesis (Scheme 20.11) [4850]. The peptides were
prepared by standard solid-phase synthesis, and the N-alkenylation was eected
during the assembly of the peptide by N-sulfonylation with 2-nitrobenzenesulfonyl
chloride, followed by N-alkenylation under Mitsunobu conditions and sulfona-
mide cleavage by treatment with mercaptoethanol/1,8-diazabicyclo[5.4.0]undec-7-
ene (DBU). Ring-closing metathesis could be performed either in solution or on
solid phase, but in solution higher yields were usually obtained [50]. Cyclization
experiments showed that the length of the N-alkenyl group was crucial for ring
closure. N-Allyl peptides (12) could only be cyclized to yield eight-member rings
(13). Larger ring sizes required the use of N-homoallyl or N-(4-penten-1-yl) pep-
tides. The cyclization of tripeptides (to form a 15-member ring, e.g. (14)) was
particularly dicult, and only proceeded satisfactorily with N-(4-penten-1-yl) sub-
stitution (Scheme 20.11).
Scheme 20.11. Preparation of cyclic peptides by ring-closing

metathesis in solution, and lengths of the N-alkenyl substituent
required for ring formation [49].
Other recent examples of the preparation of cyclic peptide analogs by ring-

closing metathesis in solution include the cyclic sulfamides 15 [51], cyclic sulfo-
namides 16 [37], and siloxanes 17 [52] (Scheme 20.12). The last were synthetic in-
termediates for the preparation of diols such as 18, which were used as building
blocks for the solid-phase synthesis of peptide analogs [52]. Further examples of
Scheme 20.12. Peptidomimetics prepared by ring-closing metathesis in solution.

20.3 Olefin Metathesis on Solid Phase 595
solution-phase synthesis of peptide mimetics by ring-closing metathesis have been

reported [2, 5356].
20.2.4
Examples of Library Preparation by Ring-opening Metathesis Polymerization in
Solution
Functionalized oligomers and polymers are of interest for a variety of applications.

These include their use in chromatography as the stationary phase [57] for the
separation of metals [58] or soluble receptors, and as carriers for the controlled re-
lease of drugs [59]. Oligomers functionalized with biologically relevant molecules
such as amino acids or carbohydrates can also be used to mimic various biopoly-
mers (proteins, DNA) or the surface of a cell. Such biopolymer mimetics are use-
ful tools for studying the interaction of cell surfaces with biopolymers.
Ring-opening metathesis polymerization (ROMP), in which a strained, cyclic al-
kene is polymerized with the aid of a metathesis catalyst, oers several features
which make this reaction particularly attractive for the preparation of functional-
ized oligomers [58, 6062]. ROMP can be conducted as a living polymerization
because the rate of initiation can be faster than the rate of propagation. This fea-
ture enables the preparation of oligomers with well-dened length and narrow
molecular weight distribution. Because the oligomers persist as active carbene
complexes even when one monomer has been consumed, ROMP also enables the
preparation of block copolymers, in which various dierent monomers are poly-
merized sequentially.
Kiessling and coworkers have used ROMP for the preparation of carbohydrate-
functionalized oligomers, which were used as ligands for various carbohydrate-
binding proteins (concanavalin A [63], P-selectin [64], L-selectin [65]). Initially,
ROMP was performed with norbornenes that were already covalently linked to a
carbohydrate. However, better results were later, obtained by preparing activated
oligomers by ROMP, which were then derivatized with the carbohydrate (Scheme
20.13).
Maynard et al. [67] used ROMP of exo-5-norbornene-2-carboxylic acid deriva-
tives for the preparation of oligomers displaying the peptide sequences GlyaArga
GlyaAsp and SeraArgaAsn, which play an important role in the binding of ex-
tracellular matrix proteins to cell-surface integrins. Both homopolymers and co-
polymers were prepared and characterized (Scheme 20.14). Polymers substituted
with these peptides are being considered for use in the treatment of cancer [67].
20.3
Olen Metathesis on Solid Phase
In solid-phase synthesis, the metathesis of alkenes has been used both for the
chemical transformation of support-bound intermediates as well as for the cleav-
age of products from the support. Although these techniques have not yet been
Scheme 20.13. Strategies for the preparation of carbohydrate-

functionalized oligomers by ROMP [65, 66]. DCE, 1,2-
dichloroethane.
Scheme 20.14. Preparation of peptide-functionalized oligomers by ROMP [67].
extensively used for the preparation of large libraries by parallel synthesis, solid-
phase chemistry is generally well suited for this purpose, and some of the reac-
tions described below can probably be used for the preparation of compound li-
braries.
20.3.1
Cleavage from the Support by Olen Metathesis
20.3.1.1 Scope and Limitations

With the discovery of highly ecient and robust soluble catalysts which mediate
olen metathesis under mild reaction conditions even in the presence of water
and air, the use of alkenes as linkers for solid-phase synthesis became a realistic
option. The use of alkenes as linkers is an attractive alternative to other types of
linkers because alkenes are inert toward a broad range of reaction conditions, and
because they provide for a reliable xation of intermediates to the support.
Various strategies for the cleavage of compounds from insoluble supports by
olen metathesis have been described (Scheme 20.15). Support-bound dienes
can yield either terminal alkenes or cycloalkenes, depending on how the diene is
bound to the resin. Terminal alkenes can also be prepared by cross-metathesis of
resin-bound internal alkenes with ethylene [68].
Scheme 20.15. Strategies for the cleavage of alkenes from

insoluble supports by olen metathesis.
Occasionally, carbene complex-mediated cleavage reactions give only low yields.

When an additional olen was added to the reaction mixture, however, better
yields could be obtained [69]. This eect was attributed to the irreversible xation
of the carbene complex to the support when little or no amounts of terminal
alkenes were present in the reaction mixture (Scheme 20.16).
Later studies [71] suggest that the irreversible xation of the catalyst to the sup-
port is not necessarily detrimental to the yield of the cleavage reaction if spacers of
sucient exibility are used. Thus, diene 19 (Scheme 20.17) could not be cleaved
from the support, and even in the presence of 1-octene only traces of the desired
product were obtained. The more exible diene 20, on the other hand, underwent
smoothly RCM smoothly in the absence of any additional alkene, to give the ex-
pected cyclic product (21) in high yield. The fact that the support was colored after
cleavage and catalyzed olen metathesis suggests that carbene complexes were in-
deed covalently bound to the support. The exibility of the spacer enables the
metal fragment to migrate from one attachment point to the next, so that catalytic
Scheme 20.16. Mechanism of the cleavage of dienes from supports by RCM [70].
Scheme 20.17. Dependence of cleavage yields on the exibility

of spacers and on the type of alkene used as linker [71].
amounts of the carbene complex are sucient to achieve complete metathesis of

all attachment sites. Another reason for the resistance of 19 toward carbene com-
plex-mediated cleavage may be the fact that 19 is a styrene derivative. Styrenes
usually react more slowly with ruthenium carbene complexes than unconjugated,
internal cis-alkenes.
One problem which is inherent to olen metathesis-induced cleavage is the elu-
tion of catalyst-derived byproducts together with the nal product. The currently
known metathesis catalysts (mainly ruthenium carbene complexes) decompose
slowly during the metathesis reaction to yield various ruthenium complexes, which
do not remain attached to the support. These impurities have to be removed by
chromatographic purication of the products. However, large libraries of com-
pounds for direct biological screening cannot always be puried, and cleavage by
olen metathesis will only be of limited use for the preparation of such libraries
unless more stable metathesis catalysts or selective scavengers for metal-containing
byproducts become available.
20.3.1.2 Examples of Cleavage from the Support by Olen Metathesis

Knerr and Schmidt [72, 73] have used a metathesis-based cleavage strategy for the
solid-phase synthesis of oligosaccharides (Scheme 20.18). Cleavage by treatment
with Grubbs catalyst yielded O-allyl glycosides (22), which represent versatile,
protected intermediates for further synthetic manipulations [73].
Scheme 20.18. Synthesis of allyl glycosides by RCM-mediated

cleavage from a polymeric support [72, 73].
A similar strategy has been described by Peters and Blechert [74], in which RCM
of a support-bound diene was used to release styrenes from a polystyrene-based,
insoluble support. Linkers of this type can also be cleaved by cross-metathesis with
ethylene [68].
Several groups have investigated the preparation of cyclic compounds by RCM
with simultaneous cleavage from the support [71, 75, 76]. One recent example, re-
ported by Piscopio et al. [77], is shown in Scheme 20.19. The substrate (23) for
olen metathesis was prepared in one step by an Ugi reaction. The product (24), a
Freidinger lactam, was designed to mimic b-turns, which play a pivotal role in the
Scheme 20.19. Solid-phase synthesis of b-turn mimetics by

RCM with simultaneous cleavage from the support [77].
interaction of proteins. Because styrene derivative 25 was chosen as linker, cleav-

age required prolonged heating for a long time. An unconjugated cis-alkene would
probably allow milder cleavage conditions (cf. Schemes 20.17 and 20.18).
Nicolaou et al. [78, 79] have used ring-closing metathesis with simultaneous
cleavage from the support in an elegant solid-phase synthesis of epothilone ana-
logs (Scheme 20.20). Epothilones are a group of natural products which promote
the polymerization of a- and b-tubulin subunits, and which show higher cytotox-
icity than taxol [80]. These interesting biological properties have prompted several
research groups to develop syntheses for these compounds and analogs thereof
[80, 81].
Scheme 20.20. Solid-phase synthesis of epothilone analogs [78, 79].
In Nicolaous solid-phase synthesis of epothilone analogs, a Merrield resin

(PSaCH2 Cl) with low loading (0.3 mmol g1 ) was used. After release from the
support the products were puried by preparative thin layer chromatography. More
than 100 epothilone analogs have been prepared using this methodology, and their
biological evaluation gave detailed insight into the structureactivity relationship
of this family of natural products [79].
20.3.2
Ring-closing Metathesis on Solid Phase

Ring-closing metathesis (RCM), being a reversible process, is best suited to the
preparation of unstrained cyclic compounds. In most of the reported examples
of RCM on solid phase [2], ve- or six-member rings were generated. Other ring
sizes are also accessible, but careful optimization of the reaction conditions are
often necessary. Macrocyclizations, for instance, usually require the use of sup-
ports with low loading to avoid self-metathesis (Scheme 20.21).
Scheme 20.21. Ring-closing metathesis on solid phase, and

self-metathesis as a potential side reaction.
20.3.2.2 Examples of Ring-closing Metathesis on Solid Phase

Several examples of the solid-phase synthesis of nitrogen-containing heterocycles
have been reported (Scheme 20.22) (for an example performed on soluble poly-
(ethylene glycol), see [82]). Heating and substantial amounts of ruthenium car-
bene complex are usually required to attain complete conversion of the starting
diene (e.g. 25). Eneyne 28 is an interesting example of an intramolecular eneyne
coupling, which gives ready access to highly substituted dienes (29), which in turn
are suitable starting materials for DielsAlder reactions [83].
Scheme 20.22. Examples of the preparation of nitrogen-

containing heterocycles by RCM on solid phase [8385]. PS,
crosslinked polystyrene.
Various groups have investigated the preparation of cyclic peptides by RCM on

solid phase. In Section 20.2.3, the work of Liskamp and coworkers concerning the
cyclization of peptide-derived dienes was presented. These cyclizations generally
give higher yields in solution than on solid phase [4850]. Another example on
crosslinked polystyrene is shown in Scheme 20.23.
With the aim of nding ecient routes to structurally complex, polycyclic com-
pounds, Lee et al. [86] recently developed the synthesis shown in Scheme 20.24.
With an Ugi reaction followed by an intramolecular DielsAlder reaction and an
Scheme 20.23. Preparation of cyclic peptides by RCM on solid phase [55]. TG, Tentagel.
Scheme 20.24. Synthesis of polycyclic structures using a ring-

opening ring-closing metathesis cascade [86].
allylation, strained triene (30) was generated, which upon treatment with a meta-
thesis catalysts underwent a ring-opening/ring-closing cascade to yield highly sub-
stituted, tetracyclic compounds (31). A valuable feature of this synthesis is the
ready availability of some of the four building blocks. One drawback of this reac-
tion sequence is the low selectivity of the allylation reaction, which necessitates the
protection of all nucleophilic functional groups.
20.3.3
Cross- and Self-metathesis on Solid Phase

Cross-metathesis should in principle enable the ecient preparation of unsym-
metrical, acyclic alkenes on solid phase. Unfortunately, this reaction does not
always proceed as expected, mainly because only few types of terminal alkenes
smoothly undergo cross-metathesis (see Scheme 20.7). Alkenes bearing interest-
ing functional groups (hydrogen bond donors and acceptors) sometimes react
only sluggishly or not at all, leading either to complete consumption of the catalyst
(formation of unreactive carbene complexes) and/or to formation of large amounts
of the products of self-metathesis (e.g. 33) (Scheme 20.25).
Scheme 20.25. Strategies for performing cross-metathesis on solid phase.
An interesting variant of cross-metathesis is the so-called ring-opening cross-

metathesis. Strained, cyclic alkenes (e.g. norbornene (35), cyclobutene) react rap-
idly and irreversibly with metathesis catalysts to yield a new carbene complex,
which can react with a second alkene to yield the product of cross-metathesis
(36). This reaction has also been performed successfully on solid phase (Scheme
20.25).
20.3.3.2 Examples of Cross- and Self-metathesis on Solid Phase

Some illustrative preparations of internal alkenes by cross-metathesis on solid
phase are shown in Scheme 20.26. Allylsilanes (37) appear to be well suited for this
reaction [33, 87], and substituted allylsilanes (38), which are valuable synthetic in-
termediates, can be easily prepared by cross-metathesis (Scheme 20.26). Nicolaou
et al. used cross-metathesis of support-bound, alkenyl-substituted ketophospho-
nates (39) with o-alkenols (40) in a solid-phase synthesis of muscone analogs [88]
(Scheme 20.26). Unsaturated a-amino acid derivatives (42) have also been prepared
on solid phase by cross-metathesis [35] (Scheme 20.26). The low loading of the
starting resin (0.07 mmol g1 ) was required to suppress self-metathesis.
Scheme 20.26. Cross-metathesis on solid phase [35, 87, 89].

PS, crosslinked polystyrene; 1, (Cy3 P)2 Cl2 RubCHPh.
The combination of ring-opening with cross-metathesis (ring-opening cross-

metathesis) has been realized on insoluble supports by Cuny and coworkers [90
92]. Support-bound norbornene derivative 43 was treated with styrenes 44 (which
do not undergo self-metathesis eciently) and a ruthenium carbene complex,
to yield regioisomeric mixtures of highly substituted cyclopentenes 45 (Scheme
20.27). Substituents on styrene which were tolerated included tert-butyl, alkoxy,
acyloxy, and hydroxy.
Scheme 20.27. Ring-opening cross metathesis on solid phase

[92]. (PS), crosslinked polystyrene with spacer; 1,
(Cy3 P)2 Cl2 RubCHPh.
The carbene complex-mediated coupling of alkynes with alkenes to yield 1,3-

dienes [13, 16, 93] is one of the most surprising metathesis reactions. Despite a
number of potential side reactions (polymerization of the alkyne, self-metathesis of
the alkene), high yields of dienes can be obtained. This reaction can also be con-
ducted on insoluble supports, with either the alkene or the alkyne attached to the
resin (Scheme 20.28). The resulting dienes can be further transformed by 2 4
cycloaddition with suitable dienophiles to yield substituted cyclohexenes [94].
Scheme 20.28. Examples of alkene/alkyne cross-metathesis on

solid phase [29, 95]. PS, crosslinked polystyrene; 1,
(Cy3 P)2 Cl2 RubCHPh.
Self-metathesis of support-bound N-alkenoylated peptides was used by Conde-

Friboes et al. [96] for the preparation of symmetric peptidomimetics (Scheme
20.29). Peptides were prepared on crosslinked polystyrene by standard uorenyl-
methoxycarbonyl (Fmoc) chemistry and then acylated with an o-alkenoic acid.
In accordance with similar results of Boger and Chai [44] (Section 20.2.2), neither
3-butenamides nor 4-pentenamides underwent self-metathesis eciently. With
longer alkenoic acids, however, the peptide dimers 46 were formed in high yield
and purity as mixtures of E/Z isomers.
Scheme 20.29. Self-metathesis of support-bound, N-alkenoyl peptides [96].

20.4
Conclusion
With the development of highly ecient and selective catalysts for olen meta-
thesis in recent years, this reaction has become a valuable tool for organic chem-
ists. Cross-metathesis and ROMP in solution can now be performed with func-
tionalized alkenes, and can oer interesting new possibilities for the preparation of
compound libraries. In particular, the selective cross-metathesis of dierent al-
kenes, for which the underlying principles are now slowly emerging, has huge
potential and could become a process with an impact similar to those of the Wittig
or the DielsAlder reactions if its scope and limitations are clearly understood.
Solid-phase synthesis has also greatly beneted from these new catalysts, and new
cleavage strategies and other methodologies based on carbene complex-mediated
olen metathesis on solid phase have been developed successfully.
The properties of the currently available catalysts are, however, far from ideal.
Because of their limited stability, large amounts of catalyst are often required
to drive reactions to completion. This feature can lead to signicant amounts of
metal-derived impurities in the crude products. Moreover, most carbene complexes
suitable for olen metathesis are also highly sensitive toward amines, azoles, and
other nucleophiles, which severely limits the choice of functional groups tolerated
in the starting materials. This facet is particularly problematic for the preparation
of libraries of biologically active compounds because nucleophilic functional groups
are often of crucial importance for biological activity. Future research should aim
to overcome these limitations of current catalysts by further enhancing their selec-
tivity and stability.
References
1 A. Furstner, Angew. Chem. Int. Ed. 9 M. Scholl, T. M. Trnka, J. P.

2000, 39, 30123043. Morgan, R. H. Grubbs, Tetrahedron
2 F. Zaragoza, Metal Carbenes in Lett. 1999, 40, 22472250.
Organic Synthesis. Wiley-VCH, 10 J. Huang, E. D. Stevens, S. P.
Weinheim 1999. Nolan, J. L. Petersen, J. Am. Chem.
3 R. H. Grubbs, S. Chang, Tetrahedron Soc. 1999, 121, 26742678.
1998, 54, 44134450. 11 A. Furstner, O. R. Thiel, L.
4 K. J. Ivin, J. C. Mol, Olen Metathesis Ackermann, H. J. Schanz, S. P.
and Metathesis Polymerization. Nolan, J. Org. Chem. 2000, 65, 2204
Academic Press, London 1997. 2207.
5 M. Schuster, S. Blechert, Angew. 12 A. Briot, M. Bujard, V.
Chem. Int. Ed. 1997, 36, 20372056. Gouverneur, S. P. Nolan, C.
6 H. S. Eleuterio, J. Mol. Catal. 1991, Mioskowski, Org. Lett. 2000, 2, 1517
65, 5561. 1519.
7 R. Streck, J. Mol. Catal. 1992, 76, 13 R. Stragies, U. Voigtmann, S.
359372. Blechert, Tetrahedron Lett. 2000, 41,
8 P. Schwab, R. H. Grubbs, J. W. 54655468.
Ziller, J. Am. Chem. Soc. 1996, 118, 14 A. K. Chatterjee, R. H. Grubbs, Org.
100110. Lett. 1999, 1, 17511753.
References 607
15 M. Scholl, S. Ding, C. W. Lee, 34 W. E. Crowe, D. R. Goldberg, J. Am.

R. H. Grubbs, Org. Lett. 1999, 1, 953 Chem. Soc. 1995, 117, 51625163.
956. 35 S. C. G. Biagini, S. E. Gibson, S. P.
16 J. A. Smulik, S. T. Diver, Tetrahedron Keen, J. Chem. Soc. Perkin Trans. 1
Lett. 2001, 42, 171174. 1998, 24852499.
17 J. D. Rainier, J. M. Cox, S. P. 36 S. E. Gibson, V. C. Gibson, S. P. Keen,
Allwein, Tetrahedron Lett. 2001, 42, Chem. Commun. 1997, 11071108.
179181. 37 D. D. Long, A. P. Termin,
18 C. W. Bielawski, R. H. Grubbs, Angew. Tetrahedron Lett. 2000, 41, 67436747.
Chem. Int. Ed. 2000, 39, 29032906. 38 S. C. Schurer, S. Gessler, N.
19 W. Apichatachutapan, L. J. Buschmann, S. Blechert, Angew.
Mathias, J. Appl. Pol. Sci. 1998, 67, Chem. Int. Ed. 2000, 39, 38983900.
183190. 39 Q. Yao, Angew. Chem. Int. Ed. 2000,
20 D. M. Lynn, B. Mohr, R. H. Grubbs, 39, 38963898.
J. Am. Chem. Soc. 1998, 120, 1627 40 L. Jafarpour, S. P. Nolan, Org. Lett.
1628. 2000, 2, 40754078.
21 D. M. Lynn, S. Kanaoka, R. H. 41 M. Ahmed, T. Arnauld, A. G. M.
Grubbs, J. Am. Chem. Soc. 1996, 118, Barrett, D. C. Braddock, P. A.
784790. Procopiou, Synlett 2000, 1007
22 J. Louie, R. H. Grubbs, Angew. Chem. 1009.
Int. Ed. 2001, 40, 247249. 42 D. L. Boger, W. Y. Chai, R. S. Ozer,
23 D. M. Lynn, B. Mohr, R. H. Grubbs, C. M. Andersson, Bioorg. Med. Chem.
L. M. Henling, M. W. Day, J. Am. Lett. 1997, 7, 463468.
Chem. Soc. 2000, 122, 66016609. 43 D. L. Boger, W. Chai, Q. Jin, J. Am.
24 S. B. Garber, J. S. Kingsbury, B. L. Chem. Soc. 1998, 120, 72207225.
Gray, A. H. Hoveyda, J. Am. Chem. 44 D. L. Boger, W. Y. Chai, Tetrahedron
Soc. 2000, 122, 81688179. 1998, 54, 39553970.
25 M. S. Sanford, L. M. Henling, M. 45 T. Giger, M. Wigger, S. Audetat,
W. Day, R. H. Grubbs, Angew. Chem. S. A. Benner, Synlett 1998, 688691.
Int. Ed. 2000, 39, 34513453. 46 K. C. Nicolaou, R. Hughes, S. Y.
26 H. Katayama, H. Urushima, T. Cho, N. Winssinger, C. Smethurst,
Nishioka, C. Wada, M. Nagao, F. H. Labischinski, R. Endermann,
Ozawa, Angew. Chem. Int. Ed. 2000, Angew. Chem. Int. Ed. 2000, 39, 3823
39, 45134515. 3828.
27 M. S. Sanford, M. Ulman, R. H. 47 C. Brandli, T. R. Ward, Helv. Chim.
Grubbs, J. Am. Chem. Soc. 2001, 123, Acta 1998, 81, 16161621.
749750. 48 J. F. Reichwein, B. Wels, J. A. W.
28 H. E. Blackwell, D. J. OLeary, A. K. Kruijtzer, C. Versluis, R. M. J.
Chatterjee, R. A. Washenfelder, D. Liskamp, Angew. Chem. Int. Ed. 1999,
A. Bussmann, R. H. Grubbs, J. Am. 38, 36843687.
Chem. Soc. 2000, 122, 5871. 49 J. F. Reichwein, C. Versluis, R. M. J.
29 M. Schuster, S. Blechert, Tetra- Liskamp, J. Org. Chem. 2000, 65,
hedron Lett. 1998, 39, 22952298. 61876195.
30 R. Stragies, M. Schuster, S. 50 J. F. Reichwein, R. M. J. Liskamp,
Blechert, Angew. Chem. Int. Ed. 1997, Eur. J. Org. Chem. 2000, 23352344.
36, 25182520. 51 J. M. Dougherty, D. A. Probst, R. E.
31 A. Furstner, G. Seidel, Angew. Chem. Robinson, J. D. Moore, T. A. Klein,
Int. Ed. 1998, 37, 17341736. K. A. Snelgrove, P. R. Hanson,
32 W. E. Crowe, Z. J. Zhang, J. Am. Tetrahedron 2000, 56, 97819790.
Chem. Soc. 1993, 115, 1099810999. 52 T. M. Gierasch, M. Chytil, M. T.
33 W. E. Crowe, D. R. Goldberg, Z. J. Didiuk, J. Y. Park, J. J. Urban, S. P.
Zhang, Tetrahedron Lett. 1996, 37, Nolan, G. L. Verdine, Org. Lett. 2000,
21172120. 2, 39994002.
53 Y. Gao, P. Lane-Bell, J. C. Vederas, Moriggi, Tetrahedron Lett. 2000, 41,

J. Org. Chem. 1998, 63, 21332143. 36813685.
54 R. M. Williams, J. Liu, J. Org. Chem. 72 L. Knerr, R. R. Schmidt, Eur. J. Org.
1998, 63, 21302132. Chem. 2000, 28032808.
55 S. J. Miller, H. E. Blackwell, R. H. 73 L. Knerr, R. R. Schmidt, Synlett
Grubbs, J. Am. Chem. Soc. 1996, 118, 1999, 18021804.
96069614. 74 J. U. Peters, S. Blechert, Synlett
56 A. S. Ripka, R. S. Bohacek, D. H. 1997, 348350.
Rich, Bioorg. Med. Chem. Lett. 1998, 8, 75 J. Pernerstorfer, M. Schuster, S.
357360. Blechert, Chem. Commun. 1997,
57 M. R. Buchmeiser, N. Atzl, G. K. 19491950.
Bonn, J. Am. Chem. Soc. 1997, 119, 76 J. H. van Maarseveen, J. A. J. den
91669174. Hartog, V. Engelen, E. Finner, G.
58 F. Sinner, M. R. Buchmeiser, R. Visser, C. G. Kruse, Tetrahedron Lett.
Tessadri, M. Mupa, K. Wurst, G. K. 1996, 37, 82498252.
Bonn, J. Am. Chem. Soc. 1998, 120, 77 A. D. Piscopio, J. F. Miller, K. Koch,
27902797. Tetrahedron 1999, 55, 81898198.
59 A. Godwin, M. Hartenstein, A. H. 78 K. C. Nicolaou, N. Winssinger, J.
E. Muller, S. Brocchini, Angew. Pastor, S. Ninkovic, F. Sarabia, Y.
Chem. Int. Ed. 2001, 40, 594597. He, D. Vourloumis, Z. Yang, T. Li,
60 S. C. G. Biagini, V. C. Gibson, M. R. P. Giannakakou, E. Hamel, Nature
Giles, E. L. Marshall, M. North, 1997, 387, 268272.
Chem. Commun. 1997, 10971098. 79 K. C. Nicolaou, D. Vourloumis, T.
61 V. C. Gibson, E. L. Marshall, M. Li, J. Pastor, N. Winssinger, Y. He,
North, D. A. Robson, P. J. Williams, S. Ninkovic, F. Sarabia, H.
Chem. Commun. 1997, 10951096. Vallberg, F. Roschangar, N. P.
62 C. Fraser, R. H. Grubbs, King, M. R. V. Finlay, P.
Macromolecules 1995, 28, 72487255. Giannakakou, P. Verdier-Pinard, E.
63 M. Kanai, K. H. Mortell, L. L. Hamel, Angew. Chem. Int. Ed. 1997,
Kiessling, J. Am. Chem. Soc. 1997, 36, 20972103.
119, 99319932. 80 K. C. Nicolaou, N. P. King, M. R. V.
64 D. D. Manning, L. E. Strong, X. Hu, Finlay, Y. He, F. Roschangar, D.
P. J. Beck, L. L. Kiessling, Vourloumis, H. Vallberg, F.
Tetrahedron 1997, 53, 1193711952. Sarabia, S. Ninkovic, D. Hepworth,
65 E. J. Gordon, J. E. Gestwicki, L. E. Bioorg. Med. Chem. 1999, 7, 665697.
Strong, L. L. Kiessling, Chem. Biol. 81 J. D. Winkler, J. M. Holland, J.
2000, 7, 916. Kasparec, P. H. Axelsen, Tetrahedron
66 L. E. Strong, L. L. Kiessling, J. Am. 1999, 55, 81998214.
Chem. Soc. 1999, 121, 61936196. 82 S. Varray, C. Gauzy, F. Lamaty, R.
67 H. D. Maynard, S. Y. Okada, R. H. Lazaro, J. Martinez, J. Org. Chem.
Grubbs, Macromolecules 2000, 33, 2000, 65, 67876790.
62396248. 83 D. A. Heerding, D. T. Takata, C.
68 R. B. Andrade, O. J. Plante, L. G. Kwon, W. F. Huffman, J. Samanen,
Melean, P. H. Seeberger, Org. Lett. Tetrahedron Lett. 1998, 39, 68156818.
1999, 1, 18111814. 84 M. Schuster, J. Pernerstorfer, S.
69 J. J. N. Veerman, J. H. van Blechert, Angew. Chem. Int. Ed. 1996,
Maarseveen, G. M. Visser, C. G. 35, 19791980.
Kruse, H. E. Schoemaker, H. 85 J. Pernerstorfer, M. Schuster, S.
Hiemstra, F. P. J. T. Rutjes, Eur. J. Blechert, Synthesis 1999, 138144.
Org. Chem. 1998, 25832589. 86 D. Lee, J. K. Sello, S. L. Schreiber,
70 F. Zaragoza, Organic Synthesis on Solid Org. Lett. 2000, 2, 709712.
Phase; Wiley-VCH, Weinheim 2000. 87 M. Schuster, N. Lucas, S. Blechert,
71 R. C. D. Brown, J. L. Castro, J.-D. Chem. Commun. 1997, 823824.
References 609
88 K. C. Nicolaou, J. Pastor, N. Hauske, Tetrahedron 1999, 55, 8169

Winssinger, F. Murphy, J. Am. 8178.
Chem. Soc. 1998, 120, 51325133. 93 A. Kinoshita, N. Sakakibara, M.
89 J. Barluenga, F. Aznar, S. Mori, J. Am. Chem. Soc. 1997, 119,
Barluenga, A. Martn, S. Garca 1238812389.
Granda, E. Martn, Synlett 1998, 94 S. C. Schurer, S. Blechert, Synlett
473474. 1999, 18791882.
90 G. D. Cuny, J. R. Cao, J. R. Hauske, 95 S. C. Schurer, S. Blechert, S.
Tetrahedron Lett. 1997, 38, 52375240. Synlett 1998, 166168.
91 J. Cao, G. D. Cuny, J. R. Hauske, 96 K. Conde-Frieboes, S. Andersen, J.
Mol. Diversity 1998, 3, 173179. Breinholt, Tetrahedron Lett. 2000, 41,
92 G. D. Cuny, J. Cao, A. Sidhu, J. R. 91539156.
611
Part III
Special Synthetic Topics

ISBN: 3-527-30509-2
613
21
Solid-phase Synthesis of Natural Products and
Natural Product-like Libraries
K. C. Nicolaou and Jerey A. Pfeerkorn
21.1
Introduction
Natural products have always played, and continue to play, important roles in
both drug discovery and chemical biology. In fact, from 1989 to 1995, 60% of all
approved drugs and new drug application (NDA) candidates were derived from
natural sources [1]. Furthermore, natural products have been used extensively for
studying complex biological processes such as signal transduction and cell cycle
regulation [2]. Yet, in spite of their importance to both biology and medicine, it
was only recently that solid-phase chemistry has been applied to the synthesis of
natural products and their analogs. Initial attempts were hampered by the limited
scope of early solid-phase reactions for the construction of nonoligomeric struc-
tures as well as the lack of appropriate solid-phase analytical techniques [3]. How-
ever, given the remarkable advances in solid-phase chemistry over the last decade,
it is not surprising that numerous research groups are now actively engaged in
the construction of structurally complex, natural product-based libraries using
solid-phase combinatorial synthesis techniques [3, 4]. Figure 21.1 shows a diverse
collection of naturally occurring structures which have been synthesized using
solid-phase technologies. Within this chapter, we seek to highlight these accom-
plishments, focusing particular attention on the novel strategies developed to solve
each problem and on how the synthetically demanding complexity of natural
products has spurred the development of new linking and cleavage devices and
protocols, as well as on the chemical biology contributions made possible by these
technologies. The discussion will be divided into three sections paralleling, chro-
nologically, the trends which have emerged in the solid-phase synthesis of natural
products. These include: (1) combinatorial derivatization of immobilized natural
product skeletons; (2) solid-phase target-oriented total synthesis of natural prod-
ucts; and (3) construction of diversity-oriented natural product-like libraries for
chemical biology and drug discovery purposes.

ISBN: 3-527-30509-2
614 21 Solid-phase Synthesis of Natural Products and Natural Product-like Libraries
Fig. 21.1. Selected natural products synthesized and/or

diversied through solid-phase chemistry.
21.2
Solid-phase Derivatization of Natural Product Scaolds Combinatorial
Semisynthesis
The earliest examples of the solid-phase library construction of natural product

analogs focused on the immobilization of natural product skeletons on solid sup-
ports so as to facilitate installation of diversity elements in either a parallel or split-
and-pool format. This strategy has been used both to create focused libraries
around a particular natural product for the development of structureactivity data
as well as to create diversity-based libraries for high-throughput screening in drug
discovery programs. Regardless of the nal application, the success of such com-
binatorial chemistry eorts is contingent upon several key factors which include:
(1) the ready availability of natural product scaolds from natural sources, degra-
dation chemistry, or solution-phase synthesis; (2) the identication of appropriate
sites on the scaold for attachment onto solid support so as to facilitate reliable
21.2 Solid-phase Derivatization of Natural Product Scaffolds -- Combinatorial Semisynthesis 615
loading/release, as well as installation of maximum structural diversity; and (3) the

development or application of an appropriate encoding technology in order to
facilitate rapid structural identication of individual library members. In order to
illustrate better both the applicability of this approach and the experimental pro-
cedures involved in this scaold-based solid-phase strategy, we will discuss below
several studies which employed a variety of natural product skeletons, including
yohimbine, purine, Taxol TM , sarcodictyns A and B, and vancomycin.
21.2.1
Solid-phase Semisynthesis of Rauwolfa Alkaloids
In an early example of this scaold-based approach, researchers at the Aymax

Research Institute enlisted the pentacyclic framework of the Rauwola alkaloids as
a template for combinatorial derivatization to create a 792-member library [5]. The
indole alkaloid yohimbinic acid (14) was selected as a scaold by virtue of its rigid
framework and rich functionality for elaboration and derivative formation. Al-
though this natural product exhibits a wide range of biological activities, the pri-
mary objective of these investigations was not to optimize the activity toward a
specic target, rather, the researchers sought to generate a diverse library of com-
pounds to be used in high-throughput screening studies against various therapeu-
tic targets. Preliminary eorts focused on the development of a linking and diver-
sication strategy, which when tested resulted in the construction of an unencoded
792-member library, as outlined in Scheme 21.1 wherein the nal compounds
were obtained in 22 pools, each containing 36 compounds. As shown, TentaGel-S-
NH2 , functionalized with a triuoroacetic acid (TFA)-labile Rink amide linker 13,
Scheme 21.1. Non-encoded solid-phase synthesis of alkaloids.

DIEA, diisopropylethylamine; 4-DAMP, 4-dimethyl amino
pyridine; HATU, O-(7-azabenzotriazol-1-yl)-N,N,N 0 ,N 0 -
tetramethyluronium hexauorophosphate; TFA, triuoroacetic
acid [5].
was deprotected with piperidine to furnish free amine 15 which was then coupled
to a series of N-uorenylmethoxycarbonyl (Fmoc)-protected amino acids (16) via
HATU activation. These 36 amino acids represented the rst element of diversity
in the library. After piperidine-mediated deprotection of the newly coupled amino
acid 17, the liberated amine was coupled to the free C1 carboxylic acid of yo-
himbinic acid (14) to eect loading of the natural product skeleton onto the solid
support. A second element of diversity was then installed at the C2 hydroxyl posi-
tion of yohimbinic acid through reaction with the symmetrical anhydrides of a
variety of carboxylic acids [(R2CO)2 O] to aord esters of type 20. After acidic cleav-
age, 22 pools each containing 36 compounds were obtained with the structures of
selected pools conrmed by ow injection mass spectroscopy (MS) analysis. While
validating the overall strategy, this rst approach required extensive deconvolution
eorts to identify the active component(s) of any of the pools. As such, the authors
then elaborated on the above approach by cosynthesizing surrogate analytes, or
tags, onto each bead which could be cleaved under conditions orthogonal to the
chemistry of the actual library member on the same bead. In this way, if during
biological assay the subanalytical amount of cleavage product from a given bead
demonstrated activity, the tag on that bead could be subsequently cleaved and
identied by MS, thereby revealing the structure of the active compound. The suc-
cess of this strategy hinged upon construction of orthogonally dierentiated beads;
this was accomplished by treatment of TentaGel-S-NH2 with a 9:1 mixture of Fmoc-
Cl and allyl chloroformate, giving a resin with a @5:1 ratio of Fmoc/Alloc sites.
The N-Fmoc-protecting group was then cleaved with piperidine and the generated
amine was acetylated with the N-Fmoc Rink amide (RAM) linker to give resin 22.
The spacer for the amine tag was installed by removal of the Alloc protecting
group [Pd(PPh3 )4 /TMSN3/TBAF] and reaction with N-Alloc iminodiacetic anhy-
dride, leading to carboxylic acid 25. The free carboxylic acid of 25 was subsequently
coupled with 36 secondary amines ( n Ry NH) through the intermediacy of an acti-
vated pentauorophenolate ester. These 36 amines (each with a distinct molecular
weight) served as the tags, and each of them encoded for a dierent amino acid
to be coupled in the next step. After deprotection of 26 using piperidine, each of the
36 N-Fmoc-protected amino acids (16) were coupled to their respective resins us-
ing HATU activation to provide amides of type 28. Upon completion of this opera-
tion, the resins were pooled and then split into 22 new reaction vessels where the
C2 hydroxyl group was acylated using a symmetrical acid anhydride as described
above. This nal acylation did not require tagging since the beads were already
spatially segregated for the reactions. The products of this nal reaction were then
maintained in the 22 separate pools for screening. Since the synthesis was en-
coded, if any of the products released from a particular bead proved biologically
active the surrogate amine tag from that bead could then be cleaved to provide
identication, as illustrated at the bottom of Scheme 21.2. Treatment of the resid-
ual resin with HCl followed by Li 2 CO3 and subsequent labeling of the released
amine with dansyl chloride would provide conjugate 32, which could be readily
analyzed by MS to determine the structure of the active library member.
Scheme 21.2. Encoded solid-phase synthesis of alkaloids [5].
21.2.2
Solid-phase Synthesis of Purine Derivatives
In a second example, the Schultz group employed two complementary solid-phase

strategies to construct libraries of purine derivatives [6, 7]. Since the purine ring
system is a key structural element of many endogenous ligands which act as
regulatory and signal transduction-mediating molecules, it was envisaged that li-
braries based on this scaold might facilitate the discovery of novel inhibitors of
these biological processes. These libraries were specically designed for the pur-
pose of identifying small molecule inhibitors of key cell cycle kinases which could
potentially nd applications as both biological probes and therapeutic leads. In
order to retain spatial separation of library members, and thereby avoid the need
for deconvolution, this solid-phase chemistry was conducted using the Geysen pin
apparatus [8]. For the construction of the rst library (Scheme 21.3a), the purine
scaold was linked to the Rink resin through a glycinamide moiety, furnishing
structure 35. The initial diversity element was installed by acylation of the C2 exo-
cyclic amine with various acid chlorides (R1COCl). The second diversity element
was then introduced by nucleophilic displacement of the C6 chloride with various
primary amines (R2NH2 ). Upon completion, these purine derivatives were re-
leased from the solid support by treatment with TFA to aord structures of type
38. To enable greater diversication at the C2 amino group, a complementary
linking strategy was also developed as outlined in Scheme 21.3b. The tetrahy-
dropyranyl-derivatized purine 40 was linked to the Rink resin via an intermediary
an activated pentauorophenolate ester to furnish 41. Elaboration of the C2
exocyclic amino group commenced with acylation using triuoroacetic anhydride,
Scheme 21.3. Solid-phase synthesis of 2-(acylamino)-6-

aminopurines and 2,6-diaminopurines. DIEA,
diisopropylethylamine; PFP, pentauorophenolate; PNP,
p-nitrophenolate [6].
followed by alkylation, under Mitsunobu conditions with a variety of alcohols

(R1OH) to give structures of type 42. As before, the chloride at C6 was then dis-
placed with a series of primary amines (R2NH2 ) with concomitant cleavage of the
triuoroacetate group from the C2 amino group. Once complete, library members
were then released from solid support by treatment with TFA to provide purine
analogs of type 44. The combined application of the strategies in Schemes 21.3
and 21.4 resulted initially in the construction of 362 purine derivatives while sub-
sequent eorts expanded these libraries. More importantly, through the screening
of these libraries, several potent protein kinases inhibitors were identied and
used to probe the role of protein kinases in biochemical processes [6, 7, 9].
21.2.3
Solid-phase Semisynthesis of a Taxoid Library
In a third example of combinatorial natural product diversication, researchers

at Irori Quantum Chemistry, now a division of Discovery Partners International,
employed radiofrequency (RF) encoding to facilitate the combinatorial split-and-
Scheme 21.4. Radiofrequency (RF)-encoded solid-phase split-

and-pool synthesis of taxoid library [10].
pool construction of a 400-member focused library based on paclitaxel (4, Fig.

21.1), also known as Taxol TM [10]. Taxol TM (Bristol-Myers Squibb) was originally
isolated from the bark of the Pacic yew (Taxus brevifolia) and was approved in
1992 by the Food and Drug Administration (FDA) as a drug for the treatment of
refractory ovarian cancer [11]. Since then its indications have been expanded and it
is often the drug of choice for treating ovarian, breast, nonsmall cell lung, bladder,
esophagus, head, and neck carcinomas. Despite its impressive record, however, the
poor water solubility of Taxol TM and its susceptibility to drug resistance prompted
numerous eorts to construct analogs with improved pharmacological properties.
The Irori group utilized RF-encoding technology in its synthesis of the taxoid li-
brary. Developed in 1995, this technology employs microreactors polypropylene-
made vessels with porous side panels capable of encapsulating both a solid-phase
resin and a radiofrequency-addressable semiconductor tagging device [12]. These

semiconductor tagging devices are capable of receiving, storing, and emitting RF
signals to a suitably interfaced computer programmed with the synthetic algo-
rithm [12]. The starting scaold for these eorts was baccatin III (45, Scheme
21.4), a diterpene obtained from the European yew tree (Taxus baccata) and used
for the semisynthesis of taxol. In order to attach this scaold to the resin, a gluta-
mate spacer unit was rst installed on a Troc-protected variant of baccatin III by
a PyBOP-mediated coupling with N-Fmoc-O-(trichloroethyl)-l-glutamic acid 47 to
provide ester 48. After simultaneous removal of both the Troc and trichloroethyl
groups with zinc dust, carboxylic acid 49 was reacted with excess 2-chlorotrityl
resin in the presence of diisopropylethylamine to aord resin-bound ester 50.
Resin 50 was then divided into 400 microreactors, each containing a radiofre-
quency tag. In a pooled operation, the N-Fmoc protecting group of 51 was removed
by treatment with piperidine, after which the reactors were sorted into 20 pools
and each set coupled with carboxylic acids (R2CO2 H) using PyBOP activation con-
ditions to eect N-acylation. After recombining and then splitting the microreac-
tors into 20 new pools, each set was then coupled to a second carboxylic acid under
DIC-mediated coupling conditions to induce O-acylation at both the side-chain and
C7 sites. The resin in the individual microreactors was then subjected to cleavage
using standard acid conditions (AcOH) to release library members of type 55 in 2-
to 4-mg quantities with purities ranging from 50% to 100% as determined by thin
layer chromatography (TLC) and high-performance liquid chromatography (HPLC)
analysis. The structures of randomly selected members were also conrmed by
1
H-NMR (nuclear magnetic resonance) and ES/MS techniques.
21.2.4
Solid-phase Semisynthesis of Sarcodictyns A and B and Libraries Thereof
A fourth scaold-driven natural products solid-phase synthesis from the Nicolaou

group focused on sarcodictyns A and B (5 and 6, Fig. 21.1): two members of a
family of marine-derived diterpenoids with potent cytotoxicities against various tu-
mor cell lines [13]. Preliminary investigations revealed that these compounds, like
Taxol TM , exert their cytotoxic eects through induction of tubulin polymerization
and microtubule stabilization. At the time of isolation, little was known about
which structural features of these marine natural products were required for activ-
ity, and their relative scarcity signicantly hampered further investigations [14]. As
a consequence, several groups undertook the challenge of their total synthesis and,
today, two syntheses have been reported: one from our laboratory [15] and the
other from Professor Danishesfkys group [16]. With the completion of these syn-
theses came an opportunity to explore the structureactivity relationships of this
family of marine natural products through the generation of analog libraries.
Given the eciency that solid-phase-based combinatorial chemistry could bring to
such a task, the Nicolaou group embarked on a strategy employing this tool in the
construction of sarcodictyn libraries. In contrast to the previous two examples, the
parent natural product was only available in trace quantities from natural sources;
therefore, the operation of library construction had to rely on the solution-phase

total synthesis to produce a key advanced intermediate which could be attached to
a solid support and subsequently diversied.
The rst step of this combinatorial approach was to develop a linking strategy
wherein such an advanced intermediate from the synthesis could be tethered so as
to allow for maximum installation of diversity elements while maintaining a reli-
able and ecient cleavage protocol [13]. It became evident that tricyclic hemiketal
57 could be employed as the library scaold and that this intermediate could be
linked through a mixed ketal moiety at C(4), as outlined in Scheme 21.5. Hence,
compound 57, obtained from -carvone (56) in 22 synthetic steps, was rst per-
acetylated to give diacetate 58, and the latter compound was then treated with 1,6-
hexanediol and PPTS to provide 59. In preparation for resin loading, the terminal
hydroxy group of 59 was oxidized to the corresponding aldehyde 60, which upon
treatment with a resin ylide underwent smooth loading via olenation to give the
resin-bound sarcodictyn scaold 61. To conrm the viability and delity of this
linking strategy, the total syntheses of both sarcodictyns A (5) and B (6) were com-
pleted from intermediate 61 in a fashion analogous to the solution-phase synthe-
sis. Briey, treatment of 61 with NaOMe revealed the free C(8) hydroxyl group
which was esteried with the (E )-N-(6 0 )-methylurocanic acid side-chain. This was
followed by deprotection and oxidation of the C(15) alcohol leading to carboxylic
acid 65. DCC-mediated esterication of 65 with either methanol or ethanol gave 66
or 67, respectively, which were independently cleaved from the resin via treatment
with CSA to provide sarcodictyns A (5) and B (6).
Scheme 21.5. Solid-phase total synthesis of sarcodictyns A and B [13].

With the linker-cleavage protocol validated, the avenue toward library construc-
tion was then open, as illustrated in Scheme 21.6. Inspection of the sarcodictyn
structure suggested the following three sites for diversication; (1) the side-chain
appended to C(8), (2) the hemiketal at C(4) and (3) the C(15) ester moiety. As out-
lined in Scheme 21.7, each of these sites was modied in a sequential fashion.
Thus, the previously linked scaold 61 was rst esteried at the C(8) hydroxyl
moiety employing ve distinct (R1COX) acyl donors to give 68. After desilylation of
Scheme 21.6. Radiofrequency (RF)-encoded solid-phase split-

and-pool synthesis of sarcodictyn analog library [13].
Scheme 21.7. Synthesis of novel polystyrene-based selenyl

bromide resin (82) and selenoether resin (84) [17].
the C(15) hydroxy group, intermediate 69 was split along three pathways. The rst
entailed acylation (R2COX) of the C(15) hydroxyl group followed by transketaliza-
tion release with a series of alkyl alcohols (R3OH), ultimately yielding structures of
the general type 75. The second pathway involved oxidation of the C(15) hydroxyl
group of 69 to the corresponding carboxylic acid, which was converted to either an
amide or an ester (74) by coupling with a series of amines (R4NH2 ) or alcohols
(R4OH) respectively. These derivatives were then released by transketalization as
before, giving rise to 76. The nal path involved conversion of alcohol 69 to the cor-
responding amine (71), which was subsequently acylated (R5COX) giving structures
of the general type 74. Release of the latter structures by transketalization provided
77. This approach yielded a 66-member library which was evaluated using the col-
orimetric tubulin polymerization assay. Active compounds were also tested in cyto-
toxicity assays employing ovarian cancer cells (1A9) and two Taxol TM -resistant cell
lines (1A9PTX10 and 1A9PTX22), leading to a number of promising antitumor
agents with higher potencies than those exhibited by the naturally occurring sub-
stances themselves [14].
21.2.5
Solid-phase Semisynthesis of Vancomycin
Our nal example in this section involves the solid-phase semisynthesis of

the glycopeptide antibiotic vancomycin (12, Fig. 21.1) [17]. This solid-phase con-
struction provides an example of how the multitude of functionality commonly
found in complex natural products can necessitate the development of novel link-
ing and release strategies. Vancomycin, renowned for its activity against methi-
cillin-resistant Staphylococcus auerus (MRSA), has been used for the past 40 years
to treat Gram-positive bacterial infections. The emergence of vancomycin-resistant
enterococci strains (VRE) has raised serious health concerns and prompted a re-
newed vigor in the eld of glycopetide antibiotics [18]. Researchers from Eli Lilly
have demonstrated that modication of the oligosaccharide portion of vancomycin
can enhance its activity against VRE to a clinically signicant level [19]. However,
more in-depth investigations of the role of the oligosaccharide in the glycopeptides
biological activity have been hampered by the synthetic inaccessibility of analogs.
With completion of the total synthesis of vancomycin in these laboratories, the
stage was set for studies directed toward a solid-phase semisynthesis of vancomy-
cin libraries for biological screening purposes.
The carboxylic acid group of vancomycin was identied as the most suitable site
for linkage to a solid support since it is the only singularly present handle on van-
comycin and, therefore, does not require some form of selective derivatization. The
criteria for the selection of a linker included acid and base stability, as well as mild
loading and cleavage conditions compatible with silyl protecting groups. After nu-
merous unsatisfactory attempts with conventional linkers, attention was turned to
our recently reported preparation of polystyrene-based selenenyl bromide [20]. We
reasoned that the facile oxidation/elimination of the polymer-bound phenylseleno
group could be used to mask an allylic functionality, thereby serving as precursor
to an Alloc protecting group in a safety-catch fashion. Thus, selenenyl bromide

resin 82 (Scheme 21.7) was prepared from commercial polystyrene 78 via lithiation
followed by treatment with dimethyl diselenide to give methyl selenide 80, a con-
jugate whose subsequent oxidation with bromine led to adduct 81 which, upon
heating in ethanol, aorded resin 82. Treatment of 82 with LiBH4 then furnished
83, which was quenched with 1,3-diiodopropane to provide the requisite linker 84.
The essential feature of this new safety-catch linker is outlined in Scheme 21.8.
Carboxylic acids are loaded onto the resin under basic conditions, and can then be
liberated in a two-step procedure in which the desired compound is initially re-
leased from the resin by oxidation of the selenide to the corresponding selenoxide,
which undergoes a facile syn-elimination to aord the O-Alloc derivative, and then
liberation of the carboxylic acid upon treatment with n-Bu3 SnH and catalytic
amounts of Pd(PPh3 )4 . The application of this strategy to the loading and release
of vancomycin is outlined in Scheme 21.9. Thus, the free carboxylic acid of per-
silylated vancomycin 90 was reacted with resin 84 in the presence of CsHCO3 to
aord resin-bound species 91. As before, release was accomplished by oxidation
with hydrogen peroxide to aord the Alloc-protected derivative, which was then
deprotected.
Scheme 21.8. Use of selenoether 84 as a safety-catch linker for carboxylic acids [17].
Scheme 21.9. Loading and cleavage of vancomycin scaold

using a selenium-base safety-catch linker [17].
With the resin-bound vancomycin 91 in hand, the solid-phase construction

of vancomycin from the corresponding aglycone, obtained from the plentiful nat-
ural product via deglycosidation, became feasible. As shown in Scheme 21.10, after
loading, the disaccharide moiety was hydrolyzed from 91 under acidic conditions
Scheme 21.10. Solid-phase synthesis of vancomycin (12) using

a selenium-based safety-catch linker [17].
to provide polymer-bound phenol 92, which was then glycosylated with the tri-
chloroacetimidate 93 to aord monosaccharide 94. Removal of the C2 Alloc group
from glucose using palladium(0)-mediated allyl transfer conditions aorded com-
pound 95 in excellent yield. The polymer-bound conjugate 95 was then subjected
to a second glycosidation reaction with glycosyl uoride 96 to deliver fully pro-

tected polymer-bound vancomycin derivative 97, which was then cleaved with
H2 O2 thus releasing allyl derivative 98. Finally, vancomycin (12) was obtained from
98 via a deprotection sequence involving deacetylation (K2 CO3 -MeOH), desilylation
(CsF), deprotection of the carboxylic acid group [Pd(PPh3 )4 -n-Bu3 SnH] and Cbz
cleavage (10% Pd/C, NH4 HCO3 ) via intermediate 99. The developed technology
was combined with parallel solution-phase chemistry to produce an extensive
library whose biological screening revealed a number of interesting and highly
potent vancomycin analogs.
21.3
Solid-phase Total Synthesis of Natural Products Combinatorial Total Synthesis
The excitement generated in the 1990s by combinatorial chemistry did not escape
the attention of synthetic chemists involved in the total synthesis of natural prod-
ucts. The attractiveness of solid-phase chemistry and the lure of the possibility of
using the split-and-pool strategy for library construction prompted several studies
directed toward diversity-oriented total synthesis on solid support. In a typical case,
the natural product itself is rst targeted for synthesis on solid phase an en-
deavor that provides the opportunity to develop the necessary chemistry for load-
ing, elaborating, and cleaving the nal target. Once the technology is developed,
the practitioner then employs a pool of building blocks to construct a library of
small to medium size, depending on the complexity of the target molecules in-
volved. Below, we discuss several such solid-phase syntheses, paying particular at-
tention to the novel linking and cleavage strategies developed during these pro-
grams and as a consequence of the challenges posed by each natural product.
21.3.1
Solid-phase Synthesis of Prostaglandins and Libraries Thereof
One of the early examples of total synthesis on polymeric support was reported by
Chen and Janda in which the construction of prostaglandin E2 (PGE2 ) methyl ester
was carried out using a soluble polystyrene polymer; although, strictly speaking,
this is not a solid-phase synthesis, it is included here for its elegance and for his-
torical reasons [21]. The practical features of soluble polymeric supports have been
well known for some time and include solubility in most organic solvents [tetra-
hydrofuran (THF), CH2 Cl2 , CHCl3 ], thus allowing reactions to be carried out
under standard solution-phase conditions and, more importantly, allowing stan-
dard analytical techniques, especially NMR, to be used to monitor reaction prog-
ress [22]. When necessary, however, the polymer support can be precipitated out of
the reaction mixture since it is insoluble in solvents such as methanol and water
so that the benets of easy purication typically associated with solid-phase chem-
istry can still be realized [22].
21.3 Solid-phase Total Synthesis of Natural Products -- Combinatorial Total Synthesis 627
In their prostaglandin synthesis (Scheme 21.11), the Janda group employed

an acid-labile pyran linker 101 constructed by the treatment of a noncrosslinked
chloromethylated polystyrene resin with hydroxymethyl pyran derivative 100 in
the presence of NaH. The requisite prostaglandin core, hydroxycyclopentenone,
was then loaded under nonaqueous acid catalysis to aord resin-bound enone 102,
which was subsequently subjected to a 1,4-cuprate conjugate addition and the re-
sulting enolate was trapped as the corresponding silyl enol ether 103. Installation
of the second appendage was accomplished by cleavage of the silyl enol ether with
MeLi, followed by quenching with an alkynyl triate to provide alkyne 104. Con-
trolled hydrogenation of 104 followed by treatment of the resulting conjugate 105
with HF resulted in release of PGE2 methyl ester (106) in 37% overall yield, while
reduction of the carbonyl group with l-selectride, followed by saponication of the
methyl ester, furnished the polymer-bound PGFa 108. Cleavage via exposure to HF
then provided PGFa (2) in 30% overall yield. The sequential installation of key
structural elements made this synthesis particularly amenable to the construction
of prostaglandin-like libraries through the use of structurally diverse pools of build-
ing blocks, and, in fact, the Janda group subsequently reported the construction of
the prostanoid library shown in Scheme 21.12 [23]. Resin-bound enone 102 was
reacted with four dierent cuprates to aord structures of type 109. Pools contain-
ing a portion of these various silyl enol ethers were then derivatized with a set of
Scheme 21.11. Soluble polymer-supported synthesis of prostaglandins [21].

Scheme 21.12. Synthesis of a prostanoid library on soluble polymeric support [23].
four dierent a-chains to furnish structures of the general type 110. After reduc-
tion of the alkyne of the a-chain to the alkene moiety of the natural prostaglandins,
the pools were cleaved with aqueous HF to aord four new pools of prostanoids,
each consisting of four compounds. These mixtures were then assayed for inhibi-
tion of cytomegalovirus (CMV) a member of the herpesvirus family and de-
convolution of an active pool led to the identication of a lead compound.
A similar solid-phase synthesis of a related series of prostaglandins was reported
by Ellman and coworkers, who employed a traditional, crosslinked polystyrene-
based resin [24]. The Ellman approach relied on tethering the cyclopentene build-
ing block 113 (Scheme 21.13) through its hydroxyl group to a suitably derivatized
resin. Thus, treatment of the polystyrene-derived di-n-butylsilyl chloride resin with
113 in the presence of imidazole aorded conjugate 114. The tri-(4-methox-
yphenyl)methyl (TMT) protecting group of 114 was then removed from the mole-
cule by treatment with formic acid and the a-side-chain was installed through a
Suzuki coupling with a borane derivative to provide structure 116. DessMartin
oxidation of 116 followed by attachment of the lower side-chain via a conjugate
addition provided 118. The sulfonamide moiety of the a-side-chain was then acti-
vated with bromoacetonitrile and coupled with various alcohols (R1OH) and
amines (R1NH2 ). Cleavage of the silyl ether bridge with HFpyridine resulted in
the formation of 120, whereas l-selectride reduction of 119 followed by a similar
cleavage resulted in the formation of prostaglandins of type 122. As with the Janda
approach, the strategy developed by Ellman allowed the construction of a small li-
brary demonstrating its usefulness in combinatorial chemistry.
21.3.2
Solid-phase Synthesis of Epothilone A and Libraries Thereof
Another early example of the solid-phase synthesis of natural products is the

olen metathesis-based total synthesis of epothilone A emanating from these lab-
oratories in 1997 [24]. Epothilones A (7, Fig. 21.1) and B were originally isolated
from a series of myxobacteria by Hoe, Reichenbach, and coworkers at the Gesell-
Scheme 21.13. Solid-phase synthesis of prostaglandins [24].
shaft fur Biotechnologische Fonschung in Germany, and subsequently by scien-

tists at Merck, who also determined their tubulin-binding properties. Once their
Taxol TM -like mechanism of action and their potent activities against Taxol TM -
resistant tumor cells became known, interest in these natural products soared [26].
Following our solution-phase chemical synthesis of these natural products, we
became interested in a solid-phase total synthesis which could allow us to apply
the split-and-pool strategy to construct combinatorial libraries of such substances.
Our olen metathesis approach to epothilone A, developed previously, appeared to
be ideally suited to such a solid-phase approach. To this end, a novel cyclorelease
strategy was devised and executed as shown in Scheme 21.14 [27]. In addition to
its inherent eciency, the cyclorelease strategy is also advantageous in that it re-
quires a compound to have successfully undergone all the requisite reaction pro-
cesses for it to be released, thereby assuring against contamination of the cleavage
products. The essential features of the epothilone synthesis include convergent
assembly of building blocks, a ring-closing metathesis reaction which releases
the generated macrocycle, and a nal deprotection/epoxidation sequence in solu-
tion. As shown in Scheme 21.14, a resin-bound ylide (129) is used to load
the rst building block giving rise to 130, which is then deprotected and oxidized
to aord aldehyde 132. Subsequent aldol condensation provided acid 133, which
was coupled to the heterocycle side-chain as shown to furnish metathesis precur-
sor 134. Cyclorelease via ring-closing metathesis then aorded olens 135139,
which could be further elaborated. The advantage of this approach is enhanced by
the three somewhat controllable steps which can be coached to deliver optimum
Scheme 21.14. General cyclorelease strategy (a) and solid-

phase synthesis of epithilone A (7) via an olen metathesis
[25].
diversity: aldol reaction (syn/anti-stereoisomers); metathesis reaction (cis/trans-

olens); and epoxidation (a/b-epoxides). These advantages have been exploited in
the expedient construction of a combinatorial library, as summarized in Scheme
21.15. In addition, these compounds have been added to a series of other analogs
obtained via solution-phase methods and screened for their tubulin polymerization
and cytotoxicity properties, leading to a useful set of structureactivity relation-
ships within the epothilone eld.
21.3.3
Solid-phase Synthesis of (S)-Zearalenone
Continuing the theme of cyclorelease (see Scheme 21.14a), the Nicolaou group re-
ported the solid-phase synthesis of (S)-zearalenone (10) using a Stille coupling re-
action to form and simultaneously release the macrocyclic product from the resin
Scheme 21.15. Radiofrequency (RF)-encoded split-and-pool

solid-phase synthesis of epithilone library [25].
(Scheme 21.16) [28]. (S)-Zearalenone (10) is a naturally occurring substance pos-

sessing anabolic, estrogenic, and antibacterial properties and whose multitude of
solution-phase syntheses include the one developed by Hegedus and coworkers
which utilizes a Stille coupling reaction for the formation of the large ring [29].
Relying on the reported methodology, the Nicolaou group demonstrated a highly
ecient and convenient solid-phase synthesis of this natural product, as shown in
Scheme 21.17. Thus, the sequence began with oxidation of Merrield resin to af-
ford styrene 150, which was then stannylated to provide resin 151. Treatment of
151 with a vinyl lithium species furnished vinyl stannane 152, the terminal alcohol
of which was oxidized to aord aldehyde 154. Grignard addition followed by oxi-
dation provided access to structure 156, which was deprotected and coupled with
an iodocarboxylic acid to provide 158 as the cyclorelease precursor. In the nal
palladium-catalyzed step, the zearalenone derivative 159 was released and then
deprotected to aord (S)-zearalenone (10) in high overall yield and purity. A key
advantage of this strategy was that all tin residues remained bound to the solid
support.
Scheme 21.16. Solid-phase synthesis of (S)-zearalenone (160)

via a palladium-mediated cyclorelease strategy [28]. DMSO,
dimethyl sulfoxide.
Scheme 21.17. Solid-phase total synthesis of (dl)-muscone via

a HornerWadsworthEmmons-mediated cyclorelease strategy
[30].
21.3.4
Solid-phase Synthesis of (DL)-Muscone and Libraries Thereof
In an eort to develop a resin suitable for the solid-phase version of the powerful
HornerWadsworthEmmons reaction, we targeted (dl)-muscone and a library
thereof [30]. The adopted strategy represents yet another example of the cyclo-
release strategy (see Scheme 21.15, top) in which the cyclic product is simulta-
neously formed and released, leaving the troublesome phosphorous residues on

the resin. As illustrated in Scheme 21.17, Merrield resin was derivatized with 1,4-
butanediol in the presence of NaH to aord resin 160, which was then reacted
with MeP(O)(OMe)Cl and Et3 N to give resin-bound methylphosphonate 161. This
versatile resin was then deprotonated with n-BuLi and quenched with an alkenyl
ester leading to terminal olen conjugate 162, whose cross-metathesis reaction
with a hydroxy alkene resulted in the new resin 163 (cis/trans mixture). Oxidation
to the aldehyde 164 was then followed by smooth cyclorelease (K2 CO3/18-crown-6),
furnishing enone 165, which underwent 1,4-addition with LiCuMe 2 to aord 166
and, hence, (dl)-muscone (11) upon hydrogenation. Application of the developed
chemistry in a split-and-pool fashion using the radiofrequency-encoding system
also allowed the synthesis of a small muscone library.
21.3.5
Solid-phase Synthesis of the Vitamin D3 System
Among the most recent examples of the solid-phase synthesis of natural products
and their analogs is one reported by Takahashi and coworkers around the vitamin
D3 skeleton [31]. As shown in Scheme 21.18, the Takahashi group employed
the trialkylsilane linker 168, which was alkylated with the presynthesized bicyclic
upper unit of vitamin D3 to furnish intermediate 169. The ketone of 169 was then
subjected to a HornerWittig condensation with the presynthesized lower unit in
the presence of n-BuLi to aord triene 170. The side-chain was then installed by a
Grignard reaction in which the tosylate moiety of 170 was displaced to furnish
compound 171, which was ultimately cleaved to provide the 1a,25-(OH)2 -vitamin
D3 analog 172.
Scheme 21.18. Solid-phase synthesis of vitamin D3 system

173. DCDMH, 1,3-dichloro-5,5-dimethylhydantoin [31].
21.3.6
Solid-phase Synthesis of Carpanone-like Molecules
The Shair group has described the synthesis of a small library of carpanone-like
molecules employing a solid-phase variant of the biomimetic carpanone synthe-
sis rst reported by Chapman et al. [33]. The strategy, as outlined in Scheme
21.19, relied on initial tethering of a series of electron-rich o-hydroxystyrenes to a
solid support to generate adducts of type 173. These styrenes were then treated
with a series of electron-poor o-hydroxystyrenes in the presence of PhI(OAc)2 to
eect an oxidative coupling furnishing 174, which underwent a spontaneous in-
verse electron-demand DielsAlder reaction to aord a small library of benzox-
anthenones (175) representing the carpanone skeleton. Cleavage with HF led to
the release of carpanone-like compounds 176. The researchers minimized oxida-
tive homocoupling of the resin-bound styrenes species through electronic consid-
erations, low resin loading, and linker optimization.
Scheme 21.19. Biomimetic solid-phase synthesis of carpanone-like compounds (176) [32].
21.4
Combinatorial Solid-phase Synthesis of Natural Product-like Libraries
Over the past centuries, nature has served as a most generous source supplier of
cures and, in more recent times, leads for drug discovery purposes. Indeed, many
of the clinically used drugs of the twentieth century have their origins in nature,
whose library of compounds exceeds our wildest imagination in terms of both
numbers and molecular diversity. However, the tremendous strides made by biol-
ogy and high-throughput screening technologies in recent times demand a much
faster pace of isolation and characterization of new natural products than currently
possible [34]. This problematic phenomenon is compounded by the pressure to
discover new drugs and to fulll the promise of the human genome project, the
fruits of which will soon be available for further biomedical advances [35]. The
advent of combinatorial chemistry provided a powerful alternative to nature, for
now chemists can design and rapidly synthesize large libraries of natural product
analogs or even libraries of natural product-like molecules. The value of such en-
deavors should be measured by various factors, such as novelty of the chemistry
developed, the molecular diversity generated, the practicality of library construc-
tion, and the relevance of the designed structures to biology.
The rst examples of combinatorial synthesis of natural product analog libraries
are those already discussed above. More recently, several research groups have
21.4 Combinatorial Solid-phase Synthesis of Natural Product-like Libraries 635
described the solid-phase combinatorial syntheses of larger libraries of natural

product-like compounds. Many of these libraries attempt to emulate the structural
characteristics observed in natural products, but, at the same time, provide more
rapid access to larger collections of products that possess greater diversity and in-
corporate optimized physical and pharmacological properties into their structures.
Several strategies for the construction of such libraries have been described. Below,
we discuss a number of representative examples from the Schreiber and Nicolaou
laboratories.
To achieve the construction of larger diversity-oriented libraries, Schreiber and
coworkers have described several combinatorial solid-phase synthetic strategies
used to create libraries of complex structures for screening in various chemical
genetics applications [3639]. One of these strategies, shown in Scheme 21.20,
targeted a 2.18 million-compound library [36]. In this eort, researchers converted
both enantiomers of shikimic acid (177) to epoxycyclohexenol carboxylic acid 178,
which was then coupled via a photolabile linker to solid support to give conjugate
179. Subsequent treatment of enone 179 with a series of nitrone carboxylic acids
Scheme 21.20. Solid-phase synthesis of a natural product-like library [36].

under esterication conditions furnished polycyclic compounds of type 180 to be

used as library scaolds. The rigid, highly functionalized octahydrobenzisoxazole
core 180 was further functionalized through a variety of reactions, as shown at the
bottom of Scheme 21.20. These reactions included palladium couplings, epoxide
openings, lactone openings, acylations, and others. The reaction pathways and
building blocks were validated through a number of testing protocols, and a test
library of 456 compounds was constructed and analyzed by LC/MS to establish the
validity of the library strategy. Upon completion of the full-sized library, it was
employed in several miniaturized cell-based assays to screen for cell-permeable,
protein-binding ligands [36].
More recently, our group has introduced a strategy for the construction of natu-
ral product-like libraries using naturally occurring privileged structures as templates
[4042]. The concept of privileged structures was rst introduced by a Merck group
to describe select structural types (originally benzodiazepines and benzazepines)
that bind to multiple, unrelated classes of protein receptors as high anity ligands
[43]. These privileged structures are typically rigid, polycyclic heteroatomic sys-
tems capable of orienting varied substituent patterns in a well-dened three-
dimensional space. The tendencies of derivatives of these privileged structures to
exhibit binding anity toward various receptors and enzymes has made them at-
tractive scaolds for discovery libraries, particularly in cases where there is only
limited structural information available about the target. Given the success of
privileged structures in medicinal chemistry, we envisaged a similarly advanta-
geous application of this principle to the construction of natural product-like li-
braries, especially since the principal use of such libraries is to discover ligands for
either unknown or recently discovered biological targets. We were particularly in-
trigued by the possibility that using scaolds of natural origin, which presumably
have undergone evolutionary selection, might confer favorable bioactivities and bio-
availabilities to library members. Thus, we sought to identify privileged structural
subunits found in biologically active natural products and to develop novel solid-
phase chemistries to allow these structures to be employed as templates for the
construction of versatile compound libraries. These eorts have resulted in the
development of a number of unique solid-phase cycloloading strategies (shown in
Scheme 21.21) which capitalized on the electrophilicity of the selenenyl bromide
resin described previously [20]. Thus, as shown, various alkenyl systems contain-
ing an internal nucleophile can be treated with the selenium bromide resin to
eect an electrophilic cyclization reaction concomitant with loading. Once loaded,
the stability of the resulting selenoether tether enables further functionalization of
the polycyclic scaolds, and, upon completion, the target molecules can then be
released either through oxidation elimination or through radical hydride transfer
conditions. To date, this process has been demonstrated for both heterocyclic and
carbocylic ring systems. As illustrated at the bottom of Scheme 21.21, benzopyrans
can be constructed by the cycloloading of o-prenylated phenols (194) followed by
functionalization and oxidative cleavage to give 2,2-dimethylbenzopyrans of type
197 [44]. Notably, this benzopyran motif and its derivatives have been found in
over 12,000 natural and designed structures with wide-ranging biological activities,
21.4 Combinatorial Solid-phase Synthesis of Natural Product-like Libraries 637
Scheme 21.21. General strategy for solid-phase cycloloading

reactions using an electrophilic selenyl bromide resin (a) and
representative hetero- and carbocyclic resin-bound scaolds
useful in the construction of natural product-like libraries (b)
[4446].
thereby making it an optimal template for construction of a natural product-like

library (see below). The cycloloading of o-allylanilines (198) aords resin-bound
indolines 199 which can be further functionalized and then cleaved under radical
hydride conditions [45]. Interestingly, if a conjugated radical acceptor is placed in a
suitably proximal position to the generated carbon-centered radical, complex poly-
cyclic indolines reminiscent of alkaloid-type natural products can be obtained.
Lastly, cycloloading of alkenyl-substituted b-ketoesters 202 provided access to a
series of resin-bound bicyclic scaolds which could be derivatized and cleaved to
aord highly functionalized carbocycles of type 205. The last compounds resemble
a family of natural products from the Guttiferae classication with promising bio-
logical activities [46].
As an illustration of the utility of such cycloloading strategies in the construction
of large natural product-like libraries, the benzopyran strategy was recently em-
ployed in the construction a 10,000-member natural product-like library, as out-
lined in Scheme 21.22 [4042]. This library was constructed by directed split-and-
pool techniques employing the NanoKan TM optical encoding platform recently
developed by Irori, a Discovery Partners International Company [47]. Synthesis of
this diverse library commenced with a series of resin-bound benzaldehydes (207)
which were subjected to various reactions, including organometallic additions, re-
ductive aminations, condensations, acylations, Mitsunobu inversions, and glyco-
638
21 Solid-phase Synthesis of Natural Products and Natural Product-like Libraries
Scheme 21.22. Optically encoded split-and-pool solid-phase

synthesis of 10,000-member natural product-like library based
on 2,2-dimethylbenzopyran template [4042].
21.6 Addendum 639
sidations. An automated cleavage protocol employing H2 O2 furnished 2- to 3-mg

quantities of each library member in high purity (often > 90%) with the entire li-
brary formatted in 96-well microtiter plates for use in various chemical biology
studies [48].
21.5
Conclusion
Merrields pioneering work on solid-phase chemistry revolutionalized the eld of

peptide synthesis. It subsequently inuenced profoundly the eld of oligonucleo-
tide synthesis where similar concepts were utilized to construct much-needed
DNA sequences for the genetic engineering revolution. The same philosophy of
solid-phase chemistry is now being implemented in the latest revolution in or-
ganic synthesis to deliver small organic molecules urgently needed to confront the
human genome via biological screening. Indeed, in the 1990s, we have seen a
strong push in research directed at the discovery and invention of new methods
for solid-phase synthesis and the application of the latter for the construction of
compound libraries for, among others, biological screening purposes. Many of
these eorts focused on developing new resins and linkers for convenient loading
and cleavage, others focused on suitable synthetic strategies to construct specic
libraries, and yet others focused on designing and synthesizing novel molecular
diversities. Given their molecular complexities, natural products are playing a cru-
cial role in this process by serving as challenging targets for solid-phase synthesis,
frequently demanding the development of new linking and synthesis strategies.
When successful, such endeavors can deliver, in addition to the natural substances,
highly valuable analog libraries of these compounds for biological investigations.
In contrast to the repetitive nature of peptide and oligonucleotide synthesis, the
construction of small nonoligomeric natural products demands a mastery of a
much wider range of synthetic chemistry. For this reason, chemists will remain
busy for some time inventing, discovering, and developing enabling technologies
that will enhance the power of solid-phase synthesis, and, in turn, sharpen the
tools of combinatorial chemistry. The benets of such eorts to biology and medi-
cine are already becoming apparent and are bound to increase in the future.
21.6
Addendum
Since the submission of this chapter for publication, an important contribution

to the eld of natural product-based combinatorial chemistry has been reported.
Specically, the laboratory of Shair and coworkers described the biosynthetically
inspired construction of a 2527-membered library using the natural product gal-
anthamine as a scaold. The galanthamine skeleton was functionalized at four
sites using solid phase split-and-pool chemistry. While the natural product itself is
a potent acetylcholinesterase inhibitor, the authors were interested in creating a

non-focused, diversity oriented library. The resulting library was screened and a
molecule capable of interfering with protein tracking was identied for use as a
chemical probe. The interested reader is referred to a full account of this work: H.
E. Pelish, N. J. Westwood, Y. Feng, T. Kirchhausen, M. D. Shair, J. Am. Chem. Soc.
2001, 123, 67406741.
References
1 a) G. M. Cragg, D. J. Newman, K. M. 12 a) K. C. Nicolaou, X.-Y. Xiao, Z.

Snader, J. Nat. Prod. 1997, 60, 5260; Parandoosh, A. Senyei, M. P. Nova,
b) Y.-Z. Shu, J. Nat. Prod. 1998, 61, Angew. Chem. Int. Ed. Engl. 1995, 107,
10531071. 24762479; b) E. J. Moran, S.
2 a) K. Hinterding, D. Alonso-Daz, Sarshar, J. F. Cargill, M. J. M.
H. Waldmann, Angew. Chem. Int. Ed. Shahbaz, A. Lio, A. M. M. Mjalli, R.
1998, 37, 688749; b) D. T. Hung, T. W. Armstrong, J. Am. Chem. Soc.
F. Jamison, S. L. Schreiber, Chem. 1995, 117, 1078710788.
Biol. 1996, 3, 623639. 13 K. C. Nicolaou, N. Winssinger, D.
3 C. Watson, Angew. Chem. Int. Ed. Vourloumis, T. Ohshima, S. Kim, J.
1999, 38, 19031908. Pfefferkorn, J. Y. Xu, T. Li, J. Am.
4 S. Bertels, S. Frormann, G. Jas, K. Chem. Soc. 1998, 120, 1081410826.
U. Bindseil, Drug Discovery Nat. 14 For a review, see: K. C. Nicolaou, J.
1999, 72105. Pfefferkorn, J. Xu, N. Winssinger,
5 A. Atuegbu, D. Maclean, C. T. Ohshima, S. Kim, S. Hosokawa,
Nguyen, E. M. Gordon, J. W. Jacobs, D. Vourloumis, F. van Delft, T. Li,
Bioorg. Med. Chem. 1996, 4, 1097 Chem. Pharm. Bull. 1999, 47, 1199
1106. 1213.
6 T. C. Norman, N. S. Gray, J. T. Koh, 15 K. C. Nicolaou, J. Xu, S. Kim, J.
P. G. Schultz, J. Am. Chem. Soc. Pfefferkorn, T. Ohshima, D.
1996, 118, 74307431. Vourloumis, S. Hosokawa, J. Am.
7 N. S. Gray, L. Wodicka, A.-M. W. H. Chem. Soc. 1998, 120, 86618673.
Thunnissen, T. C. Norman, S. 16 X.-T. Chen, B. Zhou, S. K.
Kwon, F. H. Espinoza, D. O. Bhattacharya, C. E. Gutteridge, T.
Morgan, G. Barnes, S. LeClerc, L. R. Pettus, S. J. Danishefsky, Angew.
Meijer, S.-H. Kim, D. J. Lockhart, Chem. Int. Ed. 1998, 37, 789792.
P. G. Schultz, Science 1998, 281, 17 K. C. Nicolaou, N. Winssinger, R.
533538. Hughes, C. Smethurst, S. Y. Cho,
8 H. M. Geysen, S. J. Rodda, T. J. Angew. Chem. Int. Ed. 2000, 39, 1984
Mason, G. Tribbick, P. G. Schoofs, 1989.
J. Immunol. Methods 1987, 102, 259 18 For reviews, see: a) K. C. Nicolaou,
274. C. N. C. Boddy, S. Brase, N.
9 G. R. Rosania, J. Merlie, Jr, N. Gray, Winssinger, Angew. Chem. Int. Ed.
Y.-T. Chang, P. G. Schultz, R. 1999, 111, 22302287; b) D. H.
Heald, Proc. Natl. Acad. Sci. USA Williams, B. Bardsley, Angew. Chem.
1999, 96, 47974802. Int. Ed. 1999, 38, 11721193.
10 X.-Y. Xiao, Z. Parandoosh, M. P. 19 R. Nagarajan, J. Antibiot. 1993, 46,
Nova, J. Org. Chem. 1997, 62, 6029 11811195.
6033. 20 a) K. C. Nicolaou, J. Pastor, S.
11 For a review, see: K. C. Nicolaou, Barluenga, N. Winssinger, Chem.
W.-M. Dai, R. K. Guy, Angew. Chem. Commun. 1998, 19471948; for
Int. Ed. Engl. 1994, 33, 1544. preparation of related selenium-based
References 641
resins, see: b) T. Ruhland, K. 30 K. C. Nicolaou, J. Pastor, N.

Andersen, H. Pedersen, J. Org. Winssinger, F. Murphy, J. Am.
Chem. 1998, 63, 92049211; c) K. Chem. Soc. 1998, 120, 51325133.
Fujita, K. Watanabe, A. Oishi, Y. 31 T. Doi, I. Hijikuro, T. Takahashi, J.
Ikeda, Y. Taguchi, Synlett 1999, 11, Am. Chem. Soc. 1999, 121, 6749
17601761. 6750.
21 S. Chen, K. D. Janda, J. Am. Chem. 32 C. W. Lindsley, L. K. Chan, B. C.
Soc. 1997, 119, 87248725. Goess, R. Joseph, M. D. Shair, J. Am.
22 For an early use of soluble polymers Chem. Soc. 2000, 122, 422423.
in peptide synthesis, see: a) M. 33 O. L. Chapman, M. R. Engel, J. P.
Narita, M. Hirat, K. Kusano, S.-I. Springer, J. C. Clardy, J. Am. Chem.
Itsuno, M. Ue, M. Okawara in: Soc. 1971, 93, 6696.
Peptide Chemistry. Yonehara, J. (ed.), 34 S. L. Schreiber, Bioorg. Med. Chem.
Protein Research Foundation, Osaka 1998, 6, 11271152.
1979, vol. 99, pp. 107112; b) M. 35 a) G. R. Lenz, H. M. Nash, S. Jindal,
Narita, Bull. Chem. Soc. Jpn. 1978, 51, Drug Discovery Today 2000, 5, 145
1477; c) E. Bayer, M. Mutter, Nature 156; b) E. S. Razvi, L. J. Leytes, Mod.
1972, 237, 512513; for a review, see: Drug Discovery 2000, 4142; c) J.
d) C. W. Harwig, D. J. Gravert, K. Rosamond, A. Allsop, Science 2000,
D. Janda, Chemtracts 1999, 12, 126. 287, 19731976; d) M. D. Garrett, P.
23 K. J. Lee, A. Angulo, P. Ghazal, K. Workman, Eur. J. Cancer 1999, 35,
D. Janda, Org. Lett. 1999, 1, 1859 20102030; e) C. E. Barry, R. A.
1862. Slayden, A. E. Sampson, R. E. Lee,
24 a) L. A. Thompson, F. L. Moore, Biochem. Pharmacol. 1999, 59, 221
Y.-C. Moon, J. A. Ellman, J. Org. 231.
Chem. 1998, 63, 20662067; b) D. R. 36 D. S. Tan, M. A. Foley, B. R.
Dragoli, L. A. Thompson, J. Stockwell, M. D. Shair, S. L.
OBrien, J. A. Ellman, J. Comb. Schreiber, J. Am. Chem. Soc. 1999,
Chem. 1999, 1, 534539. 121, 90739087.
25 a) K. C. Nicolaou, N. Winssinger, J. 37 D. Lee, J. K. Sello, S. L. Schreiber, J.
Pastor, S. Ninkovic, F. Sarabia Y. Am. Chem. Soc. 1999, 121, 10648
He, D. Vourloumis, Z. Yang, T. Li, 10649.
P. Giannakakou, E. Hamel, Nature 38 D. Lee, J. K. Sello, S. L. Schreiber,
1997, 387, 268272; b) K. C. Org. Lett. 2000, 2, 709712.
Nicolaou, D. Vourloumis, T. Li, J. 39 D. R. Spring, S. Krishnan, S. L.
Pastor, N. Winssinger, Y. He, S. Schreiber, J. Am. Chem. Soc. 2000,
Ninkovic, F. Sarabia, H. Vallberg, 122, 56565657.
F. Roschangar, N. P. King, M. R. V. 40 K. C. Nicolaou, J. A. Pfefferkorn,
Finlay, P. Giannakakou, P. Verdier- G.-Q. Cao, A. J. Roecker, S.
Pinard, E. Hamel, Angew. Chem. Int. Barluenga, H. J. Mitchell, J. Am.
Ed. Engl. 1997, 36, 20972103. Chem. Soc. in press.
26 For a review, see: a) K. C. Nicolaou, 41 K. C. Nicolaou, J. A. Pfefferkorn,
F. Roschangar, D. Vourloumis, H. J. Mitchell, A. J. Roecker, S.
Angew. Chem. Int. Ed. 1998, 37, 2014 Barluenga, G.-Q. Cao, R. L. Affleck,
2045. J. E. Lillig, J. Am. Chem. Soc. in
27 For a review, see: J. H. van press.
Maarseveen, Comb. Chem. High 42 K. C. Nicolaou, J. A. Pfefferkorn,
Throughput Screening 1998, 1, 185214. S. Barluenga, H. J. Mitchell, A. J.
28 K. C. Nicolaou, N. Winssinger, J. Roecker, G.-Q. Cao, J. Am. Chem.
Pastor, F. Murphy, Angew. Chem. Int. Soc. in press.
Ed. 1998, 37, 25342537. 43 B. E. Evans, K. E. Rittle, M. G. Bock,
29 K. Kalivretenos, J. K. Stille, L. S. R. M. DiPardo, R. M. Freidinger,
Hegedus, J. Org. Chem. 1991, 56, W. L. Whitter, G. F. Lundell, D. F.
28832894. Veber, P. S. Anderson, R. S. L.
Chang, V. J. Lotti, D. J. Cerino, T. 46 a) K. C. Nicolaou, J. A. Pfeffer-

B. Chen, P. J. Kling, K. A. Kunkel, korn, G.-Q. Cao, S. Kim, J. Kessabi,
J. P. Springer, J. Hirsheld, J. Med. Org. Lett. 1999, 5, 807810; b) K. C.
Chem. 1988, 31, 22352246. Nicolaou, J. A. Pfefferkorn,
44 a) K. C. Nicolaou, J. A. Pfeffer- S. Kim, H. X. Wei, J. Am. Chem. Soc.
korn, G.-Q. Cao, Angew. Chem. Int. 1999, 121, 47244725.
Ed. 2000, 39, 734739; b) K. C. 47 X.-Y. Xiao, C. Zhoa, H. Potash, M.
Nicolaou, G.-Q. Cao, J. A. Pfeffer- P. Nova, Angew. Chem. Int. Ed. Engl.
korn, Angew. Chem. Int. Ed. 2000, 39, 1997, 36, 780782.
739743. 48 K. C. Nicolaou, J. A. Pfefferkorn,
45 K. C. Nicolaou, A. J. Roecker, J. A. F. Schuler, A. J. Roecker, G.-Q.
Pfefferkorn, G.-Q. Cao, J. Am. Cao, J. E. Casida, J. Chem. Biol. in
Chem. Soc. 2000, 122, 29662967. press.
643
22
Solid-phase Synthesis of Heterocyclic Systems
(Heterocycles Containing One Heteroatom)
Roland E. Dolle
22.1
Introduction
The synthesis of chemical libraries is now widely practiced in academic and

industrial laboratories. The rst examples of small-molecule libraries were collec-
tions of heterocycles, e.g. Ellmans 1,4-benzodiazepines and b-lactams from Ay-
max. Of the 1250 libraries published since 1992, over 80% are based on a hetero-
cyclic theme [1]. The impetus for the development and application of high-speed
synthesis is tied to the pharmaceutical industrys quest for discovering new bio-
logically active agents; heterocycles enjoy a rich history of providing leads for this
multibillion dollar industry. This chapter presents a systematic examination of the
solid-phase synthesis of heterocycles containing a single heteroatom. This treatise
is organized by atom type (nitrogen, oxygen, sulfur), ring size, and degree of un-
saturation. Table 22.1AH lists the generic structures of all solid- and solution-
phase heterocyclic libraries containing a single heteroatom that were published
during 19922000.
22.2
Solid-phase Synthesis of Heterocycles Containing One Nitrogen Atom
22.2.1
Aziridines
The GabrialCromwell reaction involving the conjugate addition of an amine to a-

haloacrylate and intramolecular ring closure is a classical method for preparing
aziridine-2-carboxylates. This reaction sequence was adapted to solid phase by Fili-
gheddu and coworkers [2] in a construction of aziridine-containing peptidomi-
metics (Scheme 22.1). Wang resin esteried with amino acids 1 serves as resin-
bound amine substrates. A direct synthesis of the heterocyclic unit was carried out
upon the Michael addition of a-bromoacrylates 2 or a-bromoacrylamides 35 in
tetrahydrofuran (THF) in the presence of triethylamine (25 C, 12 h). Cleavage

ISBN: 3-527-30509-2
644 22 Solid-phase Synthesis of Heterocyclic Systems (Heterocycles Containing One Heteroatom)
Tab. 22.1. Generic structures of heterocyclic libraries containing a single heteroatom: 1992
2000. *Solid-phase attachment point.
22.2 Solid-phase Synthesis of Heterocycles Containing One Nitrogen Atom 645
[85] [84]
[38] [39] [40] [37] [36]

I. 10-membered nitrogen heterocycles


Scheme 22.1. GabrielCromwell aziridine synthesis on solid phase.
of the aziridine carboxylic acids 6 with triuoroacetic acid (TFA) aords products
in >70% yield and in high purity. A second complementary method for azir-
idine synthesis was described in which substrates 1 are acylated with activated 2,3-
dibromopropane 7 to yield resin-bound a-bromoacrylamides 8. The use of 7
required as an alternative three-step acylation of 1 with acrylic acid chloride, bro-
mine addition, and HBr elimination gave a low yield of 8 owing to premature
cleavage. Treatment of Michael substrates 8 with a range of primary amines and
amino acid esters, followed by TFA cleavage, aords aziridines 10 in high purity.
22.2.2
b-Lactams
2-Azetidinones are important constituents of b-lactam antibiotics and are useful

intermediates in the synthesis of chiral b-amino acids. The [2 2] cycloaddition
reaction of ketones with resin-bound imines to yield b-lactams was one of the rst
successful examples of cycloaddition chemistry on solid phase. The solid-phase
version of the Staudinger reaction, initially described by researchers at Aymax

(Scheme 22.2A,B) [3, 4], proceeds via condensation of amino acid-esteried Sasrin
resin 1 with alkyl, aromatic, or a,b-unsaturated aldehydes to furnish quantitatively
resin-bound imines 11. Cycloaddition is eciently carried out by the slow addition
Scheme 22.2. b-Lactam solid-phase syntheses.

Scheme 22.2. (continued)
of acid chlorides to a methylene chloride suspension of imine resins 11 in the

presence of triethylamine. Large molar excess of acid chloride is used to convert
hindered imines to b-lactams. Sasrin resin is preferred over Wang resin because of
Sasrins increased sensitivity to acid, resulting in mild cleavage of the b-lactams
from solid support. Product yields are uniformly high (>80%) with the expected
cis disposition of 3- and 4-substituents on the b-lactam ring. Diastereomeric ratios
are modest and range from 1:1 to 3:1 for chiral amine substrates. Analogous
chemistry was employed in the synthesis of N-unsubstituted b-lactams using pho-
tolysis as the cleavage method (Scheme 22.2B).
In a reverse strategy, Singh and Nuss showed that the Staudinger reaction can
be carried out using immobilized imines 18 generated from resin-bound aryl alde-
hydes 17 (Scheme 22.2C) [5]. In their sequence, resins 18 are reacted with acetox-
yacetyl chloride [triethylamine (TEA), 0 C] to give cis-azetidinones 19 which may
be further elaborated to carbamates 22.
b-Lactams (relative stereochemistry not dened) are also prepared by condensa-
tion of resin-bound imines 24 with titanium enolates derived from b-substituted
propionic acid pyridinylthioesters (Scheme 22.2D) [6].
22.2.3
Pyrrolidines and Derivatives
Another early example of heterocyclic synthesis on solid support is the 1,3-dipolar
cycloaddition reaction of resin-bound azomethine ylides with olens to furnish
functionalized pyrrolidines (Scheme 22.3A). This work was carried out by pioneers
at Aymax in 1995 [8, 9]. In situ ylide formation occurs upon treatment of resin-
Scheme 22.3. Pyrrolidines via cycloaddition on solid phase.
bound amino acid imines (11) with AgNO3 and triethylamine in acetonitrile. Re-
action of these silver azomethine ylides with electron-poor olens (28) furnishes
proline derivatives after resin cleavage. The synthetic scheme was optimized using
gel-phase 13 C-NMR (nuclear magnetic resonance) analysis. Product yields range
from 50% to 80% and diastereoselectivities from 2.5:1 to >10:1. Because the pyr-
rolidine ring is a structural component of angiotensin-converting enzyme (ACE)

inhibitors, intermediate prolines 29 were acylated with mercaptoacyl chlorides
yielding mercaptoacyl prolines 31 after thioester deprotection and resin cleavage.
Biological evaluation of a split-and-pool library prepared from 240 building blocks
led to the identication of an exceptionally potent series of ACE inhibitors (Ki
values < 1 nM). This same library was subsequently encoded using oligomeric
amine tags, providing more detailed structureactivity relationship (SAR) infor-
mation [9].
The reverse strategy for pyrrolidine synthesis is also known, in which electron-
decient olens prepared on solid support via the condensation of immobilized
3-hydroxyacetophenone with aryl aldehydes are reacted with metalated azome-
thine ylide (derived from PhCHbNCH2 CO2 Me) [10]. In this synthesis, high regio-
and diastereoselectivity is observed.
A solid-phase synthesis of highly substituted pyrrolidines was conducted via
[2ps 4ps] cycloaddition of 2-azaallyl anions with alkenes (Scheme 22.3B) [11].
Hydroxyaldehydes are loaded onto resin via a dihydropyridine (DHP) linker to give
bound aldehydes 33 and are condensed with stannyl amine 35. Resin-bound 2-
(azaallyl) stannanes 34 so obtained are transmetalated (n-BuLi), in the presence of
electron-rich alkenes, to furnish pyrrolidine anions 37 which may be alkylated
upon subsequent addition of an electrophile. Six fully substituted pyrrolidines (38,
39) were prepared in 3250% overall isolated yield.
Other reports of solid-phase methods for generating pyrrolidines include appli-
cation of N-acyliminium ion chemistry [12], the imino-Sakurai and Pd-catalyzed
cyclization cleavage of allylic amine systems [13], radical cyclization of oxime
ethers [14], and intramolecular amino-zinc-enolate cyclization [15].
Cyclic imides (2,5-dioxopyrrolidines) form another class of compound that often
possesses interesting biological properties. Solid-phase strategies for the synthesis
of cyclic imides include a variant of the classical amine/cyclic anhydride conden-
sation [16] and DielsAlder reaction of N-substituted maleimide with resin-bound
dienes [17, 18]. In the latter example, Barn and Morphy at Organon [16] optimized
the coupling of succinic and phthalic anhydrides to hydroxymethyl polystyrene
resin using dimethylaminopyridine (DMAP) in dimethylformamide (DMF) (Scheme
22.4). Acids 41 are converted to amides 42 using a primary amine in the presence
of dicyclohexylcarbodiimide (DCC) and hydroxybenzotriazole (HOBT). Heating the
resulting resin 42 in 5% acetic acid/DMF at 130 C for 18 h promotes cyclative re-
lease of the cyclic imide 43 from resin. Although the yields for nine examples
range from 20% to 71%, the purity of the products are excellent owing to the fact
the resin cleavage can only occur upon imide formation. The new chemistry was
used to construct a @40-member d-opioid optimization library of cyclic imides.
22.2.4
Tetramic Acids
Three publications appeared in 1998 from three independent laboratories describ-

ing the synthesis of tetramic acids in high yield and purity [1921]. Each method
Scheme 22.4. Solid-phase synthesis of cyclic imides.
relies on some variation of the following three-step sequence: (1) reductive alkyla-
tion of resin-bound a-amino acids with aldehydes (44); (2) acylation of the second-
ary amine (44 to 4850); and (3) base-promoted Claisen-type intracyclative cleavage
(4850 to 5153; Scheme 22.5). Acylating reagents include Meldrumss acid, ma-
Scheme 22.5. Tetramic acid synthesis on solid support.

lonic half esters, aryl acetic acids, and acetic acids bearing electron-withdrawing
groups, with the last two reagents providing convenient access to diversity at posi-
tion C3 on the heterocycle.
22.2.5
Pyrroles
Tetra- and penta-substituted pyrroles were rst prepared by Mjalli and co-
workers via the 1,3-dipolar cycloaddition of alkynes to polymer-bound munch-
nones (Scheme 22.6A) [22]. Resin-bound amino acids 54 are subjected to a four-
component condensation with aldehydes, carboxylic acids, and either phenyl or
pyridinylisocyanates to yield Ugi products (55, 56). Hydrolysis of the terminal
amide bond in 55 and 56 to 57 is carried out after Boc anhydride activation. The
selection of either phenyl or pyridinylisocyanate stems from the necessity to hy-
drolyze the amide bond in 55 and 56 under conditions compatible with resin link-
age. Originally, benzylisocyanate was used in this process, but the rate of hydroly-
sis of the corresponding amide is too slow (t1=2 > 7 days) to be of practical utility.
The reaction of 57 with electron-decient alkynes either in neat acetic anhydride as
solvent or in a toluene solution of Et3 N and isobutyl chloroformate at 100 C (24
48 h) leads to sequential in situ formation of munchnones 58 and 1,3-dipolar cy-
cloaddition. Some ten pyrroles were obtained in 2676% overall yield using this
protocol (TFA cleavage). The purity of all the products was exceptional.
A slight variant of this reaction was reported by Armstrong wherein resin-bound
succinate 61 is used in the Ugi condensation employing 1-isocyanocyclohexene as
a convertible isocyanide (Scheme 22.6B) [23]. Munchnone precursors 62 are su-
ciently reactive such that heating 62 in toluene containing 10 equiv. HCl and 25
equiv. dimethyl acetylenedicarboxylate (DMAD) aords the pyrrole ring, negating
the earlier requirement for intermediate amide hydrolysis (55, 56 to 57; Scheme
22.6A).
Resin-bound enaminones 69 are particularly versatile intermediates with respect
to pyrrole synthesis (Scheme 22.7). They are prepared from the condensation of
resin derivative 68 and primary amines [trimethylorthoformate (TMOF)] as the
dehydrating reagent in DMF. The intramolecular net reaction of 69 with a-alkyl-
substituted nitroalkenes (neat or prepared in situ from nitroalkanes and aldehydes)
aords pyrroles in 4690% yields [24]. Enaminones 69 readily react with a-bromo-
ketones in the classical Hantzch pyrrole synthesis [25]. The key to the success of
this reaction is the use of the non-nucleophilic Lewis base 2,6,-di-t-butyl-pyridine
and DMF as solvent.
22.2.6
Piperidine and Derivatives
The aza-DielsAlder reaction provides convenient access to a range of nitrogen-

containing heterocycles. In an operationally simple one-pot solid-phase synthesis
of 3,4-dihydropiperidines 76 [26], a solution of aminomethylated polystyrene resin
nchnones.
Scheme 22.6. Pyrroles via immobilized mu
71, an aldehyde (72), a diene (73), and ytterbium triate (10 mol%) in methylene
chloride is shaken at room temperature for @24 h (Scheme 22.8). Traceless cleav-
age of adducts 75 is performed using ACE chloride (N-debenzylation) to give col-
lections of 76. Electron-rich dienes in combination with ethyl glyoxylate, phenyl-
glyoxal, and 37% aqueous formaldehyde are the preferred reagents.
Scheme 22.7. Pyrroles from enaminones.
Scheme 22.8. Multicomponent condensation to dihydropiperidines.
The construction of b-aryl-2,3-dihydro-4-pyridones 80 on solid support has been

described by Wang and Wilson (Scheme 22.9) [27]. Resin-bound imines 78, pre-
pared from resin-bound aldehyde 77 (Mitsunobu reaction of 4-hydroxyben-
zaldehyde and Wang resin) and primary amines, undergo a tandem Mannich
Michael reaction with Danishefskys diene 78 catalyzed by Yb(OTf )3 in dry THF.
A wide range of amines may be employed in the chemistry, including aliphatic
and arylalkyl amines, as well anilines. Product purities average over 85% after TFA
cleavage.
A resin-bound divinyl ketone equivalent (82) was utilized in the construction of
2-substituted-piperidine-4-ones (Scheme 22.10) [28]. Reagent 82 is generated via a
six-step sequence: (1) reaction of Merrields chloromethyl resin with potassium
thioacetate; (2) LiBH4 -mediated reduction of the thioester to methylmercaptan; (3)
Scheme 22.9. Ecient solid-phase synthesis of piperidinones.
Scheme 22.10. Piperidinone synthesis via cyclorelease strategy.
Michael addition with 3-butenone in EtOH; (4) oxidation to the sulde to sulfone
81; (5) bromination; and (6) reaction with triphenylphosphine. Phosphonium salt
82 undergoes Wittig condensation to 83 in high yield with a variety of aldehydes
using NaOMe as base. Treatment of vinyl ketones 83 with an excess of benzyl-
amine for 3 days at room temperature provides N-benzyl-2-subsititued-piperidin-4-

ones 86 in 5075% yield. Benzylamine serves as both nucleophile (Michael addi-
tion; 83 to 84) and base (1,4-elimation; 84 to 85) in this ring construction.
A second example of a traceless linker strategy utilizing Ru-catalyzed ring-
closing metathesis (RCM) was reported by Rutjes and coworkers (Scheme 22.11)
[29]. Substrates 89, readily prepared from the Mitsunobu coupling of 87 with al-
lylic sulfonamide 88, undergo RCM in >90% yield at 50 C in toluene.
Scheme 22.11. Metathesis release method for the synthesis of N-heterocycles.
22.2.7
Dihydropyridines
The dihydropyridine (DHP) pharmacophore, well known for its anity for cal-
cium channels, is regarded as a privileged scaold possessing broad-based biologi-
cal activity. The synthesis of DHPs has been largely explored by Gordeev and co-
workers at Aymax [30, 31]. Their synthesis is based on the multicomponent
cyclocondensation of resin-bound enamino esters 92 with either 2-benzylidine b-
keto esters 93 or b-keto esters and aldehydes (94, 95) followed by TFA cleavage
from solid support (Scheme 22.12A). The success of the cyclocondensation relies
upon the use of pyridine as solvent, which facilitates the formation of the thermo-
dynamically favored enamine 97 from imine 96 (isomerization of the p-bond).
An elegant application of 13 C-labeled substrates and 13 C-NMR was used to dene
the reaction mechanism. Acyclic adducts 97 are cleaved from resin prior to cycli-
zation. The solid-phase protocol is suciently robust for the construction of a 300-
member DHP library (Scheme 22.12B). Rink amine resin was split into ten por-
tions and condensed with one of ten b-keto esters. The enamines were then com-
bined and portioned into 30 reaction vessels. Each enamine lot was treated with
one of three 1,3-dicarbonyl building blocks and ten aldehydes in pyridine at 45 C.
Each resin lot was cleaved with 3% TFA in CH2 Cl2 to yield 30 pools of ten DHPs
per pool. All 30 pools were evaluated for Ca 2 channel binding (rat brain mem-
branes). Two of the pools displayed binding anities at @10 nM. All 20 com-
Scheme 22.12. Dihydropiperidine library synthesis.

pounds from the two pools were resynthesized as discrete analogs from which 3,5-
dicarboxymethyl-2,6-dimethyl-4-(2-uorophenyl) DHP 105 was identied with an
IC50 14 nM.
22.2.8
Pyridines
The facile oxidation of dihydropyridines to pyridines prompted the development

of a solid-phase pyridine synthesis exploiting this transformation (Schemes 22.13
and 22.14) [32]. Immobilized b-keto esters 106 are reacted with aliphatic or aryl al-
dehydes 95 to furnish Knoevenagel derivatives 107 (Scheme 22.13). These products
then undergo Hantzsch-type condensation with g-oxo-enamines 108 to yield DHPs
that in turn are oxidized to pyridines 110 with cerium ammonium nitrate (CAN).
TFA-mediated cleavage aords 111. This chemistry also serves as the basis for the
solid-phase synthesis of 2,2 0 -bipyridines [33].
Scheme 22.13. Solid-phase synthesis of pyridines.
Ellingboe and coworkers [35] generated 1,5-diketones (114) on resin from im-
mobilized hydroxyacetophenones via ClaisenSchmidt reaction with an aromatic
aldehyde followed by Michael addition of trimethylsilyl enol ether (112 ! 113 !
114; Scheme 22.14). Heterocycle formation 116 occurs upon heating 114 with
NH4 OAc in HOAc/DMF at 100 C in an atmosphere of air. Presumably, DHPs 115
initially form and spontaneously oxidize to the corresponding aromatic pyridines.
The yield and purity of ten examples (117) range from 19% to 62% and 21% to
70%, respectively.
Jung [34] condensed the same enone substrates 113 with 1-(2-oxo-2-arylethyl) pyr-
idinium salts (118) and ammonium acetate in a Krohnke-type pyridine synthesis
Scheme 22.14. Pyridine-derived biaryls.
(Scheme 22.14). DMF containing glacial acetic acid (1:1) is the preferred solvent.
Conducting the reaction in the absence of acetic acid gives a side product arising
from the addition of pyridine to 113.
22.2.9
Azepanes, Benzazepines, and Derivatives
To date, the solid-phase synthesis of seven- and eight-member ring nitrogen het-
erocycles has relied primarily on the use of the ring-closing metathesis (RCM) re-
action (Schemes 22.1522.17) [3638]. Metathesis reactions generally proceed in
good yield with minimal intermolecular cross-linking. The challenge is devising a
synthetic scheme that permits the introduction of diversity elements in the requi-
site bis-olen substrates. The traceless linker strategies reported by Piscopio intro-
duce up to three points of diversity in azepinone structures (Schemes 22.15 and
22.16). In one example, bis-olen substrates 123 with two points of diversity are
prepared by sequential FukuyamaMitsunobu and acylation reactions [39]. Ugi
four-component coupling of resin-bound cinnamyl amine 125, aldehyde 128, iso-
cyanate 127, and olen-bearing carboxylic acid 126 conveniently introduces three
diversity parameters in a single reaction (Scheme 22.16) [36]. Elevated temperature
is generally required for successful RCM. For example, treatment of substrate 129
with Grubbs catalyst (510 mol%) in CH2 Cl2 at 25 C fails to generate metathesis
products. However, conducting the RCM reaction in dichloroethane at 80 C for 24
h gives the corresponding lactams as a 1:1 mixture of diastereomers in good yield.
Scheme 22.15. Solid-phase azepine synthesis.
Scheme 22.16. Azepines via multicomponent condensation and metathesis cyclorelease.
Immobilized diene substrates for azepane synthesis may also be prepared by the
addition of allyl lithium to tethered imine ethers (132 to 133 to 134; Scheme 22.17)
[37].
Polyhydroxylated azepane scaold 137 was obtained upon the reaction of Rink
linker 71 with chiral l-iditol bis-epoxide 135 (Scheme 22.18) [40]. The intramo-
lecular ring closure required heating for 5 days at 80 C in DMF. Azepanes 137 are
obtained following acylation of diol 136 and resin cleavage.
Bolten and Hodges [41] at Parke-Davis Pharmaceuticals (now Pzer) developed
a solid-phase synthesis of substituted benzazepines (147) via intramolecular Heck
reaction of allyl or propargyl glycines bearing a 2-iodophenyl group (140, 144)
Scheme 22.17. Metathesis approach to azepines.
Scheme 22.18. Solid-phase azepine synthesis via a chiral pool.
(Scheme 22.19A,B). Resin-bound N-(3-nitro)sulfonyl allylglycine is methylated

with MeI in the presence of 7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene (MTBD)
to give the key cyclization precursor 140, after N-deprotection and acylation with
o-iodobenzoyl chloride. Heating 140 in DMF with catalytic Pd(0) cleanly provides
the benzazepinone 142 in @65% overall yield following TFA-mediated resin cleav-
age and treatment with diazomethane. The propargyl substrates 144 give the anal-
ogous Heck products 146 following the same protocol. The latter sequence was
further exemplied via the synthesis of several benzazepinones (148153). Yields
for the multistep sequence ranged from 40% to 70%.
Octahydrobenzazepinones [42] were synthesized via intracyclative ring closure
of resin-bound intermediate 156 (Scheme 22.20). Intermediate 156 is eciently
prepared via sequential yneene cross-metathesis (154 and an alkyne) and Diels
Alder cycloaddition reactions (155, 156).
Scheme 22.19. Intramolecular Heck reaction to produce benzazepinones.
22.2.10
Indoles
The synthesis of the indole system has received more attention from combinatorial
chemists than any other heterocycle. This is a reection of the broad-based biolog-
ical activity ascribed to indole-containing compounds. Some 11 reports from eight
laboratories describe the solid-phase methodology used to synthesize substituted
Scheme 22.20. Tetrahydroazepinones on solid phase.
indoles [4352; see also 141, 144]. With the exception of the classical Fischer in-
dole synthesis by Merck [51], all of the examples employ Pd catalysis as a central
theme. The requisite o-iodoanilines are generally tethered to solid support through
an appended carboxylate function. The immobilized substrates are then subjected
to the Sonogashira protocol for terminal alkyne coupling followed by Pd-catalyzed
cyclization. The overall yield and eciency of the reaction sequence are highly de-
pendent on the structure of the alkyne and the base used in the heteroannulation
step (Schemes 22.21 and 22.22) [44]. Because of its ability to provide homogeneous
reaction conditions, tetramethylguanidine (TMG) is the preferred base in many of
the reported protocols.
Indoles with three points of diversity were generated by Collini and Ellingboe
(Scheme 22.23) [45] by coupling triuoracetylated alkyne intermediates 168 with
vinyl triates 170 using catalytic Pd(PPh3 )4 and potassium carbonate as base. Re-
moval of the triuoroacetyl protecting group followed by N-alkylation gave a set of
functionalized indoles (173).
Using an intramolecular Heck reaction, o-iodoanilines 176, bearing a N-allyl sub-
stituent, may be cyclized to give indoles 177 (Scheme 22.24) [43, 46]. Several varia-
tions on this theme have been published, including the synthesis of 2-oxindoles [52]
(178 to 179; 180 to 181).
Solid-phase reaction conditions have been optimized for Fischer indole synthesis
(Scheme 22.25) [51]. In a single step, resin-bound arylketones 182 are treated with
a solution of an arylhydrazine (183) and ZnCl2 in glacial acetic acid at 70 C for
1820 h. Methanolysis of the resin generates indole esters 186. Because acid catal-
Scheme 22.21. Indoles via intramolecular Heck cyclization.
Scheme 22.22. Application of tetrahydropyran linkage to indole synthesis.
ysis is required for the reaction, the acid-stable hydroxymethylbenzoic acid (HMB)
is the preferred linker (ester linkage). A survey of resins revealed that polystyrene
was superior to polyethylene glycol (PEG) polystyrene (PEG-PS), minimizing
resin-based impurities in the indole products. Electron-rich, electron-decient, and
even sterically demanding 2,5-disubstituted hydrazines can be used in this solid-
phase synthesis.
Scheme 22.23. Multicomponent indole synthesis on solid phase.
22.2.11
Tetrahydroquinolines
In a series of three publications, Kiselyov and coworkers described the synthesis

of diverse arrays of tetrahydroquinolines via a three-component condensation re-
action (Schemes 22.26 and 22.27) [5355]. Approximately a decade earlier, Grieco
reported this multicomponent reaction in solution based on the condensation of
substituted anilines, electron-rich olens, and aldehydes in the presence of TFA in
acetonitrile.
In his initial disclosure, Kiselyov anchored 4-nitrobenzoic acid (191) to Wang
resin (Scheme 22.26) [53]. The nitro group is selectively reduced to the aniline 192
by SnCl2 in DMF/water. Aniline 121 is then suspended in a 1M solution of ben-
zaldehyde (189) and cyclopentadiene (188) with a catalytic amount of TFA. After 12
h at room temperature, the resin is ltered, washed, and treated with 15% TFA to
give tetrahydroquinoline 190 in 76% yield, free of any byproducts. A library of 80
members was generated using aniline (192), ve alkenes (187, 194197), and eight
aldehydes (189, 198204). With the exception of 189, aliphatic aldehydes do not
participate in the reaction. Thus, the inputs are largely limited to aryl aldehydes.
The yield of library compounds ranges from 53% to 92% with purities in excess of
90%. The highest yields were obtained using electron-decient aryl aldehydes.
Scheme 22.24. Indoles via intramolecular Heck reaction.
Scheme 22.25. Fisher indole synthesis on solid phase.

Scheme 22.26. Multicomponent condensation yielding a tetrahydroisoquinoline library.
In further studies, it was observed that, with certain synthons, substantial

amounts of nonreacted Schi base was present in the cleaved products [54], which
prompted a survey of Lewis acids to replace TFA as catalysts. Ultimately, a 0.1%
solution of Yb(OTf )3 in MeCN/CH2 Cl2 (1:1) was identied as a superior catalyst
system for the three-component condensation. The scope of the reaction was then
expanded to resin-bound phenolamine substrate 209 and the synthesis of other
tricyclic tetrahydroquinolines (Scheme 22.27) [55].
Scheme 22.27. Variations on the preparation of tetrahydroisoquinolines.
22.2.12
Quinolinones
The synthesis of a 4140-member library of 3,4-dihydro-2-(1H)-quinolinones was

achieved through rearrangement of resin-bound b-lactams [56]. Boc-protected
amino acids are attached to resin via standard peptide coupling conditions in ei-
ther dichloromethane (DCM) or DMF depending on amino acid solubility and the
deprotected (Gly resin 211 shown; Scheme 22.28). Condensation of 211 with o-
nitrobenzaldehyde in DCM using Na2 SO4 as a water scavenger furnishes imine
213. Imine 213 is then subjected to [2 2] cycloaddition with the ketene derived in
situ from phenoxyacetyl chloride and TEA at 78 C. The aryl nitro-containing cis-
b-lactam (structure conrmation by cleavage and 1 H-NMR analysis) is reduced
with SnCl2 to the anilino species 215. This intermediate spontaneously rearranges
to the desired aminoquinolinone 216 in high yield and in >85% purity. In the
model studies, methylbenzylhydryl amine (MBHA) resin was identied as the
resin most compatible with the reaction scheme. Interestingly, when Wang resin
was used, the alternative bicyclic system 217 (Scheme 22.28, reaction b) became a
Scheme 22.28. Solid phase of quinolinones via b-lactams.
signicant contaminant. A split-and-pool protocol using tea-bags created a 4140

(2070 pairs of enantiomers)-member library: 69 amino acids (R1) 6 o-nitro-
benzaldehydes (R2) 5 acid chlorides (R3). In the actual production run, the R1
position was in mixture format and R2 and R3 were formatted in a two-dimensional
array.
Other quinolinone heterocycles synthesized on solid support include substituted
quinolin-2-(1H)-one-3-carboxylic acids 222 [57] and the antibacterial quinolones
[58]. The former heterocycle 222 can be synthesized in three steps: (1) acylation of
the malonic esteried Wang resin 219 with o-aminophenones 220; (2) intra-
molecular Knoevenagel condensation (220 to 221); and (3) resin cleavage (221 to
222; Scheme 22.29). Aminophenones containing electron-donating and electron-
withdrawing substituents are equally tolerated. Quantitative yields were obtained
in some examples.
22.2.13
Quinolines
A four-step solid-phase synthesis of 2-aryl-6-alkoxyquinolines 232 was reported by

the Schering group (Scheme 22.30) [59]. Reaction conditions were initially devel-
oped in solution, and the chemistry was transferred to solid phase. Esters 224 and
225, derived from 5-hydroxy-2-nitrobenzaldehyde 223, were the starting materials
for the solution- and solid-phase synthesis, respectively.
Scheme 22.29. Synthesis of tetrahydroisoquinolones from resin-bound malonic acid ester.
Scheme 22.30. Quinoline synthesis on solid support.
The rst step in both sequences is an aldol condensation of 224 (225) with
an aryl ketone. Optimal reaction conditions in solution employ K2 CO3 in CH3 CN
at room temperature. Optimal reaction conditions for the solid-phase synthesis
require CH2 Cl2 /THF (1:1) and K2 CO3 at reux temperature for 2 days. Dichloro-
methane was used as a cosolvent to ensure resin swelling (polystyrene hydroxy-
methyl resin). In solution, the nitro reduction to quinoline N-oxide (226 to 227)
was eected with SnCl2 in reuxing EtOH for 2 h. This same transformation on
solid phase requires a 4-h reaction time, and again preswelling the resin with
CH2 Cl2 is essential. The solution- and solid-phase reaction conditions for the re-
maining two-steps, deoxygenation (TiCl3 ) and aminolysis (amine, AlMe3 ), are vir-
tually identical. Solid-phase reaction monitoring was conveniently achieved via
fourier transform infrared FT-IR spectroscopy. A small parallel array of 12 quino-
lines was synthesized and the products were puried by silica gel chromatography
(yields 2065%).
The solid-phase synthesis of quinolines based on the Doebner quinoline synthe-
sis (multicomponent condensation) has been described by Gopalsamy and Pallai
[60].
22.2.14
Tetrahydroisoquinolines
The tetrahydroisoquinoline nucleus is a common structured feature in many bio-

logically active alkaloids. The reaction of an imine with a cyclic anhydride yields a
4-carboxy-substituted tetrahydroisoquinoline. This transformation was a key step
in the construction of a 43,000-tetrahydroisoquinoline library (236; Scheme 22.31)
[6163]. Sets of aldehydes, cyclic anhydrides, and amines were sources of diversity
in the library. MBHA resin was superior to TentaGel resin with respect to purer
products obtained upon release of the library compounds with HF.
Scheme 22.31. Addition of cyclic anhydrides to imines aording tetrahydroisoquinolones.
Researchers at Merck developed a general synthetic strategy for the preparation

of tetrahydroisoquinolines via thermal cyclization of resin-bound imines under
mild conditions (Scheme 22.32) [64]. Heating resin-bound m-tyramine 237 with
aldehydes (pyridine, 100 C) leads to cyclocondensation, and standard cleavage con-
ditions give the target compounds 238. The reaction accommodates a variety of
substituted m-tyramine derivatives.
Two reports describe the solid-phase synthesis of tetrahydroisoquinolines using
the BischlerNapieralski reaction [65, 66]. The key step in the synthesis is the in-
22.3 Solid-phase Synthesis of Heterocycles Containing One Oxygen Atom 675
Scheme 22.32. Tetrahydroisoquinolines via solid-phase imine cyclization.
tramolecular cyclization of m-phenoxyphenethylacetamides with POCl3 , substrates,

which survive the rather harsh reaction conditions, attached through ester-type
linkages to Merrield resin.
22.3
Solid-phase Synthesis of Heterocycles Containing One Oxygen Atom
22.3.1
Tetrahydrofurans and g-Butyrolactams
Intramolecular radical cyclizations of unsaturated carboncarbon bonds to access

heterocyclic systems have been known for over 20 years. Two publications explored
the synthesis of tetrahydrofurans using such methodology [67, 68]. In research
carried out by Balasubramanian and coworkers [67], radical cyclizations to form
tetrahydrofurans (243) were achieved upon treatment of substrates 241 with Bu3 SuH
and catalytic 2,2 0 -azobisisobutyronitrile (AIBU) (Scheme 22.33). The synthesis was
initially attempted on polystyrene support, but the yields were poor. Use of Tenta-
Gel resin results in substantially improved yields of >90%. It is thought that the
failure of the reaction on polystyrene is due to competing hydrogen abstraction from
Scheme 22.33. Tetrahydrofurans via intramolecular radical cyclization.

the benzylic position of the polymeric backbone. The polyethylene spacing units in
TentaGel minimize the formation of backbone radicals. No byproducts are pro-
duced, and tin residues are conveniently washed out of the resin to give pure cy-
clized products. This chemistry is also useful for constructing dihydrobenzofurans.
As further conrmation of the observations made by Balasubramanians group,
Toru and coworkers [68] found that linear spacing groups on polystyrene support
were necessary to enable high-yielding radical cyclization of substrates 245 en route
to g-butyrolactones 247 (Scheme 22.34). The traceless linker solid-phase synthesis
begins with the preparation of b-bromoacetals (245). Intramolecular radical cycli-
zation furnishes cyclic actetals (246), whereupon g-butyrolactones are isolated after
Jones oxidation. Six g-butyrolactones were prepared using this methodology, with
yields ranging from 47% to 93%. The same six examples based on Merrield resin
with linear spacing groups gave reduced yields on the order of 2343%.
Scheme 22.34. Radical cyclization and oxidative cleavage to butyrolactones.
Several other g-butyrolactone syntheses have been described using nonradical

chemistry [6974].
22.3.2
Furans
A general method for the construction of substituted furans on solid support is

described by Austin and coworkers [75] and by Gororavram and Gallop [76]. Fur-
ans are assembled in aqueous medium via the 1,3-dipolar cycloaddition reaction of
acetylenes with resin-bound isomunchnones. Upon heating, the transient cyclo-
adducts experience a facile retro-DielsAlder reaction (cycloreversion) to release
tetra-substituted furans in solution while isocyanate is retained on resin.
Model solid-phase studies began with amide 248 Wang resin esteried with
N-acyl-protected amino caproic acid (Scheme 22.35) [75]. Acylation of 249 with
methylmalonyl chloride and diazo transfer yields the isomunchnone precursor
250. Rhodium-mediated decomposition of 250 in the presence of DMAD at room
temperature aords adduct 251. The reaction is easily monitored by infrared (IR)
22.3 Solid-phase Synthesis of Heterocycles Containing One Oxygen Atom 677
Scheme 22.35. Cycloadditioncycloreversion approach to furans.
spectroscopy. Furans 252 are obtained in 70% yield and in 98% purity upon ther-
molytic cleavage of 251 in benzene at 70 C.
The solid-phase chemistry was applied to a split-and-pool synthesis of a small
furan library (18 members). Both aryl and alkyl groups may be incorporated into
the furan ring using a rhodium(II) peruorobutyramidate catalyst. The chemistry
appears to be limited to acetylenes possessing electron-withdrawing groups.
22.3.3
Benzofurans
Given the structural similarity of benzopyrans and indoles, many of the solid-
phase approaches developed for indoles have been applied to benzofuran syn-
thesis. Solid-phase strategies to this class of compounds utilize Pd-catalyzed hetero-
annulation of terminal acetylenes in the presence of o-hydroxyaryl iodides [77,
78]. Fancelli and coworkers prepared 254 by esterifying TentaGel S-OH resin (Mit-
sunobu reaction) with acetate-protected 3-iodo-4-hydroxy benzoic acid (Scheme
22.36) [77]. Heteroannulation with terminal acetylenes is carried out using Pd(0)
Scheme 22.36. Intramolecular Heck cyclization to furnish benzofurans.

catalyst, CuI, and tetramethylguanidine as a soluble base. Saponication of the

products gives essentially pure benzofuran carboxylic acids in 4070% yield. The
methodology is exemplied using ten dierent terminal acetylenes possessing
amino- and hydroxyalkyl substituents and is suitable for automated synthesis in
96-well format.
Other methods for preparing benzofurans and derivatives on solid support in-
clude SmI2 -mediated radical cyclization/anionic capture of aryl iodides [79, 80]
and intramolecular condensation of aryl keto-b-alkoxyesters [81].
22.3.4
Pyrans, Benzopyrans, and Derivatives
In contrast to furans, there are few reports on the synthesis of pyrans and their
derivatives. Solid-phase chemistries for the construction of dihydropyrans (241)
have been reported that utilize a hetero-DielsAlder reaction of oxabutadienes
(239) with enol ethers (Scheme 22.37) [82]. Baldwin and coworkers at Pharmaco-
peia, have described the solid-phase synthesis of a dihydrobenzopyran library using
molecular tagging technology [83]. In this chemistry, resin-bound o-hydroxyaryl
methylketones are attached to resin and condensed with a variety of cyclic and
acyclic ketones. When bifunctional ketones were used, four points of diversity
were achieved (Scheme 22.38).
Scheme 22.37. Dihydropyrans via hetero-DielsAlder reaction on solid phase.
Nicolaou and coworkers have prepared natural product-like libraries based on a

benzopyran template; this process is reviewed in Chapter 21.
22.4
Solid-phase Synthesis of Thiophenes
3-Aminothiophenes have been synthesized on solid phase by Zaragoza and col-

leagues at Novo Nordisk [84, 85]. The reaction sequence is an adaptation of solu-
22.5 Summary 679
Scheme 22.38. Encoded benzopyran library.
tion chemistry originally described by Laliberte. Resin-bound cyanoacetamide 247

is reacted with aliphatic or aromatic isothiocyanates in DMF/1,8-diazabicyclo[5.4.0]-
undecene-7 (DBU) (Scheme 22.39). Subsequent S-alkylation of intermediates 248
with a set of aryl a-haloketones and acidolytic cleavage furnishes 3-aminothio-
phenes in high yield. The reaction sequence precludes the use of strongly electron-
donating isothiocyanates or aliphatic a-haloketones. In subsequent studies, resin-
bound isothiocyanates were found to be useful in this synthesis.
Scheme 22.39. Solid-phase thiophene synthesis.
22.5
Summary
The solid-phase syntheses of all the major classes of heterocycles containing a sin-
gle heteroatom have been described in the literature. Much of the solid-phase het-
erocyclic chemistry published thus far is synthetic methodology that is typically
exemplied by fewer than a dozen compounds. Relatively few libraries containing

thousands of members are known. In general, methodology developed on solid
support is a direct adaptation of solution chemistry. Solid-phase chemistries re-
quire extended reaction times and excess reagents to drive them to completion. In
this regard, extensive reaction development and synthon proling must be en-
gaged to optimize solid-phase chemistry. Yields of solid-phase synthesis are gener-
ally equal to or lower than that observed in solution, although the ease of purica-
tion is greatly facilitated by solid support. Several examples are cited in which the
type of resin is critically important for selected chemistries. A case in point is the
failure (or greatly reduced yields) of radical-mediated cyclizations on Merrield
versus TentaGel resin.
References
1 a) R. E. Dolle, J. Comb. Chem. 2000, 13 R. C. D. Brown, M. Fisher, Chem.

2, 383433; b) R. E. Dolle, K. H. Commun. 1999, 15471548.
Nelson, Jr, J. Comb. Chem. 1999, 1, 14 H. Miyabe, H. Tanaka, T. Naito,
235282; c) R. E. Dolle, Mol. Diversity Tetrahedron Lett. 1999, 40, 83878390.
1998, 3, 199233; d) R. E. Dolle, Mol. 15 P. Karoyan, A. Triolo, R.
Diversity 1998, 4, 233256. Nannicini, D. Giannotti, M.
2 S. N. Filigheddu, S. Masala, M. Altamura, G. Chassaing, E.
Taddei, Tetrahedron Lett. 1999, 40, Perrotta, Tetrahedron Lett. 1999, 40,
65036506. 7174.
3 B. Ruhland, A. Bhandari, E. M. 16 D. R. Barn, J. R. Morphy, J. Comb.
Gordon, M. A. Gallop, J. Am. Chem. Chem. 1999, 1, 151156.
Soc. 1996, 118, 253254. 17 M. Crawshaw, N. W. Hird, K. Irie,
4 B. Ruhland, A. Bombrun, M. A. K. Nagai, Tetrahedron Lett. 1997, 38,
Gallop, J. Org. Chem. 1997, 62, 7820 71157118.
7826. 18 E. M. Smith, Tetrahedron Lett. 1999,
5 R. Singh, J. M. Nuss, Tetrahedron Lett. 40, 32853288.
1999, 40, 12491252. 19 J. Matthews, R. A. Rivero, J. Org.
6 V. Molteni, R. Annunziata, M. Chem. 1998, 63, 48084810.
Cinquini, F. Cozzi, M. Benaglia, 20 B. A. Kulkarni, A. Ganesan,
7 S. Hanessian, R. Y. Yang, Tetrahedron 21 L. Weber, P. Iaiza, G. Biringer, P.
Lett. 1996, 37, 58355838. Barbier, Synlett, 1998, 1156.
8 M. M. Murphy, J. R. Schullek, E. M. 22 A. M. M. Mjalli, S. Sarshar, T. J.
Gordon, M. A. Gallop, J. Am. Chem. Baiga, Tetrahedron Lett. 1996, 37,
Soc. 1995, 117, 70297030. 29432946.
9 D. Maclean, J. R. Schullek, M. M. 23 A. M. Strocker, T. A. Keating, P. A.
Murphy, Z. J. Ni, E. M. Gordon, M. Tempest, R. W. Armstrong,
A. Gallop, Proc. Natl. Acad. Sci. USA Tetrahedron Lett. 1996, 37, 11491152.
1997, 94, 28052810. 24 A. W. Trautwein, G. Jung, Tetra-
10 S. P. Hollinshead, Tetrahedron Lett. hedron Lett. 1998, 37, 82638266.
1996, 37, 91579160. 25 A. W. Trautwein, R. D. Submuth, G.
11 W. H. Pearson, R. B. Clark, Tetra- Jung, Bioorg. Med. Chem. Lett. 1998, 8,
hedron Lett. 1997, 38, 76697672. 23812384.
12 J. J. N. Veerman, F. P. J. T. Rutjes, J. 26 W. Zhang, W. Xie, J. Fang, P. G.
H. vanMaarseveen, H. Hiemstra, Wang, Tetrahedron Lett. 1999, 40,
References 681
27 Y. Wang, S. R. Wilson, Tetrahedron 45 M. D. Collini, J. W. Ellingboe,

28 A. Barco, S. Benetti, C. De Risi, P. 46 H. C. Zhang, B. E. Maryanoff, J.
Marchetti, G. P. Pollini, V. Org. Chem. 1997, 62, 18041809.
Zanirato, Tetrahedron Lett. 1998, 39, 47 H. C. Zhang, K. K. Brumeld, B. E.
75917594. Maryanoff, Tetrahedron Lett. 1997, 38,
29 J. J. N. Veerman, J. H. van 24392442.
Maarseveen, G. M. Visser, C. G. 48 A. L. Smith, G. I. Stevenson, C. J.
Kruse, H. E. Schoemaker, H. Swain, J. L. Castro, Tetrahedron Lett.
Hiemstra, F. P. J. T. Rutjes, Eur. J. 1998, 39, 83178320.
Org. Chem. 1998, 25832589. 49 H. C. Zhang, K. K. Brumeld, L.
30 M. F. Gordeev, D. V. Patel, B. P. Jaroskova, B. E. Maryanoff,
England, S. Jonnalagadda, J. D. Tetrahedron Lett. 1998, 39, 44494452.
Combs, E. M. Gordon, Bioorg. Med. 50 H. Stephensen, F. Zaragoza,
Chem. Lett. 1998, 6, 883889. Tetrahedron Lett. 1999, 40, 57995802.
31 M. F. Gordeev, D. V. Patel, E. M. 51 S. M. Hutchins, K. T. Chapman,
Gordon, J. Org. Chem. 1996, 61, 924 Tetrahedron Lett. 1996, 37, 48694872.
928. 52 V. Arumugam, A. Routledge, C.
32 M. F. Gordeev, D. V. Patel, J. Wu, E. Abell, S. Balasubramanian,
M. Gordon, Tetrahedron Lett. 1996, Tetrahedron Lett. 1997, 38, 64736476.
37, 46434646. 53 A. S. Kiselyov, R. W. Armstrong,
33 S. Tadesse, A. Bhandari, M. A. Tetrahedron Lett. 1997, 38, 61636166.
Gallop, J. Comb. Chem. 1999, 1, 184 54 A. S. Kiselyov, L. Smith, A.
187. Virgilio, R. W. Armstrong,
34 P. Grosche, A. Holtzel, T. B. Walk, Tetrahedron Lett. 1998, 54, 79877996.
A. W. Trautwein, G. Jung, Synthesis 55 A. S. Kiselyov, L. Smith, R. W.
1999, 11, 19611970. Armstrong, Tetrahedron Lett. 1998,
35 C. Chiu, Z. Tang, J. W. Ellingboe, J. 54, 50895096.
Comb. Chem. 1999, 1, 7377. 56 Y. Pei, R. A. Houghten, J. S. Kiely,
36 A. D. Piscopio, J. F. Miller, K. Tetrahedron Lett. 1997, 38, 3349
Koch, Tetrahedron Lett. 1999, 55, 3352.
81898198. 57 B. T. Watson, G. E. Christiansen,
37 J. Pernerstorfer, M. Schuster, S. Tetrahedron Lett. 1998, 39, 9839
Blechert, Synthesis 1999, 1, 138144. 9840.
38 J. H. van Maarseveen, J. A. J. den 58 A. A. MacDonald, S. H. DeWitt, E.
Hartog, V. Engelen, E. Finner, G. M. Hogan, R. Ramage, Tetrahedron
Visser, C. G. Kruse, Tetrahedron Lett. Lett. 1996, 37, 48154818.
1996, 37, 82498252. 59 T. Ruhland, H. Kunzer, Tetrahedron
39 A. D. Piscopio, J. F. Miller, K. Lett. 1996, 37, 27572760.
Koch, Tetrahedron Lett. 1998, 39, 60 A. Gopalsamy, P. V. Pallai, Tetra-
26672670. hedron Lett. 1997, 38, 907910.
40 L. Gauzy, Y. Le Merrer, J. C. 61 M. Lebl, V. Krchnak, G. Ibrahim, J.
Depezay, Tetrahedron Lett. 1999, 40, Pires, C. Burger, Y. Ni, Y. Chen, D.
60056008. Podue, P. Mudra, V. Pokorny, P.
41 G. L. Bolton, J. C. Hodges, J. Comb. Poncar, K. Zenisek, Synthesis 1999,
Chem. 1999, 1, 130133. 11, 19711978.
42 S. C. Schurer, S. Blechert, Synlett, 62 M. Lebl, Bioorg. Med. Chem. Lett.
1999, 12, 18791882. 1999, 9, 13051310.
43 W. Yun, R. Mohan, Tetrahedron Lett. 63 M. C. Griffith, C. T. Dooley, R. A.
1996, 37, 71897192. Houghten, J. S. Kiely, Mol. Diversity
44 M. C. Fagnola, I. Candiani, G. Comb. Chem.: Libr. Drug Discovery,
Visentin, W. Cabri, F. Zarini, N. Conf. 1996, 5057.
Mongelli, A. Bedeschi, Tetrahedron 64 S. M. Hutchins, K. T. Chapman,
65 W. D. F. Meutermans, P. F. 87 J. G. Breitenbucher, H. C. Hui,

Alewood, Tetrahedron Lett. 1995, 36, Tetrahedron Lett. 1998, 39, 82078210.
77097712. 88 K. C. Nicolaou, G. Q. Cao, J. A.
66 K. Rolng, M. Thiel, H. Kunzer, Pfefferkorn, Angew. Chem. Int. Ed.
Letters, 1996, 1036. 2000, 39, 739743; b) K. C. Nicolaou,
67 A. Routledge, C. Abell, S. J. A. Pfefferkorn, G. Q. Cao, Angew.
Balasubramanian, Synlett 1997, 61. Chem. Int. Ed. 2000, 39, 734739; c) K.
68 Y. Watanabe, S. Ishikawa, G. Takao, C. Nicolaou, A. J. Roecker, J. A.
T. Toru, Tetrahedron Lett. 1999, 40, Pfefferkorn, G. Q. Cao, J. Am.
34113414. Chem. Soc. 2000, 122, 29662967; d)
69 M. Rottlander, P. Knochel, J. K. C. Nicolaou, J. A. Pfefferkorn,
Comb. Chem. 1999, 1, 181183. F. Schuler, A. J. Roecker, G. Q.
70 D. H. Ko, D. J. Kim, C. S. Lyu, I. K. Cao, J. E. Casida, Chem. Bio. 2000, 7,
Min, H. Moon, Tetrahedron Lett. 1998, 979992; e) K. C. Nicolaou, J. A.
39, 297300. Pfefferkorn, A. J. Roecker, G. Q.
71 S. Kobayashi, T. Wakabayashi, M. Cao, S. Barluenga, H. J. Mitchell,
Yasuda, J. Org. Chem. 1998, 63, 4868 J. Am. Chem. Soc. 2000, 122, 9939
4869. 9953; f ) K. C. Nicolaou, J. A.
72 C. Le Hetet, M. David, F. Carreaux, Pfefferkorn, S. Barluenga, H. J.
B. Carboni, A. Sauleau, Tetrahedron Mitchell, A. J. Roecker, G. Q. Cao,
Lett. 1997, 38, 51535156. J. Am. Chem. Soc. 2000, 122, 9968
73 X. Beebe, C. L. Chiappari, M. M. 9976.
Olmstead, M. J. Kurth, N. E. 89 C. Pothion, J. A. Fehrentz, A.
Schore, J. Org. Chem. 1995, 60, 4204 Aumelas, A. Loffet, J. Martinez,
74 X. Beebe, N. E. Schore, M. J. Kurth, 90 J. Pitlik, C. A. Townsend, Bioorg.
J. Org. Chem. 1995, 60, 41964203. Med. Chem. Lett. 1997, 7, 31293134.
75 D. L. Whitehouse, K. H. Nelson, S. 91 K. Rossen, J. Sager, L. M.
N. Savinov, R. S. Lowe, D. J. Austin, DiMichele, Tetrahedron Lett. 1997, 38,
Bioorg. Med. Chem. Lett. 1998, 6, 1273 31833186.
1282. 92 G. C. B. Harriman, Tetrahedron Lett.
76 M. R. Gowravaram, M. A. Gallop, 1997, 38, 55915594.
Tetrahedron Lett. 1997, 38, 69736976. 93 G. D. Cuny, J. Cao, J. R. Hauske,
77 D. Fancelli, M. C. Fagnola, D. Tetrahedron Lett. 1997, 38, 5237
Severino, A. Bedeschi, Tetrahedron 5240.
Lett. 1997, 38, 23112314. 94 W. Yun, R. Mohan, Tetrahedron Lett.
78 Y. Wang, T. Huang, Tetrahedron Lett. 1996, 37, 71897192.
1998, 39, 96059608. 95 M. D. Collini, J. W. Ellingboe,
79 X. Du, R. W. Armstrong, Tetrahedron Tetrahedron Lett. 1997, 38, 79637966.
Lett. 1998, 39, 22812284. 96 M. C. Griffith, C. T. Dooley, R. A.
80 X. Du, R. W. Armstrong, J. Org. Houghten, J. S. Kiely, Mol. Diversity
Chem. 1997, 62, 56785679. Comb. Chem. 1996, 5057.
81 T. L. Boehm, H. D. H. Showalter, J. 97 M. F. Gordeev, H. C. Hui, E. M.
Org. Chem. 1996, 61, 64986499. Gordon, D. V. Patel, Tetrahedron Lett.
82 L. F. Tietze, T. Hippe, A. Steinmetz, 1997, 38, 17291732.
Synlett 1996, 1043. 98 D. A. Goff, R. N. Zuckermann, J.
83 J. J. Baldwin, Mol. Diversity 1996, 2, Org. Chem. 1995, 60, 57485749.
8188. 99 a) G. L. Bolton, Tetrahedron Lett.
84 H. Stephensen, F. Zaragoza, J. Org. 1996, 37, 34333436; b) G. L. Bolton,
Chem. 1997, 62, 60906097. J. C. Hodges, J. R. Rubin, Tetrahedron
85 F. Zaragoza, Tetrahedron Lett. 1996, 1997, 53, 66116634.
37, 62136216. 100 K. M. Short, B. W. Ching, A. M. M.
86 B. T. Watson, G. E. Christiansen, Mjalli, Tetrahedron 1997, 53, 6653
References 683
101 T. T. Romoff, L. Ma, Y. Wang, D. A. 120 J. Habermann, S. V. Ley, R. Smits, J.

Campbell, Synlett 1998, 13411342. Chem. Soc. Perkin Trans. 1999, 17,
102 A. R. Far, T. T. Tidwell, J. Org. 24212423.
Chem. 1998, 63, 86368637. 121 S. Sun, W. V. Murray, J. Org. Chem.
103 I. C. Cotterill, A. Y. Usyatinsky, J. 1999, 64, 59415945.
M. Arnold, D. S. Clark, J. S. 122 P. Garibay, P. H. Toy, T. Hoeg-
Dordick, P. C. Michels, Tetrahedron Jensen, K. D. Janda, Synlett 1999, 9,
Lett. 1998, 39, 11171120. 14381440.
104 M. W. Creswell, G. L. Bolton, J. C. 123 E. M. Smith, Tetrahedron Lett. 1999,
Hodges, M. Meppen, Tetrahedron 40, 32853288.
1998, 54, 39833998. 124 C. Chen, B. Munoz, Tetrahedron Lett.
105 G. R. Pabst, K. Schmid, J. Sauer, 1999, 40, 34913494.
Tetrahedron Lett. 1998, 39, 6691 125 J. Zhang, A. Jacobson, J. R. Rusche,
6694. W. Herlihy, J. Org. Chem. 1999, 64,
106 D. G. Powers, D. S. Casebier, D. 10741076.
Fokas, W. J. Ryan, J. R. Troth, D. L. 126 M. L. Greenlee, J. B. Laub, J. M.
Coffen, Tetrahedron 1998, 54, 4085 Balkovec, M. L. Hammond, G. G.
4096. Hammond, D. L. Pompliano, J. H.
107 D. Craig, M. J. Robson, S. J. Shaw, Epstein-Toney, Bioorg. Med. Chem.
Synlett 1998, 13811383. Lett. 1999, 9, 25492554.
108 D. Jonsson, H. Molin, A. Unden, 127 S. Kobayashi, S. Nagayama, J. Am.
Tetrahedron Lett. 1998, 39, 10591062. Chem. Soc. 1996, 118, 89778978.
109 M. M. Sim, C. L. Lee, Tetrahedron Lett. 128 H. A. Dondas, R. Grigg, W. S.
1998, 39, 63996402. MacLachlan, D. T. MacPherson, J.
110 R. Baudelle, P. Melnyk, B. Deprez, Markandu, V. Sridharan, S.
A. Tartar, Tetrahedron 1998, 54, Suganthan, Tetrahedron Lett. 2000,
41254140. 41, 967970.
111 B. A. Kulkarni, A. Ganesan, Chem. 129 J. G. Breitenbucher, G. Figliozzi,
Commun. 1998, 785786. Tetrahedron Lett. 2000, 41, 4311
112 C. Hulme, J. Peng, G. Morton, 4315.
J. M. Salvino, T. Herpin, R. 130 J. M. Alvarez-Gutierrez, A. Nefzi,
Labaudiniere, Tetrahedron Lett. 1998, R. A. Houghten, Tetrahedron Lett.
39, 72277230. 2000, 41, 609612.
113 K. E. Frank, M. Jung, L. A. 131 S. Ma, D. Duan, Z. Shi, Org. Lett.
Mitscher, Comb. Chem. High 2000, 2, 14191422.
Throughput Screening 1998, 1, 7387. 132 S. Leconte, G. Dujardin, E. Brown,
114 D. G. Powers, D. S. Casebier, D. Eur. J. Org. Chem. 2000, 639643.
Fokas, W. J. Ryan, J. R. Troth, D. L. 133 S. Schunk, D. Enders, Org. Lett.
Coffen, Tetrahedron 1998, 54, 4085 2000, 2, 907910.
4096. 134 A. R. Katritzky, L. Serdyuk, C.
115 W. Chai, W. V. Murray, Tetrahedron Cassaing, D. Toader, X. Wang, B.
Lett. 1999, 40, 71857188. Forood, B. Flatt, C. Sun, K. Vo, J.
116 Y. Watanabe, S. Ishikawa, G. Takao, Comb. Chem. 2000, 2, 182185.
T. Toru, Tetrahedron Lett. 1999, 40, 135 A. S. Wagman, L. Wang, J. M.
34113414. Nuss, J. Org. Chem. 2000, 65, 9103
117 P. C. Miller, T. J. Owen, J. M. 9113.
Molyneaux, J. M. Curtis, C. R. 136 N. Gouault, J. F. Cupif, A. Sauleau,
Jones, J. Comb. Chem. 1999, 1, 223 M. David, Tetrahedron Lett. 2000, 41,
234. 72937297.
118 D. A. Goff, Tetrahedron Lett. 1999, 40, 137 C. Hulme, L. Ma, M. P. Cherrier,
87418745. J. J. Romano, G. Morton, C.
119 J. Zhang, A. Jacobson, J. R. Rusche, Duquenne, J. Salvino, R. Labaud-
W. Herlihy, J. Org. Chem. 1999, 64, iniere, Tetrahedron Lett. 2000, 41,
10741076. 18831887.
138 K. Paulvannan, T. Chen, J. Org. 145 S. C. Schurer, S. Blechert, Synlett

Chem. 2000, 65, 61606166. 1999, 12, 18791882.
139 C. Brandli, T. R. Ward, J. Comb. 146 A. S. Bhat, J. L. Whetstone, R. W.
Chem. 2000, 2, 4247. Brueggemeier, J. Comb. Chem. 2000,
140 S. Sato, Y. Kubota, H. Kumagai, T. 2, 597599.
Kumazawa, S. Matsuba, J. I. 147 E. J. Guthrie, J. Macritchie, R. C.
Onodera, M. Suzuki, Heterocycles Hartley, Tetrahedron Lett. 2000, 41,
2000, 53, 15231532. 49874990.
141 D. M. Ketcha, L. J. Wilson, D. E. 148 L. S. Harikrishnan, H. D. H.
Portlaock, Tetrahedron Lett. 2000, 41, Showalter, Tetrahedron 2000, 56,
62536257. 515519.
142 A. Barco, S. Benetti, C. De Risi, P. 149 M. Nettekoven, Tetrahedron Lett.
Marchetti, G. P. Pollini, V. 2000, 41, 82518254.
Zanirato, J. Comb. Chem. 2000, 2, 150 M. Ramaseshan, J. W. Ellingboe, Y.
337340. L. Dory, P. Deslongchamps,
143 Y. Kondo, K. Inamoto, T. Sakamoto, Tetrahedron Lett. 2000, 41, 4743
J. Comb. Chem. 2000, 2, 232233. 4749.
144 H. C. Zhang, H. Ye, A. F. Moretto, 151 C. W. Lindsley, L. K. Chan, B. C.
K. K. Brumeld, B. E. Maryanoff, Goess, R. Joseph, M. D. Shair, J. Am.
Org. Lett. 2000, 2, 8992. Chem. Soc. 2000, 122, 422423.
685
23
Multicomponent Reactions
Arounarith Tuch and Stefan Walle
23.1
Introduction
Multicomponent reactions (MCRs) are usually condensation reactions involving

three or more educts; they are fundamentally dierent from two-component re-
actions. During the past decades, this type of reaction has been recognized as a
very ecient method that can be used in all elds of organic synthesis. Especially
in both liquid- and solid-phase combinatorial chemistry, these reactions have been
accepted as an indispensable tool for library construction. This chapter describes
the most important multicomponent reactions and their applications to combina-
torial chemistry; examples of the synthesis of combinatorial libraries on solid sup-
port as well as in solution phase will be given.
23.2
Mannich Reaction
The Mannich reaction is a classic three-component reaction in which a component

containing at least one hydrogen atom of pronounced reactivity reacts with an
imine species formed from the condensation of an amine and an aldehyde.
Although Mannich chemistry in traditional solution-phase organic synthesis is
of general utility [1], its application to resin-bound substrates as well as to parallel
synthesis in solution has not been so widespread.
Independently, and almost simultaneously, the Katritzky [2] (Scheme 23.1) and
Showalter groups [3] (Scheme 23.2) described the synthesis of polymer-supported
benzotriazole and its application to the generation of Mannich adducts. Secondary
[2] and tertiary [2, 3] amines (1, 3) and tosylamides [2] formed by Mannich reac-
tion were cleaved from the resin with Grignard [2, 3] and organozinc reagents [2].
The reactions were performed with a large excess of aldehyde (5 mol equiv. [2], 10
mol equiv. [3]) and amine (5 mol equiv. [2], 10 mol equiv. [3]) in tetrahydrofuran
(THF)/methoxyethanol (1:1) at 60 C for 812 h [2] or THF/EtOH at reux or in
dimethylformamide (DMF) at 70 C for @17 h [3]. These solvents were chosen

ISBN: 3-527-30509-2
686 23 Multicomponent Reactions
Scheme 23.1. Tertiary amines and tosylamide [2].
Scheme 23.2. Mannich-type adducts from polymer-supported benzotriazoles [3].
because they led to better swelling of the polymer. The aldehydes tested by Ka-
tritzky were of diverse reactivity HCHO, PhCHO, and iso-BuCHO and only
secondary amines were used, whereas Showalter also used primary amines. In the
case of the less reactive benzaldehyde, harsher conditions were necessary to carry
out the reaction: toluene, reux, and a DeanStark trap for 12 h [2]. These Man-
nich adducts (1, 3) were then cleaved from the polymer-supported benzotriazole
with Grignard (4 mol equiv., THF, reux, 4 h) [2], (5 mol equiv., toluene, reux,
overnight) [3], or organozinc reagents (5 mol equiv., THF, 60 C, 12 h) [2]. After
work-up, the amines (2, 3) were isolated in good overall yields [2, 3].
In their synthesis of tertiary methylamines (8), Blaney et al. [4] (Scheme 23.3)
also used benzotriazole, but this component was not polymer supported. In this
alternative strategy, the reaction conditions are milder than those in the previous
two strategies [2, 3]. The resin-bound secondary hydroxylamine 5 reacted with an
excess of aliphatic or aromatic aldehyde (10 mol equiv.) in the presence of an ex-
cess of benzotriazole (10 mol equiv.) in CH2 Cl2 at room temperature (rt) for 18 h
Scheme 23.3. Tertiary methylamines via resin-bound oxyiminium ions [4].

23.2 Mannich Reaction 687
to form the resin-bound benzotriazole Mannich adduct 6. The latter was then dis-
placed with Grignard reagents (10 mol equiv., THF, rt, 16 h). Quaternization of 7
(5 mol equiv. MeOTf, CH2 Cl2 , rt, 16 h) followed by base-induced cleavage (5 mol
equiv. NEt3 , CH2 Cl2 , rt, 16 h) gave very pure amines (8).
3-Aminomethylindoles [5] (Scheme 23.4), which are interesting because of their
biological activity, were prepared from polymer-bound indoles (10) by Mannich re-
action. The resin-supported 2-substituted indoles 10 obtained in three steps from
Rink amide resin and 4-amino-3-iodobenzoic acid [5b] were subjected to Mannich
reaction conditions with an excess of formaldehyde (28 mol equiv.) and secondary
amines (28 mol equiv.) at rt for 1.5 h in 1,4-dioxane/HOAc (4:1). The reactions
were reported to proceed more eectively in this mixture than in only HOAc. After
acidic cleavage, the 2-substituted 3-aminomethylindoles 11 were isolated in good
yields and purities.
Scheme 23.4. Resin-bound indoles [5].
Any Mannich partner can be immobilized on an appropriate solid support. Re-

searchers at the R. W. Johnson Pharmaceutical Research Institute [6] elegantly
demonstrated this versatility. Terminal alkynes can also serve as components in
the Mannich reaction. In such cases, a copper(I) salt is necessary to promote the
aminomethylation [6]. Youngman and Dax [6a] (Scheme 23.5) reported the rst
Mannich reaction with resin-bound alkynes. After binding propargylamine to 2-
chlorotrityl resin, the Mannich chemistry was performed with secondary amines (5
mol equiv.), cuprous chloride (1 mol equiv.), and paraformaldehyde (10 mol equiv.)
in 1,4-dioxane at 7075 C for 3 h. The overall isolated yields and purities were re-
ported to be >90% and >95%, respectively. The reaction seemed to be a general
one, as evidenced by the diversity of the compounds synthesized.
Scheme 23.5. Resin-bound terminal alkynes [6a].

However, the number of commercially available acetylenes is limited. This

problem was clearly overcome by a combination of the Sonogashira and Mannich
reactions [6b] (Scheme 23.6). The Sonogashira reaction was run prior to Mannich
chemistry, thus generating diverse building blocks (15) for the Mannich reaction.
The overall yields and purities of 17 were reported to be good. The Mannich part-
ner amine was then bound to solid support (Scheme 23.7), e.g. piperazine was
bound to 2-chlorotrityl resin [6c]. The Mannich reaction was carried out under the
reaction conditions described above. The Mannich adducts 19 were isolated as bis-
triuoroacetic acid (TFA) salts with high purity.
Scheme 23.6. Resin-bound terminal alkynes [6b].
Scheme 23.7. Resin-bound terminal alkynes [6c].
Finally, a Wang resin-supported aldehyde [6c] (Scheme 23.7) was subjected to

the same reaction conditions as described above. The Mannich adducts 21 were
isolated with lower yields: the incomplete iminium formation was suspected to be
the cause.
Compounds of the Mannich reaction having a hydrogen atom of pronounced
reactivity can be successfully substituted by silyl enol ethers. The Kobayashi group
23.3 Hantzsch Reaction 689
[7] eciently applied this Mannich-type reaction to solid phase to prepare suc-
cessfully a 48-amino alcohol library [7b] (Scheme 23.8). Aldehyde (1.2 mol equiv.),
primary amine (1.2 mol equiv.), Drierite, and scandium triate (0.1 mol equiv.)
were stirred in CH2 Cl2 at rt for 1 h prior to the addition of the polymer-supported
silyl enol ether 22. The mixture was then stirred at rt for 20 h and, after comple-
tion of the reaction, the desired amino alcohols (24) were reductively cleaved from
the support in good overall yields.
Scheme 23.8. Mannich-type reaction [7b].
Furthermore, this method worked in solution phase as well as on solid support

[7c] (Scheme 23.9). b-Amino esters 25 were thus eciently prepared in parallel in
large quantities, with high yields and purities. The ease of the work-up and puri-
cation procedure could render this method amenable to automation.
Scheme 23.9. Mannich-type reaction [7c].
23.3
Hantzsch Reaction
The Hantzsch reaction is a condensation involving 2 mol of b-ketoester or b-ketoa-

mide, 1 mol of aldehyde, and 1 mol of ammonia. The product of the condensation
1,4-dihydropyridine can then be oxidized to the corresponding pyridine deriv-
ative.
Patel et al. [8] (Scheme 23.10) used Rink resin-bound enamino esters for the
synthesis of a 300-member dihydropyridine library via the Hantzsch condensa-
tion. The reaction was performed with resin-supported enamino esters (26), an al-
dehyde (2 mol equiv.), and a b-dicarbonyl derivative (2.3 mol equiv.) in dry pyridine
in the presence of 4A molecular sieves at 45 C for 24 h. Pyridine was found to be
the most eective solvent in this heterocyclization. An acidic cleavage with 3%
TFA in CH2 Cl2 gave the desired 1,4-dihydropyridines (28), whose yields and pu-
rities were not reported.
Breitenbucher and Figliozzi [9] (Scheme 23.11) reported a small 272-member
4-aryl-1,4-dihydropyridine library using a slightly dierent approach. Resin-bound
Scheme 23.10. Hantzsch reaction [8].
Scheme 23.11. Hantzsch reaction [9].
b-acetoacetate (29) was formed upon treatment of diverse amino alcohol linkers
with 2,2,6-trimethyl-1,3-dioxanone. The Hantzsch reaction was then carried out
with aminocrotonate derivatives and aryl aldehydes in DMF at 80 C. The desired
4-aryl-1,4,-dihydropyridines (30) were obtained along with the byproduct (31)
(15%). This Knoevenagel product (31) was selectively removed by washing the
resin with hydrazine. After acidic cleavage and supported liquid extraction, the 4-
aryl-1,4,-dihydropyridines 30 were obtained in modest to good overall yields (44
88%) and in good purities (7790%).
23.4
BaylisHillman Reaction
To date, there is only one publication on a multicomponent version of the Baylis

Hillman reaction, reported by the Jung group [10] (Scheme 23.12). The three-
component reaction was performed with 2-chlorotrityl resin-bound acrylic acid
(32), aryl aldehydes (16 mol equiv.), sulfonamides (1620 mol equiv.), and 1,4-dia-
23.5 Grieco Three-component Reaction 691
Scheme 23.12. BaylisHillman reaction [10].
zabicyclo[2.2.2]octane (DABCO) (1.6 mol equiv.) as catalyst in dioxane at 70 C for

20 h. The substituted sulfonamides 33 were obtained in good purities (5390%),
but overall yields were not reported.
23.5
Grieco Three-component Reaction
The Grieco three-component reaction [11a] is a condensation involving anilines,

aldehydes, and electron-rich olens catalyzed by TFA [11b,c], Yb(OTf )3 [11d], or
Sc(OTf )3 [11e] as Lewis acid catalysts to form nitrogen-containing six-member
heterocycles.
Kiselyov and Armstrong reported the rst version of this reaction on solid phase
[11b] (Scheme 23.13). Furthermore, they elegantly immobilized every Grieco part-
ner on appropriate solid support [11bd] (Scheme 23.14), thus demonstrating the
Scheme 23.13. Grieco three-component reaction [11b].
Scheme 23.14. Grieco three-component reaction [11c].

versatility of this multicomponent reaction. The typical reaction conditions were

an excess of aldehydes (1.58 mol equiv.), anilines (1.5 mol equiv.), and alkenes
(2.55 mol equiv.) catalyzed by TFA [11b,c] or Yb(OTf )3 [11d] in MeCN [11b,c] or
MeCN/CH2 Cl2 (2:1) [11d] at rt for 1224 h. Other catalysts, namely FeCl3 [11b],
LiBF4 [11c], BF3 Et2 O, TiCl 4 , and InCl3 [11d], aorded lower yields of the prod-
ucts. Several other solvents such as dioxane, DMF, MeOH, and THF were found to
be inferior to MeCN [11b,d]. The yields and purities of the synthesized tetrahy-
droquinoline derivative (3436) were reported to be good [11bd].
This three-component condensation was successfully carried out in solution by
the Kobayashi group [11e] (Scheme 23.15) using a polymer-supported scandium
catalyst. The quinoline derivatives (37) were reported to be obtained in high yields
(65100%) and quantity. Given the number of commercially available Grieco
partners and the eectiveness of this method, a quinoline library of more than 1
million members could be prepared.
Scheme 23.15. Grieco three-component reaction [11d].
23.6
Biginelli Reaction
In 1893, Biginelli rst reported the synthesis of 3,4-dihydropyrimidine-2-(1H)-ones

of type 38 by a very simple one-pot condensation reaction of acetoacetate, benzal-
dehyde, and urea in ethanolic solution [12] (Scheme 23.16).
Scheme 23.16. Biginelli reaction: synthesis of dihydropyrimidinones.
A major drawback of this so-called Biginelli reaction is the moderate yield asso-
ciated with it only 2060% of the expected product is usually obtained. Since 4-
aryldihydropyrimidinones have emerged as an integral backbone of several drugs
such as calcium channel blockers or antihypertensive agents during the past few
decades, some improved procedures for their preparation have been reported, in-
cluding various solid-phase modications suitable for combinatorial chemistry
[13].
Recently, the synthesis of Biginelli compounds involving the use of BF3 OEt2 /
CuCl and polyphosphate ester leading to high yields of dihydropyrimidinones was
published [14]. The use of ferric chloride hexahydrate as a mild catalyst in ethanol
as the solvent consistently produced yields of 8090% of the desired dihydropyr-
imidinones [15].
23.7
Multicomponent Reactions with Isocyanides
23.7.1
History of Isocyanides
A large and important class of multicomponent reactions involve isocyanides. Iso-

cyanides, also known as isonitriles, are compounds with remarkable reactivity.
Their unusual valence structure and reactivity have been discussed for more than a
century, and they belong to the only class of stable organic compounds with a for-
mally divalent carbon (carbon monoxide also contains a divalent carbon). In exo-
thermic reactions, the C(II) of isocyanides is oxidized to C(IV); this feature was
originally noted by Nef in 1892 [16].
Hundreds of natural products containing an isocyano function have been iso-
lated over the years, mostly from marine organisms (xanthocillin was commer-
cially available from Arzneimittelwerk Dresden) [17]. Many of these natural iso-
cyanides show antibiotic and fungicidal eects as well as the potential to be used
in crop protection [18]. In addition to the isolated isocyanides, many natural prod-
ucts have been found as N-formamides. These can be regarded as products of the
hydrolysis of isocyanides or even as their precursors, meaning that probably more
isocyanides occur naturally than is generally assumed. Table 23.1 shows a few ex-
amples of naturally occurring isocyanides [19].
Isocyanide chemistry began in the middle of the nineteenth century. In 1859,
Lieke succeeded in synthesizing allyl isocyanide by reacting allyl iodide and silver
cyanide; however, he did not recognize the synthesized species to be an isocyanide,
believing it instead to be a nitrile [20]. His attempts to transform the compound
into the corresponding carboxylic acid failed, leading instead to the formamide. It
took another 8 years for isocyanides to become generally available. In 1867, Ho-
mann published [21] a new method of preparation of isocyanides involving the re-
action of primary amines, chloroform, and potash. Despite that synthetic success,
the chemistry of isocyanides stagnated for almost a century since they could be
obtained only in low yields. All preparative methods known at that time were
complicated and were poorly generalizable, and, in addition, the desired com-
pounds were known to have a very unpleasant smell, which forced chemists to
work outside [22]. During the rst 100 years of isocyanide chemistry, only 12 of
Tab. 23.1. Examples of naturally occurring isocyanides.
Xanthocillin
Leptocillin
4-((E )-2-carboxyvinyl)-3,4-epoxy-
1-cyclopentenyl isocyanide
Acenthellin 1
Aerocyanidine
these compounds were known; by 1971, more than 300 isocyanides had been de-
scribed in the literature.
The synthesis of tetrazoles by Olivieri-Mandala and Malagna in 1910 was an
important and remarkable event that took place during the period when isocy-
anide chemistry was not very popular [23]. In the 1920s Passerini worked on the
synthesis of a-acyloxy carbonamides [22, 24, 25], inventing a new type of three-
component reaction utilizing carbonyl compounds, carboxylic acids, and isocy-
anides. Again, the lack of a general method to synthesize isocyanides in good
yields postponed the general use of the Passerini reaction by another 30 years. In
1958, a breakthrough in isocyanide chemistry occurred: a high number of various
isocyanides could be synthesized in good yields by the dehydration of N-formyl
amines. Even though dozens of methods for the preparation have been described
[26], the reaction of N-formyl amines with phosgene, triphosgene, or other inor-
ganic dehydratants and matching bases is still the method of choice regarding
costs and yields of the desired products [27, 28]. Various organic bases such as
triethylamine, pyridine, quinoline, diisopropylamine, or DABCO have been used.
Depending on further functionalities, many alternative isocyanide synthesis meth-
ods have been developed, some of which are summarized in Table 23.2 [19].
23.7.2
Isocyanide Chemistry
The chemistry of isocyanides is characterized by three properties: a-addition, a-

acidity, and the formation of radicals. The synthetically most important property is
Tab. 23.2. Various synthetic routes to isocyanides.
Reference
20
29
30
31
32
33
34
the reaction of the isocyanide carbon with electrophiles and nucleophiles. (Most
other functional groups in organic chemistry react with nucleophiles and electro-
philes at dierent centers, only carbenes and carbon monoxide share this behavior
with isocyanides.) A very important eld of chemistry to which isocyanides con-
tribute is the synthesis of heterocyclic compounds. Among others, useful imida-
zoline, oxazoline [35], thiazoline, pyrrole [36], imidazole [37], oxazole [38], and
thiazole [39] syntheses have been described [40].
23.7.3
Isocyanides on Solid Phase [41]
Isocyanide-bearing polymers are generally prepared by dehydration of the corre-

sponding formamido resins. Among the various dehydrating agents [42, 43] for
the preparation of low-molecular-weight isocyanides, diphosgene and toluene-
sulfonyl chloride have been found to be the most eective. However, the use of
TsCl in pyridine is certainly the most convenient method: a concentrated solution
of TsCl in pyridine is used and the reaction is carried out at 020 C. Under these
conditions, various resins swell adequately and the reaction is complete within
minutes.
23.7.4
Passerini Reaction
In 1921, the reaction between carboxylic acids, oxo components, and isocyanides
was described for the rst time by the Italian chemist Passerini. The reaction leads
to a-acyloxycarboxamides, which are produced in one step [24] (Scheme 23.17).
Scheme 23.17. Passerini reaction.
Dierent mechanisms have been discussed for the Passerini reaction [44, 45];
since the reaction is accelerated and usually carried out in aprotic solvents, a non-
ionic mechanism is indicated [46]. Most likely, the rst step of the reaction leads to
a hydrogen-bound adduct of the carbonyl compound and the carboxylic acid 39; in
the second step, the a-addition of the electrophilic carbonyl carbon and the nucle-
ophilic oxygen atom of the carboxylic acid to the isocyanide carbon forms the cyclic
transition state (40) involving all three parent compounds. The a-adduct cannot be
isolated and rearranges to the stable a-acyloxycarboxamide (41) (Scheme 23.18).
Scheme 23.18. Passerini reaction mechanism.
The solvent of choice for the Passerini reaction is CH2 Cl2 , and the reaction is
usually carried out at rt with a high concentration of the three components. There
are almost no limitations in the choice of the oxo component used: both aldehydes
and ketones can be utilized. Some sterically hindered and a,b-unsaturated ketones
as well as bicyclic extremely hindered ketones such as camphor do not react
with isocyanides in a Passerini reaction [47]. Besides normal C-isocyanides,
Me3 SiCN, which is in an equilibrium with Me3 SiNC, also reacts with mineral
acids in the presence of ZnI2 to give 2-hydroxy carboxylic acids and amides [48].
The treatment of ketones such as 42 with two equivalents of the isocyanide in
the presence of BF3 OEt3 in nonpolar solvents leads to the b,g-unsaturated a-
oxocarboxylic amide 43 (Scheme 23.19).
Scheme 23.19. Reaction of ketone 42 with tert-butyl isocyanide.
The a-acyloxy carboxamide group is a frequently recurring motif in many natu-

ral products. For that reason, the Passerini reaction is a suitable route to numerous
depsipeptides [49]. Lewis and Brnsted acids catalyze the formation of a-hydroxy
tetrazoles from isocyanides, HN3 , and oxo compounds. a-Hydroxytetrazoles were
described in 1931 as a cyclic version of the Passerini reaction as products of
the reaction of hydrazoic acid, oxo compounds, and isocyanides [50]. The Passerini
reaction has had a renaissance in the last few years, and there are numerous ex-
amples of this reaction that lead to interesting structures [19].
23.7.5
The Ugi Reaction
The Ugi four-component condensation was discovered in 1959. Basically, a carbox-

ylic acid reacts with a ketone or an aldehyde, an amine, and an isocyanide [51, 52]
(Scheme 23.20).
Scheme 23.20. Ugi reaction.
In a simplied mechanism, the oxo component and the amine react in the rst
step to the imine (Scheme 23.21). Then, the acid component protonates the nitro-
gen atom of the imine, increasing the electrophilicity of the CbN bond. In the
third step, the electrophilic iminium cation as well as the nucleophilic acid anion
add to the isocyanide carbon atom. An intramolecular acylation of the nitrogen
atom of the former amine and the subsequent rearrangement to an a-acylamino-
amide follow, forming the stable Ugi product. All the steps of the reaction sequence
are equilibria; however, the sequence for the last step lies completely on the
product side. In this respect, this type of MCR is dierent from other MCRs. The
Scheme 23.21. Ugi reaction, proposed mechanism.
driving force for the reaction sequence is the oxidation of the isocyanide C(II)
atom to the amide C(IV) atom. Changes in the nucleophiles and electrophiles of
the components of the Ugi condensation can be observed during the reaction se-
quence: the reactive centers of the acid component and the imine change the sign
of their reactivity several times. First, the CbN bond of the imine behaves like a
base toward the acid component. Then, the protonated Schi base functions as the
electrophilic and the acid anion as the nucleophilic component of the a-addition.
In the cycloaddition and elimination that follows the addition, the reactive centers
change their signs once again. In the course of the Ugi reaction, one CaC bond
and several heteroatomC bonds are newly formed.
Reactivity tables for isocyanides have been generated; the formation of the prod-
uct with dierent isocyanides has been examined as a function of solvent and
concentration [53]. The reactivity is mainly inuenced by inductive, mesomeric,
and steric eects the last of which play the least important role; in addition, the
concentration of the reactants has a signicant inuence on the reactivity and the
products of the reaction!
The Ugi reaction can be carried out in solution as well as on solid phase. In so-
lution phase, low-molecular-weight alcohols, such as methanol, ethanol, or tri-
uoroethanol, are used as typical solvents. Aprotic polar solvents such as DMF,
chloroform, dichloromethane, THF, or dioxane have also been described in many
cases. However, the choice of the solvent has a decisive inuence on the product of
the reaction: benzoic acid, benzyl amine, dichloroacetic aldehyde, and tert-butyl
isocyanide react in methanol at 0 C almost quantitatively to form the Ugi product;
in methylene chloride the Passerini product of benzoic acid, dichloroacetic aldehyde
and tert-butyl isocyanide is formed [54].
The Ugi condensation is an exothermic reaction and usually proceeds at a fast
rate at room temperature or below; for large batches, an external cooling of the re-
action mixture is recommended. If the reactants are present in high concen-
trations, the reaction proceeds better this is typical behavior for many multi-
component reactions.
23.7.6
The Ugi Reaction on Solid Phase
The Ugi reaction has also been described on solid phase. Basically, each of the re-
actions components can be attached to resin; which component is best attached to
the solid phase certainly depends on the structure and the electronic properties of
each component and varies from case to case.
In 1997, the synthesis of small-molecule combinatorial libraries on solid phase
by the Ugi reaction was published [56]. Besides pyrroles [57, 58] and imidazoles
[58], the solid-phase preparations of small ring lactams [59], a-(dialkylamino)-
amides, hydantoin-4-imides, 2-thiohydantoin-4-imides, and 5-(1-aminoalkyl)tetra-
zoles have been described. The last are prepared by replacing the carboxylic acid
with HN3 (Scheme 23.22).
Scheme 23.22. Synthesis of tetrazoles 44 on solid phase via Ugi reaction.
The reaction on solid phase has been carried out using NaN3 ; thus, the exposure
of various isocyanides to a range of amines, aldehydes, and sodium azide with
pyridine hydrochloride in a methanol/dichloromethane/water (3:3:1) mixture for
4 days led to the Ugi product [60]. The resin was washed with methanol and
dichloromethane (DCM), then agitated with 20% TFA in DCM. After removing
the solvent, the residues were puried by preparative thin layer chromatography
(TLC).
With the isocyanides immobilized on Wang resin, 45 was obtained by stirring
the isocyanides with aldehydes, amines, and in situ-generated HOCN [HXCN can
be conveniently generated in situ by the addition of pyridineHCl to form KXCN
(X O, S)] for 24 h in methanol/chloroform/water (5:5:1). The TFA/CH2 Cl2
cleavage provided the desired hydantoin-4-imides 46 in yields up to 80% (Scheme
23.23).
The synthesis of the a-(acylamino)amides 47 was also carried out by an Ugi re-
action, starting from pyrimidine carboxylic acids [44] (Scheme 23.24).
Scheme 23.23. Synthesis of hydantoin-4-imides on solid phase via Ugi reaction.
Scheme 23.24. Synthesis of a-(acylamino)amides on solid phase via Ugi reaction.
A mixture of a primary amine and an aldehyde was shaken at rt in dry dioxane

for 3 h, then the isocyanide and the polymer-bound pyrimidine carboxylic acid
were added. After a reaction time of 48 h at 55 C, the a-(acylamino)amides were
obtained.
23.7.7
Other Multicomponent Reactions with Isocyanides
During the last few years, several new multicomponent reactions have been
discovered, mostly involving isocyanides. In 1998, Bienayme and Bouzid [61],
Blackburn et al. [62], and Groebke et al. [63] described a synthesis of fused 3-
aminoimidazoles 48. Heteroaromatic amidines, such as 2-aminopyridine or pyr-
imidine, react with isocyanides and aldehydes in the presence of a catalytic
amount of protic acids in a very ecient three-component reaction to form the
corresponding imidazo-pyridines and -pyrimidines respectively (Scheme 23.25).
Many heteroaromatic amidines have been tested in this reaction with good results;
only electron-poor amidines tend to react slowly, with the frequent appearance of
side-products.
Scheme 23.25. Synthesis of aminoimidazo-pyridines (XbC) and

aminoimidazo-pyrimidines (XbN) respectively via three
component condensation.
A probable mechanism involves [4 1] cycloaddition between the protonated

Schi base of the 2-aminopyridines holding the electrophilic and the nucleophilic
centers and the isocyanide that behaves as a vinylidene carbenoid. A subsequent
prototropic shift gives the nal aromatic fused 3-aminoimidazole 48.
The above-described reaction has also been carried out on solid phase. A resin-
bound aldehyde, prepared by anchoring 3-carboxybenzaldehyde to Rink amide
resin in the presence of HATU [O-(7-azabenzotriazol-1-yl)-N,N,N 0 ,N 0 -tetramethyl-
uronium hexauorophosphate], was converted to an imine by reaction with 2-
aminopyridine in a solution of CH2 Cl2 /CH3 OH (3:1) with Sc(OTf )3 as a catalyst
and allowed to react with benzyl isocyanide. After 48 h, the TFA-induced cleavage
aorded the condensation product in a similar yield to that obtained in solution
phase (Scheme 23.26).
Scheme 23.26. Aminoimidazoles on solid phase: amine bound to the polymer.
Another attractive strategy for the solid-phase synthesis of the aminoimidazoles

is to anchor the least readily available compound to the resin, namely the iso-
cyanide. N-Fluorenylmethoxycarbonyl (Fmoc)/g-amino butyric acid (GABA) was

attached to Rink amide resin and deprotected with piperidine/DMF. The amine
was then formulated by treatment with 2,4,5-trichlorophenylformiate [64]. The de-
hydration to the isocyanide was accomplished using PPh3 , CCl 4 , and NEt3 . The
imine formation of 2-aminopyridine and benzaldehyde was followed by the ad-
dition to the resin-bound isocyanide. After a reaction time of 48 h and a TFA-
induced cleavage, the product was obtained in low yield but good purity (Scheme
23.27).
Scheme 23.27. Aminoimidazoles on solid phase: isocyanide bound to the polymer.
In conclusion, the three-component reaction of amidines, aldehydes, and iso-

cyanides can be carried out on solid phase with any of the three components
anchored to the solid support, aording moderate to good yields of high-purity
imidazoles for most amine inputs.
The very interesting three-component reaction of a phenylhydrazine, cyclo-
hexanone, and an isocyanide, leading to a 4-amino-dihydrocinnoline 49, was de-
scribed in 1996 for the rst time by the Weber group [65, 66] (Scheme 23.28).
Scheme 23.28. Synthesis of dihydrocinnolines via three-component condensation.
The four-component reaction of arylglyoxals, primary amines, carboxylic acids,

and isocyanides was reported by Zhang et al. in 1996 [58]. First carried out in so-
lution, the reaction of phenylglyoxal, isobutylamine, benzoic acid, and n-butyliso-
cyanide gave amide 50 and was cyclized to the imidazole 51 (16 h at 100 C) with
an overall yield of 43% (Scheme 23.29).
The solid-phase synthesis began with the formulation of aliphatic amino acids
attached to Wang resin with HCOOEt or HCOOH/Ac2 O followed by the dehydra-
tion with PPh3 /NEt3 /CCl 4 to provide the resin-bound isocyanides. The reaction
with phenylglyoxal, isobutylamine, and benzoic acid in CHCl3 /CH3 OH/pyridine
(1:1:1) at 65 C for 3 days led to the tetrasubstituted imidazole. The construction of
References 703
Scheme 23.29. Synthesis of the imidazole 51 on solid phase via four-component condensation.
the imidazole nucleus using the above-described methodology increases the overall
diversity and size of an imidazole library.
References
1 a) F. F. Blicke, Org. React. 1947, 1, 8 a) D. V. Patel, M. F. Gordeev, B. P.

303; b) J. H. Brewster, E. L. Eliel, England, E. M. Gordon, Mol.
Org. React. 1953, VIII, 99197. Diversity Combin. Chem: Lib. Drug
2 A. R. Katritzky, S. A. Belyakov, D. Discovery 1996, 5869; b) M. F.
O. Tymoshenko, J. Comb. Chem. Gordeev, D. V. Patel, B. P. England,
1999, 1, 173176. S. Joannalagadda, J. D. Combs, E. M.
3 K. Schiemann, H. D. H. Showalter, Gordon, Bioorg. Med. Chem. 1998, 6,
J. Org. Chem. 1999, 64, 49724975. 833889.
4 P. Blaney, R. Grigg, Z. Rankovic, 9 J. G. Breitenbucher, G. Figliozzi,
M. Thoroughgood, Tetrahedron Lett. Tetrahedron Lett. 2000, 41, 43114315.
2000, 41, 66396642. 10 H. Richter, G. Jung, Tetrahedron Lett.
5 a) H.-C. Zhang, K. K. Brumeld, L. 1998, 3, 27292730.
Jaroskova, B. E. Maryanoff, 11 a) P. A. Grieco, A. Bahsas, Tetra-
Tetrahedron Lett. 1998, 39, 44494452; hedron Lett. 1988, 29, 58555858;
b) H.-C. Zhang, K. K. Brumeld, B. b) A. S. Kiselyov, R. W. Armstrong
E. Maryanoff, Tetrahedron Lett. 1997, Tetrahedron Lett. 1997, 38, 61636166;
38, 24392442. c) S. Kiselyov, L. Smith II, A.
6 a) M. A. Youngman, S. L. Dax, Virgilio, R. W. Armstrong, Tetra-
Tetrahedron Lett. 1997, 38, 63476350; hedron 1998, 54, 79877996; d) S.
b) A. B. Dyatkin, R. A. Rivero, Kiselyov, L. Smith II, R. W.
Tetrahedron Lett. 1998, 39, 36473650; Armstrong, Tetrahedron 1998, 54,
c) J. J. McNally, M. A. Youngman, S. 50895096; e) S. Kobayashi, S.
L. Dax, Tetrahedron Lett. 1998, 39, Nagayama, J. Org. Chem. Soc. 1996,
967970. 118, 89778978.
7 a) S. Kobayashi, I. Hachiya, S. 12 a) P. Biginelli, Gazz. Chim. Ital.
Suzuki, M. Morikaki, Tetrahedron 1893, 23, 360; b) for a review, see: C.
Lett. 1996, 37, 28092812; b) S. O. Kappe, Tetrahedron 1993, 49, 6937;
Kobayashi, M. Morikaki, R. c) C. O. Kappe, Molecules, 1998, 3, 1.
Akiyama, S. Suzuki, I. Hachiya, 13 a) B. C. OReilly, K. S. Atwal,
Tetrahedron Lett. 1996, 37, 77837786; Heterocycles 1987, 26, 1185; b) B. C.
c) S. Kobayashi, S. Komiyama, H. OReilly, K. S. Atwal, J. Z.
Ishitani, Biotechnol Bioeng (Comb Gougoutas, F. M. Malley,
Chem) 1998, 61, 2331. Heterocycles 1987, 26, 1189; c) K. S.
Atwal, G. C. Rovnyak, B. C. Comprehensive Organic Functional

OReilly, J. Schwartz, J. Org. Chem. Group Transformations, Vol. 3.
1989, 54, 5898; d) R. Gupta, A. K. Katritzky, A. R., Meth-Cohn, D. C.,
Gupta, S. Paul, P. L. Kachroo, Ind. Rees W. (eds), Pergamon, Oxford
J. Chem. 1995, 34B, 151. 1995, p. 963; c) for a review of
14 a) P. Wipf, A. Cunningham, uorinated isocyanides: D. Lentz,
Tetrahedron Lett. 1995, 36, 7819; b) A. Angew. Chem. 1994, 106, 1377; Angew.
Studer, S. Hadida, R. Ferritto, S.-Y. Chem. Int. Ed. Engl. 1994, 33, 1315; d)
Kim, P. Jeger, P. Wipf, D. P. P. Hoffmann, G. Gokel, D.
Curran, Science 1997, 275, 823; c) A. Marquarding, I. Ugi in: Isonitrile
Studer, P. Jeger, D. P. Curran, J. Chemistry. Ugi, I. (ed.), Academic
Org. Chem. 1997, 62, 2917. Press, New York 1971, p. 9.
15 J. Lu, H. Ma, Synlett 2000, 1, 6365. 27 a) G. Skorna, I. Ugi, Angew. Chem.
16 a) J. U. Nef, Justus Liebigs Ann. Chem. 1977, 89, 267; Angew. Chem. Int. Ed.
1892, 270, 267; b) J. U. Nef, Justus Engl. 1977, 16, 259; b) H. Eckert, B.
Liebigs Ann. Chem. 1899, 309, 126. Forster, Angew. Chem. 1987, 99, 927;
17 a) P. J. Scheuer, Acc. Chem. Res. Angew. Chem. Int. Ed. Engl. 1987, 26,
1992, 25, 433439; b) M. S. 1221.
Edenborough, R. B. Herbert, Nat. 28 R. Obrecht, R. Herrmann, I. Ugi,
Prod. Rep. 1988, 5, 229245. Synthesis 1985, 400.
18 a) I. Ugi, U. Fetzer, W. 29 a) E. Meyer, J. Prakt. Chem. 1866, 147;
Unterstenhofer, P. E. Behrenz, P. b) P. Boullanger, G. Descotes,
E. Frohberger, H. Schinpug, G. Tetrahedron Lett. 1976, 38, 4327.
Unterstenhofer (Bayer AG), DE-B 30 A. W. Hofmann, Justus Liebigs Ann.
1,209,789 1962/1966; b) U. Fetzer, I. Chem. 1867, 144, 114.
Ugi, G. Unterstenhofer (Bayer AG), 31 A. W. Hofmann, Ber. Dtsch. Chem.
DE-B 1,235,298 1964/1967; c) U. Ges. 1870, 3, 766.
Eholzer, U. Fetzer, I. Ugi, I. 32 a) I. Ugi, R. Meyr, Angew. Chem.
Hammann, G. Unterstenhofer 1958, 70, 702; b) I. Ugi, R. Meyr,
(Bayer AG), DE-B 1,215,141, 1964/ Chem. Ber. 1960, 93, 239.
1966; d) H. L. Yale AS-A 33 R. Appel, R. Kleistuck, K. D. Ziehn,
1970.000098106, 1970. Angew. Chem. 1971, 83, 143; Angew.
19 A. Domling, I. Ugi, Angew. Chem. Chem. Int. Ed. Engl. 1971, 10, 132.
Int. Ed. 2000, 39, 31683210. 34 D. H. R. Barton, T. Bowles, S.
20 W. Lieke, Justus Liebigs Ann. Chem. Husinec, J. E. Forbes, A. Llobera, A.
1859, 112, 316. E. A. Porter, S. Z. Zard, Tetrahedron
21 A. W. Hoffmann, C. R. Acad. Sci. Lett. 1988, 29, 3343.
1867, 65, 484. 35 A. M. van Leusen, Synthesis 1991, 531.
22 I. Ugi, Isonitrile Chemistry, Vol. 20. 36 A. M. van Leusen, H. Siderius, B. E.
Academic Press, New York 1971. Hoogenboom, D. van Leusen,
23 E. Olivieri-Mandala, E. B. Malagna, Tetrahedron Lett. 1972, 13, 5337.
Gazz. Chim. Ital. 1910, 40 (II), 441. 37 A. M. van Leusen, J. Wildeman, O.
24 a) M. Passerini, Gazz. Chim. Ital. H. Oldenziel, J. Org. Chem. 1977, 42,
1921, 51, 126; b) M. Passerini, Gazz. 1153.
Chim. Ital. 1921, 51, 181. 38 R. Schroder, U. Schollkopf, E.
25 I. Ugi, S. Lohberger, R. Karl in: Blume, I. Hoppe, Liebigs Ann. Chem.
Comprehensive Organic Chemistry for 1975, 533 .
Synthesis Eciency, Vol. 2. Trost, B. 39 U. Schollkopf, P. H. Porsch, E.
M., Heathcock, C. H. (eds), Pergamon, Blume, Liebigs Ann. Chem. 1976, 2122
Oxford 1991, pp. 10831109. .
26 For reviews of isocyanides, see: a) C. 40 S. Marcaccini, T. Torroba, Org.
Grundman, Methoden Org. Chem, Prep. Proced. Int. 1993, 25, 141.
1952, 4th edn. Houben-Weyl 1985, 41 a) G. Skorna, I. Ugi, Chem. Ber. 1978,
Vol. E5, p. 1611; b) I. A. ONeil in: 111, 3965; b) R. Ashady, I. Ugi, Z.
References 705
Naturforsch. B 1981, 36, 1202; c) R. 72; c) B. Zeeh, E. Muller, Justus

Ashady, I. Ugi, Angew. Chem. 1982, Liebigs Ann. Chem. 1968, 715, 47.
94, 367; Angew. Chem. Int. Ed. Engl. 52 J. W. McFarland, J. Org. Chem. 1963,
1982, 21, 374; Angew. Chem. Suppl. 28, 2179.
1982, 761; d) R. Ashady, I. Ugi, 53 a) I. Ugi, H. Aigner, M. L. V.
Talanta 1984, 31, 842; e) for a review, Arnaez, G. Glahsl, P. Lemmen, R.
see: R. Ashady, I. Ugi, Polymer 1990, Stocklein-Schneiderwind, M.
31, 1164. Balla-Tamasi in: Vortrage anlasslich
42 U. Casellato, B. Corain, R. der Konigsteiner Chromatographie-
Craziani, R. Michelin, M. Mozzon, Tage. Aigner, H. (ed.), Waters,
M. Zecca, in press. Eschborn 1984, p. 1; b) H. Aigner,
43 R. Obrecht, R. Hermann, I. Ugi, PhD dissertation, Technische
Synthesis, 1985, 400. Universitat Munchen, 1984.
44 a) M. Passerini, Gazz. Chim. Ital. 54 I. Ugi, D. Marquarding, R. Urban,
1922, 52, 432; b) M. I. S. Dewar, Chemistry and Biochemistry of Amino
Electronic Theory of Organic Chemistry. Acids, Peptides and Proteins, Bd. 6.
Clarendon, Oxford 1949, p. 116; c) R. Marcel Decker, New York 1982, pp.
H. Baker, D. Stanonis, J. Am. Chem. 245.
Soc. 1951, 73, 699; d) I. Hagedorn, U. 55 K. M. Short, B. W. Ching, A. M. M.
Eberholz, H. D. Winkelmann, Mjalli, Tetrahedron 1997, 53, 6653
Angew. Chem. 1994, 76, 583; Angew. 6679.
Chem. Int. Ed. Engl. 1964, 3, 647; e) T. 56 A. M. Strocker, T. A. Keating, P. A.
Carglio, P. G. Cozzi, C. Floriani, Tempest, R. W. Armstrong,
A. Chiesi-Villa, C. Rizzoli, Organo- Tetrahedron Lett. 1996, 37, 1149.
metallics 1993, 12, 2726; f ) D. 57 A. M. M. Mjalli, S. Sarshar, T. J.
Seebach, G. Adam, T. Gees, M. Baiga, Tetrahedron Lett. 1996, 37,
Schiess, W. Weigand, Chem. Ber. 2934.
1988, 121, 507. 58 C. Zhang, E. J. Moran, T. F.
45 a) I. Ugi, R. Meyr, Chem. Ber. 1961, Woiwode, K. M. Short, A. M. M.
94, 2229; b) I. Hagedorn, U. Mjalli, Tetrahedron Lett. 1996, 37, 751.
Eholzer, Chem. Ber. 1965, 98, 59 K. M. Short, A. M. M. Mjalli,
46 I. Ugi, R. Meyr, Angew. Chem. 1962, 60 K. M. Short, B. W. Ching, A. M. M.
74, 9; Angew. Chem. Int. Ed. Engl. Mjalli, Tetrahedron 1997, 42, 7489
1962, 1, 8. 7492.
47 E. Muller, B. Zech, Liebigs Ann. 61 H. Bienayme, K. Bouzid, Angew.
Chem. 1966, 696, 72. Chem. Int. Ed. 1998, 37, 16.
48 G. L. Grunewald, W. J. Brouillette, 62 C. Blackburn, B. Guan, P. Fleming,
J. A. Finney, Tetrahedron Lett. 1980, K. Shiosaki, S. Tsai, Tetrahedron Lett.
21, 1219. 1998, 39, 36353638.
49 a) U. Fetzer, I. Ugi, Justus Liebigs 63 K. Groebke, L. Weber, F. Mehlin,
Ann. Chem. 1962, 659, 184; b) J. Synlett 1998, 661663.
Rachon, Chimia 1983, 37, 299. 64 J. Martinez, J. Laur, Synthesis 1982,
50 M. Passerini, G. Ragni, Gazz. Chim. 979.
Ital. 1931, 61, 826. 65 O. Lack, L. Weber, Chimica 1996, 50,
51 a) M. Passerini, Gazz. Chim. Ital. 9.
1924, 54, 529; b) E. Muller, B. Zeeh, 66 L. Weber, K. Illgen, M. Almstetter,
Justus Liebigs Ann. Chem. 1966, 696, Synlett 1999, 3, 366374.
706
24
Strategies for Creating the Diversity of
Oligosaccharides
Pamela Sears and Chi-Huey Wong
24.1
Introduction
Carbohydrates are essential for many important biological functions [14]. When
conjugated to protein to form glycoproteins, they can alter protein structure and
function. As components of glycolipids, they can play pivotal roles in intercellular
recognition and signaling. The extracellular matrix contains proteoglycans that not
only modify the physicochemical properties of the matrix, but also are involved in
a variety of recognition processes such as cell adhesion in response to inammatory
factors and cancer metastasis. Although numerous carbohydrate structures occur
in nature, in general the role of saccharide structure in function at the molecular
level has been minimally studied. This longstanding problem can be attributed
mainly to the diculty of synthesizing saccharides, especially when compared
to proteins and nucleic. Nucleic acids can now be easily made via chemical and
biological synthetic techniques, and proteins, which are encoded by DNA, can
therefore be easily produced and manipulated through recombinant DNA technol-
ogy. In addition, automatic synthesizers are available for the synthesis of poly-
peptides and oligonucleotides. Saccharides, however, are made in nature with a
diverse set of enzymes competing to produce very diverse products [1]. There is no
information carrier that encodes a particular saccharide structure, and so creat-
ing libraries of saccharides with methods analogous to protein mutagenesis is not
possible. Furthermore, unlike proteins and nucleic acids, saccharides are more dif-
cult to synthesize chemically because (1) oligosaccharides are typically branched
rather than linear; (2) the monosaccharide units can be connected by a- or b-
linkages; and (3) oligosaccharide synthesis requires multiple selective protection
and deprotection steps, a process called protecting group manipulation.
This last requirement is quite formidable, and currently there is no general
route for combinatorial saccharide synthesis. In a glycosidation reaction, both do-
nors (monosaccharides activated for reaction) and acceptors (which receive the ac-
tivated monosaccharide) contain many hydroxyl and other functional groups that
must be dierentially and selectively protected. The product must then be se-
lectively deprotected for the next round of reactions. The complexity of protecting

ISBN: 3-527-30509-2
group manipulation increases with each additional glycosidic linkage. Develop-

ment of stepwise solid-phase synthesis can simplify the intermediate work-up and
purication steps, but the complexity of protecting group manipulation remains
the same. Because of this problem, there is currently no single stepwise method
that is applicable to the synthesis of all oligosaccharides or even just the >15 mil-
lion possible tetrasaccharides that can be assembled from the nine common mon-
osaccharides found in humans. In contrast, solid-phase synthesis of peptides and
oligonucleotides involves only one protecting group manipulation in the iterative
process.
In the last few decades, however, the work of many research groups has started
to open up new paths to saccharide and glycoconjugate synthesis. Coupling tech-
niques with better yields and stereoselectivity have been worked out, and new pro-
tecting group chemistries have also become available. The possibility of construct-
ing libraries of saccharides, which was considered at one time to be a hopeless
prospect, is now starting to appear feasible. The next step in making oligosac-
charides widely accessible will be the automation of saccharide synthesis. This
chapter will focus on the current state of the subject and emphasize the develop-
ments with potential application to automated combinatorial synthesis of saccha-
rides, glycopeptides, and glycoproteins.
24.2
Chemical Synthesis of Oligosaccharides
Several practical approaches have been taken with success for the chemical syn-
thesis of oligosaccharides (Fig. 24.1) [524]. Most involve the activation of the
anomeric leaving group with a Lewis acid and then displacement of that leaving
group by the free hydroxyl of the acceptor sugar. The KoenigsKnorr method of
coupling glycosyl halides, one of the rst techniques to gain widespread use, is still
employed [5] and most other glycosidation reagents used to date proceed by the
same basic mechanism. The relative instability of the sugar halide necessitates
the construction of the saccharide from the reducing end, and in fact, many of the
most successful approaches are those that minimize side-reactions of the activated
sugar. New leaving groups have been further developed to improve the stability of
the glycosyl donors and their reactivity. Trichloroacetimidates [6], prepared by the
reaction of free sugars with trichloroacetonitrile and base, are used most fre-
quently for coupling, as are glycosyl sulfoxides [7], phosphites [8, 9], phosphates
[10], thio-glycosides [11], and pentenyl-glycosides [12]. Another scheme for glyco-
side synthesis is to build the saccharide from the nonreducing to the reducing
end using glycals [13], which can be activated through epoxidation for either direct
attack of the epoxide with the aglycon or intermediate formation of, for example,
the thioacetal or phosphate (Fig. 24.2).
The control of anomeric conguration of the product can be complicated, espe-
cially because the reaction can occur readily via either an SN 1- or an SN 2-type pro-
cess. The anomeric conguration of the activated sugar, therefore, does not ensure
708 24 Strategies for Creating the Diversity of Oligosaccharides
Fig. 24.1. (A) Common mechanisms for phosphites will not activate thioglycosides or
glycosidation. (B) Commonly used pentenyl glycosides. Tf, triate; TMSOTf,
glycosidation reagents and their activators (in trimethylsilyl triate; TfOH, triic acid; NIS,
parentheses). Some of these glycosidation N-iodosuccinimide; Et, ethyl; DMDO, 3,3-
reagents can be used orthogonally. For dimethyldioxirane; DMTST, dimethylthiosul-
example, the activator for glycosyl uorides or fonium triate.
the anomeric conguration of the product. Furthermore, which products form can
be heavily inuenced by the protecting groups used. Acyl protecting groups at C2
can strongly direct the trans conguration at C1 by forming an intermediate diox-
ocarbenium ion (Fig. 24.1A). In general, a-1,2-cis-glycosides such as a-d-glucosides
and a-d-galactosides can be formed either by taking advantage of the kinetic
anomeric eect [14] in the displacement of glycosyl halides and thioglycosides or
by direct displacement of b-trichloroacetimidates under conditions that favor in-
version (with no participating substituent at C2 and a nonpolar solvent) [15]. b-1,2-
trans-Glycosides such as b-d-glucosides and -galactosides can be obtained by using
neighboring group eects mediated by the 2-O-acyl protecting group or polar me-
dia to favor SN 1 displacement and formation of the dioxocarbenium species. Glu-
Fig. 24.2. Glycal approach to the solid-phase synthesis of

oligosaccharides from the nonreducing to the reducing end.
cosyl and galactosyl phosphates have, in all cases explored, produced the b-1,2-
trans-glycoside, regardless of the anomeric conguration of the phosphate [10],
and glycal chemistry also produces mainly the b-anomer. a-1,2-trans-Glycosides,
such as a-d-mannosides, are simple to obtain as they are favored both by the kinetic
anomeric eect and by the presence of participating groups at C2, but b-1,2-cis-
glycosides are still quite dicult to construct. Preparation of the b-d-glucoside
followed by inversion at C2 has been one common method, and recent attempts to
direct the attack of the incoming sugar by tethering it in a position that allowed
only b-attack have met with success [1619].
In general, control of anomeric stereochemistry is still a problem, especially
when neighboring group participation is lacking. Also, there are certain chem-
istries that do not work well with some sugars. In nature, only a-sialic acid link-
ages are observed, but sulfoxide and trichloroacetimidate chemistries only give the
b-anomer, a problem that can be solved by using other activating groups such as
phosphites [8, 9], thioglycosides [20], and 2-xanthates [21].
In automating oligosaccharide synthesis, it is convenient for the reactions to be
performed on solid phase. This approach allows rapid removal of reactants, rela-
tively easy purication, and (in the case of library construction) the encoding of the
product either by position (as in a two-dimensional array chip format) or, for
mix-and-split type library construction, by an accessory encoding reaction [7] in
which labels are added to the solid support as the chain is extended or by radio-
frequency-encoded combinatorial chemistry technology [22]. Most of the saccha-
ride synthetic techniques outlined above have been applied to solid-phase synthetic
strategies on a variety of supports [7, 13, 2226]. Polystyrene-based resins such as
the Merrield resin are commonly used [6, 24], although these do not necessarily
have the optimal characteristics for synthesis of sugars with regard to swelling
properties and reactant accessibility, particularly in hydrophilic media [26]. More
hydrophilic supports such as polyethylene glycol-based resins have been used with
good success [26], as have hybrid resins such as TentaGel that have a polysty-
rene core coated in polyethylene. To a lesser extent, soluble supports such as poly-
ethylene glycols and derivatives as well as thermoresponsive polyacrylamide de-
rivatives [27] have been used in oligosaccharide synthesis.
However, there are many disadvantages to using a solid support earlier. As
mentioned, protecting group manipulation on a solid support is extremely di-
cult, and with the protecting group chemistry known to date, it is impossible to
create true diversity based on this stepwise solid-phase method. In addition, oligo-
saccharides and glycopeptides are sterically hindered compounds. Blocking one
side of the molecule further with a solid support is likely to drop yields dramati-
cally. Long, exible linkers can be used to alleviate this problem somewhat, but
such linkers must be both cleavable and yet still compatible with the coupling
and protectiondeprotection reactions (e.g. photo- or enzyme-sensitive linkers or
linkers which can be cleaved by Pd(0) or by olen cross-metathesis). Monitoring
reaction progress on solid phase is also not trivial. In addition, protecting group
manipulation on resins is extremely dicult, as non-soluble reagents are generally
not amenable to solid-phase synthesis. Palladium nanoparticles, however, have
been found to be useful in the debenzylation of sugars attached to a polyethylene
glycolacrylamide (PEGA) resin [28].
The most challenging task, however, is the selection of orthogonal protecting
groups and their selective manipulation during synthesis. Commonly used pro-
tecting groups include benzyl or silyl ethers and derivatives, as well as acid- or
base-sensitive protecting groups [15, 23, 29] (Fig. 24.3). Although conditions have
been developed for their selective deprotection, in general their application to the
synthesis of oligosaccharide libraries with great diversity has not been demon-
strated. To date, the largest oligosaccharide made by solid-phase synthesis is that
reported by Nicolaou et al. (Fig. 24.4) [25] and Seeberger and coworkers (Fig. 24.5)
[30]. Both groups synthesized the same branched dodecasaccharide on solid phase
using phenyl thioglycosides [25] or glycosyl phosphates and imidates [30], and the
products were released from the support with photolysis [25] or olen cross-meta-
thesis [30]. In the Nicolaou groups synthesis, trisaccharide blocks were coupled
successively, with typically 5060% yields on the coupling steps, while Seebergers
group alternated mono- and disaccharide couplings to obtain the repeating tri-
saccharide unit of the phytoalexin elicitor, and the process has been automated
using a modied peptide synthesizer. Although the individual coupling yields were
not tabulated, making direct comparison of the two strategies dicult, the overall
yield of Seebergers synthesis was very good, in excess of 50%. The approaches are
similar in principle. The diculty of these approaches is the generality of the
methods. In both cases, building blocks were tailor-made to t the synthesis of this
particular compound. The blocks used by the Seeberger group are more general
only in that they are less complex, but the pattern of protecting and activating
groups still pigeonholes them into the synthesis of a certain class of compounds,
namely b1,2/6-linked polymers. The use of either type of scheme for the general
synthesis of many dierent polysaccharides will require the maintenance of a very
large stock of building blocks that are appropriate for the construction of dierent
types of links.
Fig. 24.3. Commonly used protecting groups toluenesulfonic acid; MsOH, methanesulfonic
and their removal conditions (in parentheses). acid; TFA, triuoroacetic acid; Tr, trityl; All,
See references 523 and citations therein. allyl; DMAP, 4,-N,N-dimethylaminopyridine;
Ar, aryl; DDQ, 2,3-dichloro-5,6-dicyano-1,4- Lev, levulinoyl; Piv, pivaloyl; Bn, benzyl; Phth,
benzoquinone; TBDMS, tert-butyl-dimethylsilyl; phthalimidyl; Ph, phenyl; Troc, trichloro-
TBDPS, tert-butyl-diphenylsilyl; TsOH, p- ethoxycarbonyl.
24.3
Enzymatic Synthesis of Oligosaccharides
Over the past few decades, enzymatic approaches have been gaining popularity for
the synthesis of saccharides and glycopeptides [31, 32]. Enzymes feature exquisite
stereo- and regioselectivity and catalyze the reaction under very mild conditions.
Extensive protectiondeprotection schemes are thus unnecessary, and the control
of anomeric conguration is simple. Both glycosyltransferases, the enzymes which
are naturally used to synthesize saccharides, and glycosidases, enzymes normally
used to hydrolyze glycosidic bonds, have been used. Drawbacks to an enzymatic
approach are the availability and cost of the catalysts and substrates, which can be
high. The enzymes themselves are in many cases only just becoming available,
particularly in the case of glycosyltransferases. The substrates, which for glycosyl-
Fig. 24.4. The Nicolaou groups solid-phase synthesis of a

dodecasaccharide phytoalexin elicitor. Trisaccharide blocks were
added in succession to provide the nal dodecasaccharide.
DMTST, (dimethylthio) methylsulfonium triate; TMU,
tetramethylurea.
transferases are the nucleotide-activated sugars, are relatively expensive, but can be
prepared from sugars or sugar phosphates through enzymatic or biological meth-
ods that have been worked out [31, 33]. Glycosidases, which use cheaper substrates
such as sugar halides and p-nitrophenyl glycosides, can be used but the yields
have typically been lower. However, the Withers group recently found that muta-
genesis of glycosidases to remove one of the two catalytic carboxylates in the active
site produces an enzyme, coined a glycosynthase, that can catalyze the synthesis
of a saccharide from a uorosugar donor but cannot catalyze hydrolysis of the re-
Fig. 24.5. The Seeberger groups solid-phase synthesis of the

dodecasaccharide phytoalexin elicitor. A modied peptide
synthesizer was used to couple mono- and disaccharide
phosphate donors alternately, providing the repeating trimer of
the structure.
sulting product [34] (Fig. 24.6). Whether this approach will be applicable to other
exo-glycosidases remains to be investigated.
Another drawback of the enzymatic approach is that while enzymes are excellent
at catalyzing the synthesis of natural products, their ability to accept novel saccha-
rides with unusual or unnatural sugars as substrates may be poor; at best, it will
be unknown. Models for the substrate preferences of glycosyltransferases are cur-
rently unavailable, and alteration of their specicity using protein engineering has
experienced limited success. Prediction of reaction products with novel substrates
will become easier as the enzymes begin to enjoy more widespread use and their
substrate specicities become better characterized. Since the preparative scale en-
zymatic synthesis of N-acetyllactosamine involving sugar nucleotide regeneration
in the 1980s [35], enzymatic and chemoenzymatic approaches have been used in
the synthesis of a great number of oligosaccharides and glycoconjugates [32]. For
example, the synthesis of sialyl trimeric Lewis X [36] was accomplished through
Fig. 24.6. Synthesis of an oligosaccharide with glycosynthases.

In principle, exo-glycosidases can be genetically altered to
accept glycosyl uorides as donors to perform glycosidation.
the transfer of sialic acid and fucose to a chemically synthesized trimeric LacNAc
acceptor. Further improvement in the area with the multiple enzymes required
for sugar nucleotide regeneration immobilized on beads has been developed (Fig.
24.7) [37]. The four enzymes required for the (re)generation of UDP-galactose
from uridine diphosphate (UDP), galactose, and phosphoenol pyruvate [with cata-
lytic amounts of glucose-1-phosphate and adenosine diphosphate (ADP)] are
coimmobilized on a bead, which can be added to the reaction medium to allow in
situ generation of the galactosyltransferase substrate, UDP-galactose. This process
both facilitates the reaction by removing the product, UDP (a galactosyltransferase
inhibitor), and can reduce the cost of the reaction by allowing the use of cheaper
substrates, assuming that the immobilized enzymes are stable enough to be reused
multiple times. However, if one or more of the immobilized enzymes is in-
activated, replacement of that enzyme will be dicult.
Application of enzymes to an automated scheme is possible. The logic of such a
reaction scheme is conceptually simple, as it is determined by the enzymes pre-
ferred reaction: the saccharide must be built stepwise, in a linear fashion, from the
reducing end (Fig. 24.8). Conducting the reaction on solid phase requires sup-
plying the enzymes in solution, from which they must be either recovered for re-
cycling or discarded. Recovery can be achieved via a variety of techniques such as
anity-based capture (of anity-tagged enzymes), passage through a microlter,
or enzyme precipitation. Enzymes are large molecules, and thus care must be
taken in choosing the support for solid-phase synthesis. The support, if porous,
should have pores large enough to accommodate these macromolecules and
Fig. 24.7. Preparation of superbeads for the kinase (PyrK), galactose-1-phosphate

facile regeneration of UDP-galactose. uridylyltransferase (GalPUT), glucose-1-
Galactosyltransferase (GalT), an enzyme that phosphate uridylyltransferase (GalU), and
transfers galactose from the UDP-galactose to galactose kinase (GalK) is used. Gal, galactose;
an alcohol donor, releases UDP, which inhibits Glc, glucose; Gal-1-P, galactose-1-phosphate;
the enzyme. (A) In order to prevent inhibition Glc-1-P, glucose-1-phosphate. (B) These
of the enzyme and to limit the use of the enzymes can be produced with a polyhistidine
expensive UDP-galactose substrate, a tag that allows them to be puried and
regeneration scheme using pyruvate immobilized onto a nickel resin.
should be hydrophilic to allow good swelling in water, or the support should be

rigid so that the enzyme will not become entrapped [31]. Use of long cleavable
tethers to attach the growing saccharide may also help the substrate to enter the
enzymes active site. Many resins have been used, including polysaccharide-based
resins such as Sepharose, polyethylene-based resins such as SPOCC (polyoxy-
ethylene-polyoxethane), and polyacrylamide supports [23, 26]. However, more
standard solid-phase supports such as derivatized silica and polystyrene have also
been used with success [38, 39]. Solution-phase synthesis, while solving the prob-
lem of enzymatic accessibility, adds problems of product recovery, which may be
substantial, given the frequent complexity of the reaction buer required for enzy-
matic reactions. A good approach may be to couple the substrate to a water-soluble
polymer, which can be easily removed from solution either by precipitation of the
polymer or by anity-based capture (if an anity label is attached to the support).
Water-soluble supports such as uncrosslinked polyacrylamide have been used in
the enzymatic synthesis of saccharides and glycoconjugates such as pseudo-GM3
(Fig. 24.9) [40]. Other water-soluble polymers such as polyethylene glycol [41] and
Fig. 24.8. Approaches to automated soluble polymer, which is passed across

enzymatic saccharide synthesis. In (A), the columns of immobilized enzymes. Product
enzymes are left in solution and the growing recovery at the end can be accomplished by
saccharide is immobilized on the solid phase. precipitating the polymer or by anity
This approach simplies purication, but techniques if the polymer is tagged with an
requires an enzyme recovery step to avoid anity ligand (such as biotin). Alternatively,
losing the expensive catalyst. In (B), the both enzymes and substrates can be used in
growing saccharide is attached to a water- free form.
thermoresponsive polyacrylamide [27] may nd use in enzymatic oligosaccharide

synthesis. One can thus envision a scheme in which glycosyltransferases (and, if
necessary, the enzymes required for the regeneration of their substrates) are im-
mobilized onto a resin and packed into dierent columns. The substrate, free or
bound to a water-soluble resin with an anity tag, is passed through the columns
in sequence depending on the glycosyltransferases desired. Intermediate isolation,
if necessary, can be achieved via capture of the substrate using, for example, an-
ity capture. Attachment of enzymes and substrates to a support is, however, not
trivial. In the end, given the high yields observed with glycosyltransferase-catalyzed
glycosidations and the simplicity of product isolation, the choice of the reactor
conguration is probably not critical, and both solution and solid-phase methods
can be used for automated synthesis.
Fig. 24.9. Enzymatic synthesis of the ganglioside from the support. Polymer-bound
ganglioside pseudo-GM3 on a polymeric versions of GM3 have also been shown to be
support. Ceramide glycanase-catalyzed useful as picomolar inhibitors of inuenza
transglycosidation can be used to remove the hemagglutinin [48].
24.4
Programmable One-pot Synthesis
A recent approach that shows promise for automation is the use of one-pot reac-
tion schemes that use the reactivity prole of dierent protected sugars [42, 43] to
determine the outcome. The reactivity of a sugar is highly dependent on the pro-
tecting groups and the anomeric activating group used. By adding substrates in
sequence from the most to least reactive, one can assure the predominance of a
desired target compound (Fig. 24.10). Compared with the stepwise solid-phase
method, the one-pot method involves no protecting group manipulation in the
iterative process. The key to this approach is to have extensive quantitative data re-
garding the relative reactivities of dierentially protected sugar building blocks. A
large amount of reactivity data for more than 100 protected p-methylphenyl thio-
glycosides (Fig. 24.11) were recently generated and used as the basis of a computer
program, termed OptiMer, which selects the best reactants for the one-pot synthesis
Fig. 24.10. (A) Traditional step-wise solid- database of relative reactivities. This approach
phase synthesis requires on-resin protecting requires preparation of a number of building
group manipulation, which can become very blocks with their glycosidation reactivities
complicated as the number of glycosidic quantitatively measured. A reactivity dierence
linkages increases. (B) OptiMers one-pot greater than 1000 between the building blocks
approach. OptiMer is a program which will give a high-yield in coupling. No protecting
predicts the optimal type and order of addition group manipulation and intermediate isolation
of partially protected sugars, based on a are required during the one-pot synthesis.
of a target compound [32, 43]. p-Methylphenyl thioglycosides were chosen as they

are applicable to most monosaccharides and are more reactive toward thiophilic ac-
tivators such as N-iodosuccinimide (NIS) and dimethylthiosulfonium triate
(DMTST) than other thioglycosides [11, 20, 44, 45] which have been used in practi-
cal synthesis.
This approach has been used with success in the synthesis of a large number of
oligosaccharides including the cancer antigen Globo-H hexasaccharide (Fig. 24.12)
[46]. In practice, the sequence of Globo-H was entered into the computer program
OptiMer, three building blocks and their corresponding relative reactivities were
shown. One simply mixes the building blocks and NIS in sequence, and after a
few minutes the desired product is generated in protected form. After deprotection
and purication, the target is obtained. If necessary, the trisaccharide building
blocks can be prepared separately by the one-pot approach using the same proce-
dure. While the one-pot strategy is quite eective, further work is needed to design
a complete set of building blocks (probably @500 or so are needed) for use in
the synthesis of most bioactive saccharides. So far, branchpoints have been incor-
porated by using the thioglycosides of disaccharides as reactants in the linear
Fig. 24.11. Building blocks and their relative reactivities (in

parentheses) used for OptiMers one-pot approach.
Fig. 24.12. Synthesis of the cancer antigen reactive one, in the presence of an activator.
Globo-H using OptiMer technology. In brief, The product obtained is then puried and
the sequence of Globo-H is entered into the deprotected to give the target. Ac, acetyl;
computer, which predicts the best building Bn, benzyl; Bz, benzoyl; Tol, tolyl; Troc,
blocks to be used. These building blocks are trichloroethoxycarbonyl.
then mixed in sequence, starting with the most
scheme. These reactions are typically performed in solution, but, in order to facili-
tate removal of reactants at the end, the nal acceptor may be attached to solid
support or other aglycons.
Future development in this approach is to expand the building-block repertoire
and to ensure its applicability in programmable one-pot synthesis. Compared with
stepwise solid-phase synthesis, the one-pot approach requires protecting group
manipulation only at the stage of building-block synthesis, and thus holds greater
potential for automation and for a greater diversity of oligosaccharide structures.
Other solution-phase syntheses of oligosaccharide libraries have been reported,
especially the method for the synthesis of mixtures [47], but the methods have
not been demonstrated to create great diversity. In addition, characterization of the
mixture represents a dicult problem.
24.5
Conclusions
Recent advances in synthetic carbohydrate chemistry have provided new strategies

for creating the diversity of oligosaccharides needed to tackle many interesting
problems in glycobiology. Many technical problems that hinder the development of
combinatorial carbohydrate chemistry still exist and remain to be solved. Of par-
ticular importance is development of convenient and eective automated systems
References 721
for the synthesis of oligosaccharides. Future eorts to reach this goal include,
for example, the development of new methods and strategies for rapid assembly of
oligosaccharides, the design of new orthogonal protecting groups, and the simpli-
cation of protecting group manipulation. Development of such automated sys-
tems easily accessible to both biologists and chemists will have a signicant im-
pact on our understanding of carbohydrates in biological systems and on the
development of new therapeutics to modulate or to control carbohydrate functions.
References
1 P. Sears, C.-H. Wong, Cell. Mol. Life Large, D. G., Warren, C. D. (eds),
Sci. 1998, 54, 223252. Dekker, New York 1997, pp. 207
2 A. Varki, Glycobiology 1993, 3, 97 243.
130. 16 D. Crich, S. Sun, J. Am. Chem. Soc.
3 H. Lis, N. Sharon, Eur. J. Biochem. 1998, 120, 435436.
1993, 218, 127. 17 F. Barresi, O. Hindsgaul, J. Am.
4 T. Kolter, K. Sandhoff, Angew. Chem. Soc. 1991, 113, 83769377.
Chem. Int. Ed. Engl. 1999, 38, 1532 18 G. Stork, J. J. La Clair, J. Am. Chem.
1568. Soc. 1996, 118, 247248.
5 H. Paulsen, Angew. Chem. Int. Ed. 19 Y. Ito, T. Ogawa, J. Am. Chem. Soc.
Engl. 1982, 21, 155173. 1997, 119, 55625566.
6 J. Rademann, A. Geyer, R. R. 20 P. J. Garegg, Adv. Carbohyr. Chem.
Schmidt, Angew. Chem. Int. Ed. Engl. 1997, 52.
1998, 37, 12411245. 21 H. Lonn, K. Stenvall, Tetrahedron
7 R. Liang, L. Yan, J. Loebach, M. Ge, Lett. 1992, 33, 115116.
Y. Uozomi, K. Sekanina, N. Horan, 22 K. C. Nicolaou, X. Y. Xiao, Z.
J. Gildersleeve, C. Thompson, C. Parandoosh, A. Senyei, M. P. Nova,
Smith, K. Biswas, W. C. Still, D. Angew. Chem. Int. Ed. Engl. 1995, 34,
Kahne, Science 1996, 274, 15201522. 22892291.
8 T. J. Martin, R. R. Schmidt, 23 P. H. Seeberger, W.-C. Haase, Chem.
Tetrahedron Lett. 1992, 33, 61236126. Rev. 2000, 100, 43494393.
9 H. Kondo, Y. Ichikawa, C.-H. Wong, 24 J. T. Randolph, K. F. McClure, S. J.
J. Am. Chem. Soc. 1992, 114, 8748 Danishefsky, J. Am. Chem. Soc. 1995,
8750. 117, 57125719.
10 S. Hashimoto, T. Honda, S. 25 K. C. Nicolaou, N. Watanabe, J. Li,
Ikegami, J. Chem. Soc. Chem. J. Pastor, N. Winssinger, Angew.
Commun. 1989, 685. Chem. Int. Ed. Engl. 1998, 37, 1559
11 R. J. Ferrier, R. W. Hay, N. 1561.
Vethaviyasar, Carbohydr. Res. 1973, 26 P. M. St. Hilaire, M. Meldal, Angew.
27, 5561. Chem. Int. Ed. Engl. 2000, 39, 1162
12 B. Fraser-Reid, J. R. Merritt, A. L. 1179.
Handlon, C. W. Andrews, Pure Appl. 27 X. Huang, K. Witte, D. E.
Chem. 1993, 65, 779786. Bergbreiter, C.-H. Wong, Adv.
13 S. J. Danishefsky, K. F. McClure, J. Synth. Catal. 2001, 343, 17.
T. Randolph, R. B. Ruggeri, Science 28 O. Kanie, G. Grotenberg, C.-H.
1993, 260, 13071309. Wong, Angew. Chem. Int. Ed. Engl.
14 R. U. Lemieux, K. B. Hendriks, R. V. 2000, 39, 45454546.
Stick, K. James, J. Am. Chem. Soc. 29 B. Ernst, G. W. Hart, P. Sinay,
1975, 97, 40564062. Carbohydrates in Chemistry and
15 S. L. Flitsch, G. M. Watt in: Glyco- Biology, Wiley-VCH-Verlag, Weinheim
peptides and Related Compounds. 2000.
30 O. J. Plante, E. R. Palmacci, P. H. Nishimura, Chem. Commun. 1999,

Seeberger, Science 2001, 291, 1523 507508.
1527. 41 S. P. Douglas, D. M. Whiteld, J. J.
31 C.-H. Wong, R. L. Halcomb, Y. Krepinsky, J. Am. Chem. Soc. 1991,
Ichikawa, T. Kajimoto, Angew. Chem. 113, 50955097.
Int. Ed. Engl. 1995, 34, 412546. 42 N. L. Douglas, S. V. Ley, U. Lucking,
32 K. M. Koeller, C.-H. Wong, Chem. S. L. Warriner, J. Chem. Soc. Perkin
Rev. 2000, 100, 44654493. Trans. 1 1998, 5165.
33 J. E. Heidlas, K. W. Williams, G. M. 43 Z. Zhang, I. R. Ollmann, X.-S. Ye,
Whitesides, Acc. Chem. Res. 1992, 25, R. Wischnat, T. Baasov, C.-H.
307314. Wong, J. Am. Chem. Soc. 1999, 121,
34 L. F. Mackenzie, Q. Wang, R. A. J. 734753.
Warren, S. G. Withers, J. Am. 44 S. Hanessian, C. Bacquet, N. Lehong,
Chem. Soc. 1998, 120, 55835584. Carbohydr. Res. 1980, 80, C1722.
35 C.-H. Wong, S. L. Haynie, G. M. 45 K. C. Nicolaou, S. P. Seitz, D. P.
Whitesides, J. Org. Chem. 1982, 47, Papahatjis, J. Am. Chem. Soc. 1983,
54165418. 105, 24302434.
36 K. Koeller, C.-H. Wong, Chem. Eur. 46 F. Burkhart, Z. Zhang, S.
J. 2000, 6, 12431251. Wacowich-Sgarbi, C.-H. Wong,
37 X. Chen, J. Fang, J. Zhang, Z. Liu, J. Angew. Chem. Int. Ed. Engl. 2001, 40,
Shao, P. Kowal, P. Andreana, P. G. 12741277.
Wang, J. Am. Chem. Soc. in press. 47 O. Kanie, F. Barresi, Y. Ding, J.
38 M. Schuster, P. Wang, J. C. Labbe, A. Otter, L. S. Forsberg, B.
Paulson, C.-H. Wong, J. Am. Chem. Ernst, O. Hindsgaul, Angew. Chem.
Soc. 1994, 116, 11351136. Int. Ed. Engl. 1995, 34, 27202722.
39 K. Witte, O. Seitz, C.-H. Wong, J. 48 H. Kamitakahara, T. Suzuki, N.
Am. Chem. Soc. 1998, 120, 1979 Nishigori, Y. Suzuki, O. Kanie, C.-
1989. H. Wong, Angew. Chem. Int. Ed. Engl.
40 K. Yamada, S. Matsumoto, S.-I. 1998, 37, 152428.
723
Part IV
Molecular Design and Combinatorial
Compound Libraries

ISBN: 3-527-30509-2
725
25
Design Criteria
Josef Pernerstorfer
25.1
Introduction
The original goal of combinatorial synthesis was to synthesize huge numbers of

organic compounds. The simple belief that a certain number of test compounds
had to be evaluated to identify a new drug led to the assumption that the numbers
game of combinatorial chemistry could speed up the drug development process. It
was several years before scientists realized that it was not only the number of
compounds but also their quality that was essential for medicinal chemistry proj-
ects. This chapter deals with the design of reasonable combinatorial libraries for
drug development. First, some general aspects of drug-like compounds will be con-
sidered, followed by diversity concepts and the synthesis of diverse compound
libraries. A discussion of preferred structural motifs in medicinal chemistry will
complete the chapter.
25.2
Properties of Combinatorial Libraries for Drug Development
Generally, the drug development process aims to synthesize chemical entities

which are, apart from their biological eects on specied targets, orally bioavail-
able. A major criterion for good absorption of these compounds is that certain
physiological properties will allow them to be reasonably absorbed into the gastro-
intestinal system. In a landmark paper, Lipinski and coworkers [1] from Pzer
were looking for factors which inuence absorption and permeability of drugs and
which could be considered even at the stage of the drug discovery process. They
studied a database of 2245 drug compounds which had passed clinical phase I and
had entered clinical phase II. Lipinski and coworkers assumed that these com-
pounds had good absorption properties since insoluble and poorly permeable sub-
stances had been eliminated from further research at an earlier stage of the drug
development process. The properties which were taken into account had to be
easily calculable and could be expected to have a pronounced eect on permeabil-

ISBN: 3-527-30509-2
726 25 Design Criteria
ity. These authors identied: (1) molecular weight, (2) lipophilicity, (3) number of
hydrogen bond donor groups (i.e. number of NH and OH bonds), and (4) number
of hydrogen bond acceptors (i.e. number of N O) as the key properties which
have an essential eect on the permeation through lipid bilayers and therefore on
the intestinal absorption process. Properties 1, 3, and 4 are obviously easily calcu-
lable from the structural formula. As a measure of lipophilicity, Lipinski and co-
workers used the partition coecient of the substance between n-octanol and
water, P, which can be approximated by increment systems. The authors used two
such systems. The rst was the Pomona College Medicinal Chemistry program
which calculated log P values (C log P) from structural fragments and gave very
accurate results, but failed in many instances because of fragments in the mole-
cule which were not assigned in the program. The other system they used had
been described by Moriguchi et al. [2]. This system gives less but still reasonably
accurate results and allows the calculation of M log P directly from the structural
formula [2].
Lipinski et al. determined the distribution of these four properties among the
drug database and found cut-o levels for each parameter such that @90% of the
drugs were within these levels. From these, they stated that poor absorption and
permeation are more likely when:
1 the molecular weight (MW) is >500;

2 C log P is >5 (or M log P is >4.15);
3 the number of N O is >10 (H-bond acceptors);
4 the number of NH OH is >5 (H-bond donors);
5 compound classes which are substrates for biological carriers are exceptions to
the rule.
These became known as Lipinskis rule of 5. Lipinski and coworkers found

that no more than 10% of drugs obeyed any combination of two of these rules.
For example, only 1% of the drugs had both MW and log P outside the cut-o
levels. Orally bioavailable substances which violate the rst four rules mainly be-
long to a few therapeutic categories, i.e. antibiotics, antifungals, vitamins, and car-
diac glycosides. These substances are assumed to be substrates for naturally oc-
curring transporters.
Using these results, Lipinski and coworkers examined the lead generation pro-
cess at Pzer, which is representative of that used by many large pharmaceutical
companies. The advent of high-throughput screening (HTS) allowed testing of
huge numbers of chemical compounds. In contrast to earlier techniques, it was
not necessary to obtain thermodynamically stable aqueous solutions of the com-
pounds for biological testing: the compounds were delivered as dimethyl sulfoxide
(DMSO) stock solutions, which allowed for testing of very lipophilic compounds.
At the same time, combinatorial chemistry enabled the synthesis of vast numbers
of test compounds for in vitro HTS screening. Lipinski and coworkers compared
the properties of test compounds which were synthesized 1986 and 1994 (pre- and
post-HTS era) (Table 25.1). They found that test compounds were becoming much
25.2 Properties of Combinatorial Libraries for Drug Development 727
Tab. 25.1. Distribution of M log P and molecular weight in the pre- and post-HTS era [1].
Percentile M log P MW
1986 1994 1986 1994
90 4.30 4.76 514 726

75 3.48 3.90 415 535
50 2.60 2.86 352 412
more lipophilic and heavier. Both these factors led to the discovery of a number of
highly active compounds in vitro but caused severe problems in developing orally
bioavailable drugs owing to insucient solubility and permeability in vivo. Ob-
viously, the strategy in combinatorial chemistry of taking a multifunctional central
building block and decorating it with organic residues runs the risk of generating
very high MW compounds which are furthermore very lipophilic since all polar
groups (acids, amines, alcohols, and phenols) would be masked by combinatorial
variation (acid amides, ureas, ethers, esters). Although this can be useful during
the late stages of the optimization process, it is not a good procedure for generat-
ing lead compound libraries.
In accordance with these results, Teague et al. [3] studied the drug optimization
process at Astra Zeneca. They found that only very few lead compounds have such
desirable properties and that it would be very unlikely for one of them to pass on
to clinical development directly. Generally, potency and pharmacokinetic prole
have to be further optimized this goal is accomplished by the addition of suitable
groups and side-chains and causes an increase in MW and lipophilicity of the drug
compared with the initial lead. Teague et al. divided the properties of lead struc-
tures identied by HTS into three groups with respect to anity, MW, and log P:
1 Intermediate anity (> 0.1 mM), low MW (< 350), and low C log P (< 3). These
are classical lead structures which can be optimized by introducing lipophilic
groups to increase potency and improve pharmacokinetic properties.
2 High anity (f 0.1 mM), high MW (g 350), and low C log P (< 3). These leads
are often derived from natural products and can be optimized by derivatization
to improve pharmacokinetics while potency is retained.
3 Intermediate anity (> 0.1 mM), high MW (g 350), and high C log P (> 3).
These leads are often generated in HTS assays of combinatorial libraries. An
optimization of these drug-like leads normally proves dicult, since the anity
results from many nonoptimized interactions between lead and target and a
further optimization produces very lipophilic, poorly soluble compounds.
Teague et al. concluded that combinatorial libraries for lead identication should
be fundamentally dierent from those for lead optimization. Lead structure li-
braries have to produce compounds with low MW (100350) and low C log P (1.0
3.0). Focused libraries based on such leads can quickly improve drug properties.
Fig. 25.1. Molecular weight distribution of drugs that have

good and poor oral bioavailability [4].
Although there is general agreement in the literature on the inuence of lip-

ophilicity and H-bond donor and H-bond acceptor properties on the bioavailability
of drugs, the inuence of MW is controversial. A set of 286 marketed drugs was
examined for the relationship between MW and oral bioavailability and a boundary
of 40% blood levels after oral application was chosen, above which no bioavail-
ability problems should be expected [4]. Of the total set of 286 drugs, 168 lay above
the 40% level and 118 lay below. As expected, about 50% of drugs that perform
well had a MW between 250 and 350 and only very few had a MW > 500. Surpris-
ingly, however, the drugs with low bioavailability had a quite similar distribution,
with an average MW of between 350 and 400, and only a few compounds had
MW > 500 (Fig. 25.1). When those drugs with obvious metabolic instabilities
(such as b-lactams), with very high lipophilicities (which cause poor water sol-
ubility), and with quaternary amines were subtracted from the 116 inferior per-
formers, 97 substances remained whose correlation between MW and oral avail-
ability did not signicantly dier from the distribution of the well-bioavailable
compounds. This indicates that MW is not a primary cause of low bioavailability
but that high MW is very often correlated with factors such as high lipophilicity
and poor solubility and with a high number of heteroatoms.
25.3
Dierentiation of Drug-like and Nondrug-like Compounds
Since an accessible virtual library is much larger than one that is actually syn-
thesized, the rst criterion when choosing compounds for synthesis should be
that they have reasonable drug-like properties. For example, toxic and reactive
substructures which can react with proteins can cause false-positive read-outs in
screening assays and should, therefore, be eliminated (Fig. 25.2) [5].
Several authors have tried to dierentiate drugs from nondrugs by looking at the
25.3 Differentiation of Drug-like and Nondrug-like Compounds 729
Fig. 25.2. Reactive functional groups leading to in vitro false positives [5].
general structural properties using computational methods [6]. Generally, data-

bases of known drug compounds are used as examples of drug-like substances
[e.g. World Drug Index (WDI)] and databases of nondrugs [e.g. Available Chem-
icals Directory (ACD)] are used for the studies. Some authors operate with neural
networks trained on drug and nondrug databases [7, 8]. These networks use large
sets of approximately 8090 descriptors for each structural parameter. After train-
ing the network on part of a database, these authors classied 8090% of the mem-
bers of each database correctly. A much smaller set of only 15 molecular descriptors
(XaH aromatic, XaH nonaromatic, CaH (any), CbO, C sp 2 conj, bNa, N non-
aromatic, NbC, O nonaromatic, O s 2 (any), P s 2 , F any, Cl any, number of atoms,
total charge) was used to gain essentially equally good results in dierentiating be-
tween drugs and nondrugs [9]. However, the authors had diculties in explaining
the decision processes of such trained black box neuronal networks. A similar
quality of dierentiation between drug-like and nondrug-like compounds was ob-
tained using a fairly simple decision tree which dierentiates on the presence/
absence of functional groups. By simply checking for the presence of hydroxyl,
tertiary/secondary amino, carboxyl, phenol, and enol groups, 75% of the drugs
were correctly recognized, whereas nondrugs were shown to have an aromatic
nature and a low content of functional groups except for halogens. Further rene-
ment of the decision tree allowed a prediction quality of around 80% [10]. Another
approach used the deviation of 25 structural parameters from a global drug-like

cluster center which was calculated from a drug database in a 25-dimensional
parametric space. This deviation produced a drug-like index (DLI) value between
0 and 1. It could be shown that compounds from drug databases have a signif-
icantly higher DLI than compounds from nondrug databases [11]. Furthermore,
complexity parameters such as numbers of ring systems (RNG), rotatable bonds
(RTB), and rigid bonds (RGB) were examined to dierentiate drugs from non-
drugs. It was found that drugs are more likely to have properties RNG b 3/
RGB b 18/RTB b 6, whereas nondrugs are more likely to have RNG a 2/
RGB a 17/RTB a 5) [12]. This nding means that more complex molecules are
more likely to be drug-like. Although the statistical signicance of the last two ap-
proaches is without doubt, it remains to be determined whether these ndings are
suciently exact to dierentiate drugs from nondrugs in practice.
25.4
Diversity in Combinatorial Chemistry for Drug Development
25.4.1
Introduction
The number of compounds theoretically accessible from all permutations of

chemical building blocks with an appropriate molecular weight goes well into the
billions [13] and by far exceeds the number of compounds which can be realisti-
cally synthesized. Therefore, considering the diversity of compounds actually pre-
pared can further exploit the potential of combinatorial synthesis [1418]. In me-
dicinal chemistry, a sine qua non for every description of chemical diversity is some
kind of neighborhood behavior. As such, similar compounds with respect to a rea-
sonable descriptor system should have similar biological properties [19]. This fea-
ture allows compounds that are dissimilar to a certain degree to be synthesized
and screened without losing relevant information about their biological eects.
Thus, a much larger chemical and biological space can be evaluated using an
acceptable amount of eort.
The diversity of combinatorial libraries is also dependent on the actual scope of
the library and on the information which is available for library design. One can
dierentiate focused libraries, targeted libraries, and primary screening libraries
[20]. Focused libraries are designed to evaluate a given lead structure in more de-
tail. The information content for the library design is very high and the chemical
space which has to be evaluated is rather small since key pharmacophoric ele-
ments are already known. Targeted or biased libraries are directed toward a partic-
ular biological target that belongs to a specic protein class such as a kinase or a
G-protein-coupled receptor. Information about key structural features addressing
the target class can be derived from literature, but is much less than for focused
libraries. Therefore, the structural space which the library has to evaluate is much
larger. Finally, primary or general screening libraries are designed for screening
against new pharmaceutical targets. Generally, there is no information about the

type of molecule that will interact with a biological target. The only limitation
which can be made to these libraries is to generate drug-like structures, but no
further limitation can be made initially.
25.4.2
Descriptors
To evaluate the diversity of compounds and of combinatorial libraries, there rst

needs to be some kind of description system for each substance in the form of a
number or a set of numbers which allows a quantitative comparison of the struc-
tural dierences between two entities. Instead of a set of numbers, a bitstring is
often used which displays properties just in terms of absent (i.e. 0) or present
(i.e. 1). This system allows a fast comparison of two bitstrings.
Descriptors can be dierentiated according to their dimensionality [2123]:
. One-dimensional (1D) descriptors describe the molecular properties of mole-

cules holistically with a unique number such as log P, molecular weight, or
number of hydrogen bond donors and acceptors. These values have a large im-
pact on pharmacokinetic parameters and are often used as lters in library de-
sign rather than as actual descriptors for molecular similarity and diversity [20].
. Two-dimensional (2D) descriptors are based on the 2-dimensional representation
of molecules, i.e. the structural formula. They normally use bitstrings to describe
the presence or absence of structural fragments (e.g. carboxylic acids or certain
ring systems) or of certain atom patterns of 27 atoms length (molecular n-
gerprints) [24]. For the use of structural fragments, the MACCS (Molecule
Accessing System) structural fragment keys [25] are often used, which were
originally developed for substructure searching in chemical databases. These
fragment keys suer from their lack of generality, since not all possible struc-
tural fragments can be described by a reasonable set of fragment keys. Molecular
ngerprints generate a bitstring from indexing all possible paths of dened
lengths through a molecule. Since the number of all possible paths is too high to
assign every dierent path to unique bits, the ngerprints are hashed, meaning
that bits are associated with several paths. This hashing causes a lack of accuracy
in the description.
. Three-dimensional (3D) descriptors take the spatial relationships of chemical
features into account. Since distances and angles between functional groups can
adopt continuous values, a distance or angle range (e.g. 210 A or 0180 ) is de-
ned which is subdivided into a number of bins of certain bin width. A set of
bits is then assigned to these bins to encode all possible conformations of pre-
dened pairs of features between which the distances or the angles are deter-
mined. These descriptors do not consider high-energy conformations but treat
all possible conformations which descend from the rotation around CaC bonds
as being equal. The computational eort used for these exible descriptors is
very high. Therefore, sometimes rigid descriptors are used, which only consider
one or a few minimum energy conformations of the molecule.
Pharmacophores are also used as 3D descriptors. These pharmacophores are

specied by three interaction centers of seven-center types which are responsible
for the interaction with molecular receptor sites: these are hydrogen bond donors,
hydrogen bond acceptors, hydrogen bond donors and acceptors, aromatic rings,
hydrophobic regions, acidic sites, and basic sites. While the arrangement of three
pharmacophores does not allow the dierentiation of enantiomeric compounds, a
further renement of this concept uses four pharmacophoric points, which also
consider the chirality of the centers. A major drawback to the use of three- or four-
point pharmacophores is the need for rather long calculation times (about 1 min
per compound in the case of four-point pharmacophores) [26], which can be a
limiting criterion in the evaluation of whole virtual libraries containing numerous
compounds.
25.4.3
Selection Algorithms
After diversity has been assessed using a descriptor system, compounds can be
subdivided into classes which cover the available chemical space with representa-
tive molecules. A widely used system to evaluate the similarity between the bit-
strings of two compounds is the Tanimoto coecient. If two molecules have A and
B bits set in their fragment bitstrings and C of these in common [27], then:
Tanimoto C=A B C
The Tanimoto coecient can adopt values between 1 (identical substances with
respect to the descriptor system) and 0 (no similarity).
Using this similarity metric, the set of compounds can be subdivided into clus-
ters of similar compounds which are dierent from the members of other clusters.
There are two categories of clustering: hierarchical and nonhierarchical. Hierar-
chical clustering can be divided into agglomerative and divisive approaches. The
agglomerative approach begins with all the molecules as singleton clusters and
combines these gradually into larger clusters by successively joining the most
similar compounds. Divisive clustering begins from one large cluster containing
all entities and splits this cluster successively into smaller clusters of dissimi-
lar compounds. Both methods continue until the desired number of clusters
is reached. An example of a nonhierarchical clustering algorithm is the Jarvis
Patrick method. For this approach, in the rst stage, the K nearest neighbors for
each member are calculated, according to the Tanimoto coecient. In the next
step, clustering is performed. Two structures are assigned to the same cluster,
when the following three conditions are met:
1 A is in the top K nearest neighbor list of B.

2 B is in the top K nearest neighbor list of A.
3 A and B have at least M of their top nearest neighbors in common (M < K).
Fig. 25.3. Clustering may produce diverse sets of compounds,

in which diversity occurs along one dimension.
Depending on the values of K and M, the JarvisPatrick procedure tends to pro-

duce either very large clusters (if M and K are rather low) or many singleton clus-
ters (if M and K are high), but it is a relatively fast algorithm compared with the
hierarchical clustering methods.
A major drawback to clustering is that it gives no information about the chemi-
cal space which is covered. The clusters may appear to be very widespread, but if
diversity occurs just along one or a few dimensions of chemical space, the other
dimensions still may not be covered at all. In Fig. 25.3, the compound clusters
seem to be diverse, but they are almost exclusively spread along the x-axis. There is
hardly any diversity along the y-axis. Another approach which circumvents this
problem is a partition-based selection. In this method, chemical space is divided
into a number of segments along each axis. These segments generate a number of
smaller volume elements (bins) in the chemical space envisaged. A diverse set
of compounds can then be chosen to maximize the number of dierent bins lled
with representatives. The same set of compounds as in Fig. 25.3 shows in Fig. 25.4
that the chemical space along the x-axis is covered very uniformly, whereas the
space along the y-axis is hardly covered at all.
Fig. 25.4. Partitioning of chemical space shows that diversity

only appears along the x-axis (lled squares).
25.4.4
Diversity Assessment
There is much discussion in the literature about the relevance of dierent de-
scriptors and diversity selection processes [2835]. Although 3D descriptors can
encode more information on molecules, it was shown that 2D descriptors perform
better in separating biologically active molecules from inactive ones. Hierarchical
clustering in combination with MACCS 2D descriptors performed best in several
dierent datasets of enzyme assays, high-throughput screening results, and activ-
ities in an monoamine oxidase assay. JarvisPatrick clustering was shown to be
rather ineective since it generated either singleton clusters of actives or very large
clusters containing the actives together with many inactives. Using hierarchical
clustering, it was possible to separate active clusters containing 3050% actives on
average whereas only 0.82% of the whole dataset was active. It appeared that a
reasonable cluster size is around ve molecules per cluster, which means that
about 20% of a dataset still has to be sampled in order to obtain valid results [21].
The MACCS structural keys also performed best in predicting hydrophobicity,
electrostatics, sterics, dispersion interaction, and hydrogen bonding of molecules.
These factors are relevant for ligandreceptor interaction and molecular recogni-
tion. This result is the reason why this descriptor system performs well in biologi-
cal clustering [36].
Another statistical evaluation of random selection methods and of designed
compound subsets for biological screening systems proved that the latter were, in-
deed, superior. About 3.5 times more compounds have to be sampled randomly to
obtain results equivalent to a rational design approach. For initial screening, a Ta-
nimoto similarity radius of 0.7 between similar compounds in the subset is ex-
pected to be sucient to cover relevant biological eects, whereas, for lead rene-
ment, a Tanimoto similarity radius of 0.85 is recommended [37].
The question of which level of diversity of combinatorial libraries should be
assessed has also been widely discussed in the literature. Three main strategies
have been proposed [38]: reactant-based design means that the diversity of the re-
agents is evaluated and these diverse reactants are assumed to give a diverse prod-
uct library. The number of reagents is orders of magnitude lower than the number
of products, therefore this design process is very fast. However, it is not guaran-
teed that a maximum diverse set of reagents also provides a maximum diverse set
of products. Therefore, product-based design uses fully enumerated combinatorial
libraries and picks the most diverse products thereof. During this process, the com-
binatorial nature of the products gets lost and, therefore, the process loses e-
ciency. A compromise between these two approaches is a reactant-biased/product-
based algorithm. This means maintaining the combinatorial nature of chemistry
at the reactant level, but optimizing the diversity at the product level by use of
mathematical models such as genetic algorithms and simulated annealing [39
41]. A general problem with these product-based approaches is that diversity has to
be calculated for the whole virtual library, which needs very large computational
resources. Which of these methods is nally more ecient remains unclear. On

one hand, there are reports which show that diversity design at the product level
results in more diverse libraries than if design is performed at the reagent level
[42]. On the other hand, it could be shown that eciency of selection is equivalent
both at the product level and at the reagent level if the number of building blocks
is suciently high. Just with a very few building blocks (e.g. <7), diversity at
product level is signicantly higher since unique features might not be repre-
sented in the building blocks [43].
25.5
Privileged Structures
25.5.1
Introduction
When Evans et al. [44] were looking for new cholecystokinin (CCK) antagonists in
1988, they introduced the concept of privileged structures for structural motifs
which are capable of providing useful ligands for more than one single target. As
shown in Fig. 25.5, the benzodiazepine skeleton is a recurring structural motif ad-
dressing not only CCK but the structurally similar Triuadom 2 shows high an-
ity to the opiate receptor [45] and 3 is an NK-1 antagonist [46].
This nding contradicts the common principles of individuality and selectivity of
biological receptors. According to Evans et al., a possible explanation for this phe-
nomenon might be that these G-protein-coupled receptors descend from the same
ancestral genes and that they still remain structurally related. Similarly, Wiley and
Rich [47] have reasoned that the similar structure of G-protein-coupled receptors
which are characterized by seven transmembrane a-helices might favor a recurring
binding element. These hydrophobic pockets might be complementary to the dif-
ferent conformations of privileged structures [47]. Therefore, libraries of such
privileged structures can give rise to a number of lead compounds in new screen-
ing assays [26, 48, 49].
Fig. 25.5. Phenylbenzodiazepines as privileged substructures.

Fig. 25.6. Biphenyltetrazoles as privileged substructures.
25.5.2
Further Examples of Privileged Structural Motifs
The biphenyltetrazole moiety is an example of a privileged structure which is

found in angiotensin I antagonists such as Losartan (4) [50] and Valsartan (5) [51]
and in growth hormone (GH) secretagogue agonist MK-0751 (6) [52] (Fig. 25.6).
The diphenyl methane moiety is another structural motif which is active in a
variety of biological targets. The rigidity of the template prevents the aromatics
from intramolecular hydrophobic interaction in aqueous media (hydrophobic
collapse) so that the hydrophobic interaction can promote receptor binding in-
stead [47]. On one hand, it is part of the 5-phenyl-1,4-benzodiazepine substructure
(see Sect. 25.5.1); on the other, it is, for example, part of the NPY Y1 antagonist (7)
BIBP 3226 [48], of angiotensin AT-2 ligand (8) PD 132 177 [26], and of neurokinin
NK1 antagonist quinuclidine (9) CP 96345 [53] (Fig. 25.7).
As shown in Fig. 25.8, arylspiropiperidines also display a broad range of activ-
ities. Examples include the chemotaxin C5a receptor agonist 10 [54], the oxytocin
antagonist 11 [55], and the growth hormone secretagogue 12 [52] (Fig. 25.8).
A more general description of central nervous system (CNS) drugs shows that
many of them descend from a simple aromatic system and an amine which is
xed via a two- to ve-atom chain to the hydrophobic core [56]. For example, the
dopamine antagonist chlorpromazine (10) and the 5-hydroxytryptamine (5-HT)
Fig. 25.7. Diphenylmethanes as privileged substructures.

Fig. 25.8. Arylspiropiperidines as privileged substructures.
Fig. 25.9. Arylalkylamines as CNS drugs.
uptake inhibitor imipramine (11) contain this substructure, as do the anticon-

vulsant drug procyclidine (12) and the heroin substitute analgesic methadone (13)
(Fig. 25.9).
This principle is not only limited to CNS drugs. The calcium antagonist verapa-
mil (14), the b-blocker propanolol (15) and tamoxifen (16), an antiestrogen, share
the same substructural unit [57] (Fig. 25.10).
The 2,2-dimethylbenzopyran substructure is a common subunit in natural
products as well as in pharmaceutically active substances. Nicolaou et al. presented
a solid-phase synthesis of a series of libraries based on this scaold (Scheme 25.1)
[5860]. They used a selenium-based linker which proved to be stable over a range
of reaction conditions (e.g. reductions, Li-organyls, Stille coupling conditions, con-
densation reactions, hydrazines), but was selectively cleaved with hydrogen perox-
ide, thus yielding the benzopyran in kind of a traceless linker system.
Fig. 25.10. Arylalkylamines which are not CNS drugs.

Scheme 25.1. Synthesis of dimethylbenzopyrans on solid phase.
25.5.3
Substructure Analysis of Drugs
In a paper by Bemis and Murcko [61], a database of 5120 known drugs [Compre-
hensive Medicinal Chemistry (CMC)] was analyzed for the molecular frameworks
of the drugs. These authors dened the framework of a drug as the union of all
ring systems and linker atoms on the direct path between the ring systems. On the
basis of the two-dimensional representations of the drugs (ignoring atom type, hy-
bridization, and bond order), they found 1179 dierent frameworks, but only 32 of
these accounted for half of all frameworks. A few representative samples of these
are outlined in Fig. 25.11. The numbers show the frequency of each framework
within the database.
Fig. 25.11. Frequently occurring frameworks.

Fig. 25.12. Most frequently occurring side-chains.
Although the trivial six-member ring appears most often, the other frameworks
indicate a clear preference for certain ring systems. The aforementioned 5-phenyl-
1,4-benzodiazepine also belongs to these privileged frameworks (45 occurrences).
With regard to the atom type, hybridization, and bond order, Bemis and Murcko
found more than 2500 dierent frameworks in the database, but only 42 of these
accounted for 25% of the total. In another paper [62], the same authors studied
the frequencies of side-chains in the CMC database. The side-chains are all parts
of the drug which do not belong to the framework. They found an average number
of four side-chains per molecule, including the trivial oxygen side-chain of the car-
bonyl groups. When ignoring the carbonyl group (3545 occurrences) as a side-
chain, only 20 dierent side-chains account for 75% of the total. Examples of these
are given in Fig. 25.12. The number gives the frequency of occurrence among the
5090 drugs studied.
These data clearly show that certain substructures within a drug appear more
often than others, a nding which can aect the design of new drug-like libraries.
An interesting application of these ndings is the Retrosynthetic Combinatorial
Analysis Procedure (RECAP) [63]. In this approach to the design of biased com-
binatorial libraries, all compounds in the World Drug Index (WDI) were broken
down into fragments by dissection of 11 classes of bonds which are easily formed
by combinatorial chemistry until structurally nontrivial building blocks were ob-
tained (Fig. 25.13). Trivial residues such as methyl ethers were not broken down
further so that pharmacophoric information was not lost.
Clusters of compounds which exhibit potency toward a given biological target
were examined for common building blocks. In the next step, the frequency of
these building blocks in the specic cluster was compared with the frequency in
Fig. 25.13. RECAP dissection bonds.
the total WDI in order to dierentiate pharmacophoric subunits from trivial com-
mon substructures. Combinatorial libraries using these building blocks are ex-
pected to lead to rapid identication of novel hits and lead compounds for a given
biological target. A possible drawback is the similarity of the compounds synthe-
sized in this way to known drugs. Many leads produced according to this approach
might therefore be under patent protection. Furthermore, it is unlikely that new
bioisosteric pharmacophores will be produced using this method.
25.6
Conclusion
Combinatorial chemistry has allowed the productivity of synthetic organic chem-

ists to be multiplied by orders of magnitude. Nevertheless, it will not only be a
pure numbers game to nd new chemical entities; combinatorial libraries will also
have to be designed carefully. Otherwise, combinatorial chemistry tends to produce
compounds whose physicochemical parameters such as lipophilicity and molecu-
lar weight reach undesired values. Furthermore, the diversity of synthesized com-
pounds must respond to the problems that have to be solved since diversities that
are either too large or too small within libraries will reduce the eciency of the
synthetic process. Although diversity space is incredibly large, it is worth consider-
ing that certain structural features are occurring in diverse drug motifs and these
deserve special attention when synthesizing drug-like libraries for general screen-
ing purposes.
References
1 C. A. Lipinski, F. Lombardo, B. W. 2 I. Moriguchi, S. Hirono, Q. Liu, I.

Dominy, P. J. Feeney, Adv. Drug Deliv. Nakagome, Y. Matsushita, Chem.
Rev. 1997, 23, 325. Pharm. Bull. 1992, 40, 127130.
References 741
3 S. J. Teague, A. M. Davies, P. D. 24 D. R. Flower, J. Chem. Inf. Comput.

Leeson, T. Oprea, Angew. Chem. 1999, Sci. 1998, 38, 379386.
111, 39623967. 25 MACC II; Molecular Design Ltd.:
4 R. A. Fecik, K. E. Frank, E. J. 14600 Catalina St. San Leandro, CA
Gentry, S. R. Menon, L. A. 94577, (510)-895-1313.
Mitscher, H. Telikepalli, Med. Res. 26 J. S. Mason, I. Morize, P. R.
Rev. 1998, 18, 149185. Menard, D. L. Cheney, C. Hulme, R.
5 G. M. Rishton, Drug Discov. Today F. Labaudiniere, J. Med. Chem. 1999,
1997, 2, 382384. 42, 32513264.
6 W. P. Walters, Ajay, M. A. Murcko, 27 V. J. Gillet, Molecular Diversity in
Curr. Opin. Chem. Biol 1999, 3, 384 Drug Design. Kluwer Academic
387. Publishers, Dordrecht 1999.
7 J. Sadowski, H. Kubinyi, J. Med. 28 R. E. Higgs, K. G. Bemis, I. A.
Chem. 1998, 41, 33253329. Watson, J. H. Wikel, J. Chem. Inf.
8 Ajay, W. P. Walters, M. A. Murcko, Comput. Sci. 1997, 37, 861870.
J. Med. Chem. 1998, 41, 33143324. 29 E. J. Martin, R. E. Critchlow, J.
9 T. M. Frimurer, R. Bywater, L. Comb. Chem 1999, 1, 3245.
Naerum, L. N. Lauritsen, S. Brunak, 30 J. M. Blaney, E. J. Martin, Curr.
J. Chem. Inf. Comput. Sci. 2000, 40, Opin. Chem. Biol. 1997, 1, 5459.
13151324. 31 R. D. Cramer, R. D. Clark, D. E.
10 M. Wagener, V. J. v. Geerestein, J. Patterson, A. M. Ferguson, J. Med.
Chem. Inf. Comput. Sci. 2000, 40, 280 Chem. 1996, 39, 30603069.
292. 32 J.-L. Fauchere, J. A. Boutin, J.-M.
11 J. Xu, J. Stevenson, J. Chem. Inf. Henlin, N. Kucharczyk, J.-C.
Comput. Sci. 2000, 40, 11771187. Ortuno, Chemometrics Intelligent Lab.
12 T. I. Oprea, J. Comp. Aid. Mol. Des. Syst. 1998, 43, 4368.
2000, 14, 251264. 33 D. Gorse, A. Rees, M. Kaczorek, R.
13 D. L. Coffen, Med. Chem. Res. 1998, Lahana, Drug Discovery Today 1999, 4,
8, 206218. 257264.
14 D. C. Spellmeyer, P. D. J. 34 P. Willett, Curr. Opin. Biotechnol.
Grootenhuis, Ann. Rep. Med. Chem. 2000, 11, 8588.
1999, 34, 287296. 35 J. S. Mason, M. A. Hermsmeier,
15 W. A. Warr, J. Chem. Inf. Comput. Curr. Opin. Chem. Biol. 1999, 3, 342
Sci. 1997, 37, 134140. 349.
16 D. M. Bayada, H. Hamersma, V. J. 36 R. D. Brown, Y. C. Martin, J. Chem.
van Geerestein, J. Chem. Inf. Inf. Comput. Sci. 1997, 37, 19.
Comput. Sci. 1999, 39, 110. 37 T. Potter, H. Matter, J. Med. Chem.
17 S. L. Schreiber, Science 2000, 287, 1998, 41, 478488.
19641969. 38 D. Gorse, R. Lahana, Curr. Opin.
18 L. Weber, Curr. Opin. Chem. Biol. Chem. Biol. 2000, 4, 287294.
2000, 4, 295302. 39 A. C. Good, R. A. Lewis, J. Med.
19 D. E. Patterson, R. D. Cramer, A. M. Chem. 1997, 40, 39263926.
Ferguson, R. D. Clark, L. E. 40 V. J. Gillet, P. Willet, J. Bradshaw,
Weinberger, J. Med. Chem. 1996, 39, D. V. S. Green, J. Chem. Inf. Comput.
30493059. Sci. 1999, 39, 169177.
20 D. H. Drewry, S. S. Young, 41 J. Mount, J. Ruppert, W. Welch, A.
Chemometrics Intelligent Lab. Syst. N. Jain, J. Med. Chem. 1999, 42, 60
1999, 48, 120. 66.
21 R. D. Brown, Y. C. Martin, J. Chem. 42 V. J. Gillet, P. Willett, J. Bradshaw,
Inf. Comput. Sci. 1996, 36, 572584. J. Chem. Inf. Comput. Sci. 1997, 37,
22 R. D. Brown, Perspect. Drug Disc. Des. 731740.
1997, 7/8, 3149. 43 A. Linusson, J. Gottfries, F.
23 P. Willet, J. Chem. Inf. Comput. Sci. Lindgren, S. Wold, J. Med. Chem.
1998, 38, 983996. 2000, 43, 13201328.
44 B. E. Evans, K. E. Rittle, M. G. Bock, A. Lowe III, K. P. Longo, W. S.

R. M. DiPardo, R. M. Freidinger, Lebel, H. A. Woody, S. E. Drozda,
W. L. Whitter, G. F. Lundell, D. F. M. C. Desai, F. J. Vinick, R. W.
Veber, P. S. Anderson, R. S. L. Spencer, H.-J. Hess, Science 1991,
Chang, V. J. Lotti, D. J. Cerino, T. 251, 435437.
B. Chen, P. J. Kling, K. A. Kunkel, 54 S. E. de Laszlo, E. E. Allen, B. Li, D.
J. P. Springer, J. Hirsheld, J. Med. Ondeyka, R. Rivero, L. Malkowitz,
Chem. 1988, 31, 22352246. C. Molineaux, S. J. Siciliano, M. S.
45 D. Romer, H. H. Buscher, R. C. Springer, W. J. Greenlee, N.
Hill, R. Maurer, T. J. Petcher, H. Mantlo, Bioorg. Med. Chem. Lett.
Zeugner, W. Benson, E. Finner, W. 1997, 7, 213218.
Milkowski, P. W. Thies, Nature 1982, 55 B. E. Evans, J. L. Leighton, K. E.
298, 759760. Rittle, K. F. Gilbert, G. F. Lundell,
46 D.-R. Armour, N. M. Aston, K. M. L. N. P. Gould, D. W. Hobbs, R. M.
Morriss, M. S. Congreve, A. B. DiPardo, D. F. Veber, D. J.
Hawcock, D. Marquess, J. E. Pettibone, B. V. Clineschmidt, P. S.
Mordaunt, S. A. Richards, P. Ward, Anderson, R. M. Freidinger, J. Med.
Bioorg. Med. Chem Lett. 1997, 7, 2037 Chem. 1992, 35, 39193927.
2042. 56 P. R. Andrews, E. J. Lloyd, Med. Res.
47 R. A. Wiley, D. H. Rich, Med. Res. Rev. 1982, 2, 355393.
Rev. 1993, 13, 327384. 57 F. S. LaBella, Biochem. Pharmacol.
48 A. A. Patchett, R. P. Nargund, Ann. 1991, 42, S1S8.
Rep. Med. Chem. 2000, 35, 289298. 58 K. C. Nicolaou, J. A. Pfefferkorn,
49 D. C. Rees, Ann. Rep. Med. Chem. A. J. Roecker, G.-Q. Cao, S.
1993, 28, 5968. Barluenga, H. J. Mitchell, J. Am.
50 D. J. Carini, J. V. Duncia, P. E. Chem. Soc. 2000, 122, 99399953.
Aldrich, A. T. Chiu, A. L. Johnson, 59 K. C. Nicolaou, J. A. Pfefferkorn,
M. E. Pierce, W. A. Price, J. B. H. J. Mitchell, A. J. Roecker, S.
Santella III, G. J. Wells, R. R. Barluenga, G.-Q. Cao, R. L. Affleck,
Wexler, P. C. Wong, S.-E. Yoo, P. B. J. E. Lillig, J. Am. Chem. Soc. 2000,
M. W. M. Timmermans, J. Med. 122, 99549967.
Chem. 1991, 34, 25252547. 60 K. C. Nicolaou, J. A. Pfefferkorn,
51 P. Buhlmayer, P. Furet, L. S. Barluenga, H. J. Mitchell, A. J.
Criscione, M. de Gasparo, S. Roecker, G.-Q. Cao, J. Am. Chem.
Whitebread, T. Schmidlin, R. Soc. 2000, 122, 99689976.
Lattmann, J. Wood, Bioorg. Med. 61 G. W. Bemis, M. A. Murcko, J. Med.
Chem. Lett. 1994, 4, 2934. Chem. 1996, 39, 28872893.
52 R. P. Nargund, K. H. Barakat, K. 62 G. W. Bemis, M. A. Murcko, J. Med.
Cheng, W. W.-S. Chan, B. R. Butler, Chem. 1999, 42, 50955099.
R. G. Smith, A. A. Patchett, Bioorg. 63 X. Q. Lewell, D. B. Judd, S. P.
Med. Chem. Lett. 1996, 6, 12651270. Watson, M. M. Hann, J. Chem. Inf.
53 R. M. Snider, J. W. Constantine, J. Comput. Sci. 1998, 38, 511522.
743
26
Estimation of Physicochemical and ADME
Parameters
Michael W. Harter, Jorg Keldenich, and Walter Schmitt
26.1
Introduction
The advent of combinatorial chemistry has added a new momentum to the early
stages of drug discovery and drug development. Nowadays, combinatorial libraries
are produced that serve dierent purposes in the drug discovery process. Random
libraries are generated with the aim of identifying one or more hits, i.e. identi-
fying one or more members of a library which bind to a given target in a screening
approach. Here, the term random is not precisely dened: complete randomness
is never realized. The preference for a certain template structure and the limi-
tations set by the chemistry that can be performed with the given template as well
as practical reasons confer restrictions even on a random library. Once a hit (or an
island of activity) has been identied, so-called focused libraries might be syn-
thesized in order to explore the chemical space close to that hit. These focused li-
braries are usually smaller in size and are used to gain structureactivity relation-
ship (SAR) information. The properties of the initial hit are usually improved and
a member of the focused library might serve as a lead structure; eventually after
repeated cycles of optimization a compound can be obtained that fullls the re-
quirements of a drug candidate and enters the stages of preclinical and clinical
development.
In the early days of combinatorial chemistry, library design centered exclusively
on the aim of nding molecules which bind to a given target or optimize binding
anity, as mentioned above. There has been debate in the pharmaceutical indus-
try as to why the number of successful development candidates has not grown at
the same or a similar pace as the number of molecules which are synthesized and
tested for pharmacological eects. A possible answer to that question might be the
limited attention that has been paid during library design to the overall properties
of the intended test compounds. This response is surprising since it has been
known for a long time that it takes more than just one pharmacophore to produce
a potential drug molecule. Assessing the reasons why a drug candidate fails in
preclinical development (i.e. the development stage that follows the discovery
stage) might be helpful in realizing any additional properties that might be neces-

ISBN: 3-527-30509-2
744 26 Estimation of Physicochemical and ADME Parameters
sary for a molecule to become a successful drug candidate [1, 2]. Beside commer-
cial and strategic reasons, which consitute about one-third of all discontinued
projects at that stage, toxicity and safety issues cause a further 30% of all drop
outs. Another 17% of all discontinued development projects are due to poor phar-
macokinetics or an unfavorable physicochemical compound prole. Depending on
the source of information, this gure rises up to 3550% when all stages of pre-
clinical and clinical drug development are considered. It is this last fraction of
molecules that we will discuss in this chapter.
26.2
ADME/PK Considerations in Combinatorial Library Design
It is only very recently that the need to design libraries of drug-like molecules
has become a central topic among the practitioners of combinatorial or parallel
synthesis in the life science arena [3, 4]. A number of rules have been estab-
lished from the analysis of various databases in order to aid chemists in library
design with respect to drug-likeness [59], some of which were discussed in
Chapter 25. In some companies, rules of that kind have been implemented in
software tools that are used as guides in library design. But what exactly does
drug-likeness mean?
Most potential drugs are intended for oral application. In order for a compound
to reach its site of action, it has to cross several barriers within the body. After in-
take, it has to be suciently water soluble in the lumen of the gastrointestinal (GI)
tract for it to be absorbed. It also has to be suciently stable in this environment,
which has, for instance, marked dierences in pH values. On the other hand, the
compound should not be too hydrophilic or too bulky because then it might re-
main in the gut lumen and eventually be excreted rather than being absorbed.
Hence, some degree of lipophilicity is required for a compound to be absorbed
through the lipid membrane of the gut wall, but compounds with a molecular
volume greater than a certain threshold range are restricted from being (passively)
absorbed. However, if the compound is too lipophilic, it might remain in the
membrane or stick to other biological material in the gut and might not reach the
portal vein. In the following sections, the factors which govern absorption, for ex-
ample permeability and solubility, will be discussed in greater depth. After being
absorbed, a compound has to pass through the liver, where it might be metabo-
lized, it might be transformed into active, inactive or even toxic metabolites, or it
might be excreted via the bile. Having passed through the liver, the compound is
part of systemic circulation. As such, it has to be stable against plasma components,
e.g. certain enzymes. It has to be distributed within the body and must penetrate
the respective target tissue. For that purpose, it is likely that the compound again
has to cross one or even several lipid membranes. Simultaneously, the compound
is subject to continued hepatic and renal clearance.
From this brief description, it is obvious that a drug is more than just a phar-
macophore. It must possess properties that allow a sucient proportion of the ad-
ministered amount of drug molecules to reach their site of action in order to trig-
ger the desired pharmacological eect. In recent literature, these properties are re-
ferred to as ADME/PK properties, where ADME stands for absorption, distribu-
tion, metabolism, and excretion and PK stands for pharmacokinetics.
Once the importance of ADME/PK properties has been recognized, it is desir-
able to incorporate ADME/PK considerations early into the hit- or lead-nding
process because the likelihood of successful optimization is higher and the time it
would take to nd a suitable drug candidate is shortened when the starting point
already possesses some quality features [10]. Especially in library design, it would
be advantageous to lter virtual libraries in order to select a sublibrary containing
discrete members with some minimum likelihood of being orally bioavailable and
to synthesize and screen just the subset [3]. For that purpose, tools are needed
which allow an estimation of the ADME/PK properties from the chemical struc-
ture [11]. The physicochemical properties of a compound that underlie ADME/PK
behavior and how these can be predicted are discussed below. A review that sum-
marizes the current status of the entire eld of ADME/PK optimization was pub-
lished recently [12].
26.3
Estimation of ADME/PK from Physicochemical Parameters
As stated above, ADME/PK properties have to be incorporated into library design

in order to increase the likelihood of successful optimization. PK parameters,
which in that respect are crucial for good in vivo ecacy, are the systemic exposure
of the compound (dependent on absorption, distribution, metabolism, and excre-
tion), its bioavailability (dependent on absorption and metabolism), and its elimi-
nation, i.e. its half-life in the body (dependent on metabolism, distribution, and
excretion). All these parameters are well dened in pharmacokinetic textbooks
[13], but are only determined through expensive animal studies. Owing to the tre-
mendous eorts required, animal data for absorption, distribution, metabolism,
and excretion are measured for only a small number of the synthesized com-
pounds during optimization, resulting in little information in terms of the struc-
tural space of the investigated compounds. First, in vitro PK measurements must be
determined, assessing the absorption ability of compounds by measuring their
permeation through tissue or cell layers or by assessing the metabolic stability via
measurements with hepatocytes or microsomes. In addition, for permeation
studies, new approaches have appeared very recently which focus on the use of
articial membrane layers consisting of either an organic liquid (hexadecane)
or mixtures of such liquids with phospholipids [14, 15]. Although all the above-
mentioned in vitro assays can be performed with relatively high throughput, quan-
titative structureactivity relationship (QSAR) models for these in vitro parameters
over an appropriate structural space are rare in the scientic literature.
Therefore, models are needed that describe the majority of ADME/PK properties
in terms of simple, easily accessible parameters, which can be measured and cal-
culated from the structure. For library design, these calculations have to be fast
enough to calculate the property space even for very large virtual libraries.
Most of the ADME/PK properties at least those which are driven by passive
processes can be explained by appropriate physiological and physicochemical
models having physicochemical parameters as their input. Some ADME/PK pa-
rameters are partly or exclusively dependent on active processes with partially un-
clear or insucient scientic background and, therefore, are not covered in this
chapter. Physiological and physicochemical models have the advantage that they
can be generalized much more easily than QSAR models and are less dependent
on the molecular space of the compounds they are derived from.
The aim of this chapter is to describe briey some of the models that explore the
physicochemical parameter space in which drug-like molecules are found.
26.3.1
Models for Permeation Through Membranes (Absorption)
Biological membranes are built up either by complex cell layers as they are found
in the gut wall, the skin, and the endothelia cell layers dividing organs from the
blood cycle (e.g. bloodbrain barrier), or by lipids and proteins dividing the cell
plasma from its environment. Overviews of in vitro models for measuring perme-
ation through such membranes either in vitro or in vivo are given in the literature
[1619].
The physicochemical model used most frequently today is one where the per-
meation of compounds through membranes is described as follows [20, 21]. The
model consists of a layer of thickness X with area A (the membrane) dividing
aqueous compartments from each other. Adjacent to both sides of this layer, un-
stirred water layers (thickness Y,Y 0 ) are located. The transport of a compound
through such a model layer is then described by two phenomena:
. diusion inside the water layers and inside the membrane, and
. distribution into and out of the membrane.
The permeation constant Pe for this process depends on the diusion coe-
cient (Df ) of the compound in the water layer (Dfa ) and in the membrane (Dfm ) as
well as on the distribution coecient of the compounds to the membrane Km . The
mathematics have been well described in the literature and are beyond the scope
of this chapter [21].
For the chemist, real biological barriers have the disadvantage that they are not
well dened with respect to such a model. The necessary parameters for exam-
ple thickness of the individual layers, or area of the membrane are unknown or
can only be roughly estimated. A practical approach toward this problem is the t
of Eq. (1) to permeation coecients from in vivo or in vitro measurements [20].
Dfa; m Km
Pe A cm s1 1
Dfa BDf m Km
Such an approach averages the above-mentioned thickness constants X,Y,Y 0 and

area A into the t constants A and B. Consequently, these t parameters are then
dierent for every permeated membrane (e.g. parameters for gut wall permeation
dier from those for bloodbrain barrier permeation).
Next, one only has to dene descriptors, which characterize the phenomena of
diusion and distribution. It is well known from physicochemical textbooks that
diusion coecients depend on the molecular volume MV [or the molecular
weight (MW)] of a compound. The distribution of a compound to the membrane
can be estimated by distribution coecient DpH between aqueous buer and lipid
phases such as octanol, oil, or lipid model membranes at the appropriate pH. In-
serting these physicochemical descriptors into Eq. (1) leads to Eq. (2). a and b are
also t constants and describe the dependence of the diusion coecients Dfa and
Dfm on the molecular volume MV. These parameters, especially b, vary from mem-
brane to membrane; a should be around 0.707, which is the known dependence of
Dfa on molecular volume.
MVab DpH
Pe A cm s1 2
MVa B MVb DpH
The parameters MV, which can be substituted by MW, and DpH can be calcu-
lated from structure (see Section 26.3) and are therefore key parameters in library
design for assessing the permeation of compounds through biological barriers.
Examples of the use of such a model for gut wall permeation (absorption) [20], in-
testinal cell layer [22], bloodbrain barrier [23], and skin [24] are given in the lit-
erature.
In addition to absorption, a term characterizing paracellular (pore) transport for
very small compounds (MW < 250 g mol1 ) has to be included (Eq. 3).
MVab DpH MVg

Pe A C g cm s1 3
a b
MV B MV DpH D MVg
As a proof, Eq. (3), Fig. 26.1 shows a comparison of 133 compounds with mea-
sured fraction dose absorbed in humans [2529], and predictions have been made
by tting Eq. (3) to these data. As input, only measured lipophilicity (membrane
anity, see Section 26.4.1) and MW were used. The fraction dose absorbed is cal-
culated from Pe (using Eq. (9) in [30]) for compounds exhibiting complete solu-
bility while being absorbed.
The t parameters of Eq. (3) used for Fig. 26.1 are:
A B C D a b g
3940 1:1 10 7 2:5 107 202 0.6 4.25 16
Some authors go beyond such a model and further divide the distribution coef-
cient into volume-dependent and polarity terms, which in most cases are related
Fig. 26.1. Comparison of the percentage fraction doses

absorbed in humans (from dierent literature sources) with
those calculated from Eq. (3). The denoted outliers are known
to be actively transported via the gut wall. (FA fraction
absorbed)
to the hydrogen-bonding capacity of the compound. In these cases, the result is a

correlation between permeation and a combination of size and hydrogen-bonding
descriptors [3038]. Furthermore, correlation equations exist which use more
solute-specic descriptors than just hydrogen-bonding capacity [3941]. Although
it is very unlikely that one parameter is sucient for describing a complex matter
like absorption [42], some literature data are available in which a correlation be-
tween one parameter and absorption is described [25, 43]. In our opinion, this
large number of dierent descriptors is not necessary because methods exist to
correlate experimental distribution coecients with structural elements, especially
when these measured distribution coecients are available for lipid-like phases
other than octanol (see Section 26.3).
The absorption of compounds from the gut into the circulation can also be re-
stricted by the solubility of the compound. Because only the soluble part of the
dose administered orally can be absorbed, the compounds need to have a su-
ciently high solubility compared with this dose. The total dose administered has to
dissolve during transit through the parts of the gut where absorption takes place.
An oral drug transport and absorption model has been described in the literature
[44].
Solubility itself is dicult to calculate directly from structure because the crystal
and dissolution properties of a real compound depend also on the presence of
varying amounts of impurities which cannot be modeled well with simple and fast
calculation algorithms (see Section 26.3). Moreover, high-quality datasets with
measured solubility over a wide range of chemical space are not yet available. Last,
but not least, the solubility in the intestinal environment is dicult to dene, be-
cause compounds are administered in tablets with dierent vehicles. Even when
solutions are administered, it is not possible to know whether the compounds stay
in solution or whether they precipitate; if they do precipitate, it is not possible to
know to what extent this takes place (e.g. in the stomach) nor to know which crys-
tal form or the crystal diameter. Therefore, until now, in most cases it has only
been appropriate to apply solubility in a qualitative way.
Nevertheless, it is a very important parameter, and it is common sense that a
compound with low solubility will have absorption problems especially when
higher doses are needed. The limit of when the solubility is suciently high de-
pends strongly on the vehicle used, the animal species, the dose, the volume ad-
ministered with the compound, and the permeability of the gut wall.
26.3.2
Models for Distribution in the Body
A prerequisite for the action of a drug in vivo is that it must not only enter the
systemic circulation, because the site of action is only rarely found in the blood it-
self, but the drug must also be distributed into the target organs. A drugs concen-
tration at its target is important for the strength of the pharmacological response.
Depending on the mode of action, this requirement can be a mean tissue concen-
tration or an unbound concentration, which is the concentration of free drug that
is not bound to lipids or proteins. The last case is of interest if, for example, the
binding site for the drug is available directly from the aqueous phase of the tissue
(cytoplasm or interstitial uid). While the unbound concentration can in the rst
instance for all organs be regarded as being equal to the free concentration in
plasma (which is precisely true for steady-state conditions), the mean concentra-
tion is dependent on the composition of the organs. For an estimation of the con-
centration at the site of action, the steady-state distribution coecient between tis-
sue and plasma K tp C tissue =Cplasma is often very helpful.
As is evident from this discussion, no general rule can be drawn for optimum
distribution behavior. This fact is also true for binding to lipids and proteins. The
optimum properties depend very much on the purpose for which a particular
active compound shall be optimized. A very simple and obvious example is that of
a membrane-bound protein with a lipophilic binding site. It is desirable to design
compounds with a certain degree of lipophilicity in order to achieve high concen-
trations at the binding site. In contrast, for cytosolic proteins (in solution in the
cytoplasm) the opposite is true. In this case, a lower lipophilicity leads to a higher
unbound concentration, which is then available at the target. As a result, the dis-
cussion in this section is more important if a library is to be designed for optimiz-
ing a lead structure for a known target and is less important for random libraries.
Nevertheless, it is very desirable to estimate the unbound fraction in plasma
( fup ), which determines the free concentration (Cfree plasma fup Cplasma ), and the
distribution coecients as early as possible. Both fup and the K tp can be deter-
mined experimentally. The rst by separating the protein fraction of plasma sam-
ples and determining the concentration in the water phase, and the latter from
in vivo animal experiments or in vitro, e.g. by microdialysis of the substance
from plasma into homogenized tissue. However, these experiments are rather
time-consuming because in all cases quantitative analyses of concentrations in
complex biological matrices have to be carried out. Thus, they cannot be carried
through for large numbers of compounds in the early stages of research. This
problem is especially true for animal studies. Methods of estimating this distribu-
tion behavior from other properties or even from the chemical structure directly
are therefore very desirable.
The tissue/plasma distribution coecients are determined by the anity of a
drug to the dierent constituents of the tissues and the blood. In some cases, spe-
cic binding to biological macromolecules may play a signicant role. However,
generally, distribution between lipids and water as well as unspecic adsorption
to proteins are the main factors determining K tp . It is generally accepted that
these eects are related to other distribution coecients that describe a drugs
lipophilicity, therefore it may be considered that K tp can be correlated with such
lipophilicity descriptors. Several attempts to estimate the tissueplasma distribu-
tion coecients depend on this relationship and can be found in the literature (see
below).
The simplest approach is to nd a correlation function between K tp and, for ex-
ample, the octanolwater distribution coecient using tting [4547]. The core of
the correlation functions is a potential function in both cases. Because this
approach alone is not sucient to describe the correlation correctly, additional pa-
rameters have to be incorporated. These are the fraction of nonionized compound
[45] or some information about the tissue composition, either in the form of water
content and a so-called binding capacity factor [46], or as water and lipid content
[47]. Several other approaches take the composition of the organ tissues as the
starting point for the calculation of K tp . In most cases, only the fractions of water
and dierent lipids (neutral and phospholipids) are taken into consideration [48
53]. The binding to proteins in the organs and plasma is explicitly taken into ac-
count only in [54], whereas in [51, 52] protein binding is incorporated only in the
form of a free fraction in plasma. Generally, the calculation of K tp relies on linear
functions in which the dierent fractions of the tissue components are multiplied
by a parameter describing the distribution between the respective component and
water. The general form is shown in Eq. (4),
K tissue=plasma C tissue =C plasma K tissue=water =K plasma=water 4

Fig. 26.2. Comparison of calculated skinblood distribution

coecients according to Eq. (4) and Eq. (5) with measured
data from [51]. As input parameters for the equations, the
membrane anity (see Section 26.4.1) and the binding to
human serum albumin (see Section 26.4.3) were used.
with
K tissue=water f lipid K lipid=water f protein K prot=water f water 5
Correspondingly, K plasma=water 1=fup can be calculated using the binding con-

stant for human serum albumin (HSA) as K protein=water . The distribution coe-
cients K lipid=water and K protein=water can be determined explicitly. Support for this
statement is given in Fig. 26.2, in which the correlation between calculated
(according to Eq. (4) and Eq. (5)) and experimental values for skin is shown.
For less exact estimations, one can alternatively assume that these distribution
coecients are equal to, or can be replaced by, other parameters that describe lip-
ophilicity, e.g. by Collander-type potential functions specifying empirical correla-
tions between octanolwater distribution coecients and the respective organ dis-
tribution coecients. In some of the cases mentioned here, the tissue to blood or
plasma distribution coecients are not calculated directly. Instead, the methods
are used to estimate tissueair and bloodair distribution coecients of volatile

compounds. However, these parameters can be easily converted into K tp .
In principle, K lipid=water and K protein=water can be estimated directly from the
structure (see Section 26.4), but until now no published method has been available
for that purpose. However, this problem can be circumvented because acceptable
estimations of tissueplasma distribution coecients are also possible using only
one descriptor for the lipophilicity of a compound. Such descriptors can, on the
other hand, be calculated from chemical structure, and therefore it is also possible
to estimate the K tp values from structure directly; hence, the assessment of virtual
libraries in terms of the distribution behavior of their members is possible. Inter-
estingly, only a few cases of direct quantitative structureproperty relationships for
tissueplasma distribution can be found. One of these estimated adipose tissue
plasma distribution coecients for PCBs [55].
A more general approach has been applied to the brainblood distribution coef-
cient [56, 57]. Here, the distribution coecient is linearly associated with ve pa-
rameters that describe the interaction of the molecules with organic phases and
water. Some of these descriptors have to be determined experimentally from other
distribution coecients, but they can also be estimated directly from structure
[58].
Although estimated equilibrium distribution coecients between tissue and
plasma give valuable information about the expected behavior of a compound in
the body, they have limited use because the relation between dose and concentra-
tion in plasma and, moreover, the time-course of the compounds plasma concen-
tration, are not known. It would also be very useful to have methods to estimate
these properties at an early stage for a large number of compounds. Indeed,
knowledge of the K tp values together with estimates of oral absorption and meta-
bolic clearance would enable pharmacokinetic proles to be calculated. The key to
this approach is physiology-based pharmacokinetic modeling (PBPK) [59]. This
simulation method allows the calculation of concentration versus time curves for
the dierent compartments or organs of the body on the basis of physiological
data (e.g. organ volumes and blood ows) and the substance-specic parameters
mentioned above [46, 48, 51, 60]. As all of these parameters can be determined in
vitro or can even be estimated directly from chemical structure, it is possible to
evaluate the suitability of the compounds or compound classes for dierent appli-
cations in terms of their availability at the target site at a very early stage.
26.3.3
Models for Clearance and Metabolism
Clearance is dened as the irreversible removal of a drug substance from the body,
the rate constant that correlates the elimination rate of a drug with its plasma
concentration. In principle, a compound can be eliminated in two dierent ways:
excreted unchanged in its original chemical form, or modied chemically, i.e. me-
tabolized, with the metabolite(s) still being part of the systemic circulation. The
main metabolizing organ in the human body is the liver, but it should be noted
that metabolism also takes place in other parts of the body, such as the gut wall
[61, 62]. Hepatic metabolism is characterized by so-called phase I and phase II
transformations. Oxidation, reduction, and hydrolyses are all phase I reactions that
are employed by the liver to introduce functional groups into (mostly) lipophilic
drug molecules. These reactions are catalyzed by various enzyme families. Among
the oxygenases the cytochrome P450-dependent monooxygenases are the most
important ones [63]. Phase II reactions are conjugation reactions. Drug molecules
or their phase I metabolites are coupled with endogenous, highly hydrophilic mole-
cules such as glucuronic acid or sulfate anion in order to enhance their solubility
in water. As a result, urinary excretion is accelerated. Thus, it is not surprising that
lipophilicity is a useful physicochemical parameter for the estimation of renal
clearance. Renal clearance happens by ltration of blood serum at the glomerulus
into the kidney tubules from which reabsorption of most of the water content and
solutes occurs. If the logarithm of the distribution coecient log D at pH 7.4 (i.e.
log D7:4 ) between octanol and aqueous buer of a drug molecule (or its metabolite)
is <0, reabsorption is almost completely prevented and the molecule will be ex-
creted in the urine. However, if the molecule is strongly bound to plasma proteins,
it will escape rapid urinary excretion even if its lipophilicity is low. This feature
occurs because only the unbound fraction of a drug molecule in the plasma is l-
tered into the kidney tubules. Most drug molecules, however, are rather lipophilic,
rendering them subject to metabolic (hepatic) clearance. Thus, predicting the
metabolic stability of a molecule could be of great value in compound design.
Of all the physicochemical parameters, lipophilicity was linked rst to metabo-
lism by generating QSAR models for cytochrome P450 data [64, 65]. Unfortu-
nately, these and other examples of correlating physicochemical parameters with
metabolic stability [66, 67] do not seem to be widely applicable [67]. They work
quite well within a series of highly analogous compounds, but lose almost any
predictive power when dierent chemical entities are considered [11]. This dichot-
omy might reect the complex nature of these multienzyme-catalyzed biotrans-
formations.
Further approaches have been taken to predict metabolism, including three-
dimensional QSAR, pharmacophoric, and protein-modeling and articial neural
networks [6871]. All of these dierent approaches share a rather limited reliabil-
ity when they are used to predict the clearance of molecules that are not very sim-
ilar to the training set from which the models were derived. But, as metabolic
databases become larger, combinations of the above methods and perhaps also
new tools will arise and make in silico metabolism screening a part of an integrated
approach toward lead structure identication and optimization.
26.4
Estimation of Physicochemical Parameters
The estimation of physicochemical parameters has a long tradition [72]. The esti-
mation methods range from those using physicochemical theory, for example the
theory of ideal solutions, to those using molecular structural elements and corre-
lation equations with experimentally available parameters, e.g. log P.
The aim of this chapter is not the detailed description of how to measure and
predict the relevant physicochemical parameters. As such, the reader is referred to
handbooks and overviews [56, 73]. Instead, this chapter gives an overview of cur-
rently available tools for the estimation of these parameters from the structure of
compounds. These methods have to be fast and valid in order to help the combi-
natorial chemist prole even very large libraries.
26.4.1
Lipophilicity
Descriptors of lipophilicity are all distribution coecients between a buer (at dif-
ferent pH values) and a lipid-like phase, such as octanol, reversed phase (RP) high-
performance liquid chromatography (HPLC) column stationary phase, lipid mem-
branes, and so forth, as stated in Section 26.3. The most prominent member of
this distribution coecient family is the coecient between octanol and water. For
the neutral form of the desired molecule, this coecient is called the partition coef-
cient (K ow ). More commonly, its log P value is used. Also available are logarithms
for the distribution between octanol and buer at various pH values, log DpH (dis-
tribution coecient), or log K, which is the logarithm of the capacity factor from RP-
HPLC measurements. Some recently developed methods are distribution coe-
cients that have stationary phases on RP-HPLC columns built up by covalently
bound single lipid molecules log IAM (immobilized articial membranes) [74] or
those using liposomes [75], or complete lipid bilayers immobilized on silica beads
log MA (membrane anity) [76]. Only for log P and log D do commercially avail-
able calculation methods exist.
In general, one can divide the prediction methods for log P (log D) into three
groups:
1 Atom contribution methods (A log P) [ 77]. With this approach, methods are gath-
ered that fragment a molecule into its heavy atoms. Once the contribution of an
atom fragment (dened before analysis) to the molecules log P value is eval-
uated by a correlation analysis with measured log P values, the log P of a new
structure is calculated by summing up the contribution of all atoms. In some
cases, the contributions are somehow weighted when an atom is an exposed pe-
ripheral one compared with more shielded interior atoms.
2 Molecular property methods (B log P) [ 77]. These methods use structural features,
such as number of nitrogen and oxygen atoms or ring structures available, or
semiempirical molecular descriptors derived from quantum chemical calcu-
lations or solvatochromic parameters, for example hydrogen-bonding acceptor/
donor ability, and correlate these to known log P values of experimental datasets
of varying size.
3 Fragmental contribution methods (C log P) [ 77]. These methods are the most es-
tablished in the literature and are based on the contribution of molecular frag-
ments (substituents). Additional constants or correlation factors may be em-

ployed depending on the interconnectivity of the fragments.
All of these methods have their own advantages and disadvantages, e.g. the
fragmental approaches give higher correlation coecients than the atomic contri-
bution methods but sometimes in the fragmental approaches a parameterization
is not possible because a fragment is missing from the training set. A benchmark
can be found in the literature [77].
It is our belief that a method using computer-automated structure evaluation
[78], which is now commercially available [79], is a special case. This method en-
codes the structural fragments into binary bitstrings, known as ngerprints. Two
ways of ngerprinting have been described:
1 a structural key approach with predened functional groups, and

2 an approach of hashing of unique structural paths.
The latter has the advantage that the ngerprints generated are characterized by
the nature of the chemical structures in the experimental dataset. Various con-
ditions can be selected to determine the uniqueness of a fragment. The fragment
length can be predened or can be kept exible in a length region, for example
between 1 and 5 atom units, and the program itself nds the most relevant frag-
ments by a multilinear regression analysis with measured properties. Alternatively,
neuronal networks can be trained with these ngerprints as input patterns. These
methods are very useful if a large dataset of measured properties, such as log P,
log K, log D, and log MA values, is available. The advantage is that for distribution
coecients such as log K and log MA, where neither commercial programs nor
public databases are available, a calculation prior to synthesis is possible even for
very large libraries.
26.4.2
Solubility Including pKa Eects
As discussed earlier, the solubility of a drug may play a crucial role in the process
of absorption from the gut. Although the solvent medium in the gut is not pure
water, aqueous solubility (Sa ) is usually taken as the surrogate parameter. Several
methods of calculating water solubility from chemical structure have been de-
scribed in the literature (see below). However, their accuracy is signicantly lower
than that of distribution coecients, particularly if they are applied to very chemi-
cally diverse compounds. The reason for this fault is that, at least for substances
which form solid crystals under normal conditions, the solubility is mainly deter-
mined by two energy contributions. One of them describes the energy required to
place the solute molecules in the solvent and is given mainly by the chemical po-
tential. This part is very much related to distribution coecients, such as log P,
and can be estimated from the two-dimensional chemical structure suciently ac-
curately. The second energy contribution arises from the need for the molecules to
leave the energetically favorable crystal structure. This energy relies very much on
the interactions of the drug molecules with each other and on their ability to be
densely packed, and is therefore strongly dependent on the three-dimensional
structure of the molecules. This feature is the principal reason why the accuracy of
prediction on the basis of two-dimensional structures is limited.
A broad survey of the dierent prediction methods is given in [80], including
examples of applications. A review of various methods with a critical discussion of
their quality can be found in [81]. Below, we give a short overview of the dierent
approaches. Basically, three classes of methods can be distinguished: fragment-
based methods, quantitative correlations with log P or with molecular descriptors,
and the universal quasi-chemical functional group activity coecient (UNIFAC)
method.
The fragment-based methods [82, 83] rely on the assumption that Sa is an addi-
tive property which can be calculated by summing up the contributions of the dif-
ferent chemical groups of a molecule. These methods have the advantage of being
easily applicable. However, their applicability is restricted to structures for which
all groups contained within the structure are parameterized in terms of their con-
tribution to solubility.
Because methods for calculating log P are commonly available (see Section
26.4.1), using a log Sa /log P correlation is a very convenient method to estimate
Sa . A quite simple physicochemical consideration [80] leads to the result that, for
nonionic liquid solutes, a relationship of the form
log Sa a b log P 6
should exist. This relation is a quantication of the qualitative rule that water is a
good solvent for polar and a poor solvent for nonpolar, lipophilic solutes. Depend-
ing on the dataset, the parameters a and b have values of 0.251.5 and 0.951.2
respectively [81]. In its simplest form, the correlation gives good estimations only
for liquid compounds and can therefore generally only be used to make rough es-
timations. For compounds that are solid, a term regarding the energy required to
remove a molecule from the crystal has to be included, which can be accomplished
by considering the melting temperature of the crystal [84, 85]. However, because
the value of this property is generally not known for virtual structures and sub-
stances produced by combinatorial chemistry, these approaches cannot be helpful
for the evaluation of combinatorial libraries and are therefore not discussed in
greater detail here.
Several relationships between solubility and molecular connectivity have been
described [8689]. The advantage of these methods is that their application is quite
simple because the connectivity indices needed can easily be calculated from the
structure. On the other hand, their applicability is somewhat restricted because the
single relationships are in each case restricted to one single or only a few classes of
chemical structures.
The diverse approaches relying on the UNIFAC method [90] represent

mixed methods which are partly fragment based and partly quantitative property-
solubility relationships. They rely on the assumption that solubility is determined
by the so-called activity coecient, which describes the interaction between solute
and solvent. This activity index consists of a term which describes the work needed
to form a cavity within the water that is able to take up the solute molecule and a
second term which describes the interactions between the solute molecule and
water. The rst term is connected with molecular size and surface area and can
be calculated directly from the structure. The second term can be estimated
using a fragment contribution method [81]. Again, when taking into account
only the activity index, the properties of the crystal to be dissolved are not consid-
ered. A possible way to overcome this, problem again, is to take into account the
melting temperature, which is not usually practical in combinatorial chemistry.
However, recently a related method unied physical property estimation rela-
tionship (UPPER) has been published [91] which combines symmetry and exi-
bility properties of the structures with the activity indices. These additional pa-
rameters are related to the entropy of fusion and at least partly incorporate the
contribution of crystal energy.
As mentioned above, water solubility is only a surrogate for the solubility which
actually determines the absorption from the gut, not only because the gut contents
deviate in their composition from pure water, but also because the pH value within
the GI tract varies over a wide range. In the stomach, a very acidic medium with
pH values around 2 is present in the fasting state, rising to pH 56 after eating. At
the beginning of the small intestine, the pH value jumps to about 5, and then in-
creases constantly with increasing distance from the stomach to a value of around
7.5. Consequently, at least for compounds with basic or acidic groups, during the
passage through the GI tract the ionization state and thus the solution properties
may change with time if their pKa values are close to the pH values in the GI tract.
The reason for this eect is that the ionized form is usually much more soluble
than the neutral form, which means that for acids solubility may increase while for
bases it decreases during the passage through the GI tract. Bearing in mind that
most of all currently marketed drugs are ionizable compounds, this eect is far
from negligible. With regard to the estimation of solubility, the situation is even
more complicated owing to the fact that the majority of the methods used for such
estimations (see above) are explicitly valid only for nonelectrolytes, which limits
their value signicantly.
The change in solubility can be roughly estimated from the change in log P ac-
cording to the relationship between those properties, as discussed above. For a
good estimation of this eect, the knowledge of the pK a value of the compound is
necessary. Unfortunately, no reliable method for the prediction of pK a values is
known.
In conclusion, it can be stated that solubility is an important parameter and
should be taken into account in library design. However, at present, the possibil-
ities of making useful predictions of this property on the basis of chemical struc-
ture are limited.
26.4.3
Plasma Protein Binding
As stated in Section 26.3.2, plasma protein binding is one of the key factors de-
termining the distribution of a compound within the body. This parameter can be
measured using plasma itself or by using single plasma proteins such as albumin
or acidic a1 -glycoprotein to estimate plasma binding. The latter has the advantage
that the measurements can be carried out in a relatively straightforward way and
with a high throughput [92]. If a dataset of sucient size and enough chemical
space is available, this parameter can also be predicted from the structure, using
the same methods as those described in Section 26.4.1.
References
1 J. A. DiMasi, Clin. Pharmacol. Ther. Applications, Lippincott Williams &

1995, 58, 114. Wilkins, Philadelphia 1995.
2 T. Kennedy, Drug Disc. Today 1997, 2, 14 M. Kansy, F. Senner, K.
436444. Gubernator, J. Med. Chem. 1998, 41,
3 S. D. Pickett, J. M. McLay, D. E. 10071010.
Clark, J. Chem. Inf. Comput. Sci. 15 F. Wohnsland, B. Faller, J. Med.
2000, 40, 263272. Chem. 2001, 44, 923930.
4 R. A. Fecik, K. E. Frank, E. J. 16 A. Braun, S. Hammerle, K. Suda, B.
Gentry, S. R. Menon, L. A. Rothen-Rutishauser, M. Gunthert,
Mitscher, H. Telikepalli, Med. Res. S. D. Kramer, H. Wunderli-
Rev. 1998, 18, 149185. Allenspach, Eur. J. Pharm. Sci. 2000,
5 Ajay, W. P. Walters, M. A. Murcko, 11, Suppl. 2, S51S60.
J. Med. Chem. 1998, 41, 33143324. 17 A. Pagliara, M. Reist, S. Geinoz, P.
6 J. Sadowski, H. Kubinyi, J. Med. A. Carrupt, B. Testa, J. Pharm.
Chem. 1998, 41, 33253329. Pharmacol. 1999, 51, 13391357.
7 V. J. Gillet, P. Willett, J. Bradshaw, 18 L. Barthe, J. Woodley, G. Houin,
J. Chem. Inf. Comput. Sci. 1998, 38, Fundam. Clin. Pharmacol. 1999, 13,
165179. 154168.
8 C. A. Lipinski, F. Lombardo, B. W. 19 H. Lennernas, J. Pharm. Sci. 1998,
Dominy, P. J. Feeney, Adv. Drug 87, 403410.
Delivery Rev. 1997, 23, 325. 20 D. E. Leahy, J. Lynch, D. C. Taylor
9 M. Wagener, V. J. Van Geerestein, in: Novel Drug Delivery. Prexcott, L.
J. Chem. Inf. Comput. Sci. 2000, 40, F., Nimmo, W. S. (eds), Wiley & Sons,
280292. England 1989.
10 G. W. Caldwell, Curr. Opin. Drug 21 G. Camenisch, G. Folkers, H. v. d.
Discovery Dev. 2000, 3, 3041. Waterbeemd, Eur. J. Pharm. Sci. 1998,
11 S. Ekins, C. L. Waller, P. W. Swaan, 6, 321329.
G. Cruciani, S. A. Wrighton, J. H. 22 G. Camenisch, J. Alsenz, H. v. d.
Wikel, J. Pharm. Toxicol. Methods Waterbeemd, G. Folkers, Eur. J.
2000, 44, 251272. Pharm. Sci. 1998, 6, 313319.
12 H. v. d. Waterbeemd, D. A. Smith, K. 23 R. Kaliszan, M. Markuszewski, Int.
Beaumont, D. K. Walker, J. Med. J. Pharm. 1996, 145, 916.
Chem. 2001, 44, 13131333. 24 L. A. Kirchner, R. P. Moody, E.
13 M. Rowland, T. N. Tozer, Clinical Doyle, R. Bose, J. Jeffery, I. Chu,
Pharmacokinetics: Concepts and ALTA 1997, 25, 359370.
References 759
25 K. Palm, P. Stenberg, P. Luthman, 44 L. X. Yu, E. Lipka, J. R. Crison, G. L.

P. Artursson, Pharm Res. 1997, 14, Amidon, Adv. Drug Delivery Rev. 1996,
568571. 19, 359376.
26 M. D. Wessel, P. C. Jurs, J. W. 45 K. Yokogawa, E. Nakashima, J.
Tolan, S. M. Muskal, J. Chem. Inf. Ishizaki, H. Maeda, T. Nagano, F.
Comput. Sci. 1998, 38, 726735. Ichimura, Pharm Res 1990, 7, 691
27 M. Kansy, F. Senner, K. Gubernator, 696.
J. Med. Chem. 1998, 41, 10071010. 46 I. Nestorov, L. Aarons, M. Rowland,
28 K. Balon, B. U. Riebesehl, B. W. J. Pharmacokinetics Biopharmaceutics
Muller, Pharm. Res. 1999, 16, 882 1998, 28, 521545.
888. 47 J. DeJongh, H. J. M. Verhaar, J. L.
29 J. Bircher, W. Sommer, Klinisch- M. Hermens, Arch. Toxicol. 1997, 72,
pharmakologische Datensammlung, 1725.
WVG, Stuttgart, 1999. 48 M. Pelekis, P. Poulin, K. Krishnan,
30 N. El Tayar, R.-S. Tsai, B. Testa, Toxicol Ind. Health 1995, 11, 511522.
P.-A. Carrupt, C. Hansch, A. Leo, 49 P. Poulin, K. Krishnan, Toxicol.
J. Pharm. Sci. 1991, 80, 744749. Appl. Pharmacol. 1996, 136, 126130.
31 H. v. d. Waterbeemd, M. Kansy, 50 P. Poulin, K. Krishnan, Toxicol.
Chimica 1992, 46, 299303. Methods 1996, 6, 117137.
32 H. v. d. Waterbeemd, G. Camenisch, 51 P. Poulin, F.-P. Theil, J. Pharm. Sci.
G. Folkers, O. A. Raevsky, Quant. 2000, 89, 1635.
Struct.-Act. Relat. 1996, 15, 480490. 52 P. Poulin, K. Schoenlein, F.-P.
33 O. A. Raevsky, K.-J. Schaper, Eur. J. Theil, J. Pharm. Sci. 2001, 90, 436
Med. Chem. 1998, 33, 799807. 447.
34 M. Sugawara, Y. Takekuma, H. 53 S. Balaz, V. Lukcova, Quant. Struct.-
Yamada, M. Kobayashi, K. Iseki, K. Act. Relat. 1999, 18, 361368.
Miyazaki, J. Pharm. Sci. 1998, 87, 54 D. W. Connel, R. D. Braddock, S. V.
960966. Mani, Sci. Total Environ. 1993, 1338
35 J. M. Luco, J. Chem. Inf. Comput. Sci. 1396.
1999, 39, 396404. 55 F. M. Parham, M. C. Kohn, H. B.
36 H. v. d. Waterbeemd, G. Camenisch, Matthews, C. DeRosa, C. J. Portier,
G. Folkers, J. R. Chretien, O. A. Toxocol. Appl Pharmacol 1997, 144,
Raevsky, J. Drug Targeting 1998, 6, 340347.
151165. 56 M. H. Abraham, H. S. Chahda, R. C.
37 F. Yoshida, G. Topliss, J. Med. Chem. Mitchell, J. Pharm. Sci. 1994, 83,
2000, 43, 25752585. 12571268.
38 W. J. Egan, K. M. Merz Jr, J. J. 57 M. H. Abraham, K. Takacs-Novak, R.
Baldwin, J. Med. Chem. 2000, 43, C. Mitchell, J. Pharm. Sci. 1997, 86,
38673877. 310315.
39 K. Sugano, S. Yoshida, M. Takaku, 58 J. A. Platts, M. H. Abraham, D.
M. Haramura, R. Saitoh, Y. Butina, A. Hersey, J. Chem. Inf.
Nabuchi, H. Ushio, Bioorg. Med. Comp. Sci. 2000, 40, 7180.
Chem. Lett. 2000, 10, 19391942. 59 S. B. Charnik, R. Kawai, J. R.
40 M. H. Abraham, H. S. Chadha in: Nedelman, M. Lemaire, W.
Lipophilicity in Drug Action and Niederberger, H. Sato, J.
Toxicology. Pliska, V., Testa, B., Pharmacokin. Biopharm. 1995, 23,
Waterbeemd, H. v. d. (eds), VCH, 213225.
Weinheim 1996, pp. 311337. 60 B. van Ommen, J. de Jongh, J. van
41 P. Ertl, B. Rohde, P. Selzer, J. Med. de Sand, B. Blaauboer, E. Hissink,
Chem. 2000, 43, 37143717. J. Boogards, P. van Blaaderen,
42 S. D. Kramer, Pharm. Sci. Technol. Toxic. In Vitro 1995, 9, 537542.
Today 1999, 2, 373380, 744749. 61 V. J. Wacher, J. A. Silverman, Y.
43 D. E. Clark, J. Pharm Sci. 1999, 88, Zhang, L. Z. Benet, J. Pharm. Sci.
807821. 1998, 87, 13221330.
62 H. Suzuki, Y. Sugiyama, Eur. J. Folkers, G., Guy, R. (eds), Wiley-

Pharm. Sci. 2000, 12, 312. VCH-VHCA, Basel 2001.
63 D. F. Lewis, Cytochromes P450: 76 A. Loidl-Stahlhofen, T. Hartmann,
Structure, Function and Mechanism, M. Schottner, C. Rohring, H.
Taylor & Francis, London 1996. Brodowsky, J. Schmitt, J.
64 C. Hansch, Drug Metab. Rev. 1972, 1, Keldenich, Pharma. Res. submitted.
114. 77 H. v. d. Waterbeemd, R. Mannhold
65 C. Hansch, L. Zhang, Drug Metab. in: Lipophilicity in Drug Action and
Rev. 1993, 25, 148. Toxicology. Pliska, V., Testa, B.,
66 B. Walther, P. Vis, A. Taylor in: Waterbeemd, H. v. d. (eds), VCH,
Lipophilicity in Drug Action and Weinheim 1996.
Toxicology. Pliska, V., Testa, B., 78 G. Klopman, S. Wang, J. Comput.
Waterbeemd, H. v. d. (eds), VCH, Chem. 1991, 12, 10251032.
Weinheim 1996, pp. 253261. 79 HQSAR Software Package, Tripos
67 B. Testa, P. Crivori, M. Reist, P. A. Inc., Saint Louis, USA, 1999.
Carrupt, Perspect. Drug Discovery Des. 80 E. J. Baum, Chemical Property
2000, 19, 179211. Prediction. Lewis Publishers Boca
68 B. Testa, G. Cruciani in: Raton 1998.
Pharmacokinetic Optimization in 81 S. H. Yalkowsky, S. Bannerjee,
Drug Research. Testa, B., Aqueous solubility: Methods of
Waterbeemd, H. v. d., Folkers, G., Estimation for Organic Compounds.
Guy, R. (eds), Wiley-VCH-VHCA, Marcel Dekker, New York 1992.
Basel 2001, pp. 6584. 82 G. Klopman, G. Wang, D. M.
69 S. Ekins, G. Bravi, S. Binkley, J. S. Balthasar, J. Chem. Inf. Comp. Sci.
Gillespie, B. J. Ring, J. H. Wikel, S. 1992, 32, 474482.
A. Wrighton, J. Pharmacol. Exp. 83 R. Kuhne, R.-U. Ebert, F. Kleint, G.
Ther. 1999, 290, 429438. Schmidt, G. Schuurmann,
70 M. J. De Groot, M. J. Ackland, V. A. Chemosphere 1995, 30, 20612077.
Horne, A. A. Alex, B. C. Jones, J. 84 S. H. Yalkowski, S. C. Valvani, D.
Med. Chem. 1999, 52, 15151524. Mackay, Residue Rev. 1983, 85, 43
71 A. M. Ter Laak, N. P. E. Vermeulen 55.
in: Pharmacokinetic Optimization in 85 N. Jain, S. H. Yalkowsky, J. Pharm.
Drug Research. Testa, B., Water- Sci. 2001, 90, 234.
beemd, H. v. d., Folkers, G., Guy, 86 N. N. Nirmalakhandanan, R. E.
R. (eds), Wiley-VCH-VHCA, Basel Speece, Environ. Sci. Technol. 1988, 22,
2001, pp. 551588. 328338.
72 W. J. Lyman, W. F. Reehl, D. H. 87 N. N. Nirmalakhandanan, R. E.
Rosenblatt, Handbook of Chemical Speece, Environ. Sci. Technol. 1988, 22,
Estimation Methods. ACS McGraw-Hill, 610.
Washington 1990. 88 R. E. Speece, Environ. Sci. Technol.
73 V. Pliska, B. Testa, H. v. d. 1990, 24, 929930.
Waterbeemd, Lipophilicity in Drug 89 J. Huuskonen, J. Chem. Inf. Comput.
Action and Toxicology. VCH, Weinheim Sci. 2000, 40, 773777.
1996. 90 A. Fredenslund, R. L. Jones, J. M.
74 K. L. Morse, C. Pidgeon in: Prausnitz, AIChe 1975, 21, 1086
Pharmacokinetic Optimization in 1099.
Drug Research. Testa, B., 91 J. Neera, S. H. Yalkowsky, J. Pharm.
Waterbeemd, H. v. d., Folkers, G., Sci. 1999, 88, 852860.
Guy, R. (eds), Wiley-VCH-VHCA, 92 A. Loid-Stahlhofen, J. Schmitt, J.
Basel 2001. Noller, T. Hartmann, H.
75 S. D. Kramer in: Pharmacokinetic Brodowsky, W. Schmitt, J.
Optimization in Drug Research. Keldenich, Advanced Materials, 2001,
Testa, B., Waterbeemd, H. v. d., 13, 18291834.
761
27
Virtual Compound Libraries and Molecular
Modeling
Roger M. Brunne, Gerhard Hessler, and Ingo Muegge
27.1
Introduction
The introduction and establishment of high-throughput screening (HTS) led to an

increasing need for compounds to screen. Therefore, most pharmaceutical com-
panies actively purchased compounds from various external sources and increased
their own activities using combinatorial chemistry, a potential source of large
numbers of new compounds for screening.
In the early days, combinatorial chemistry was characterized by experimenting
with technology and methodology. The reactions had to be particularly robust and
produce high yields; the selected reactants used in the synthesis of libraries were
only allowed to carry functional groups that were compatible with the desired re-
action or could be protected. In addition, they had to be rather rigid, cheap, and
readily available. The limited selection or availability of reactants compatible with
these restrictions often resulted in large libraries with a rather small number of
dierent functional groups and a small range of physicochemical properties of the
products such as octanolwater partition coecients (log P) or molecular weight
(MW). Large libraries with tens of thousands of compounds were synthesized and
screened. The hit rate of these early, large libraries was very often disappointing. It
became obvious that just increasing the number of structurally similar products
did not usually increase the chance of interaction with biological targets. In addi-
tion, these large libraries often consisted of molecules with nondrug-like phys-
icochemical properties such as high average molecular weight and lipophilicity
[1].
Over the past years, computational methods have been used for the design of li-
braries with structurally diverse and more drug-like compounds as well as focused
libraries that addressed a specic drug target [e.g. 26]. In particular, for focused
libraries, in silico screening of virtual libraries increased the chance of synthesizing
biologically active compounds and improving the screening hit rate [3, 7, 8]. In the
following sections, we describe current methods of library design that are used for
these purposes.

ISBN: 3-527-30509-2
762 27 Virtual Compound Libraries and Molecular Modeling
27.2
Lead-nding Libraries
The need for large diverse screening compounds for HTS is a major reason for the
rapid technological advances in combinatorial chemistry. A combinatorial library
that is used for HTS against many cell-based or enzymatic assays with dierent
targets requires a wider range of structural and physicochemical properties than
a focused library screened against a particular target. Therefore, the assessment
of the diversity of the library compounds is an important step during the design
phase of a lead-nding combinatorial library [9, 10].
27.2.1
Diversity Assessment of Library Compounds
The meaning and quantication of diversity is not straightforward. Most ap-

proaches to measure the diversity of a library (or any collection of compounds)
depend on the representation of the molecules by topological or physicochemical
descriptors that capture the structural, physicochemical, and biological properties.
There are hundreds of molecular descriptors that have been used in the design and
analysis of libraries [11, 12]. The full range of descriptors that is typical for classi-
cal quantitative structureactivity relationship (QSAR) analysis has been used:
measured or computed physical properties such as molecular weight, octanol
water partition coecient (log P), molar refractivity, molecular surface area, mo-
lecular volume, solubility, as well as structural invariants like topological or con-
nectivity indices (Kier, Hall, etc.) and many more. In addition to these classical
descriptors, the so-called two-dimensional (2D) ngerprint keys have been widely
used for the diversity assessment of large libraries. They encode the topological or
substructural elements of a molecule derived from its connection table (a repre-
sentation of all atoms and atom bonds of a molecule). These 2D ngerprint keys
typically consist of several hundred, sometimes up to a few thousand, bit positions
(0, 1) for the absence or presence of structure elements.
Originally, these ngerprint keys had been designed to improve the eciency of
substructure searching in large structure databases using chemical database sys-
tems [13]. The ngerprint key of the structure query was compared with the n-
gerprint keys of all database structures. Only database structures that included all
query keys were submitted to the more time-consuming atom-by-atom match.
This method was only ecient if as few as possible structures were selected for the
atom-by-atom match. Therefore, the ngerprint keys were ideally designed such
that any query would lead to only a small subset of the database structures for the
atom-by-atom match and at the same time any query structure that would be rea-
sonable for the given structure database led to a nonzero ngerprint key. Thus, the
2D ngerprint keys provided a readily available descriptor that could cover a wide
range of structures and while still being sensitive to structural dierences. Since
the 2D ngerprint keys could also be computed very rapidly they represented a
27.2 Lead-finding Libraries 763
descriptor space that was eciently and generally applicable for the assessment of
the diversity of chemical structures in a combinatorial library.
Pharmacophoric or three-dimensional (3D) ngerprint keys include informa-
tion from the 3D representation of the molecules. The dierent pharmacophoric
groups of the molecule, such as hydrogen acceptor and hydrogen donor groups,
and lipophilic and aromatic centers are dened. After generation of (evenly sam-
pled) conformational models the two-, three-, and four-center distance combina-
tions between the pharmacophoric groups for each conformer are determined and
encoded in a bitstring [14, 15]. The computational eort for large libraries is con-
siderable owing to the conformational sampling step.
For a quantitative assessment of structural diversity a metre of the dissimilarity
or similarity of all pairs of structures is needed. Using ngerprint keys as the de-
scriptor this is achieved by a bit-by-bit comparison of the corresponding ngerprint
keys, as in similarity searching [16]. A widely used similarity metre is the Tani-
moto coecient, which is the quotient t of the number NAB of all common set bits
in molecules A and B divided by the number of all noncommon set bits in mole-
cules A and B (Eq. 1).
NAB
b
t 1
NA^ NB^ NAB
b
The values of the Tanimoto coecient range from 0 for most dissimilar struc-
ture pairs to 1 for pairs with all identical structure elements. Since t only refers to
set bits, it scales somewhat with the size of the molecules involved. However, the
Tanimoto coecient lacks the properties of a metre and the coecient values
do not resemble true distances [16, 17]. Nevertheless, t is computed very fast and
has even been used to assess properties such as biological activity between similar
structures [18, 19].
The diversity of a library can be computed by the pair-wise calculation of the
similarity of all structure pairs (see also Section 27.4.2.2). A representative mea-
sure is the self-similarity of a library that is determined by nding for each com-
pound the most similar but not identical structure and averaging the correspond-
ing Tanimoto coecients [13c]. The diversity of a library increases with decreasing
self-similarity.
27.2.2
Drug-likeness of Library Compounds
Early attempts in designing lead-nding combinatorial libraries have focused on

the size and diversity of the libraries [2023]. More recently, the drug-likeness of
compounds in combinatorial libraries has been addressed. The attribute of drug-
likeness combines synthetic feasibility, protein-binding functionality, favorable
ADME (absorption, distribution, metabolism, excretion), and toxicological proper-
ties of small molecules [24, 25]. In order to create drug-like libraries the phys-
icochemical parameters and functionality of the compounds must be optimized.

Simple counting rules such as the rule of ve [1] from Lipinski and coworkers,
related criteria such as the number of rotatable bonds or rings in a molecule [26],
or related functional group lters [27] are usually employed to prole a combina-
torial library. More sophisticated techniques such as neural nets [28, 29], genetic
algorithms [30], or recursive partitioning [31] can in principle also be used to in-
crease the drug-likeness of a library.
Teague and coworkers have recently pointed out that it may be more useful to
design lead-like rather than drug-like combinatorial libraries [32]. They argue
that in a typical lead-optimization phase of a drug discovery program, key phys-
icochemical parameters such as log P and molecular weight (MW) increase by
0.54 and 1200, respectively, thereby placing the resulting optimized compounds
outside of the drug-like space. Based on this assumption, Teague and coworkers
suggested a design of lead-like libraries that have a log P prole of 13 and a MW
of 100350, well below the rule of ve thresholds of clog P 5 and MW
500.
An important point, especially for smaller compounds as starting points for a
lead optimization eort, is the appropriate functionality of the molecules. Teague
and coworkers suggest using highly polar compounds or compounds bearing a
single charge at physiological pH. Suitable functionality of small molecules ac-
counts for an increased chance of sucient binding anity to a protein target but
mainly addresses the specic binding of the compound to a particular target. It is
therefore important to optimize the degree of functionality of a small molecule.
Recently, we demonstrated how simple pharmacophore lter rules help in gen-
erating a drug-like prole of compounds in a library [27]. Scheme 27.1 shows four
simple functional groups that are sucient to capture the most important func-
tional properties of small drug-like molecules. These functional groups can be
combined with what we refer to as pharmacophore points. These pharmacophore
points include the following functional groups: amine, amide, alcohol, ketone, sul-
fone, sulfonamide, carboxylic acid, carbamate, guanidine, amidine, urea, and ester.
Using these simple pharmacophore points a simple set of rules has been derived
from chemical wisdom to classify drug-like or lead-like compounds [27]:
Scheme 27.1.
1 Pharmacophore points are fused and counted as one when their heteroatoms
are not separated by more than one carbon atom.
2 Compounds with fewer than two or more than seven pharmacophore points are
dismissed.
3 Primary, secondary, and tertiary amines are considered to be pharmacophore
points but not pyrrole, indole, thiazole, isoxazole, other azoles or diazines.
4 Compounds with more than one carboxylic acid are dismissed.
5 Compounds without a ring structure are dismissed.

6 Intracyclic amines that occur in the same ring are fused (e.g. piperazine), i.e.
they count as only one pharmacophore point.
Based on these simple rules it has been shown that about two-thirds of drug-like
compounds as dened by their presence in drug-like databases such as Compre-
hensive Medicinal Chemistry (CMC) or MACCS-II Drug Data Report (MDDR) are
classied as drug-like while only one-third of the compounds in the Available
Chemicals Directory (ACD) pass the lter. Together with statistical tools that prune
distributions of such important parameters as MW or clog P to be commensurate
with those of drug-like molecules the above described pharmacophore lter pro-
vides a simple guiding tool in the design of virtual libraries that can easily be im-
plemented.
27.3
Focused Libraries
Diverse libraries and random libraries are large screening libraries synthesized
without a particular target in mind. With the advent of HTS a decade ago it was
generally assumed that lead structures could be obtained with high success rates
by screening large diverse compound libraries. However, the history of HTS that
runs throughout the pharmaceutical industry tells a dierent story. Only one in
ten HTS runs produces a viable lead compound that is subsequently optimized in
a drug discovery eort [33]. One reason for this somewhat disappointing track
record is the fact that the available chemical space is so overwhelmingly large.
Estimates for accessible small organic molecules range from 10 60 to 10 100 com-
pounds. Even if the space of drug-like compounds is considerably smaller
(maybe only 10 12 compounds) it is still six orders of magnitude larger than the
largest screening libraries processed today. From this obvious dilemma it is clear
that additional knowledge about the drug target is needed to optimize the output
of a library screen. Several strategies are available to design focused libraries that
have an increased chance of hitting a drug target:
. targeting protein families;

. use of privileged structures for a target family;
. use of similarity to HTS hits or lead structures;
. use of structure-based design methods (e.g. docking, virtual screening).
While the rst three methods exploit the knowledge about known ligands of
a target or a target family, the last and most powerful techniques require a 3D
structure of the target protein at atomic resolution to design a combinatorial li-
brary. In the following sections, we will expand on these four techniques by de-
scribing them in some detail and by giving some examples of how they may be
used.
27.3.1
Targeting Protein Families
Recent eorts to improve the eectiveness of high-throughput screens include

the design of medium-sized screening libraries (@ 10 4 compounds) that target
protein classes most relevant for drug discovery, such as G-protein-coupled re-
ceptors (GPCRs), kinases, and nuclear hormone receptors. In some cases, screen-
ing smaller libraries oers advantages over screening an entire proprietary data-
base of typically @10 6 compounds. Some assays allow only for a limited number
of compounds to be screened. Also a smaller number of compounds can be
screened in single wells at higher concentrations, thereby minimizing the number
of false negatives in the screen (active compounds that do not show up as hits in
the screen). While the current hit rate of HTS lies at about 0.01%, the hit rate of
target class-directed les is typically found to be about tenfold higher. In light of
the fact that only about one in ten HTS screens delivers a lead compound that is
subsequently optimized in a drug discovery eort [33], the quality of screening
hits is also an issue that may be more conveniently addressed in smaller focused
libraries.
Target class-directed libraries can either be assembled from available compounds
or be synthesized in combinatorial fashion. The design of target class-directed li-
braries relies on the identication of structural motifs in small molecules or in
building blocks for combinatorial libraries that can be linked to increased activity
for the target class. Target class-specic functional groups can be identied by ex-
amining ligands from the literature. For GPCRs, recurring motifs include, for ex-
ample, piperazines, morpholines, and piperidines; for kinases, they include, for
example, heterobicyclic compounds. Compounds bearing those structural motifs
are thought to have a generally higher chance of being active against the respective
target classes. A more rigorous approach to identify, for example, the GPCR-like-
ness of compounds or building blocks can be provided by a statistical analysis of
drug-like databases, such as the CMC [34] or the MDDR [35]. Since neural net-
works have been shown to be particularly useful in classifying chemical matter
[28, 29], we describe here a net that addresses the GPCR-likeness of compounds
as well as building blocks for combinatorial libraries that can be reproduced using
the known literature.
Following the literature precedent for designing neural nets for the classication
of chemical structures [28], the publicly available (free of charge) Stuttgart Neural
Network Simulator (SNNS) [36] has been employed to design a feedforward neural
net with 91 input neurons, ve hidden neurons, and one output neuron. All layers
are connected to each other. The input neuron is generated for each molecule by
converting its chemical structure into 91 Ghose and Crippen atom types [37]. Note
that only statistically signicant atom types (91 out of 120) have been used in order
to minimize the number of input neurons. Alternatively, other structural keys or
ngerprints such as ISIS keys [38] may be used. The output unit provides a
score between 0.1 (non-GPCR-like) and 0.9 (GPCR-like). The neural net has been
trained using the backpropagation with momentum scheme. The training set
consists of 5000 compounds from the MDDR that target GPCRs and 5000 com-
pounds that target other classes such as enzymes and nuclear receptors. The com-
pounds have been identied by dividing the MDDR into two structural groups:
@20,000 GPCR-like and @55,000 non-GPCR-like compounds by searching the
activity-class eld of the database for entries such as 5-hydroxytryptamine (5-
HT), leukotriene, PAF, and then randomly choosing 5000 compounds from each
class. Training of the neural net is performed for 2000 cycles with a learning rate
of 0.2 and a momentum term of 0.1 reshuing the training dataset before each
cycle. The resulting neural net classies GPCR-like compounds correctly with 80%
certainty. An independent test of compounds in our proprietary database that were
found to hit GPCRs or other targets showed a correct prediction of GPCR-like
compounds in 70% of the cases.
An important question for the design of combinatorial libraries is whether
the neural net is able to attribute the GPCR-likeness directly to possible building
blocks or whether the GPCR-likeness is an attribute of the enumerated molecule
only. Table 27.1 shows a list of possible GPCR-like primary amines taken from the
ACD [39] as putative building blocks for a virtual triazine library of 160,000 com-
pounds. Ten percent of the enumerated library was identied as GPCR-like by the
neural net. Table 27.1 shows the fraction of building blocks occurring most fre-
quently in the enumerated GPCR-like portion of the library. A high percentage
suggests that the GPCR-likeness of an enumerated compound can be directly at-
tributed to its building block (100% means that all enumerated compounds that
contain the building block have been recognized as GPCR-like a strong indicator
that the GPCR-likeness of the enumerated compound is solely due to the GPCR-
likeness of the building block). Table 27.1 shows the expected functional groups
such as piperazines, morpholines, and piperidines to be carriers of high GPCR-
likeness. This table also shows additional functional groups, such as pyrrolidines,
aliphatic tertiary amines, and acridine, that may not have been obvious to be very
GPCR-like. Other functional groups, such as imidazoles, pyrazoles, triuoro-
methyl, and benzylethers, show somewhat weaker GPCR-likeness. Table 27.1 sug-
gests that the GPCR-likeness in most cases can be attributed to the building blocks
alone. This is an enormous advantage in the design of combinatorial libraries
since a virtual library does not have to be enumerated to optimize its GPCR-
likeness. Expensive and sometimes inconclusive optimization routines such as ge-
netic algorithms [40, 41] that act on the enumerated library can be avoided. Rather,
the choice of core and building blocks becomes sucient for the library design. As
a result, there are two easy principles of designing GPCR-like libraries:
1 GPCR-like core plus drug-like building blocks (need not be GPCR-like).

2 Non-GPCR-like core plus GPCR-like building blocks.
27.3.2
Privileged Structures
The term privileged structures was introduced by Evans and coworkers for struc-
tural types of small molecules that are able to bind with high anity to multiple
classes of receptors [42]. Benzazepine analogs were found to be eective ligands for
Tab. 27.1. GPCR-like building blocks.
Structure a GPCR likeness Structure (%) Structure (%)

overlap (%)b
100 73 22
98 68 18
97 63 18
95 57 18
95 54 17
94 34 16
94 30 15
93 29 12
92 27 11
87 24 11
84 23 10
Tab. 27.1 (continued)
Structure a GPCR likeness Structure (%) Structure (%)

overlap (%)b
82 22 10
a Building blocks were taken from the Available Chemicals

Directory [39].
b The percentage of all GPCR-like building blocks (primary amines)
occurring in enumerated GPCR-like compounds is listed. Since
10% of the library of 160,000 compounds was classied as GPCR-
like, all building blocks with more than 10% occurrence in GPCR-
like enumerated compounds are potential carriers of the GPCR-
like property. Building blocks above 50% are strong carriers of
GPCR likeness.
an enzyme that cleaves the peptide angiotensin I while others are eective CCK-A
receptor ligands. Cyproheptadiene derivatives were found to have peripheral anti-
cholinergic, antiserotonin, antihistaminic, and orexigenic activity. Hydroxamate and
benzamidine derivatives have been shown to be privileged structures for metal-
oproteases and serine proteases respectively. For the class of 7-transmembrane G-
protein-coupled receptors a large number of privileged structures have been found,
including diphenylmethane, diazepine, benzazepine, biphenyltetrazole, spiropiper-
idine, indole, and benzylpiperidine [43]. Recently, the concept of privileged struc-
tures has also been applied to the design of natural product-like libraries [4446].
The wide use of privileged structures in the design of combinatorial libraries is evi-
dent from the large number of libraries being made for various target classes [47].
Many of the privileged structures are rigid, polycyclic heteroatomic moieties that
allow for varied substitutions in the three-dimensional space [43]. If one is inter-
ested in privileged structures that do not occur ubiquitously as structural motifs of
active compounds (such as biphenyls [48]) but are specic for a target class, it is
instructive to assess the target class likeness of the privileged structure. Privileged
structures are thought to interact directly with a specic binding site in a particular
class of proteins. However, for prominent drug target classes such as GPCRs this
assumption is not easy to validate without crystallographic evidence. An analysis of
some privileged structures that are thought to be specic for GPCRs reveals that
only some of them show high GPCR-likeness according to the above-described
neural net. For instance, benzylpiperidines, spiropiperidines, and biphenyltetra-
zoles exhibit high GPCR-likeness according to the neural net. On the other hand,
diphenylmethane, benzodiazepines, indoles, and benzamidines show mediocre to
no GPCR-likeness. Interestingly, the GPCR-likeness of ligands that bear privileged
structures is sometimes very high, e.g. PD 132,177 (an AT-2 ligand) which pos-
sesses a diphenylmethane moiety. This nding suggests that the reason why a
privileged structure hits a certain target class may not always be due to a direct and
specic interaction with the protein. Sometimes it may rather be attributed to its
ability to provide substituents with optimal vectors to interact within the protein
pocket. Not all privileged structures may therefore be optimal starting points for
the design of target class-directed libraries following principle 1 mentioned in
Section 27.3.1. They may rather be ubiquitously favored substructures that provide
an increased chance to hit almost any protein. Some of those ubiquitously privi-
leged structures have recently been identied [48]. They include; carboxylic acids,
biphenyls, diphenylmethane, and, to a lesser extent, naphthyl, phenyl, cyclohexyl,
bibenzyl, benzimidazole, quinoline, etc. This observation suggests that those sub-
structures ubiquitously enriched in active compounds among various protein
classes may be used as privileged building blocks rather than as privileged core
structures in combinatorial libraries. A more rigorous analysis of privileged drug-
like structural motifs has been published by Bemis and Murcko [49, 50].
27.3.3
Similarity
According to the similar property principle, compounds with similar chemical

structure exhibit similar biological activity [51]. Although this principle does not
hold true in a strict sense, similarity searching is a long-established technique used
to retrieve compounds similar to hit structures from a database. Recently, the sim-
ilarity principle has also been applied to the design of focused libraries [52, 53].
One example is Focus-2D [54], which combines topological indices with a Eucli-
dian distance as similarity metre for the design of a focused library. Compounds
similar to the query structure obtained, for example from a screening hit, are re-
trieved from the virtual library. The most similar compounds are subsequently an-
alyzed for the most frequently occurring building blocks that are then chosen to
generate the focused library. The described method was validated on a peptoid li-
brary, synthesized by Zuckerman and coworkers [55]. This library yielded two
molecules that showed high anity to a1 -adrenergenic and m-opiate receptors. No-
tably, using the Focus-2D approach, opioid active molecules would have been part
of a designed focused peptoid library, if met-enkephalin or morphine had been
used as query structures. With met-enkephalin as lead structure, however, twice as
many building blocks were selected that were known to be in opioid-active pep-
toids than with morphine, probably because met-enkephalin is chemically much
more similar to peptoids than morphine.
The opioid example illustrates the limitations of similarity methods that are
based predominantly on chemical similarity. Notably, the use of dierent scaolds
in designing libraries sometimes results in lower similarity values, limiting its ap-
plication for library design. Three-dimensional pharmacophoric ngerprints [18,
56, 57] promise a solution to this problem. The ngerprints are obtained by den-
ing all possible 3D arrangements of three or four individual pharmacophores (e.g.
H-bond donor, H-bond acceptor, hydrophobic). For each molecule an exhaustive
conformational analysis is performed. When a low-energy conformation satises
Fig. 27.1. Three pharmacophoric centers are distributed in

space. For each new entry in the pharmacophoric triplet, the
pharmacophoric features and the distance intervals between
them is varied.
one of the three- or four-point pharmacophore patterns a bit in the binary nger-
print is set, signaling the ability of the molecule to assume this pharmocophoric
pattern. The examination of all possible conformations and all pharmacophore
patterns results in a bitstring for each molecule that can then be used to calculate
the similarity between pairs of molecules (Fig. 27.1).
In an earlier study, 3D pharmacophoric ngerprints were found to be inferior
to standard 2D ngerprints in retrieving active compounds from databases [58].
Nevertheless, recent evidence was presented demonstrating their potential in clas-
sifying kinase inhibitors [59]. Furthermore, Pickett and coworkers could iden-
tify known brinogen antagonists hidden within a 100,000-compound subset of
Rhone-Poulenc Rorers repository using the four-point pharmacophoric ngerprint
of RGD peptide. All known inhibitors were found among only 3% of the database
[60]. They also report the application of pharmacophoric ngerprints in conjunc-
tion with a genetic algorithm-based compound selection, which maximizes the av-
erage pharmacophoric similarity of the library to a lead structure, but no practical
application is demonstrated. Thus, the use of 3D pharmacophoric ngerprints in
library design appears to be promising, although applications are restricted to vir-
tual libraries containing fewer than 100,000 compounds owing to high computa-
tional expense.
In principle, descriptors, which do not rely on chemical fragments alone but
give a more general picture of the molecular properties, may be more suitable for
library design based on the similarity principle. Especially the adequate calculation
of similarity between compounds with dierent scaolds needs to be improved
over chemical fragment similarity measures. Examples of such descriptors are fea-
ture trees [61], topological pharmacophoric ngerprints [62], and BCUTs [63] that
have the ability to cope better with changes in the scaold between lead structure
and combinatorial library because of graph theoretical and 3D pharmacophore ap-
proaches.
QSAR models have also been used for designing a focused library [64], but it
should be kept in mind that the validity of QSAR models usually is constrained to
the close chemical neighborhood of the molecules used as the training set. There-
fore, QSAR models are probably not well suited for designing libraries around a
new scaold.
27.3.4
Docking
The 3D protein structure presents valuable information for drug design, since de-
tails of the binding site of the target protein are available at atomic resolution.
Molecular docking routines use this information to match molecules to the protein
binding site and to predict the binding anity of the putative ligand [65]. There-
fore, docking is used for virtual screening to identify potential ligands from large
databases [66, 67] or from virtual combinatorial libraries. Docking can be applied
for cherry-picking only the most promising few compounds out of a virtual com-
binatorial library. On the other hand, the predicted binding anity also provides
reactant selection criteria to give the best library in terms of a large number of
highly potent molecules.
Various molecular docking programs such as DOCK [6870], FlexX [7173], or
GOLD [74, 75] are available. These programs dock only whole molecules. There-
fore, each molecule of the library has to be docked and scored individually. This is
a time-consuming process, which limits the number of virtual compounds to be
docked to about 1000 per day and processor.
In the following section, we will describe some examples of successful applica-
tions of structure-based design to combinatorial chemistry and compare structure-
based design with diversity-based library design.
At Roche a virtual library of roughly 4500 diaminopyrimidines has been chosen
to yield dihydrofolate reductase (DHFR) activity [76]. The diaminopyrimidine core
moiety of the library matches pharmacophoric key features in the folate binding
site and is part of many high-anity DHFR ligands. Therefore, a diaminopyr-
imidine library is expected to contain a fairly large fraction of DHFR active com-
pounds. The virtual library has been docked into Staphylococcus aureus DHFR [77]
with FlexX by xing the position of the diaminopyrimidine core at its key interac-
tion points. Of the 150 top-scoring ligands, 104 have been synthesized by parallel
chemistry, from which 16 have shown activity in antibacterial assays a hit rate of
about 15%. The same diaminopyrimidine virtual library has been clustered and
375 diverse molecules have been selected to span adequately its chemical space
and have been tested for antibacterial activity. Thirty-two of these compounds were
selected giving a hit rate of 8.5%. Although antibacterial activity rather than the
activity against the actual target has been monitored, the structure-based selection
has given a twofold higher hit rate than diversity selection. It has been suggested
that this encouraging result is due to the ability of the virtual screen to focus the
selection of the compounds on molecules that are most likely to interact with the
molecular target DHFR.
For library design, docking of whole compounds is only useful in a few cases
because of the limited throughput of docking programs and the size of virtual
combinatorial libraries, which usually comprise more than several hundred thou-
sand compounds. Virtual combinatorial libraries are built by combining every re-
actant from one site with N variations with any other reactant from another site
with M variations, thus giving N*M products for a library with two points of vari-
ation.
In structure-based library design, this combinatorial problem is often solved by
docking individual building blocks. Thus, instead of docking N*M products only
N M fragments have to be investigated. Experimental evidence for the validity of
this approach is given by the structureactivity relationship by nuclear magnetic
resonance (SAR by NMR) technique [78]. Here, small fragment-like molecules
are screened and the best molecules are linked to the complete drug later in the
design process.
One such approach was presented by Bohm and coworkers in a search for new
thrombin inhibitors [79]. The molecular design was divided into two steps. First,
high-anity fragments for the recognition pocket of thrombin were identied by
docking 5300 commercially available primary amines in the recognition pocket of
thrombin. Amines were chosen because they are good starting materials for a va-
riety of chemical reactions. In the second step, the complete compounds were built
up within the thrombin binding site by LUDI [80, 81], a de novo design program,
which joined small fragments to whole molecules within the protein binding
pocket. The top-scoring amine fragment, p-amino-benzamidine, was used as an
anchor to add 540 aldehydes by reductive amination with an extension of LUDI
that could dierentiate between types of chemical links. Ten of the 100 top-scoring
molecules were synthesized, producing a hit with an inhibition constant of 95 nM.
The design of a combinatorial library against cathepsin D, an aspartyl protease,
represented pioneering work in the eld of structure-based library design by Ell-
mans and Kuntzs groups [82]. The library was designed upon the (hydroxyethyl)-
amine isostere, since statins and analogs were well-known mechanism-based in-
hibitors for aspartyl proteases. The central (hydroxyethyl)amine core was modeled
in the active site with a binding mode similar to that of pepstatin. Substituents of
the central core were introduced as acids and amines selected from ACD with a
molecular weight limit of 270. The three sites of variation were independently in-
vestigated within the protein-binding site using CombiBuild [83], which employed
an exhaustive conformational search in the corresponding binding pockets. Next,
for each site of variation, ten compounds were selected from the 50 top-scoring
reactants by cost and diversity criteria. A 10*10*10 library was obtained containing
23 compounds with 50% inhibition at a concentration of 0.33 mM.
For comparison, a second library of the same size was synthesized using diver-
sity criteria alone for picking reactants. In this library, only three compounds had
inhibitory activity at a concentration of 0.33 mM. The focused library not only
showed a sevenfold increased hit rate compared with the diverse library, but also
contained compounds with higher activity.
The focused library was also assayed against plasmepsin II, another aspartyl
protease; it produced 13 hits at an inhibitor concentration of 1 mM [84]. The
lead compounds could be further optimized by selecting reactants for each site of
variation independent of diversity criteria and of structure-based design with
DOCK.
The examples presented above show that it is possible to use 3D protein struc-
tures to design combinatorial libraries with hit rates signicantly higher than
those obtained by diversity screening (twofold for the DHFR example and seven-
fold for the cathepsin D example). The examples presented above also exemplify
the usefulness of privileged structures. In both examples the designed library was
based on structures that are known to have some intrinsic anity to the corre-
sponding target [diaminopyrimidines for DHFR and (hydroxyethyl)amine for as-
partyl protease]. When these fragments are decorated with a diverse set of sub-
stituents, an impressive hit rate is obtained. Decorating a privileged core with a
diverse set of substituents appears to be especially useful when no 3D protein
structure is available.
27.4
Methods for Library Optimization
The denition of a template and the selection of available reactants easily gives
rise to virtual combinatorial libraries with millions of compounds. Only a subset of
those compounds can actually be synthesized. The reagents for the actual library
could be chosen based upon the properties of the individual reagents or on the
properties of the combinatorial products. Reagent-based selection is easy to ac-
complish and does not require an elaborate selection procedure. On the other
hand, reagent-based selection neglects the properties of the whole molecule, which
govern the interaction with the protein target.
Furthermore, a product-based approach called cherry-picking selects single
enumerated compounds from a large virtual library based on one or more favor-
able properties. Cherry-picking is unlikely to provide a set of reagents that can ef-
ciently be applied to parallel or combinatorial synthesis. Usually, multititer plates
(MTPs) are used for parallel synthesis. Whenever one reactant is selected, it is
used for the entire row or column of the MTP, generating a complete matrix of
products. If one reactant is changed to obtain another product in one well, the
products in all other wells of that row or column are changed too.
Libraries obtained from product-based selection were shown to be more diverse
than libraries that are obtained from reagent-based diversity selection [85, 86].
Furthermore, many design objectives rely on whole-molecule properties, e.g. the
similarity to a lead structure or drug-likeness. Therefore, only product-based selec-
tion procedures will be discussed further here.
Traditionally, anity has been considered as the key point in the initial phase of
lead optimization. This is still true, however, for reducing pharmacokinetic and
toxicological problems in the clinic [87]; the consideration of ADME-related prop-
erties becomes more and more important in the early phase of lead optimization.
Thus, dierent aspects have to be reconciled in the library design.
In the following section, some methods are described that are used to select an
optimal set of reagents with respect to the various design goals outlined above. The
selection procedure consists of two independent components: a search method,
which selects the subset of the virtual library space, and a tness function, which
evaluates how well the actual selection ts the desired properties. As a search
method only a genetic algorithm will be discussed, although other methods have
also been successfully applied [88, 89].
27.4.1
Genetic Algorithm
A genetic algorithm is the computer equivalent of evolution. The system is dened

by a population of chromosomes. In each generation the best chromosomes, as
judged by the tness function, are selected to produce the ospring by genetic op-
erations such as mutations or crossovers (survival of the ttest). This selection pro-
cedure is repeated over several generations until the tness function does not im-
prove signicantly any more. The initial population is randomly assigned and is
generally far from being a good solution to the problem. Genetic operations under
the evolutionary pressure of the tness function drive the actual selection of the
library to better solutions.
SELECT [41], a program developed by Willets group, uses such a genetic algo-
rithm for library optimization. It encodes a complete library on each chromosome,
which is partitioned into several sections. Each section represents a site of varia-
tion of a library. The number of genes in each section represents the number of
reactants to be selected for the library.
The matrix constraints can easily be incorporated in this chromosome layout:
if each chromosome represents one MTP, each section of the chromosome just
corresponds to the rows or columns of the MTP, and one gene corresponds to one
reactant.
During the optimization process, mutations and crossovers operate on single
genes, but the tness function is applied to the whole chromosome. Thus, a ge-
netic algorithm provides a straightforward method to select an optimal set of re-
agents that results in the desired properties in product space.
A chromosome can either encode a complete library [40], as described above, or
represent a single compound [90, 91].
27.4.2
Fitness Function
The tness function measures how well the actual selection of compounds ts the
desired properties. It can consist of only one term, if one property is to be opti-
mized, or can comprise several terms, if various properties have to be optimized
simultaneously. Examples of how the individual terms of the tness function can
be constructed are given below.
27.4.2.1 Potency
Various methods have been described above that can be used to predict the po-
tency of virtual compounds, e.g. similarity to lead structures and structure-based
design methods. These techniques can give an estimate of the activity of each
member of the virtual library. From this information the suitability of the actual
designed library can be obtained. According to the target function in Eq. (2) that
needs to be maximized, libraries are preferred that contain a large fraction of po-
tent molecules. Nactive is the number of compounds better than a threshold and
Ntotal is the total number of compounds selected.
Nactive
tness 2
Ntotal
A large number of active molecules is also reected in a high average activity

over the whole library selection. Therefore, quantities such as the averaged activity
could also be optimized with a tness function, as shown in Eq. (3), where N is the
number of compounds in the selection and property refers to the optimized quan-
tity such as the docking score or the similarity to lead structures.
1XN
tness property 3
N i
27.4.2.2 Diversity
The diversity of a library in product space can be calculated as the sum of pair-wise
dissimilarities over all selected molecules [92], as shown in Eq. (4), where N is the
number of compounds in the selection. Diversity is given by (1 similarity). The
averaged pair-wise similarity can be eciently calculated using the cosine coef-
cient and the centroid algorithm [92]. This function (Eq. 4) also allows for the
ecient comparison of the relative diversity of two datasets, simultaneously max-
imizing the diversity within the actual selection and the diversity to in-house
screening pools.
X
N X
N
similarityi; j
i j
D1 4
N2
Diversity can be measured by cell-based methods [93]. The chemical space, de-
scribed by a set of descriptors, spans a multidimensional grid. This grid is divided
into several bins along the dierent axes [94]. Now, diversity can be measured by
the number of bins that are populated by the actual selection. Similar molecules in
this context belong to the same or to neighboring bins.
27.4.2.3 Physicochemical Properties

Dierent approaches are used to describe drug-likeness. Parameters such as the
rule of ve [1] dene some limits to which the properties of the compounds
should be conned. Thus, a simple scoring scheme would just penalize every
compound that violates the rule of ve. The drug-likeness of a library is some-
Fig. 27.2. The bisarylether library used in the each reactant, three sections were reserved in
analysis had three sites of variation: R1 and R2 the chromosome. The full library is obtained by
were at xed positions, while the position of R3 combining each reactant with every other
at the second aromatic ring was varied. For reactant from the other sections.
times also measured by comparison of the prole of certain physicochemical prop-

erties between the library and a reference set of drug-like molecules, e.g. marketed
drugs. Gillet and coworkers [30] tted the distribution of rotatable bonds to the
corresponding distribution in the World Drug Index (WDI) as a reference for drug-
like molecules. The deviation between the reference distribution and the actual
distribution within the library can be measured as the root mean square deviation
[41], as shown in Eq. (5), where N is the number of bins, describing the property
distribution, A b is the fraction of compounds in the library that occupy bin b, and
Xb is the fraction of compounds in the reference collection that occupy bin b. Such
a comparison can be performed for any other property which is easily and reliably
calculable, such as polar surface area [95], log P and molecular weight.
v
uX
u A^b X^b 2
t
N
Df 5
N
We have used a genetic algorithm to analyze the interdependencies of various

design objectives for a bisarylether library with three points of variation (Fig. 27.2).
A virtual library of about 100,000 compounds was built from readily available
starting materials, which were selected from an in-house database. One thousand
molecules were selected from that virtual library in a 10*10*10 format based on
the following design objectives:
. rule of ve
. diversity
. both diversity and the rule of ve
The library was coded in one chromosome divided into three sections for the
three sites of variation, each section containing ten reactants. The enumeration of
the combination of these reactants gives the 1000 products of the library. The se-
lection is based on the product properties.
The tness function for the rule of ve-based selection is the sum of individ-
ual scores. Whenever a molecule is within the limits of the rule of ve criteria, it
obtains a score of 1. Thus, a molecule which meets all criteria obtains a score of 4.
The average of this score was optimized over the selected set of 1000 molecules,
resulting in a library design in which all molecules stayed well within the limits
given by each rule of ve. However, the averaged pair-wise diversity, calculated
from HQSAR ngerprints [96] with the cosine coecient, of this library is fairly
low at only 0.09.
In contrast, the diversity-based selection gives a signicantly higher averaged di-
versity of 0.25, however, a signicant fraction of the selected molecules violate the
rule of ve limits.
The combination of both design objectives in one scoring function as the sum
over the diversity score and the above-mentioned rule of ve score results in the
design of a diverse library with an averaged pair-wise diversity of 0.23 that is in
agreement with the rule of ve criteria.
Thus, the combination of both tness functions allows for the combined opti-
mization of dierent parameters, which results in an improved property prole for
the whole library (Fig. 27.3).
The above example illustrates the benets of combining dierent objective func-
tions in the optimization procedure. A genetic algorithm provides a simple scheme
to perform this combined optimization by adding various terms to the tness func-
tion, as shown in Eq. (6):
tness wD D wprop prop 6
The rst term represents the internal diversity of the selection. Other terms repre-
sent the distribution of any optimizable property. The weights wprop for these pa-
rameters have to be adjusted according to the problem.
Thus, powerful tools are available that allow the selection of a good set of com-
pounds out of a large virtual library. According to the intended library design, vari-
ous terms can be combined within the tness function:
. For lead nding, a diverse library, which consists of lead-like or drug-like mole-
cules, appears to be desirable. Diversity could also be dened with respect to the
existing in-house screening pool.
. For lead optimization, potency-related aspects such as similarity to HTS hits may
be optimized in conjunction with drug-likeness.
27.5
Conclusion
Over the past years combinatorial chemistry has become an established method
within drug discovery. In parallel, computational methods have played an increas-
Fig. 27.3. a) Distribution of molecular weight, library selected by a combination of the rule
27.5 Conclusion
log P, number of donors and the number of of ve and diversity. Compounds with
acceptors for the whole virtual library. (b) For properties above the rule of ve limits are
779
the library selected by the rule of ve; (c) for represented by dark grey bars.
the library selected by diversity; and (d) the
ing role in supporting this process. With relatively little computational eort vir-
tual library compounds can be optimized with respect to maximum diversity, high
similarity with an already known screening hit or lead structure, or improved drug-
likeness and ADME properties. Even the eciency of virtual screening can be in-
creased by applying appropriate lters for functional groups, molecular weight, or
other physicochemical properties that reduce the number of compounds for the
actual docking process. Depending on the intended purpose for which the library
is designed and synthesized, a combination of dierent computational methods is,
in most cases, appropriate.
A screening hit from a library that has been optimized using computational
methods can be optimized more eciently based on the design principles or rules
used for the original library. The new library can be focused on compounds similar
in structure to the screening hit while areas of the property space that have not led
to bioactive compounds can more easily be avoided.
Starting from calculated physicochemical properties and standard 2D ngerprint
keys, as available with chemical structure databases for structure searching, new
descriptors have been developed that can address more complex properties (e.g. 3D
pharmacophore keys) or encode properties more eciently (e.g. BCUT) for library
evaluation. In general, ngerprint keys or bitstrings provide an ecient way to
encode properties and can be used for the diversity assessment of combinatorial
libraries. They can be tailored according to the properties suitable for a particular
purpose.
Given the wealth of available descriptors and methods it is already becoming
more and more challenging to nd the most suitable descriptors for a particular
library design task and the best optimization method. This is reminiscent of the
situation in classical QSAR. However, the situation is much more promising with
virtual library design than with QSAR. With combinatorial chemistry a whole set
of new test compounds can be synthesized and tested, whereas in classical QSAR
projects typically only single compounds (usually only the estimated most active
ones) become available. The educated shot gun approach with a combinatorial
library has a much higher probability for success during screening. The overall
risk of failure due to insucient information on the true nature of the interaction
of bioactive compounds with their biological target or system decreases when
whole libraries of potentially active compounds (rather than single compounds)
are synthesized and screened.
While combinatorial chemistry can eciently be supported by computational
methods, support of computer-assisted drug design can be evaluated by library
synthesis and screening. As a result of the combined eorts of computer-assisted
library design and combinatorial chemistry, a new quality in the overall drug dis-
covery process has been achieved. While its usefulness has been proven for several
cases, library design is an active research eld that is expected to gain more im-
portance and applicability in the future.
References 781
References
1 C. A. Lipinski, F. Lombardo, B. W. 19 P. Willett, V. Winterman, Quant.

Dominy, P. J. Feeney, Advanced Drug Struct. Act. Relat. 1986, 5, 1825.
Delivery Reviews 1997, 23, 325. 20 M. A. Gallop, R. W. Barrett, W. J.
2 A. R. Leach, M. M. Hann, Drug Dower, S. P. A. Fodor, A. M.
Discov. Today 2000, 5, 326336. Gordon, J. Med. Chem. 1994, 37,
3 Special issue 4/5 of J. Mol. Graphics 12331251.
Mod. 2000, 18, 317512. 21 E. M. Gordon, R. W. Barrett, W. J.
4 D. K. Agraotis, J. C. Myslik, F. R. Dower, S. P. A. Fodor, M. A. Gallop,
Salemme, Mol. Diversity 1999, 4, 1 J. Med. Chem. 1994, 37, 13851401.
22. 22 E. J. Martin, J. M. Blaney, M. A.
5 D. E. Clark, S. D. Pickett, Drug Siani, D. C. Spellmeyer, A. K.
Discov. Today 2000, 5, 4958. Wong, W. H. Moos, J. Med. Chem.
6 M. G. Bures, Y. C. Martin, Curr. 1995, 38, 14311436.
Opin. Chem. Biol. 1998, 2, 376380. 23 Y. C. Martin, J. Comb. Chem. 2001, 3,
7 A. C. Good, S. R. Krystek, J. S. 120.
Mason, Drug Discov. Today (Suppl.) 24 W. P. Walters, Ajay, M. A. Murcko,
2000, 5, S61S69. Curr. Opin. Chem. Biol. 1999, 3, 384
8 M. A. Murcko, P. R. Caron, P. S. 387.
Charifson, Ann. Rep. Med. Chem. 25 B. L. Podlogar, I. Muegge, L. J.
1999, 34, 297306. Brice, Curr. Opin. Drug Discov. Dev.
9 P. Willett, Curr. Opin. Biotechnol 2001, 4, 102109.
2000, 11, 8588. 26 T. I. Oprea, J. Comput. Aided Mol. Des.
10 J. S. Mason, N. A. Hermsmeier, Curr. 2000, 14, 251264.
Opin. Chem. Biol. 1999, 3, 342349. 27 I. Muegge, D. Brittelli, S. L. Heald,
11 L. Xue, Bajorath, J. Comb. Chem. J. Med. Chem. 2001, 44, 18411846.
High Throughput Screen. 2000, 3, 363 28 J. Sadowski, H. Kubinyi, J. Med.
372. Chem. 1998, 41, 33253329.
12 D. Livingston, J. Chem. Inf. Comput. 29 Ajay, W. P. Walters, M. A. Murcko,
Sci. 2000, 40, 195209. J. Med. Chem. 1998, 41, 33143324.
13 a) D. Weininger, C. A. James, 30 V. J. Gillet, P. Willett, J. Bradshaw,
Daylight Theory Manual. Daylight J. Chem. Inf. Comput. Sci. 1998, 38,
Chemical Information Inc., 18500 Von 165179.
Karman Ave., Irvine, CA 92715, USA; 31 M. Wagener, V. J. van Geerestein, J.
b) MDL Information Systems Inc., Chem. Inf. Comput. Sci. 2000, 40, 280
14600 Cataline St., San Leandro, CA 292.
94577, USA; c) UNITY Reference 32 S. J. Teague, A. M. Davis, P. D.
Manual, Tripos Associates, 1699 Leeson, T. Oprea, Angew. Chem. Int.
Hanley Rd., St. Louis, MO 63144, Ed. 1999, 38, 37433748.
USA. 33 J. A. Landro, I. C. A. Taylor, W. G.
14 A. C. Good, I. D. Kuntz, J. Comput. Stirtan, D. G. Osterman, J. Kristie,
Aided Mol. Des. 1995, 9, 373379. E. J. Hunnicutt, P. M. M. Rae, P. M.
15 M. J. McGregor, S. M. Muskal, J. J. Sweetnam, Pharmacol. Toxicol.
Chem. Inf. Comput. Sci. 1999, 39, 569 Methods 2000, 44, 273289.
574. 34 Comprehensive Medicinal Chemistry
16 P. Willett, J. M. Barnard, G. M. is available from MDL Information
Downs, J. Chem. Inf. Comput. Sci. Systems Inc., San Leandro, CA 94577,
1998, 38, 983996. USA, and contains drugs already on
17 D. R. Flower, J. Chem. Inf. Comput. the market.
Sci. 1998, 38, 379386. 35 MACCS-II Drug Data Report is
18 T. Potter, H. Matter, J. Med. Chem. available from MDL Information
1998, 41, 478488. Systems Inc., San Leandro, CA 94577,
USA, and contains biologically active 50 G. W. Bemis, M. A. Murcko, J. Med.

compounds in the early stages of drug Chem. 1999, 42, 50955099.
development. 51 M. A. Johnson, G. M. Maggiora
36 SNNS: Stuttgart Neural Net (eds) Concepts and Applications of
Simulator; Version 4.0, University of Molecular Similarity. John Wiley, New
Stuttgart, Germany, 1995. York 1990.
37 V. N. Viswanadhan, A. K. Ghose, G. 52 D. K. Agraotis, V. S. J. Lobanov,
R. Revankar, R. K. Robins, J. Chem. Chem. Inf. Comput. Sci. 2000, 40,
Inf. Comp. Sci. 1989, 29, 163172. 10301038.
38 SSKEYS, MDL Information Systems 53 S. D. Pickett, I. M. McLay, D. E.
Inc., San Leandro, CA 94577, USA. Clark, J. Chem. Inf. Comput. Sci.
39 The Available Chemicals Directory is 2000, 40, 263272.
available from MDL Information 54 W. Zheng, S. J. Cho, A. Tropsha, J.
Systems Inc., San Leandro, CA 94577, Chem. Inf. Comput. Sci. 1998, 38, 251.
USA, and contains specialty bulk 55 R. N. Zuckerman, E. J. Martin, D. C.
chemicals from commercial sources. Spellmayer, G. B. Stauber, K. R.
Website: www.mdli.com. Shoemaker, J. M. Kerr, G. M.
40 R. D. Brown, Y. C. Martin, 1997, 40, Figliozzi, D. A. Goff, M. A. Siani,
23042313. R. J. Simon, S. C. Banville, E. G.
41 V. J. Gillet, P. Willett, J. Bradshaw, Brown, L. Wang, L. S. Richter, W.
D. Green, J. Chem. Inf. Comput. Sci. H. Moos, J. Med. Chem. 1994, 37,
1999, 39, 169177. 26782685.
42 B. E. Evans, K. E. Rittle, M. G. Bock, 56 M. J. Ashton, M. Jaye, J. S. Mason,
R. M. DiPardo, R. M. Freidinger, Drug Discov. Today 1996, 1, 71.
W. L. Whitter, G. F. Lundell, D. F. 57 S. D. Pickett, J. S. Mason, I. M.
Veber, P. S. Anderson, R. S. L. McLay, J. Chem. Inf. Comput. Sci.
Chang, V. J. Lotti, D. J. Cerino, T. 1996, 36, 1214.
B. Chen, P. J. Kling, K. A. Kunkel, 58 H. Matter, T. Potter, J. Chem. Inf.
J. P. Springer, J. Hirsheld, J. Med. Comput. Sci. 1999, 39, 12111225.
Chem. 1988, 31, 22352246. 59 B. Pirard, S. D. Pickett, J. Chem. Inf.
43 J. S. Mason, I. Morize, P. R. Comput. Sci. 2000, 40, 14311440.
Menard, D. L. Cheney, C. Hulme, R. 60 S. D. Pickett, I. M. McLay, D. E.
F. Labaudiniere, J. Med. Chem. 1999, Clark, J. Chem. Inf. Comput. Sci.
42, 32513264. 2000, 40, 263.
44 K. C. Nicolaou, J. A. Pfefferkorn, 61 M. Rarey, J. Dixon, J. Comput. Aided
A. J. Roecker, G. Q. Cao, S. Mol. Des. 1998, 12, 471490.
Barluenga, H. J. Mitchell, J. Am. 62 G. Schneider, W. Neidhart, T.
Chem. Soc. 2000, 122, 99399953. Giller, G. Schmid, Angew. Chem.,
45 K. C. Nicolaou, J. A. Pfefferkorn, Int. Ed. 1999, 38, 28942896.
H. J. Mitchell, A. J. Roecker, S. 63 R. S. Pearlman, K. M. Smith, J. Chem.
Barluenga, G. Q. Cao, R. L. Affleck, Inf. Comput. Sci. 1999, 39, 2835.
J. E. Lillig, J. Am. Chem. Soc. 2000, 64 S. J. Cho, W. Zheng, A. Tropsha, J.
122, 99549967. Chem. Inf. Comput. Sci. 1998, 38, 259.
46 K. C. Nicolaou, J. A. Pfefferkorn, 65 I. Muegge, M. Rarey, Rev. Comp.
S. Barluenga, H. J. Mitchell, A. J. Chem. in press.
Roecker, G. Q. Cao, J. Am. Chem. 66 W. P. Walters, M. T. Stahl, M. A.
Soc. 2000, 122, 99689976. Murcko, Drug Discov. Today 1998, 3,
47 R. E. Dolle, K. H. Nelson Jr, J. 160178.
Comb. Chem. 1998, 1, 235282. 67 I. Muegge, Y. C. Martin, P. J.
48 P. J. Hajduk, M. Bures, J. Hajduk, S. W. Fesik, J. Med. Chem.
Praestgaard, S. W. Fesik, J. Med. 1999, 42, 24982503.
Chem. 2000, 43, 34433447. 68 I. D. Kuntz, J. M. Blaney, S. J.
49 G. W. Bemis, M. A. Murcko, J. Med. Oatley, R. L. Langridge, J. Mol. Biol.
Chem. 1996, 39, 28872893. 1982, 161, 269.
References 783
69 I. D. Kuntz, Science, 1992, 257, 1078. 83 Y. Sun, T. J. A. Ewing, A. G.

70 T. J. A. Ewing, I. D. Kuntz, J. Skillman, I. D. Kuntz, J. Comput.
Comput. Chem. 1997, 18, 1175. Aided Mol. Des. 1998, 12, 597604.
71 M. Rarey, B. Kramer, T. Lengauer, 84 T. S. Haque, A. G. Skillman, C. E.
G. Klebe, J. Mol. Biol. 1996, 261, 470. Lee, H. Habashita, I. Y. Gluzman, T.
72 B. Kramer, M. Rarey, T. Lengauer, J. A. Ewing, D. E. Goldberg, I. D.
Proteins: Struct., Funct., Genet. 1997, 1, Kuntz, J. A. Ellman, J. Med. Chem.
221. 1999, 42, 1428.
73 B. Kramer, G. Metz, M. Rarey, T. 85 V. J. Gillet, P. Willet, J. Bradshaw,
Lengauer, Med. Chem. Res. 1999, 9, J. Chem. Inf. Comput. Sci. 1997, 37,
463. 731740.
74 G. Jones, P. Willet, R. C. J. Glen, J. 86 P. Willet, J. Comput. Biol. 1999, 6,
Mol. Biol. 1995, 254, 43. 447457.
75 G. Jones, P. Willet, R. C. J. Glen, A. 87 P. J. Eddershaw, A. P. Beresford, M.
R. Leach, R. Taylor, J. Mol. Biol. K. Bayliss, Drug Discov. Today 2000, 5,
1997, 267, 727. 409.
76 M. Stahl in: Virtual Screening for 88 W. Zheng, S. J. Cho, C. L. Waller,
Bioactive Molecules. Wiley-VCH, A. Tropsha, J. Chem. Inf. Comput. Sci.
Weinheim 2000 1999, 39, 738746.
77 G. Dale, C. Broger, A. DArcy, P. 89 J. S. Mason, B. R. Beno, J. Mol.
Hartmann, R. DeHoogt, S. Jolidon, Model. Graph 2000, 18, 438.
I. Kompis, A. M. Labhardt, H. 90 R. P. Sheridan, S. K. Kearsley, J.
Langen, H. Locher, M. G. P. Page, Chem. Inf. Comput. Sci. 1995, 35, 310.
D. Stuber, R. L. Then, B. Wipf, C. 91 L. Weber, S. Wallbaum, C. Broger,
Oefner, J. Mol. Biol. 1997, 226, 23. K. Gubernator, Angew. Chem. Int. Ed.
78 S. B. Shuker, P. J. Hajduk, R. P. 1995, 34, 2280.
Meadows, S. W. Fesik, Science 1996, 92 D. B. Turner, S. M. Tyrell, P.
274, 15311534. Willet, J. Chem. Inf. Comput. Sci.
79 H. J. Bohm, D. W. Banner, L. 1997, 37, 18.
Weber, J. Comput. Aided Mol. Design 93 D. Schnur, J. Chem. Inf. Comput. Sci.
1999, 13, 5156. 1999, 39, 3645.
80 H. J. Bohm, J. Comput. Aided Mol. 94 M. J. Bayley, P. Willet, J. Mol. Graph.
Design 1992, 6, 6178. Model. 1999, 17, 10.
81 H. J. Bohm, J. Comput. Aided Mol. 95 K. Palm, P. Stenberg, K. Luthmann,
Design 1992, 6, 593606. P. Artursson, Pharm Res. 1997, 14,
82 E. K. Kick, D. C. Roe, A. G. 568.
Skillman, G. Liu, T. J. A. Ewing, Y. 96 T. W. Heritage, D. R. Lowis, ACS
Sun, I. D. Kuntz, J. A. Ellman, Symp. Ser. 1999, 719 (Rational Drug
Chem. Biol. 1997, 4, 297. Design), 212225.
784
28
Erythropoietin Sensitizer A Case Study
Berthold Hinzen, Gabriele Braunlich, Christoph Gerdes, Thomas
Kramer, Klemens Lustig, Ulrich Nielsch, Michael Sperzel, Josef
Pernerstorfer
28.1
Introduction
In healthy individuals kidneys perform the vital functions of excretion of waste

products from the body, maintaining uid levels, and controlling blood pressure.
Furthermore, kidneys regulate the production of red blood cells by the synthesis
of erythropoietin (EPO) [1]. When kidneys fail, the production of erythropoietin
and the production of red blood cells are reduced. Thus, severe anemia is often
caused by insucient production of EPO, which circulates through the blood
stream to the bone marrow, where it stimulates the production of red blood cells
from stem cells [2]. Insucient amounts of EPO result in inadequate numbers of
red blood cells, and thus oxygen levels are reached which are too low to maintain
normal physiological conditions. Anemia leaves patients permanently fatigued and
exhausted [3].
Traditional treatments for anemic patients with renal failure have been repeated
blood transfusions and androgen therapy. Both can have severe side-eects: trans-
fusion may cause iron to accumulate in organs and can furthermore result in the
development of antibodies that can preclude patients from successfully receiving a
kidney transplant later [4].
Currently, the rst-line therapy for anemic patients is the administration of re-
combinant human erythropoietin (rhEPO) [5]. Since its approval, rhEPO has vir-
tually eliminated the need for repeated blood transfusions for dialysis patients.
Clinical studies have demonstrated that an increased hematocrit (percentage of red
blood cells in the blood volume) resulting from rhEPO administration has a sig-
nicant impact on the patients lives. The target hematocrit range for dialysis
patients is 3036%. Healthy individuals have a hematocrit in the range of 4248%
a range which possibly can be dangerous for anemic people due to the formation
of clots, etc.
Since its introduction for the treatment of patients with insucient erythrocyte
levels due to renal failure, the therapeutic use of rhEPO has broadened signif-

ISBN: 3-527-30509-2
28.2 Results 785
icantly. Today, patients receiving chemotherapy or those having received bone

marrow transplantations are treated with rhEPO as well as human immuno-
deciency virus (HIV) patients and others. In clinical trials the most frequently
observed adverse side-eects with rhEPO were hypertension, headache, tachy-
cardia, nausea/vomiting, and clotted vascular access. However, it is not clear
whether these eects are directly related to treatment with rhEPO. rhEPO has to
be administered three times a week. Because of its chemical nature as a peptide
hormone of 165 amino acids, it has to be injected parenterally. Despite these dis-
advantages, rhEPO is currently one of the best-selling drugs on the market ($5
billion annual sales in 2000).
Synthetic compounds which stimulate or sensitize endogenous EPO and can
overcome the disadvantages of rhEPO are highly attractive research targets for the
pharmaceutical industry. They would meet the needs of a large patient population
and a large market with expected annual growth rates above 10%. It is expected
that an orally active EPO substitute would attract a major share of this market.
Thus, the project goal was to nd an orally active low-molecular-weight EPO sen-
sitizer that would be able to increase hematocrit levels within 12 weeks by about
10% points in total to a nal hematocrit of approximately 3035% at a maximal
dose of 3 mg kg1 day1.
28.2
Results
28.2.1
High-throughput Screening and Biological Evaluations
The erythropoietin program began by building up a high-throughput screening

(HTS) assay using a murine cell line which was transfected with the human EPO
receptor and the luciferase reporter gene under the control of a globin promoter.
In this cell line, EPO causes the induction of luciferase activity. Since the HTS was
designed to identify sensitizers (compounds that would enhance the eect of en-
dogenous erythropoietin), testing of compounds was performed in the presence of
low concentrations of rhEPO, and the potentiation of this response was quantied.
Approximately 650,000 compounds were tested. After hit verication cluster
analysis, and structure similarity searches, 70 of the most promising compounds
were further tested in vivo.
Dihydropyridazinones showed in vitro and in vivo activity as well as preliminary
structureactivity relationships (SARs). The most active compound within this
class, 1 (Fig. 28.1), displayed an EC50 0:23 mM in the luciferase assay. This activ-
ity corresponds to a 6.5- to tenfold stimulation of erythropoiesis during treatment
with 10 milliunits (mU) Epo mL1 without sensitizer. In vivo, a 4.5% point in-
crease of hematocrit was measured after p.o. application (10 mg kg1 d1 for 5
days) to mice within a week. Such an increase is already in the desirable range for
a sensitizer. Higher increases in hematocrits can be dangerous for anemic people
because the density of their blood increases, which favors the formation of clots.
786 28 Erythropoietin Sensitizer -- A Case Study
Fig. 28.1. Dihydopyridazinone 1 was the lead treatment with 10 mU mL1 Epo without
structure of the Epo-sensitizer project sensitizer; 4.5% point increase in the
[EC50 0.23 mM (luciferase assay); 6.5- to hematocrit after p.o. application (10 mg kg1 );
tenfold stimulation of erythropoiesis over the IC50 (PDE3) 0.2 mM].
Further experiments demonstrated that 1 stimulates erythropoiesis not only

by means of an EPO-sensitizing eect but also by triggering an EPO release
from the kidney, which was due to the inhibition of phosphodiesterase (PDE)3
(IC50 0:2 mM). These PDE3-associated hemodynamic side-eects are not accept-
able in the treatment of anemia. Thus the lead 1 had to be optimized with respect
to potency and selectivity. Therefore, the lead was divided into three parts: a central
core (C), a heterocyclic moiety (D), and a rather lipophilic substituent (A) attached
to the core via an amide linkage (B). The corresponding compound with the in-
verse amide displayed good biological activity as well. All three parts were planned
to be modied in a medicinal chemistry program (Fig. 28.2).
The optimization of the lead structure was mostly based on in vitro results.
These were obtained from BaF3 cells expressing the human EPO receptor and the
luciferase reporter gene under the control of the b-globin promoter. The cells were
incubated with the test substances (01000 nM) in the presence of 10 mU mL1
EPO for 48 h. Cells were then lysed and the luciferase activity was measured. Re-
sults will be expressed as percentage activity compared with luciferase activity at 10
mU mL1 EPO in the presence of 0.1% DMSO. The second in vitro erythropoiesis
Fig. 28.2. The lead and some of the options of the chemical optimization program.
28.2 Results 787
model used human primary CD34-positive stem cells. The stimulation of the pro-
liferation of these erythroid cells was determined by counting benzidine-positive
cells after 14 days culture in methylcellulose medium. In vivo results were ob-
tained from mice, for which the increase in the hematocrit was measured after 5
days of treatment.
28.2.2
Concept for Chemical Optimization
The dihydropyridazinone moiety constitutes part of known PDE3 inhibitors and

was thought to be responsible for the undesired PDE3 activity of 1 [6]. Therefore,
in the rst phase of the project, chemistry eorts were focused on the replacement
of this moiety by other heterocyclic groups and on the modication of the dihy-
dropyridazinone scaold to reduce PDE3 activity. The para-substituted benzene
moiety was planned to remain constant during the initial phase of the program.
When the chemistry group working on this program was brought together,
the question of how combinatorial chemistry in solution phase or on solid sup-
port could participate in the project was an important topic. The modication
of the dihydropyridazinone moiety was planned to be performed by conventional
solution-phase chemistry. In addition, the left part (A) of the dihydropyridazinone
lead structure 1 was to be targeted by parallel solution-phase chemistry by synthe-
sizing a series of amides, inverted amides, sulfonamides, and ureas.
The replacement of the dihydropyridazinone by other heterocycles was to be
performed by combinatorial chemistry. This requirement was due to the fact that
the conventional synthesis of a small number of compounds (15) with new het-
erocyclic head groups would not fully explore the structural space. Furthermore,
the optimal substitution pattern of a new head group would not be known at the
beginning of the synthesis. Therefore, a proper design and selection of the rst
compounds would not be possible and the optimal substitution pattern of a mole-
cule with a new headgroup might be missed. On the other hand, we envisaged
that 200500 compounds had to be prepared within a structural class to nd initial
hits that would serve as starting points for further optimization. The necessity to
perform multistep syntheses of libraries and the need for further optimization
prompted us to use solid-phase chemistry methods. This approach would allow
not only a fast but also a very thorough and broad verication of the initial hits
with follow-up libraries.
28.2.3
4-Fluoro-3-nitroaniline as Central Core
To test a broad variety of heterocyclic head groups, the initial strategy was to use a
specic single intermediate as a central core and to modify this core with a variety
of heterocyclic nucleophiles as an approximate guide to which of these hetero-
cycles would be worth following up. 4-Fluoro-3-nitroaniline (2), because of its func-
tional group pattern, is a well-known building block in combinatorial chemistry
(Scheme 28.1). Using formyl-functionalized resin (3), this core was immobilized
by reductive alkylation. Owing to the low nucleophilicity of the aniline moiety, the
standard conditions for the imine formation [trimethylorthoformate (TMOF),
room temperature, 2 h] had to be enforced slightly: the mixture of starting mate-
rials was heated to 40 C overnight using TMOF as the dehydrating agent and sol-
vent [7]. Reduction was subsequently performed with tetrabutylammonium boro-
hydride in a mixture of acetic acid and dimethylformamide (DMF) (5:95) [8].
Acylation of the core was then performed under standard conditions to give the
left-hand part of the desired analog (4) of lead structure 1 [9].
Scheme 28.1. Fluoro-nitroaniline as central core gave access to

a variety of analogs of the lead structure 1.
In the next step, one of the heterocycles (510) was attached to the core by a
nucleophilic aromatic substitution reaction to give intermediates 11a. The reaction
worked well with reactive nucleophiles. Piperazine, for example, was coupled
quantitatively after stirring the resin with the amine (15 equiv.) in dimethyl sulf-
oxide (DMSO) at room temperature overnight. However, with poor nucleophiles
such as imidazole the alkylation reaction did not proceed in good yields at room
temperature and gave unsatisfactory results at elevated temperatures. However,
repeating the coupling reaction twice at room temperature gave products of su-
cient purity [> 85% by high-performance liquid chromatography/ultraviolet
(HPLC/UV) detection] for biological testing.
Following this route, the rst library of compounds with the general structure
11a was prepared using the indicated heterocycles 510 and aromatic carboxylic
28.2 Results 789
acid chlorides as building blocks. However, no biologically active compounds were

obtained. Therefore, the structural space around the core of 11a was investigated
more thoroughly via reduction of the nitro group to the corresponding aniline de-
rivatives (11b) (Scheme 28.1) using SnCl2 in DMF [10]. These conditions gave
much higher yields than reductions with Zn [11] or Fe reagents [12]. Derivatiza-
tion of the anilines using carboxylic acid chlorides or isocyanates gave, after cleav-
age, nal products 12 and 13. This methodology was exploited for the production
of a library of 460 compounds. Despite this rather large number, neither the urea
derivatives nor the amides showed biological activity. A possible explanation might
be a unfavorable set of building blocks. However, the size and constitution of the
library was thought to be large enough to cover such a broad range of substitution
patterns that this explanation was discarded. Thus, the cause of the lack of biolog-
ical activity of the whole library was thought to be either the heterocyclic moieties
or the presence of the meta-nitrogen substituent in the central core. If the rst ex-
planation had been the only reason for the lack of activity, it would have been
straightforward to establish the SAR of 1. However, the second reason made the
interpretation dicult. The situation was claried by the synthesis of the nitro-
substituted analog of 1, which was also inactive. Obviously, a meta substituent in
the central core was not tolerated. Since this substitution is a prerequisite for the
described chemical route the methodology was therefore abandoned.
28.2.4
Libraries Around Single Heterocycles
The approach of preparing a library of compounds with dierent heterocyclic

headgroups derived from one common intermediate had been shown to be poten-
tially misleading. Continuing the project, new routes to heterocyclic analogs of
lead structure 1 had to be developed. But rather than using one library to verify the
potential of a variety of heterocycles, future work concentrated on the preparation
of libraries with only one specic heterocyclic headgroup. Using this concept, mis-
leading chemical functionalities can be avoided more easily and individual hetero-
cycles can be veried more carefully. Thus, libraries of hydantoins and pyrazoles
were prepared. Again solid-phase chemistry was used to investigate the potential
of these structural classes.
28.2.4.1 Hydantoins
The targeted library of compounds 14 (Fig. 28.3) can be prepared retrosynthetically
from three types of building blocks: the hydantoin moiety can be built up from
an amino acid 15 and isocyanate 16, which are coupled and then cyclized under
basic conditions. The amide bond can be formed from the corresponding carbox-
ylic acid derivative 17 and an amine functionality can be prepared from the nitro
group in 16. Based on literature precedent [13], the ease of cyclo cleavage from the
support, and the fact that immobilized amino acids are commercially available,
the latter was chosen as the attachment point to the support, as indicated in Fig.
28.3.
Fig. 28.3. Building blocks for the synthesis of hydantoins and

the attachment point to the solid support.
In the rst series of experiments, the preparation of 18 and 19 started from im-
mobilized N-uorenylmethoxycarbonyl (Fmoc)-protected amino acids 20, 4-nitro-
phenylisocyanate 16, and carboxylic acid chlorides 21 (Scheme 28.2). The amino
groups of the amino acids were liberated using piperidine in DMF and then re-
acted with 16 to give urea 22. Subsequently, the nitro group was reduced to 23 us-
ing SnCl2 2H2 O in DMF at room temperature.
Scheme 28.2. Synthesis of a library of compounds having a

hydantoin moiety in common and otherwise displaying the
same structural pattern as lead 1.
The acylation of the resulting aniline 23 was rst investigated using carboxylic
acid chlorides (e.g. benzoyl chloride 21), although ultimately the synthesis of the
target amide 18 was envisaged to start from carboxylic acids since important
building blocks were not readily available as acid chlorides (e.g. nicotinoyl chlor-
ides). Benzoyl chloride (21) in dichloromethane and triethylamine (TEA) as base
gave the amide functionality in good yield and purity. The replacement of the
highly reactive acid chlorides by carboxylic acids, e.g. benzoic acid 24, proved to be
possible using TBTU as the activating agent [14]. The corresponding urea func-
28.2 Results 791
Fig. 28.4. Compound 25 was one of the few hydantoins displaying a weak biological activity.
tionality in 19 was prepared using isocyanates in ethyl acetate. This coupling reac-
tion gave signicantly better yields and purities in ethylacetate than in the more
commonly used solvents CH2 Cl2 [15] or DMF [16].
The cyclo cleavage to hydantoins 18 and 19 was highly dependent on the reac-
tion conditions. Based on literature precedent [13], the reaction temperature was
chosen to be 6070 C. Using TEA as base and a 1:1 mixture of methanol and
ethanol as solvent, only moderate yields of the cyclized products 18 and 19 were
obtained. The yield of the reaction was increased by using pure methanol as sol-
vent and a reaction time of 23 days. In accordance with the concept of cyclo
cleavage only the desired heterocyclic compounds are cleaved from the support
the purity of the products was good (>85% by HPLC) and approximately 600
compounds were tested for biological activity. Some of these compounds showed
weak activity, e.g. 25 (Fig. 28.4), which stimulated erythropoiesis approximately
1.5-fold. However, these hits were not further pursued since the activity was too
weak and, based on the already existing structural information, there was no po-
tential for further improvement.
28.2.4.2 Pyrazoles
Following the concepts outlined above, the replacement and modication of the
polar heterocyclic head group in lead structure 1 by a pyrazolyl group was the next
aim. A solid-phase synthesis of pyrazoles 26 based on 1,3-dicarbonyl compounds
27 as the key intermediates has been described by Marzinzik and Felder (Fig. 28.5)
[17]. The diketone 27 is prepared in a Claisen reaction from acetophenone 28 and
ester building block 29 [18]. Intermediate 27 is then condensed with a hydrazine
building block to give the corresponding pyrazole [19].
Following this retrosynthetic concept, two routes to the pyrazole analogs (30) of
lead 1 were investigated (Fig. 28.6). The rst route (a) proceeds via immobilized
Fig. 28.5. Literature route to pyrazoles.

Fig. 28.6. Retrosynthetic routes to the target structures.
secondary amide-substituted pyrazole (31), which is alkylated at the amide nitro-

gen atom with a variety of alkylating agents to give the nal products [20]. Since
this last step was thought to be critical (with respect to overalkylation and the re-
activity of the alkylating agents/diversity of the reagent pool) another route was
investigated rst (b): starting from a formyl resin [21] the rst step of the synthesis
is a reductive alkylation with amines to form immobilized secondary amine 32.
This intermediate is acylated with acetyl benzoic acid 28 to give diketo intermedi-
ate 27, which can be transformed to the product 30 (Fig. 28.6).
The reductive alkylation of the formyl resin 3 was performed with benzyl amines
34 in a two-step sequence using trimethylorthoformate as solvent and dehydrating
agent (Scheme 28.3). The imine was then reduced under acidic conditions using
Scheme 28.3. The Claisen condensation of substituted acetophenones. This result might
resin-bound acetophenone derivatives was be due to the fact that the immobilized enolate
reported for secondary amide-substituted is a much better nucleophile when bound to
acetophenone derivatives. However, the the support as secondary amide than as
reaction failed with resin-bound tertiary amide- tertiary amide.
28.2 Results 793
tetrabutylammonium borohydride in DMF/acetic acid (100:1). Subsequently, the

second building block, 4-acetyl benzoic acid (28), was coupled to the resin under
standard acylation conditions using TBTU as the activating agent to give 35.
Finally, attempts were made to synthesize the 1,3-dicarbonyl compound 36 rst
by a Claisen condensation using the conditions described in the literature for
monosubstituted amides [20 equiv. NaH, N,N-dimethylacetamide (DMA), 90 C,
1 h]. However, these conditions and a variety of others employing dierent sol-
vents and bases failed to give the product. In all cases, the starting material was
recovered.
In contrast to the rst result using disubstituted amides, the dicarbonyl com-
pound 37 (carrying only one substituent at the amide nitrogen) was accessible via
a Claisen condensation from 38 (Scheme 28.3). It is probably the case that the
enolate 39 formed under the strongly basic Claisen conditions from 38 is a better
nucleophile than enolate 40 (from 35) since the secondary amide can also be de-
protonated. This event is not possible when the enolate is bound as a tertiary
amide to the resin (Scheme 28.4).
Scheme 28.4. The immobilized enolate is a much better

nucleophile when bound to the support as a secondary amide
than as a tertiary amide.
The failure of route (b) (Fig. 28.6) prompted further investigation of the second
route (a): TentaGel resin TM 41 [22] was employed as support instead of Rink
amide resin [23] as used by Marzinzik and Felder since better and more reliable
results were obtained with the more solution-phase-like resin 41. Immobilization
of 4-acetyl benzoic acid (28) was performed under standard conditions. The subse-
quent Claisen condensation to 42 was achieved using benzoic acid esters in DMA
with NaH as base at 90 C (1 h). However, the reaction remained unreliable and no
general trends describing the reactivity of the ester components were observed.
Furthermore, reaction conditions could not be improved by using other bases (so-
dium methoxide [24], NaHMDS [25], sodium amide, potassium tert-butoxide [26]),
temperatures, reaction times, or solvents.
In solution phase, closely related reactions gave improved yields when 18-crown-
6 (18-C-6) was added [27]. This modication was also tested on solid support. In-
terestingly, in some cases the addition of 18-C-6 gave improved yields, but in many
other cases the reaction still did not work. The Claisen condensation remained a
critical step in the sequence, and for library production each ester building block
had to be tested prior to use. Furthermore, only esters which had no (acidic) a-
proton could be used. For the rst library, only aromatic esters were employed
(Scheme 28.5).
Scheme 28.5. Solid-phase synthesis of intermediate with hydrazines gave in all cases
primary and secondary carboxamides near equimolar mixtures of the two possible
containing the pyrazole moiety as the key regioisomers. For clarity, only one of the
fragment. Cyclization of the dicarbonyl regioisomers is shown.
The cyclization to pyrazoles 43 was cleanly achieved using a variety of hydra-

zines 44 in ethanol after stirring overnight at 70 C. No limitations concerning the
hydrazine building blocks were observed: hydrazine, and aliphatic and aromatic
derivatives thereof, gave consistently good yields and purities of the corresponding
pyrazoles (43). Isoxazoles were obtained from the reaction with hydroxylamine. In
all cases, roughly equimolar mixtures of the two regioisomers were obtained. For
initial biological testing these compounds were not separated. However, the sepa-
ration of the two regioisomers was in most cases possible by chromatography. For
clarity, only the active regioisomer is shown in the schemes.
The last step of the synthesis the alkylation of amide 43 to give, after cleavage
from the resin, the secondary amides 46 was the most critical one and required
the longest time for optimization. The deprotonation of solid-supported amides
with sodium hydride in DMSO [28] or with lithiated oxazolidinone in DMF [29] is
well described in the literature, but both bases gave unsatisfying results. Similar
results were obtained with lithium tert-butoxide in tetrahydrofuran (THF) [30] or
toluene. Best results were achieved using sodium hexamethyldisilylamide as base
in THF [31] under carefully controlled conditions (exclusion of water).
The rst library (Fig. 28.7) was prepared using a fully automated synthesizer
(Syro, MultiSyn Tech). Twenty-nine products (out of 120 theoretically accessible
compounds) of sucient purity (> 85% HPLC/UV detection) for biological testing
28.2 Results 795
Fig. 28.7. The rst libraries of pyrazoles. Within these libraries

the rst highly active compounds were identied and a SAR for
the hydrazine building block was established.
were obtained. This low success rate was due to the last modication step, which
required rigorous exclusion of any traces of water. This requirement is not readily
achieved using fully automated synthesizers.
The library was strongly inuenced by the SAR of the original lead structure 1,
and only a limited diversity was achieved. In vitro activity was not observed for this
library. However, since only a limited area of the available and accessible diversity
space was exploited, the biological activity of the entire virtual library was by far
not veried by this rst set of products. Therefore, a second library of 96 com-
pounds was prepared from 288 theoretically accessible compounds (Fig. 28.7). To
exploit further the chemical space accessible by the described chemistry, not only
the secondary amides 46 but also the primary amides 45 were submitted to testing.
Furthermore, a more diverse set of hydrazine building blocks was employed. In-
stead of using a fully automated synthesizer, the radiofrequency-encoding technol-
ogy from Irori TM (see Chapter 6) was used. This technique allows the preparation
of larger libraries as it is not restricted to spatial encoding of the products. Fur-
thermore, reaction conditions can be much better controlled and inert conditions
can be ensured more easily.
Within this second library, the rst biologically highly active compounds were
identied and a major breakthrough in the project was realized. Interestingly, it
was not the secondary amides (46) that were the active compounds but rather the
corresponding synthetic precursors (45). Furthermore, a rst SAR of the hydrazine
building block (R2) was identied: the N-methyl-substituted pyrazoles were the
Tab. 28.1. SAR of pyrazole substituent.

Entry Maximum
stimulation (%)
at [0.1 mM]
1 R H (50) 156
2 R Me (47) 410
3 R Et (48) 219
4 R i-Pr (51) 100
5 R t-Bu (52) 100
6 R Ph (49) 100
7 R Bn (53) 100
8 Isoxazole 54 314
most active compounds, e.g. 47, but already N-Et (48) and N-Bn (49) were signif-
icantly less active. The unsubstituted pyrazole 50 displayed some weak activity
(Table 28.1).
These initial results were conrmed by follow-up libraries and isoxazoles, e.g. 54
(Table 28.1), were identied as being almost as potent as N-methyl pyrazoles. Re-
sults for the R1 group were less clear and a variety of libraries were prepared using
a large set of ester building blocks. Based on the already established SAR the
number of hydrazine building blocks was kept small within these libraries. Bio-
logical testing nally established an SAR for the R1 building block (Table 28.2).
This residue was the most variable part of the molecule and many para-substituted
phenyl derivatives showed good activity; meta-Substituted phenyl derivatives were
less active and ortho-substituted compounds were inactive. Furthermore, a num-
ber of heterocyclic ester building blocks led to active compounds (Table 28.2).
Until this stage, three out of the four building blocks employed [acetophenone,
ester (R1), hydrazine (R2), and alkylating agent (R3)] had been modied. From this
optimization process involving around 600 compounds, pyrazole 55 was one of the
most active molecules in vitro (entry 1, Table 28.2). Compound 55 displayed a 4.5-
fold stimulation of erythropoiesis at rather high concentrations (0.1 mM). Based on
this result, in vivo experiments were initiated, but, disappointingly, no increase in
the hematocrit was observed. This result was most probably due to the poor phar-
macokinetic prole of 55: Cmax 0.16 kg L1 and area under the curve
(AUC) 0.11 kg h L1 after being given intraperitoneally to mice (Table 28.3).
Mono- and dialkylation of the primary amide with small alkyl groups increased
the metabolic stability [dimethylamide analog of 55 and 71 (for the synthesis, see
below): Cmax 0.193 kg L1 and AUC 0.416 kg h L1 after intraperitoneal ap-
plication to mice; Table 28.3], but was also associated with a loss of in vitro activity
[3.4-fold stimulation of erythropoiesis at a high concentration (10 mM)]. The rst
result indicated the primary amide functionality as an important point in the met-
28.2 Results 797
Tab. 28.2. SAR of arylester building block.

Entry Maximum
stimulation
(%) [ mM]
1 4-Triuoromethylphenyl (55) 450 [0.1]

2 3-Triuoromethylphenyl (56) 281 [10]
3 4-Fluorophenyl (57) 390 [0.1]
4 4-Chlorophenyl (58) 332 [0.36]
5 3-Chlorophenyl (59) 294 [1]
6 2-Chlorophenyl (60) 100 [0.1]
7 3,4-Dichlorophenyl (61) 156 [0.7]
8 4-Bromophenyl (62) 400 [0.3]
9 4-Methylphenyl (63) 390 [0.1]
10 4-Methoxy phenyl (64) 350 [0.1]
11 2-Pyridinyl (65) 360 [0.3]
12 2-Thiophenyl (66) 400 [0.03]
13 2-Benzofuryl (67) 330 [1]
14 2-(5-Ethyl)furyl (68) 370 [0.16]
15 4-Nitrophenyl (69) 330 [2]
16 4-Dimethylaminophenyl (70) 320 [0.12]
abolic degradation of 55 and probably also for the other hits within this class. To
address this problem and to obtain a thorough picture of the structureactivity
space around 55 and of the pyrazoles in general, the following issues were next
examined:
1 How can the primary amide functionality in hits 5670 be replaced to improve
metabolic stability?
Tab. 28.3. Pharmokokinetic prole of key compounds.
C (max) 0.16 kg/L 0.19 kg/L

AUC 0.11 kg h/L 0.42 kg h/L
Maximum 450 (0.5 mM) 340 (10 mM)
stimulation
AUC, area under the curve.

Fig. 28.8. Modications of the primary amide functionality in 55 to increase metabolic stability.
2 Is the pyrazole moiety the optimal central core?

3 If the pyrazole is the optimal core, does the acetophenone building block need
to be optimized?
Answering the rst question was a chemically demanding task since it required
a change in the link to the solid support and, as mentioned above, the Claisen
condensation was sensitive to substitution at the nitrogen. As potential replace-
ments for the primary amide, ve functionalities were considered: (1) carboxylic
acids prepared by hydrolysis of the primary amides, (2) (benzylic) amines as prod-
ucts of reduction of the corresponding amides, and (3) ureas, (4) sulfonamides,
and (5) inverse amides as derivatives of the benzylic amines obtained by reduction
(Fig. 28.8).
Some methods for the reduction of polymer-bound amides to the corresponding
benzylic amines have been described in the literature [32, 33]. However, we have
not obtained positive results for the reduction and subsequent acylation of pyr-
azoles on solid support, e.g. the sequence of reduction of 43 to 72, subsequent
acylation, and cleavage to give 73 failed (Scheme 28.6).
Since literature precedent is only given for easily accessible amide function-
alities, this failure was thought be due to steric hindrance around the amide func-
tionality. This problem was solved by solution-phase parallel synthesis: after cleav-
age of the products from solid phase the primary amides 45 were reduced using
borane in THF at room temperature overnight to give 74 [34]. The borane reduc-
tion proved to be superior to reductions with lithium aluminum hydride since the
work-up of the latter reaction in a parallel fashion was tedious [35]. The resulting
amines (74) were submitted to testing and, in addition, derivatized using acylating
agents and isocyanates to give analogs 73a and 73b (Scheme 28.6). However, the
activity of these libraries was very low. Therefore, these classes were abandoned.
To prepare the carboxylic acid analogs of 55 and other active pyrazoles, the linker
to the resin was redesigned. Instead of the amine-functionalized TentaGel SAM
resin TM 39 employed so far, it was thought that the corresponding Wang resin [36]
28.2 Results 799
Scheme 28.6. Amines and derivatives thereof were prepared as

analogs of 55 by a combination of solid- and solution-phase
chemistry.
would allow the preparation of acetophenone derivative 75 (Scheme 28.7), which

would then serve as the starting material for the Claisen condensation. The nal
products of this route would have been esters 76 and after cleavage the desired
carboxylic acids 77. However, the Claisen condensation of the ester-functionalized
acetophenone derivatives failed to yield the 1,3-dicarbonyl compounds. This prob-
lem could be caused by the immobilized ester reacting as an electrophile in the
Claisen reaction, and thereby being released from the support. However, the aceto-
phenone starting material was cleanly isolated after the failed reaction. Therefore,
this failure was probably the same as that observed for the condensation with im-
Scheme 28.7. Analogs of pyrazole 55 carrying tertiary amides

and carboxyl groups instead of the primary amide functionality
were prepared by a combination of solid- and solution-phase
chemistry.
Fig. 28.9. Carboxylic acid 79 the compound selected for preclinical development.
mobilized tertiary amide-functionalized acetophenone derivatives (Scheme 28.4)

a lack of nucleophilicity of the corresponding enolate.
The acid analogs of 55 were nally prepared by a combination of solid- and
solution-phase chemistry (Scheme 28.7). Primary amides 45 were synthesized
and cleaved from the resin, as described in Scheme 28.5, and were subsequently
hydrolyzed in solution to the carboxylic acids 77. This conversion was cleanly
achieved using in situ-prepared hydrochloric acid from TiCl 4 in a mixture of diox-
ane and water at 100 C [37]. Other, less sophisticated conditions (aq. HCl in THF
or alcohols; KOH in alcohols or in DMSO [38]) were also examined, but the results
were not satisfactory since the purity of the resulting products 77 was low.
The carboxylic acids 77 were tested and were also used as precursors for the
preparation of tertiary amides 78, which are not accessible by solid-phase chemis-
try (Scheme 28.7). The latter displayed only very low biological activity and were
consequently abandoned. On the other hand, the carboxylic acids 77 were as active
as the corresponding primary amides in vitro and the same SAR was observed for
the R1 and R2 groups. Consequently, 79 (Fig. 28.9) was tested for its in vivo activity
and an increased hematocrit was observed.
Although carboxylic acid 79 displayed an excellent biological prole, two features
were still open to question:
1 Is the pyrazole moiety the optimal central core?

2 If the pyrazole is the optimal core, does the acetophenone building block need
to be optimized?
The rst remaining question was answered by conventional chemistry, since

the development of a solid-phase methodology for the preparation of heterocyclic
analogs of 78 was envisaged to be too time-consuming with respect to the time
constraints at this stage of the project. Keeping the size of the heterocyclic cores
constant, the position, type, and number of heteroatoms were varied (Table 28.4).
Although the resulting structural changes were in some cases very small, e.g. 80
and 81, these molecules displayed a dierent SAR and were less active than the
corresponding pyrazoles and isoxazoles.
The second question of whether the para-acetophenone building block optimal
was resolved using established solid-phase chemistry: phenyl derivatives were the
most active class and para substitution was essential. Carboxylic acid 79 remained
the most active compound. Some pyridine analogs still displayed some activity,
whereas pyrimidine derivatives were found to be inactive.
28.2 Results 801
Tab. 28.4.
Entry Maximum
stimulation
(%) [ mM]
1 3,5-N-Methylpyrazolyl (82) 370 [0.1]

2 3,5-N-H-pyrazolyl (83) 220 [3]
3 3,5-N-Ethylpyrazolyl (84) 100
4 3,5-Isoxazolyl (85) 410 [0.4]
5 3,5-Oxadiazolyl (86) 380 [1]
7 3,5-Oxadiazolyl (87) 330 [3]
8 2,4-Triazolyl (88) 370 [1]
9 2,4-(5-Methyl)triazolyl (81) 330 [0.1]
10 3,5-(2-Methyl)-triazolyl (80) 300 [3]
The combination of the structureactivity relationship discussed above and the

biological properties which are described in the following paragraph rendered car-
boxylic acid 78 the most promising compound in the project. The compound was
promoted into preclinical development.
28.2.5
The Candidate for Preclinical Development
Carboxylic acid 79 has no PDE3 activity and dose-dependently increases the eects
of EPO (10 mU mL1 ). The EC50 is approximately 30 nM and the maximal re-
sponse is an approximately fourfold stimulation of the eects of 10 mU mL1
EPO. Thus, the sensitizing eects are displayed at the relevant EPO concentration
encountered in renal anemia. Even at high EPO concentrations, EPO-mediated ef-
fects were increased. In a mouse model, 79 (3 and 10 mg kg1 day1 orally, once
daily, 5 days of treatment) increased the hematocrit on day 8 by 1.9% points and
2.8% points respectively. However, the eects of 79 appear to be rather modest
compared with treatment with rhEPO, which gives an increased hematocrit of at
least 10% points after 5 days of treatment with 400 U kg day1 following the same
protocol.
The lack of a more pronounced increase, a fast return to baseline, and the total
absence of activity in rats were surprising. To exclude metabolic instability as a
potential explanation for these disappointing results, the kinetic parameters of 79
were determined in several species. In all species tested (mouse, rat, dog), no
pharmocokinetic problems were seen after peroral administration and very high
expositions could be achieved in mice and dogs: Cmax 0.847 kg L1 , AUC 9.9
kg h L1 and a 100% bioavailability after p.o. application to mice. These data ex-
cluded unfavorable pharmacokinetics as the reason for the modest in vivo eects.
However, a possible explanation for the limitation of the eects of EPO-sensitizing
agents can be given by the very tight regulation of the red blood cell mass in mice
and rats. Further studies concerning the biological activity of 79 are ongoing.
28.3
Combinatorial Chemistry in Drug Discovery
Over a period of 7 months approximately 700 pyrazoles and isoxazoles were pre-
pared within nine libraries with 2.5 Full-time-employees (FTEs). The libraries
varied according to size, the synthetic techniques employed (automated synthesizer,
radiofrequency tagged, manual synthesis), and the diversity of the building blocks
used. The rst libraries were mostly a verication of the method development and
the selection of building blocks was mostly ruled by the pre-existing SAR of the
lead structure dihydropyridazinone 1 and its close analogs. Still, these libraries
helped to identify the primary and not the secondary amides as relevant com-
pounds. The sizes and diversities of the next libraries were increased. These li-
braries further validated the SAR for the primary amides but did not help to solve
the lack of in vivo potency. However, based on the SAR, small and highly focused
libraries were prepared, in most cases manually, to verify the medicinal chemistry
hypotheses. By using parallel methods, this objective was carried out more quickly
and more thoroughly than would have been possible by conventional methods.
Combinatorial chemistry in solution and on solid support has been shown to be
a very successful tool in supporting drug discovery. To realize this potential, some
strategic considerations have been important:
. combinatorial chemistry joined the project early

. targeted libraries were prepared quickly (biological results were obtained within
23 weeks)
. learning cycles involving method development, production, and biological test-
ing have been short
. there has been close interaction with conventional chemistry (building block
synthesis, establishment of SAR)
The preparation of libraries of compounds not covered by the range of known

SARs is time-consuming and very risky. But once active compounds have been
identied within one of those libraries, the full potential of solid-phase chemistry
can be realized very quickly and with many advantages over conventional chemis-
try. Thus, taking the risk of preparing hundreds of inactive compounds (which will
then serve as feedstock for future HTS) is clearly outweighed by the prospect of
rapid success in medicinal chemistry programs if the project has been selected
properly.
Acknowledgements
The identication of 78 as a candidate for preclinical development was a tremen-

dous joint eort from various disciplines. However, the outline and the context of
this chapter does not allow for the presentation of all the results obtained within
the project, nor do they give sucient credit to all the people who participated
References 803
in this program. The contributions of Gabriele Braunlich and Jurgen Stoltefuss

(solution-phase chemistry), Ulrich Nielsch and Lorenz Mayr (in vitro data), Chris-
toph Gerdes (in vivo results), Klemens Lustig (pharmacokinetic data), and the
fruitful chemical discussions with Josef Pernerstorfer were essential for the project
and are gratefully acknowledged.
References
1 a) A. J. Erslev, Blood 1974, 44, 77; b) Alewood, Tetrahedron Lett. 1995, 36,
A. J. Erslev, N. Engl. J. Med. 1991, 7709; c) R. Ramage, S. L. Irving, C.
324, 1339; c) L. O. Jacobson, E. McInnes, Tetrahedron Lett. 1993, 34,
Goldwasser, W. Fried, L. Plzak, 6599; d) J.-U. Peters, S. Blechert,
Nature 1997, 179, 633. Synlett 1997, 348; e) S. Tomasi, M. Le
2 a) E. Goldwasser, Blood Cells 1984, Roch, J. Renault, J.-C. Corbel, P.
10, 147; b) W. Jelkmann, Physiol. Rev. Uriac, B. Carboni, D. Moncoq, B.
1992, 72, 449. Martin, J.-G. Delcros, Bioorg. Med.
3 R. T. Means, S. B. Krantz, Blood Chem. Lett. 1998, 8, 635; f ) S. H. Lee,
1992, 80, 1639. S.-H. Chung, Y.-S. Lee, Tetrahedron
4 W. Fried, C. Morley, Steroids 1985, Lett. 1998, 39, 9469; g) M. B. Francis,
46, 799. E. N. Jacobsen, Angew. Chem. Int. Ed.
5 J. W. Esbach, J. C. Egrie, M. R. 1999, 38, 937; h) R. C. D. Brown, M.
Downing, J. K. Browne, J. W. Fisher, Chem. Commun. 1999, 1547;
Adamson, N. Engl. J. Med. 1987, 316, i) C. Blackburn, B. Guan,
6 C. D. Demoliou-Mason, Exp. Opin. 9 a) S. M. Dankwardt, T. M. Phan, J.
Ther. Patents 1995, 5, 417. L. Krstenansky, Mol. Diversity 1996,
7 a) G. C. Look, M. M. Murphy, D. A. 1, 113; b) Y. Pei, R. A. Houghten, J.
Campbell, M. A. Gallop, Tetrahedron S. Kiely, Tetrahedron Lett. 1997, 38,
Lett. 1995, 36, 2937; b) M. M. 3349; c) S. Curtet, M. Langlois,
Murphy, J. R. Schullek, E. M. Tetrahedron Lett. 1999, 40, 8563; d) D.
Gordon, M. A. Gallop, J. Am.Chem. G. Hall, J. Tailor, M. Gravel, Angew.
Soc. 1995, 117, 7029; c) B. Ruhland, Chem. Int. Ed. 1999, 38, 3064.
A. Bhandari, E. M. Gordon, M. A. 10 a) D. A. Goff, R. N. Zuckermann, J.
Gallop, J. Am. Chem. Soc. 1996, 118, Org. Chem. 1995, 60, 5744; b) H. V.
253; d) G. C. Look, J. R. Schullek, C. Meyers, G. J. Dilley, T. L. Durgin,
P. Holmes, J. P. Chinn, E. M. T. S. Powers, N. A. Winssinger, H.
Gordon, M. A. Gallop, Bioorg. Med. Zhu, M. R. Pavia, Mol. Diversity 1995,
Chem. Lett., 1996, 6, 707; e) E. A. 1, 13; c) P. Grosche, A. Holtzel, T.
Boyd, W. C. Chan, V. M. Loh Jr, B. Walk, A. W. Trautwein, G. Jung,
Tetrahedron Lett. 1996, 37, 1647; f ) M. Synthesis 1999, 1961.
Schuster, J. Pernerstorfer, S. 11 a) S.-M. Yeh, C.-M. Sun, Tetrahedron
Blechert, Angew. Chem. Int. Ed. Engl. Lett. 1999, 40, 7247; b) P.-C. Pan,
1996, 35, 1979; g) Y. Wang, S. R. C.-M. Sun, Tetrahedron Lett. 1999, 40,
Wilson, Tetrahedron Lett, 1997, 38, 6443; c) C.-M. Yeh, C.-M. Sun, Synlett
4021; h) D. Maclean, J. R. Schullek, 1999, 810.
M. M. Murphy, Z.-J. Ni, E. M. 12 H. Perrier, M. Labelle, J. Org. Chem.
Gordon, M. A. Gallop, Proc. Natl. 1999, 64, 2110.
Acad. Sci. USA 1997, 94, 2805. 13 a) S. W. Kim, S. Y. Ahn, J. S. Koh, J.
8 a) B. Chenera, J. A. Finkelstein, D. H. Lee, S. Ro, H. Y. Cho, Tetrahedron
F. Veber, J. Am. Chem. Soc. 1995, 117, Lett. 1997, 38, 4603; b) J. Matthews,
11999; b) W. D. F. Meutermans, P. F. R. A. Rivero, J. Org. Chem. 1997, 62,
6090; c) A. Boeijen, R. M. J. 23 H. Rink, Tetrahedron Lett. 1987, 28,

Liskamp., Eur. J. Org. Chem. 1999, 3782.
2127; d) K.-H. Park, E. Abbate, S. 24 a) T. D. Penning, J. J. Tallay, S. R.
Najdi, M. M. Olmstead, M. J. Kurth, Bertenshaw, J. S. Carter, P. W.
Chem. Commun. 1998, 1679; e) A. Collins, S. Docter, M. J. Graneto,
Boeijen, J. A. W. Kruijtzer, R. M. J. L. F. Lee, J. W. Malecha, J. M.
Liskamp, Bioorg. Med. Chem. Lett. Miyashiro, J. Med. Chem. 1997, 40,
1998, 2375. 1347; b) I. Iijima, N. Taga, M.
14 a) O. Seitz, H. Kunz, Angew. Chem. Miyazaki, T. Tanaka, J. Uzawa, J.
Int. Ed. Engl. 1995, 34, 803; b) S. R. Chem. Soc., Perkin Trans. 1 1979, 3190.
Chhabra, A. N. Khan, B. W. 25 H. H. Seltzman, F. I. Carroll, J. P.
Bycroft, Tetrahedron Lett. 2000, 41, Burgess, C. D. Wyrick, D. F. Burch,
1099; c) K. Licha, S. Bhargava, C. J. Chem. Soc., Chem. Commun. 1995,
Rheinlander, A. Becker, J. 1549.
Schneider-Mergener, R. Volkmer- 26 P. Lhotak, A. Kurfuerst, P.
Engert, Tetrahedron Lett. 2000, 41, Nadenik, Collect. Czech. Chem.
1711; d) M. Antopolsky, A. Azhayev, Commun. 1992, 57, 385.
Helv. Chim. Acta. 1999, 82, 2130. 27 V. V. Popic, S. M. Korneev, V. A.
15 a) K. Burgess, D. S. Linthicum, H. Nikolaev, I. K. Korobitsyna,
Shin, Angew. Chem. Int. Ed. Engl. Synthesis 1991, 195.
1995, 34, 907; b) A. Wahhab, J. 28 a) L. A. Thompson, J. A. Ellman,
Leban, Tetrahedron Lett. 2000, 41, Chem. Rev. 1996, 555; b) J. M.
1487; c) G. Peng, A. Sohn, M. A. Ostresh, G. M. Husar, S. E.
Gallop, J. Org. Chem. 1999, 64, 8342; Blondelle, B. Dorner, P. A. Weber,
d) J. Habermann, S. V. Ley, J. S. R. A. Houghten, Proc. Natl. Acad.
Scott, J. Chem. Soc. Perkin Trans. 1, Sci. USA 1994, 91, 11138.
1998, 3127. 29 a) M. J. Plunkett, J. A. Ellman, J.
16 a) S. D. Lepore, M. R. Wiley, J. Org. Org. Chem. 1995, 60, 6006; b) M. K.
Chem. 1999, 64, 4547; b) T. Vojkov- Schwarz, D. Tumelty, M. A. Gallop,
sky, A. Weichsel, M. Patek, J. Org. Tetrahedron Lett. 1998, 39, 8397.
Chem. 1998, 63, 3162. 30 a) A. Nefzi, J. M. Ostresh, R. A.
17 a) A. L. Marzinzik, E. R. Felder, Houghten, Tetrahedron, 1999, 55,
Tetrahedron Lett. 1996, 37, 1003; b) A. 335; b) D. A. Heerding, D. T.
L. Marzinzik, E. R. Felder, Molecules Takata, C. Kwon, W. F. Huffman, J.
1997, 2, 17. Samanen, Tetrahedron Lett. 1998, 39,
18 K. H. Bleicher, J. R. Wareing, 6815.
Tetrahedron Lett. 1998, 39, 4587. 31 A. Nefzi, J. M. Ostresh, J.-P. Meyer,
19 D. R. Cody, S. H. H. DeWitt, J. C. R. A. Houghten, Tetrahedron Lett.
Hodges, J. S. Kiely, W. H. Moos, M. 1997, 38, 931.
R. Pavia, B. D. Roth, M. C. 32 a) W. Yun, R. Mohan, Tetrahedron
Schroeder, C. J. Stankovic, US Lett. 1996, 37, 7189; b) M. del
Patent no. US 5324483, 1994. Fresno, J. Alsina, M. Royo, G.
20 a) F. X. Woolard, J. Paetsch, J. A. Barany, F. Albericio, Tetrahedron
Ellman, J. Org. Chem. 1997, 62, 6102; Lett. 1998, 39, 2639.
b) S. H. H. DeWitt, J. S. Kiely, M. R. 33 a) Y. Aoki, S. Kobayashi, J. Comb.
Pavia, M. C. Schroeder, C. J. Chem. 1999, 1, 371; b) S. Kobayashi,
Stankovic, US Patent no. US Y. Aoki, Tetrahedron Lett. 1998, 39,
5582801, 1996. 7345; c) P. J. Brown, K. P. Hurley, L.
21 C. T. Bui, F. A. Rasoul, F. Arcole, Y. W. Stuart, T. M. Willson, Synthesis
Pham, N. J. Maeji, Tetrahedron Lett. 1997, 778; d) A. Nefzi, J. M. Ostresh,
1998, 39, 9279. J.-P. Meyer, R. A. Houghten,
22 P. Wright, D. Lloyd, W. Rapp, A. Tetrahedron Lett. 1997, 38, 931.
Andrus, Tetrahedron Lett. 1993, 34, 34 a) R. E. Gawley, J. Org. Chem. 1988,
3373. 53, 5381; b) H. C. Brown, P. Heim, J.
References 805
Org. Chem. 1973, 38, 912; c) H. C. 37 L. E. Fisher, J. M. Caroon, S. R.

Brown, P. Heim, J. Am. Chem. Soc. Stabler, S. Lundberg, S. Zaidi, C.
1964, 86, 3566; d) P. J. Brown, K. P. M. Sorensen, M. L. Sparacino, J. M.
Hurley, L. W. Stuart, T. M. Muchowski, Can. J. Chem. 1994, 72,
Willson, Synthesis 1997, 778. 142145.
35 a) R. A. Johnson, M. E. Herr, H. C. 38 a) J. Guillaumel, N. Boccara, P.
Murray, G. S. Fonken, J. Org. Chem. Demerseman, R. Royer, J. P. Bideau,
1968, 33, 3187; b) G. Manikumar, M. M. Cotrait, N. Platzer, J. Heterocycl.
Shamma, J. Org. Chem. 1981, 46, 386. Chem. 1990, 27, 605; b) A. C. Ellis, I.
36 S. Wang, J. Am. Chem. Soc. 1973, 95, D. Rae, J. Chem. Soc., Chem. Commun.
1328. 1977, 152.
806
29
Estimation of Stability and Shelf Life for
Compounds, Libraries, and Repositories in
Combination with Systematic Discovery of New
Rearrangement Pathways
Ferenc Darvas, Gyorgy Dorman, Tamas Karancsi, Tamas Nagy,
and Istvan Bagyi
29.1
Introduction
29.1.1
Stability and Shelf Life Characterization: the Need
With the emergence of high-throughput screening (HTS) and combinatorial

chemistry the most suitable drug candidates are selected from millions of new
chemical entities [1, 2]. Today, millions of compounds are synthesized and stored
every year with the aim of testing them in biological assays either immediately or
after a certain storage period in the hope of identifying new biologically active hit
compounds [3, 4]. It is one of the paradoxes of combinatorial chemistry that the
stability of the compounds is not considered to be as important as it is for other
chemical products. Marketed drugs, bulk, and ne chemicals normally possess an
expiry date stated explicitly by the manufacturers.
Today, practically every pharmaceutical corporation and a growing number of
academic research units with discovery research are involved in archiving discov-
ery compounds in solid state or in a frozen dimethyl sulfoxide (DMSO). Questions
as to how the purity of the substances changes as a result of prolonged storage
possibly combined with repeated melting and freezing of the DMSO solution are
largely unanswered, despite their serious implications for the new lead research.
The lack of stability of the compounds, which is due to their chemical structure,
the nature of impurities, as well as the less than optimal storage and handling,
have a primary impact on discovery research in two ways: through inventory
losses, and, which is more important, via the increased frequency of false-positive
results.
False positives resulting from the lack of stability of library members probably
cost the pharmaceutical industry $600900 million in 2000 (assuming 200 million
HTS assays worldwide with a 0.1% hit rate, a cost of $30,000 per false positive, and
1015% decomposed members among the tested libraries). In general, drug can-

ISBN: 3-527-30509-2
didates that fail to exhibit sucient stability should be stopped before investing
millions of dollars [5].
29.1.2
Stability Characterization: Empirical Studies
Giving an estimation about the purity degradation of a stored library over a time
period, such as a year, is principally a simple procedure: quality sampling before
and periodically during the storage can lead to a quantitative description about the
purity deterioration. These data can be utilized to develop a qualitative picture of
the library or repository stability. Such empirical studies of the library stability are
easy to perform and might be useful as a rst guess regarding the expected stabil-
ity issues.
To the best of our knowledge, the rst open account of an empirical stability
study was presented by Ortner in 1995 [6], in which she stated that approximately
20% of a collection of several thousand organic compounds (combinatorial library
members and individually synthesized samples) stored in ethanol degraded over a
1-year period.
At Merck [7], @10,000 compounds were stored at 20 C, 0 C and at room
temperature in DMSO for a year. The decomposition ratio, which was measured
by high-performance liquid chromatography/mass spectrometry (HPLC/MS), sug-
gested that compounds fall into two distinct classes: stable and unstable samples.
Compounds belonging to the unstable class had already decomposed to a large ex-
tent within 6 months. Storing the samples at 20 C did not signicantly improve
the stability of the compounds compared with storage at 0 C. The European
Union is also sponsoring an empirical study involving regular periodic purity
checking of 10,000 compounds by LC/MS and nuclear magnetic resonance [1 H-
nuclear magnetic resonance (NMR)] for a period of 3 years [8].
29.1.3
Stability and Shelf Life Estimation: Model-based Approaches
Empirical studies unfortunately suer from the problem that they do not deliver
an exact forecast about the future quality of the samples studied. Also, it is dicult
and subjective to extrapolate conclusions drawn from these studies to other sam-
ples. They generally do not allow conclusions to be drawn on a number of impor-
tant stability issues, such as structurestability relationships, the inuence of dif-
ferent storage conditions on the stability, or the implications of the quantity and
nature of the impurities for the stability of the compounds.
Three years ago, the authors concluded that a more qualitative stability descrip-
tion was needed in the eld of combinatorial libraries and repositories, and, as a
result, developed a model that extends beyond empirical description. As a starting
point, models introduced at stability expiry date determination of drug substances
are applied (see Section 29.7).
808 29 Estimation of Stability
The fundamental assumption is that long-term degradations are simply thermal

decomposition with a retarded rate at lower temperatures. It is assumed that deg-
radation processes are speeded up by elevating the degradation temperature. The
degradation rate at high temperature is characteristic of the structure and it can be
used to estimate the shelf life under storage conditions at a particular temperature.
The shelf life of a chemical species (compound, library, collection, or repository),
according to our denition (and essentially according to the ICH guidelines, see
Section 29.7), is a time interval that the species is expected to remain within an
approved purity specication provided that it is stored under the conditions pre-
scribed by the respective stability enforcing protocol.
The concept of expiry timing in combinatorial chemistry was rst mentioned by
Fitch and coworkers in 1998 [9], while a model and algorithm for the calculation of
expiry date/shelf life [stability expert system (Stabex TM ) approach] was suggested
by Darvas and coworkers in 1999 [10], and published in 2000 [11].
The present chapter describes the dierent elements of a new area of HT stabil-
ity studies, which we call combinatorial stability assessment. Combinatorial sta-
bility assessment deploys the computational armory (diversity, analog search, and
clustering) and experimental methodology of combinatorial chemistry in order to
obtain fast measurement-supported predictions for the stability characteristics of
libraries or repositories. This chapter introduces the authors approach and valida-
tion studies. In the course of developing this assessment, the authors found that
the experimental method used for stability studies can be utilized in the systematic
discovery of new scaold structures via thermal rearrangements of heat-stress-
challenged library members, as described in Section 29.5. Throughout the chapter,
stability is used to refer to chemical stability (as opposed to metabolic stability).
29.2
Methods and Tools for Combinatorial Stability Assessment
29.2.1
Modeling Intrinsic and Extrinsic Factors Inuencing the Stability of Individual
Compounds
The major factors of combinatorial library stability can be classied into two
groups: intrinsic and extrinsic factors [12]. Intrinsic factors are the properties that
are inherent to a compound with absolute purity and depend solely on the chemi-
cal structure. From our point of view, the decomposition rate of the pure com-
pound at dierent temperatures is the most important property. Less relevant fac-
tors of the pure compound are sensitivity to light, sensitivity to exposure to air or
oxygen, and sensitivity to humidity.
Extrinsic factors of compound stability are the conditions that are beyond the
chemical structure of the compounds being studied. Such factors are the purity of
the library members, the chemical nature and the distribution of the impurities,
such as the accumulated side products and reagent residues, and the nature of the
solvent(s) used for storage of the compounds. External factors, such as the tem-
perature of storage, the speed of the repeated freeze/thaw cycles, or the chemical
nature of the container are also included in this group.
The authors have proposed that the eect of the intrinsic factors should be
modeled by the Arrhenius equation [11], as described in Section 29.8. This model
enables a qualitative shelf life time to be predicted (and, therefore, the expiry date)
for solid compounds in a pure state or in solution for a single solvent system
under xed storage conditions, if we assume that no structure-dependent interac-
tion exists between the compounds and the impurities or the solvents respectively.
These assumptions can be investigated by statistical signicance testing calculations.
However, the model cannot be used to give a forecast of how the shelf life will be
changed if essential storage conditions are altered, for instance whether the sub-
stances are stored in DMSO instead of as a solid or in plastic instead of glass vials,
since the listed extrinsic factors are not part of the Arrhenius model. For treating
such eects, a dimensional analysis approach has been suggested by the authors
[10], but it is not detailed here.
29.2.2
Modeling: from Compounds to Libraries
Theoretically, the best stability estimation can be gained when both Arrhenius pa-
rameters (a and b) are determined for each individual compound in the library.
But, this would require vast numbers of tests to be conducted. For fast estima-
tion of the entire compound library composed of structurally similar compounds,
a single slope of the Arrhenius line (b) can be used in theory. A good approxima-
tion is to apply an average b, which is calculated from the previously determined b
values of the individual compounds or cluster representatives. According to this
assumption, a slope transposition can be used within clusters to determine the
interception of the Arrhenius line (a) for the compounds within the rest of the
library cluster.
Stability estimation of combinatorial libraries by experimental determination of
the Arrhenius parameters for individual compounds is time-consuming work. It
would be advantageous to reduce the number of experiments by identifying corre-
lation between structural similarity and stability. The correlation can be deter-
mined by performing a homogeneity test, which is a statistical parallelism test [13]
of the Arrhenius lines for library members (Fig. 29.1). If no signicant dierence
between the slopes of the regression equation can be proven, a joint regression
line can be calculated for the entire library, which will be used to estimate a shelf
life for each individual compound in the library.
29.2.3
Modeling: from Libraries to Repositories
If a repository consists of sets of libraries, and, furthermore, the homogeneity test

is successful for these libraries, a simplied stability test can be attempted on the
Fig. 29.1. Parallelism test of the Arrhenius plots.
entire repository. The stability test includes a homogeneity test for each library in
the repository followed by a decrease in the number of homogeneous libraries
using cluster analysis [14], and an experimental stability test for individual com-
pounds that represent the reduced homogeneous library clusters.
There is another way to model stability: if the collection of compounds can be
divided into several, discrete structure-related stability classes, the number of ex-
periments can be reduced by using simplied experimental techniques, plus sta-
tistical calculation, which ensures a robust classication of the products into the
stability classes.
29.2.4
Realization of Shelf Life Estimation for Individual Compounds and Combinatorial
Libraries
In a typical combinatorial library, compounds are designed around specic core

structures and the cores are surrounded by a standard substituent set. Based on
structural similarity with regard to those library elements, the compounds can be
clustered into structurally related subsets. Then, a representative sample set for
each cluster (series 1) is determined in a given library. Each compound in series 1
is stored at multiple (e.g. ten) elevated temperatures for a given time, which results
in a measurable degradation in the thermal analysis module (Fig. 29.2).
The compounds are analyzed using HPLC before and after the incubation to
determine the thermal decomposition of compounds. For structurally unrelated
individual compounds in a compound repository, a similar thermal analysis pro-
cedure is followed.
The measured data are processed in the calculation module (Fig. 29.3) for the
estimation of the shelf life. (For calculating the results of the validation studies, cal-
culation modules written in C and in Visual Basic language of the central data-
Fig. 29.2. HT thermal analysis module.
Fig. 29.3. Calculation module of the shelf life for (a) individual
compounds and (b) combinatorial libraries.
base management system at ComGenex, Inc. are utilized. Part of the information
system is an expert system, which is still under development. It is intended to pro-
vide a virtual stability screening during the evaluation phase of the library design
and to establish structurestability relationships.) The decomposition rate con-
stants for each elevated temperature are calculated from the measured degradation
according to the decomposition kinetic equation (Section 29.8, Eq. 1). The rate
constants are used to generate Arrhenius parameters by linear regression (Section
29.8, Eq. 2). If the Arrhenius line is extrapolated to lower temperatures (e.g. room
temperature), k25 and the shelf life can be calculated according to Eq. 2 (now T
refers to 25 C) and Eq. 3 (Section 29.8) respectively. The minimum acceptable
purity limit or percentage of acceptable purity loss should be dened before cal-
culation.
As noted above, in the case of structurally unrelated individual compounds, each
of them should be tested at multiple temperatures. However, for structurally clus-
tered compounds the shelf life estimation for the rest of the library (series 2) is
based on the degradation at one, optimally selected temperature, assuming that
their decomposition kinetics (the temperature dependence of the rate constants)
are similar.
29.2.5
Instrumentation
For thermal decomposition analysis, test compounds are distributed to wells and
incubated in various media at dierent temperatures in time- and temperature-
controlled multiwell heating blocks, e.g. MultiAger TM (see Fig. 29.12, [15]). The
decomposition of compounds is monitored by a HT HPLC system equipped with
ultraviolet (UV) and integrated with a two-arm robotic sample processor that in-
jects samples and collects fractions. For identication of degradation products on-
line LC/MS experiments are performed. Data acquisition and overall system oper-
ation software are integrated to a central database management system.
29.3
Validation Studies for Combinatorial Stability Assessment
29.3.1
General Experimental Conditions
Initial purities of the individual compounds were 70% or better (determined by

HPLC at 254 nm). Stability investigations were performed using dry materials,
composed of about 20% crystalline materials and 80% dry lms. For the storage
and for the thermal decomposition experiments, polypropylene wells were used.
Owing to the recognition limit for degradation monitoring, an upper limit of the
prediction of shelf life of 15 years was selected.
29.3.2
Stability Study for an Indole Library
For validation studies, from an indole library [11] of 1385 members (Fig. 29.4), ten
compounds were selected randomly as a learning set (to determine the model
Fig. 29.4. The indole core-based library investigated in the stability validation study.
parameters). Another set of 16 compounds was chosen from the same library for
the validation of the stability assessment model.
In order to check the linearity and parallelism of the correlation between log kT
and 1=T, the learning set of ten compounds was stored at ten dierent temper-
atures (115190 C) for two dierent durations (in time intervals of 1 h and 17 h).
Two rate constants for each temperature were calculated from the measured deg-
radation (Section 29.8, Eq. 1). The average values of the rate constants were used
for the generation of the Arrhenius parameters (Section 29.8, Eq. 2).
The model was validated at two levels. First, using the Arrhenius equation, the
rate constants of the compounds were calculated and extrapolated to 75 C and 100

C. The rate constants at 75 C and 100 C were used to estimate the decreased
purity of the compounds after storage for a predetermined time. The decomposi-
tion was monitored experimentally by HPLC. The estimated and the measured
purity values were compared for six compounds (shown in Table 29.1; the re-
maining four compounds did not show signicant degradation).
Two examples of linear regression calculated for the learning set are shown in Fig.
29.5. Since they are structurally related, their b values are similar. They conrm the
expected correlation between the log kT and 1=T values. Based on the temperature
dependence, kT was estimated at lower temperatures in order to estimate the shelf
life of the compounds under storage conditions.
To further validate the model, b values determined experimentally from the
learning set were used to predict the purity of the structurally similar set of 16 com-
Tab. 29.1. Comparison of the predicted and detected values of purity for the learning set of
compounds.
Entry Initial Experiment 1 (100 C, 40 h) Experiment 2 (75 C, 171 h)

purity
(HPLC) Purity Prediction Dierence Purity Prediction Dierence
(%) (HPLC) (%) (%) (HPLC) (%) (%)
(%) (%)
1 99 82 77 5 96 81 15
2 92 80 85 5 90 88 2
3 97 78 86 8 95 90 5
4 93 92 92 0 91 92 1
5 97 87 90 3 92 93 1
6 98 93 92 1 97 96 1
Fig. 29.5. Linearity checking of the temperature dependence

of the decomposition rate constants (examples of Arrhenius
plots for two members of the learning set between 115 C and
190 C).
pounds. The a and kT values for the validation set were determined from a single
thermal decomposition experiment at 150 C according to the Arrhenius law (Sec-
tion 29.8, Eq. 2). Then, a and b were used to calculate the decomposition rate con-
stants at two temperatures: 105 C and 115 C. The purity loss, estimated for a par-
ticular length of time at 105 C and 115 C, was compared with the experimental
results for the ten compounds as shown in Table 29.2 (the remaining six com-
pounds did not show signicant degradation).
The majority of the predictions (80%) t the experimental data well. However, in
some cases, the decomposition was overestimated or underestimated, possibly as a
result of dierent degradation pathways (Table 29.1, entry 1, experiment 2; Table
29.2, entries 7, 9, and 11). At these high temperatures, the overall degradation
mechanism may be dierent from that at storage temperature. The predicted HPLC
Tab. 29.2. Comparison of the predicted and detected values of purity for the validation set of
compounds.
Entry Initial Experiment 3 (115 C, 67 h) Experiment 4 (105 C, 46 h)

purity
(HPLC) Purity Prediction Dierence Purity Prediction Dierence
(%) (HPLC) (%) (%) (HPLC) (%) (%)
(%) (%)
7 97 55 71 16 72 88 16
8 95 95 95 0 95 95 0
9 95 80 66 14 85 85 0
10 99 97 97 0 98 99 1
11 97 75 10 65 96 47 49
12 97 93 91 2 95 95 0
13 95 95 88 7 92 93 1
14 99 99 99 0 99 99 0
15 98 97 98 1 98 98 0
16 97 82 85 3 95 93 2
results of the remaining test compounds were in good agreement with the mea-
sured ones.
In some cases (Table 29.2, entries 8 and 14), the initial purity and the purity after
the thermal decomposition test were identical, i.e. these compounds did not show
thermal decomposition they had a long shelf life.
Although monitoring thermal decomposition is faster at higher temperatures,
this results in a loss of reliability of the predictions because of the changes in the
overall kinetics along with the increased temperature.
29.3.3
Combinatorial Stability Investigation for a Small Repository
In these investigations, a small repository of 3000 compounds was considered that

had signicant diversity. The repository is composed of 300 libraries; each library
has ten members.
The initial study to establish the optimal temperature and time ranges valid for
the whole repository was performed with a representative set of 10% of the repos-
itory. Library members were selected and incubated at eight dierent temperatures
(6095 C) for 192 h. During the large-scale test performed for the remaining re-
pository compounds, treatment at 75 C for 192 h was selected as the experimental
conditions. The rate constants at higher and lower temperatures as well as the
Arrhenius parameters and the shelf life of compounds at 25 C were determined.
For the practical purposes of these investigations, a relative shelf life is dened as
the time period in years needed for a 10% purity loss (measured by HPLC).
The results obtained for the shelf life of 1178 compounds are shown in Fig. 29.6.
Interestingly, a particular pattern was observed for the distribution of the shelf life
of compounds, with three maxima at 3, 6, and 11 years.
Fig. 29.6. Shelf life distribution of compounds with detectable degradation.
29.4
Stability Investigations in Combinatorial Drug Discovery
The investigation of the stability of combinatorial libraries can be useful at dier-

ent stages of the drug discovery process, e.g. the pilot design phase (as exemplied
in the following lead optimization program based on cyclopentapyrroles), the library
evaluation, and the hit validation.
29.4.1
Pilot Design Phase
An early hit of a cyclopenta[b]pyrrole derivative showed very promising 5-

lipoxygenase and SRS-A antagonist activity [16]. To check the synthetic feasibility,
a core scaold of a cyclopenta[b]pyrrole derivative (Fig. 29.7) was synthesized. Un-
fortunately, the compound faced serious stability problems, with an unusually
short chemical lifetime when exposed to air. In order to stabilize the heterocyclic
core structure, electron-withdrawing groups (R3) had to be introduced to reduce
the electron density of the ring system. Alternatively, bulky substituents resulted in
the same eect by increasing the steric hindrance in the vicinity of the pyrrol ring.
These structural modications incorporated into the synthetic scheme led to a
series of stable analogs [17].
For example, introducing a NO2 group into the phenyl ring at position 4 increased
the stability vefold, when R1 and R2 were hydroxyl groups. Furthermore, if the
29.4 Stability Investigations in Combinatorial Drug Discovery 817
Fig. 29.7. Stabilization of the cyclopenta[b]pyrrole core.
hydroxyl groups were protected with bulky pivaloyl groups, sixfold higher stability
was detected. Proton NMR studies based on the downeld eect of the chemical
shift of the pyrrole proton conrmed that in the rst case the electron density was
signicantly reduced while in the second case no changes were observed, indicat-
ing that the stabilizing factors are purely steric eects.
To avoid similar problems, a two-stage stability checking procedure is advisable.
First, empirical knowledge in combination with an expert system should be used
to determine structural features which may lead to unstable library structures that
are still in the design phase. Second, during the pilot chemistry feasibility studies,
the pilot matrix representing the major reactivity classes of substituents can be
used in a combinatorial stability study. The matrix can show how the substituents
aect the chemical stability and which substituents should preferably be eliminated
from the full library. Initial stage stability investigations should be extended to
the key intermediates. Since the last intermediates can often be the main source
of impurities of the nal library, knowledge about their stability is a key factor in
ensuring that library products not only show high quality immediately after the
production but also retain their quality for a longer period of time.
Poor chemical stability often prevents the synthetic realization of a promising
new library. On the other hand, changing the substitution pattern in the library
design phase can avoid the stability problems in a number of cases.
29.4.2
Libraries
All library members reect their synthetic history through their impurity prole.
Properly designed combinatorial stability assessment of the library members could
reveal interactions between the impurities and the major product library member,
which result in a deterioration of its long-term stability. Poor stability often prevents
the optimization of a lead structure or extra eort is required to stabilize the mol-
ecule at later stages of drug development. (In one of the HIV entry inhibitor hit
Fig. 29.8. Cluster representative (entry 17) of 2-(a-aminoalkyl)-3H-quinazolin-4-one-based cores.
compounds, identied from a ComGenex library, analytical retesting revealed side

products during the hit validation procedure that were most possibly due to decom-
position [18].) Such a stability analysis can guide purication, which is designed to
maintain and ensure long-term stability for the library and its members.
29.5
A Way Towards Systematic Discovery of New Rearrangement Pathways
Combinatorial stability assessment and routine investigations can be combined

with systematic discovery of new thermally induced chemical transformations or
rearrangements, such as in the case of 2-(a-aminoalkyl)-3H-quinazolin-4-one-based
cores [17] Fig. 29.8. An almost clean thermally induced chemical transformation
was detected [19] using a special discovery module (Fig. 29.9). The HPLC/UV trace
was signicantly dierent for the parent and thermally treated entities (Fig. 29.10);
however, the molecular masses were identical in both cases (523 M 1 pseudo-
molecular ion for the sample shown in Fig. 29.10).
After analyzing several compounds, a similarly unique fragmentation pattern was
identied for the parent and daughter peaks, indicating a consistent transformation
pathway. One of these spectra is shown in Fig. 29.11.
Based on the mass spectrometry (MS) data, three possibilities were considered:
a dihydroquinolinone core (I), a spiro fused tetrahydroquinazolineimidazolidine
ring system (II), and a ring-opened structural variant (III) (Scheme 29.1). More
detailed structural determination together with further chemical and mechanistic
considerations seemed to support the third pathway. The corresponding fragmenta-
tion pattern is shown in Scheme 29.2. The transformation identied here is a ring-
chain tautomerism, consistent with literature data [20]. These results can be extra-
polated to the entire cluster, searching for the same rearrangement ngerprint.
29.5 A Way Towards Systematic Discovery of New Rearrangement Pathways 819
Thermal rearrangement discovery module.

Fig. 29.9.
820
29 Estimation of Stability
Fig. 29.10. HPLC/MS monitoring of thermal rearrangement (entry 17).

Fig. 29.11. Fragmented mass spectra of the thermally treated (upper) and the original (lower) sample (entry 17).
29.5 A Way Towards Systematic Discovery of New Rearrangement Pathways
821
Scheme 29.1. Possible rearrangement pathways.
Scheme 29.2. Fragmentation pattern.
Selected library members have already been used for the discovery and charac-
terization of thermally induced transformations by combining MS fragmentation
with standard structural analytical methods [21, 22]. To detect thermal rearrange-
ment, routine process-specic MS fragmentation patterns (rearrangement nger-
prints) need to be identied and subsequently recognized by the appropriate
software tools. The MS ngerprint species a unique fragmentation pattern that
29.7 Appendix I: Stability Testing of Drug Substances 823
indicates the formation of a new sublibrary via thermal rearrangement and will
rapidly speed up the identication of such transformations.
Such rearrangements can be transferred to a synthetic preparative protocol. This
approach can be considered as an equivalent of the Houghten library-from-library
approach [23] via thermal rearrangements.
29.6
Summary
The approach presented in this chapter for predicting shelf life and expiry date
for compounds, libraries, and repositories is based on modeling reaction kinetics,
modeling, completed with thermal decomposition experiments in which a series of
purity measurements of the compounds are involved. To save experimental time
and substances, extrapolation techniques of the experimental values for sub-
libraries, libraries, and repositories are proposed. Algorithms, software and expert
system solutions, instrumentation for thermal decomposition, and high through-
put analyses are integrated with a chemical database management system to a
uniform, high-performance stability estimation solution the Stabex TM system.
Stabex TM is capable of estimating the stability of several tens of thousands of
library members per month in the library design and synthesis phases, or, later,
during the systematic, long-term stability investigation of the whole repository.
Stability investigations of the key intermediates promise the synthesis of com-
pounds which may remain pure for a long time, thus contributing to a future total
quality discovery management system.
As a side product of the high throughput analytical procedures associated with
the stability investigation, a systematic search and discovery of new thermal re-
arrangements is proposed and has been demonstrated in this chapter.
29.7
Appendix I: Stability Testing of Drug Substances
Stability expiry date determination of drug substances is well regulated and con-
trolled by standardized international guidelines. Besides the photochemical- and
media-initiated structural changes, the most important factor that inuences chem-
ical degradation is the temperature.
Guidelines for stability testing are determined by the International Conference
on Harmonization (ICH), which dene three levels of stability testing: stress, accel-
erated, and long-term (real) stability testing. All three have dierent roles in stability
analysis [24, 25].
29.7.1
Stress Stability Testing
Stress stability testing is undertaken to elucidate intrinsic stability characteristics

of the drug substance and to provide data on forced decomposition products and
decomposition mechanisms (degradation pathways). Such testing is normally car-

ried out under more severe conditions than those used for the (normally later) ac-
celerated tests. Degradation products are collected in quantities necessary for their
chemical identication. Reference products are also collected for accelerated and
long-term studies, an expected impurity prole for the decomposition products has
also been established.
29.7.2
Accelerated Stability Testing
Accelerated stability testing is designed to increase the rate of chemical degrada-

tion or the physical change of an active drug substance or drug product using ex-
aggerated storage conditions as part of the formal, denitive, storage program.
These data, in addition to long-term stability studies, may also be used to assess
longer term chemical eects at nonaccelerated conditions.
29.7.3
Long-term Stability Testing
Long-term stability testing is carried out to evaluate the stability of the physical,
chemical, biological, and microbiological characteristics of a drug product and a
drug substance, covering the expected duration of the shelf life and retest period,
which are claimed in the submission and will appear on the labeling.
The shelf life, according to the ICH guidelines, is a time interval that a drug
product is expected to remain within an approved specication provided that it is
stored under the conditions dened on the label in the proposed containers and
with the correct closure.
A related term is the expiry/expiration date, which is a date placed on the
container/labels of a drug product designating the time during which a batch of
the product is expected to remain within the approved shelf life specication if
stored under dened conditions and after which it must not be used [24, 25].
29.8
Appendix II: The Arrhenius Model
Thermal activation is a frequently used empirical model simulating long-term de-

composition kinetics at the storage temperature [26, 27]. Forced decomposition
under thermal stress conditions (at multiple temperatures) allows Arrhenius pa-
rameters to be extracted, which are needed for extrapolation to any storage temper-
ature.
This accelerated stability proling provides a sucient approximation of selected
structural representatives of a cluster. The dened Arrhenius parameters can be
transferred to structurally related compounds to estimate the shelf life from a sin-
gle stress stability experiment.
The algorithm used for calculating shelf life involves three kinetic equations.
29.9 Appendix III: Model Realization -- the Stabex TM System 825
From the decrease in purity at a given temperature, which is determined using

HPLC, the rate constant of thermal decomposition of compounds (kT ; l/s) can be
calculated according to Eq. 1,
ln C0 =C
kT 1
t
where C0 is the initial purity (v/v, %); C is the measured concentration of the com-
pound of interest in the untreated sample (v/v, %); Ccrit is the minimum purity
requirement of compounds at a given storage temperature (v/v, %); and t is the
duration of the thermal burden treatment (h).
Having measured the rate constant at dierent elevated temperatures, a (inter-
cept of the Arrhenius line) and b (slope of the Arrhenius line) parameters can be
determined according to the Arrhenius law (Eq. 2). Using a and b, the rate con-
stant can be extrapolated to lower (including ambient) temperatures:
b
log kT a 2
T
where T is the temperature (K).

From the extrapolated kT value, the shelf life is calculated according to Eq. 3:
ln Ccrit =C0
t shl 3
kT
where t shl is the shelf life (years).

If the t shl value is low for a cluster, it can be eliminated from the initial library.
29.9
Appendix III: Model Realization the Stabex TM System
In the traditional drug development process, stability testing is a low throughput

process, which is designed individually for each drug candidate based upon a de-
tailed plan. Performing these tasks for large sets of compounds is a rather complex
procedure, which would benet from an integrated system. The Stabex TM system
has been developed to solve the following combined tasks:
1 Evaluating the shelf life of libraries under initial study before production.
2 Evaluating the shelf life of library members after production.
3 Retrospective evaluation of the shelf life of the repository already available.
4 Development and methodological studies of combinatorial stability issues.
Stabex TM has specic links to the elements of the CMT library technology [28],
which integrates library design, synthetic plan evaluation, synthesis and purica-
tion, HT analyses, storage, and data management. The overall owchart for
Stabex TM is shown in Fig. 29.12.
826
29 Estimation of Stability
Fig. 29.12. Combinatorial stability assessment system overview.

References 827
Acknowledgements
Thanks to Peter Slegel (EGIS Pharmaceuticals, Budapest Hungary) for his contri-
bution to this work and helpful discussions. The help given by Robert Ferenczi
and Gabor Pocze (ComGenex) is much appreciated.
References
1 A. Furka, Drug Dev. Res. 1995, 36, 11 F. Darvas, T. Karancsi, P. Slegel, G.

112. Dorman, Gen. Eng. News, 2000, 20,
2 R. A. Houghten, C. Pinilla, S. E. 3034.
Blondelle, J. R. Appel, C. T. Dooley, 12 F. Darvas, T. Karancsi, P. Slegel, G.
J. H. Cuervo, Nature 1985, 354, Dorman, A Stability Prediction System
8486. for Estimating Library Expiry Time.
3 J. N. Kyranos, J. C. Hogan, Jr, Proceedings of the CHI Conference
Modern Drug Discovery 1999, July/ Drug Discovery, Tokyo, Japan, 2000,
August, 7381. poster presentation 8.
4 R. Wedin, Modern Drug Discovery 13 H. Spath, Cluster Dissection and
1999, January/February, 4753. Analysis. Ellis Horwood, Chichester
5 A. Persidis in: Combinatorial 1985.
Chemistry and Technology/Principles, 14 H. Mager, Moderne Regressionsanalyse.
Methods and Applications. Miertus, Otto Salle Verlag, Frankfurt am Main
S. and Fassina, G. (eds), Marcel 1982.
Dekker, New York 1999, pp. 405422. 15 Allen P. Mills, European Patent, EP
6 M. J. Ortner, Proceedings of the CHI 1115120.
Conference on Studies on the Impact 16 Z. Kapui, G. Dorman, J. Ivanics, G.
of Solvent and Storage Conditions on Galambos, I. Stadler, Pharm. Res.
the Stability of Dierent Chemical Comm. 1988, 20, 195196.
Groups within High Throughput 17 G. Dorman, unpublished data.
Screening Libraries, Exploiting 18 A. K. Debnath, L. Radigan, S. Jiang,
Molecular Diversity, Small Molecule J. Med. Chem. 1999, 42, 32033209.
Libraries for Drug Discovery, CHI 19 F. Darvas, T. Nagy, T. Karancsi, P.
Conference, Wendy Warr & Associates, Slegel, G. Dorman, Combinatorial
Holmes Chapel UK, 1995, pp. 3738. Discovery of New Thermal Rearrange-
7 M. Valenciano, Proceedings of the ment Pathways. Proceedings of
SBS CSS Discussion Group on Sub- IKCOC-8, 2000.
stances, SBS 5th Annual Conference 20 R. E. Valters, F. Fulop, D.
and Exhibition, Edinburgh, UK 1999. Korbonits, Adv. Heterocyclic Chem.
8 H. Herklots, Modern Drug Discovery 1996, 66, 171.
2000, March, 4650. 21 D. B. Kassel, Chem. Rev. 2001, 101,
9 W. L. Fitch, G. C. Look, G. Detre 255267.
in: Combinatorial Chemistry and 22 S. Lane in: Separation Methods in
Molecular Diversity in Drug Discovery. Drug Synthesis and Purication,
Gordon, E. M., Kervin, Jr, J. F. (eds), Handbook of Analytical Separations,
Wiley-Liss, New York 1998, pp. 349 vol. 1. Valko, K. (ed.), Elsevier
368. Science B. V., Amsterdam 2000, pp.
10 F. Darvas, Proceedings of the SBS 160161.
CSS Discussion Group on Substances, 23 J. M. Ostresh, B. Dorner, S. E.
SBS 5th Annual Conference and Blondelle, R. A. Houghten in:
Exhibition, Edinburgh, UK 1999, Combinatorial Chemistry Synthesis
p. 127. and Application. Wilson, S. R.,
Czarnik, A. W. (eds), John Wiley Tripartite Guideline, ICH Steering

and Sons, New York 1997, pp. 225 Committee 2000.
240. 26 D. Dollimore, Analyt. Chem. 1996,
24 Stability Testing of New Drug 68, 63R71R.
Substances and Products, Q1A, ICH 27 S. Vyazovkin, C. A. Wight, Annu.
Harmonized Tripartite Guideline, ICH Rev. Phys. Chem. 1997, 48, 125149.
Steering Committee 1993. 28 F. Darvas, L. Kovacs in: High-
25 Stability Testing of New Drug Throughput Screening. Devlin, J. P.
Substances and Products (Revised (ed.), Marcell Dekker, New York 1997,
Guideline), Q1A(R), ICH Harmonized pp. 223242.
829
Part V
Novel Applications of Combinatorial Chemistry

ISBN: 3-527-30509-2
831
30
Concepts of Combinatorial Chemistry in
Process Development
Markus Eckert and Ulrich Notheis
30.1
Introduction
30.1.1
General
Automation, high-throughput screening, and combinatorial chemistry have already

revolutionized biological high-throughput screening and laboratory-scale prepara-
tive chemistry. The combinatorial synthesis of large libraries of small drug-like
molecules became a standard tool in medicinal chemistry. Over the last few years,
these methods have been nding their way downstream to larger scale chemis-
try, catalyst research, and process development.
Here, shorter development times and increasing numbers of clinical develop-
ment candidates have increased the pressure to identify and optimize ecient
large-scale syntheses for life science intermediates and products quickly. The prin-
ciples of combinatorial chemistry seem to be appropriate to fulll these demands,
not only for the synthesis of life science products but also for the process develop-
ment of basic and bulk chemicals.
30.1.2
Subject of this Chapter
In this chapter, we want to give a description of the possibilities and challenges for
combinatorial chemistry in the dierent phases of process development with the
focus on ne chemicals. Therefore, we review some principal issues of process
development which have had an inuence on the use of combinatorial methods in
process development. Furthermore, strategies and equipment for the implementa-
tion of parallel screening methods in the laboratory will be discussed.

ISBN: 3-527-30509-2
832 30 Concepts of Combinatorial Chemistry in Process Development
30.1.3
Literature
Although the real revolution in high-throughput screening happened only one

decade ago, some of the underlying ideas and strategies are as old as the science
of chemistry itself.
For example, parallelization can be traced back to the sixteenth century, when G.
Agricola, in the rst book on industrial chemistry in modern times, describes how
700 pairs of pots were placed in an array of rows and were used for the prepa-
ration of mercury from its ores (see Fig. 30.1) [1].
Fig. 30.1. Parallel working in the sixteenth century [1]. A, The

burning hearth; B, the timbers; C, the unlit hearth, into which
the pots are put; D, the rocks; E, the rows of the pots; F, the
upper pots; G, the lower pots. We thank the Agricola
foundation for kind permission to reprint this gure.
The pioneering work on spot test plates was performed in the 1920s and 1930s
by F. Feigl [2], who began preparing materials on spot test plates to analyze spe-
cic properties afterwards. Impressive examples of fast quantitative analysis of
heavy metals are given in the journals of that time [3].
Also, parallel catalyst screening was used by Mittasch in the development of the
ammonia process during the rst 20 years of the twentieth century [4]. The use
of parallel reactors for the testing of heterogeneous catalysts was described in the
1950s [5]. However, parallelization was limited, as, for example, Dowden and
Bridger stated in 1957: a test apparatus . . . can advantageously be multiplied to
give a greater rate of testing, providing the temptation to overtax both observer and
supervisor is avoided [6].
Obviously, this limit could not be overcome until the era of computers and pro-
cess automation. Therefore, just recently, numerous articles and books have been
published covering the topic of automated synthesis in process development. The
main emphasis has been on chemical process development in the pharmaceutical
industry.
An excellent review was published in 1999 by Harre et al. describing automated
chemistry in organic process research and development [7]. Describing the pio-
neering work that started during the 1980s, they revealed that most published ex-
amples were based on a Zymark robot system. Second, owing to the lack of other
commercially available solutions some companies launched programs with in-
house developments such as the DART (development automated reaction toolkit)
system of Glaxo Wellcome [8], or the ATLAS (assessing technologies for laboratory
automation in synthesis) initiative by SmithKline Beecham [9].
Nowadays, the user has the choice between several commercially available sys-
tems with dierent degrees of automation and features. Harre et al. presented a
table with a dozen systems available as at summer 1999 [7]. In mid-2001, the boom
for parallelization in process development is continuing, leading to a greater vari-
ety of apparatus available on the market (see Tables 30.1 and 30.2).
Since 1996, numerous examples of the optimization of organic reactions by par-
allel process development have covered almost the whole area of organic chemistry.
Recommended literature in this respect is by Hird [10], Orita et al. [11, 12], Zhang
et al. [13], Gooding et al. [14], Kirchho et al. [15], and Emiabata-Smith et al. [8].
In addition, there are two books covering special aspects of parallel process devel-
opment. The book Automated Synthetic Methods for Specialty Chemicals, edited by
William Hoyle, includes a number of papers presented at a Royal Society of Chem-
istry symposium in 1999 [16]. For process development especially, the contribu-
tions by Evens [17] and by Armitage and Smith [18] are relevant, describing their
experience with the Anachem SK233 workstation and the HEL AutoMate system.
Owen and Dewitt wrote about Laboratory automation in chemical development
in Process Chemistry in the Pharmaceutical Industry, edited by Gadamasetti [19].
They predict a shift of paradigm, where simply the emulation of manual methods
with automation is not enough, but the chemists must develop techniques that are
suited to automation, e.g. statistical experimental strategies.
30.2
Process Development
30.2.1
Overview and Denition
The task of process development is to make a dened product available to a given

specication, on a given scale, in a dened time-frame.
In life sciences, process development is usually divided into several phases. Fre-
quently, expressions such as route scouting, process screening, process opti-
mization, and process characterization and validation are used.
Process development is usually carried out by interdisciplinary teams of chemists
and chemical engineers, with the emphasis shifted from chemists to engineers as
the development proceeds. A schematic representation of the development teams
role in the whole development workow has been described by Carpenter for the
example of an agrochemical product (Fig. 30.2) [20, 21]. In particular, the important
input of the route selection step onto process development is elaborated as well as
the two targets of process development in agrochemical production:
1 optimizing the process and

2 delivering rst quantities for eld trials.
For basic chemicals, process development is carried out along similar lines, how-
ever the route scouting, the choice of dierent starting materials and routes, is
usually very limited and much more emphasis is put on process design, engineer-
ing, and plant design.
Fig. 30.2. Development process for an agrochemical product [20].

30.2.2
Combinatorial Chemistry in Process Development
In contrast to combinatorial chemistry eorts in drug discovery where hundreds

of compounds (libraries of products) are desired, in process development only one
molecule is of interest and synthetic ways of producing this molecule are the main
focus (libraries of reaction conditions). Thus, the evaluation of many possible
combinations of reaction parameters has to be achieved by parallelization, automa-
tion, and miniaturization. Furthermore, split-and-mix approaches cannot be applied
in this setting.
Proper identication of reaction conditions requires very carefully controlled re-
action parameters and the acquisition of many data sets including, for example, the
control of nonuniform temperatures and stirring rates. Furthermore, standardized
and repetitive runs have to be included to allow proper statistical validation of the
reaction yields and conditions.
Within the area of process development for basic chemicals, parallelization is
mostly used for the development of heterogeneous catalysts and, here, predom-
inately for gas-phase reactions. Catalyst screenings are classied by their degree of
parallelization, the complexity, and type of information gained from each experi-
ment. A typical primary screening classies a large number of solvents or catalysts
as good or bad according to a set of standard conditions, whereas a quaternary
screening gives detailed information for a single catalyst and an optimized set of
process parameters. These expressions do not correspond to the nomenclature used
in the context of process development for ne chemicals. The discussion of com-
binatorial chemistry in heterogeneous catalysis would go beyond the scope of this
article and the reader is referred to the corresponding literature. A current list of
examples, where combinatorial methods have been used, can be found in an arti-
cle by Senkan [22]. Recently, a special issue was devoted to topical developments in
combinatorial heterogeneous catalysis [23].
30.2.3
Demands on Process Development
For our discussion, it may be helpful to understand the special requirements that
process development has to meet in the whole business workow (Fig. 30.3).
As already mentioned, one of the main goals of process development is to en-
able the manufacture of the desired product in the desired quantity to the required
specication. But, additionally, often equally important goals include shortening
the time to market, and achieving the least expensive manufacturing process. For
the production department, robustness and simplicity of the process are the two
guiding principles in this endeavor.
The process, moreover, has to be environmentally benign and should be the best
long-term route. Last, but not least, the synthetic route must be unimpeded by ex-
ternal patents and, in order to strengthen ones intellectual property position, it
should be patentable.
Fig. 30.3. Business constraints for process development.
In this environment, time is the parameter where parallelization and combina-

torial chemistry can help to achieve the desired information faster, and valuable
information per time can serve as a measure. Another important parameter is the
cost of the process development. Increasing the eciency of the laboratories and
thus reducing the overall laboratory costs can be achieved by a rather small invest-
ment in parallel process development equipment. However, compared with the
benet of cutting the development time, those laboratory cost savings are marginal.
According to the priorities given to the topics presented in Fig. 30.3, at a rst
glance least expensive seems to be most important. This view is only true if all
the prerequisites are given: there is no prot at all, if the process is not scalable, if
it does not give the product in the demanded analytical specication, or if it is not
safe. (This statement has signicant impact on considerations in Section 30.3.1.)
Additionally, if the solution cannot be worked out in the supposed time frame, mar-
ket shares will be lost. This result can easily exceed the additional costs of a more
expensive alternative process. All these associations have to be borne in mind when
strategies for parallelization in process development are discussed.
30.2.4
Process Development for Dierent Applications
Process development is a complex and diverse eld because the targets of process
development, its strategies, and approaches dier depending on the kind of product
and the production scale. These can range from millions of tons of basic chemicals,
where an improvement in the reaction selectivity of less than 1% saves several mil-
lion Euros, to sensitive pharmaceuticals, where world production varies between
100 kg and several tons per year under strict quality requirements (GMP). For any
product in between these extremes, an adequate process needs to be developed,
taking into account a number of specic basic conditions:
. Proportion of material costs

Any given product can be classied by the ratio of material costs to total pro-
duction costs. For large-scale chemicals, material costs may exceed 70% of the
total cost, whereas for ne chemicals the percentage may be well below 10%. The
higher the percentage of the material costs in relation to total costs, and the higher
the scale, the more will the process aim at selectivity rather than at spacetime
yield.
. Available budget
The process development for the production of bulk chemicals requires a far
larger budget than the process development for the production of ne chemicals.
This factor inuences the size and dedication of the combinatorial screening
apparatus. For big projects, it is protable to design dedicated, process-tailored
workstations, whereas for small projects commercially available standard equip-
ment is usually favored.
. Timescale/milestones
The development of a new process for a bulk chemical can take more than 5
years, whereas the rst 10 kg of a new pharmaceutical development candidate
usually has to be delivered within a few months. If only a limited number of ex-
periments can be performed before the next milestone, the eort to be put into
the development of specic parallelization methods has to be considered pre-
cisely.
. Constraints given by existing equipment/plants
Since new processes in the area of ne chemicals usually have to be developed
in accordance with the existing production facilities, the chemist has to consider
whether the reactor where the target process is to be realized is already xed and
known.
In general, when developing a process for a dedicated plant, custom-made or
specially adapted equipment is recommended, whereas for multipurpose plants
a standard (commercial) parallel screening apparatus seems adequate.
Tab. 30.1. Factors which inuence the design of parallelized equipment.
Variable/constraint Basic chemicals Fine chemicals
Scale of the process 1000100,000 tons 0.011000 tons

Plant Continuous Batch
Dedicated Multipurpose
Time line 110 years 10 days to 2 years
Ratio material costs per total costs High Low
Budget for process screening High Low
Screening apparatus Dedicated, tailored Multifunctional, standard
Screening stage, where started Often primary catalyst Late-stage process screening
screening
Given that in the ne chemical business dedicated plants will only be built for
runaway successes, the production of most ne chemicals requires processes
with a high degree of simplicity which t a standard apparatus.
. Topical stage of development
Improving an existing industrial process usually includes minimizing invest-
ments and changing as little as possible in the plants equipment. Often, process
parameters are optimized within narrow margins determined by the already ex-
isting plant reactors, which can be changed only at extraordinary costs. In this
case, it is not necessary to set up a primary screening for a totally new synthesis.
If the goal is to nd a new, revolutionary route to a product using new feedstocks
or totally dierent chemistry (dream reactions), the situation is reversed.
All of these factors have to be taken into account when discussing parallelization
in process development more precisely. Table 30.1 gives a short summary of the
key issues.
30.3
Parallelization in Process Development
30.3.1
Number of Experiments Compared with Scale of Experiment
On the one hand, it is obvious that by carrying out more experiments a higher de-
gree of optimization will be achieved and, thereby, a better process. Here, paral-
lelization can help either by reducing the time for a given number of experiments
or by performing more experiments in a given time.
On the other hand, the process has to be scaled up: thermochemistry, speed of
addition, and work-up (e.g. ltration, precipitation, extraction, or distillation) have
to be adjusted to the available apparatus, or a suitable apparatus has to be con-
structed. Therefore, the reaction is run on dierent scales, and, if applicable, in dif-
Fig. 30.4. Scaling up and screening intensity.
ferent modes (batch or continuously); typically, it is run in a miniplant and a pilot

unit.
These two goals optimization and scaling up are largely independent of one
another (Fig. 30.4)!
For example, even thousands of experiments carried out on a milligram scale
cannot replace a pilot run. For an ecient process development, the hits from
primary screening have to be followed up in another screen under more dened
conditions and on a larger scale (secondary screen). Since a larger number of
hits is expected from the primary screening, the secondary screening also needs a
reasonable degree of parallelization (typically 1:5 to 1:100). The same holds for the
tertiary screen.
Therefore, the typical picture of a pyramid results (Fig. 30.5), with decreasing
numbers of reactions in consecutive screens. At the top, one optimal set of param-
eters is created and veried in a single representative and fully scalable reactor
(parallelization 1).
For high eciency in process development, the existing screens have to be
combined and experiments have to be performed at the smallest relevant scale. It
is crucial to check the results from earlier screens in the more precise later screens
as soon as possible and to set up mass and mole balances to detect artifacts stem-
ming from lack of scalability, errors in analysis, or a lack of reproducibility.
Fig. 30.5. Dierent phases in process development.
30.3.2
Requirements and Equipment for Parallelization in Dierent Development Phases
30.3.2.1 Route Scouting

During route scouting, completely dierent routes to the target molecule are dis-
cussed and investigated.
For this discussion, the knowledge and experience of process development chem-
ists regarding scalability, safety, and specic plant capabilities are highly valuable.
Therefore, the most fertile combinatorial approach lies in a parallelization of sev-
eral biocomputers, called brainstorming. In this context, the Eli Lilly Internet
venture InnoCentive recently suggested a new way of global brainstorming [24].
The venture publishes Lilly research problems in organic synthesis on the world-
wide web and oers a reward of up to US$100,000 for the best veried route. It
will be interesting to see whether this approach nds imitators in other pharma-
ceutical companies in the near future.
For experimental investigation, the more promising routes are selected on the
basis of rst-shot experiments. Based on these results, the decision as to which
route should be further developed has to be made. Sometimes, one could start
with two or three routes in an orientating process screening to obtain a better basis
for prioritization, and then cancel the worst ones. The equipment for rst-shot
experiments should be of a simple set-up adaptable to various dierent reactions.
Since this approach overlaps with process-screening equipment, details will be
discussed below.
In the future, a shift of the ratio between the discussion and the experimental
investigation of the route-scouting process is likely. The easier a large number of
rst-shot experiments can be carried out by parallel process development equip-
ment covering more dierent routes in more detail at a time, the more the specu-
lative discussion part will be replaced by early experimental facts.
This consideration has an impact on rst-shot experiments in steps where the
inherent understanding of the process is low or the parameter space is large. If,
for example, in the case of asymmetric hydrogenations a route is skipped on the
basis of only a handful of experiments, this approach would be fatal.
In those cases, the rst-shot experiments should involve several parallel runs
over the chiral ligand database (e.g. 3 96 experiments) to obtain a true estimate
of the potential of this route.
30.3.2.2 Process Screening

In process screening some basic knowledge of the reaction already exists. For ex-
ample, if a certain Lewis acid has been selected in a FriedelCrafts acylation, then
dierent solvents at dierent temperatures should be screened. In general, pro-
cess screening and route scouting proceed at the same scale and parameters
are screened with similar equipment, therefore both areas are discussed in one
section.
What parameters are screened in process screening? A number of reaction condi-

tions are screened in small-volume batch runs. The interesting target parameters
are often only conversion and selectivity with an accuracy of G10%. Sometimes, a
yes/mediocre/no answer or a relative order (X is better than Y . . .) are sucient
results from the process screening, especially in the early stage. The reaction vari-
ables screened are solvents, temperatures, additives, catalysts or other reagents,
protecting groups, stoichiometry, reaction time, etc. for each synthetic step. The
data acquisition is usually restricted to thin layer chromatography (TLC), gas chro-
matography (GC), or high-performance liquid chromatography (HPLC) analysis
of the reaction mixture, either only at the end-point or in addition to one or two
measurements at intermediate run times.
What are the requirements for parallel process screening equipment? In this devel-
opment phase, most chemists use standard apparatus such as 50- to 100 mL asks
with magnetic stirrers. If sucient starting material is available, batches of 2550
mmol are preferred. The more sophisticated the intermediates and the more valu-
able the 23 g of step 8 material are, the more opportune are microscale reactions:
however, the handling of small amounts of substances becomes more dicult when
changing from the few grams scale to the few milligrams scale.
To transfer a standard ask set-up into a parallel screening set, it is desirable
to keep the most common features constant, including working under an inert
atmosphere (degas/nitrogen purge), mixing (preferably stirring), cooling/heating,
reux, adding liquids through a dropping funnel, adding solids altogether through
an opening under counternitrogen ow, collecting small samples for analysis dur-
ing the reaction, and no cross-contamination by neighboring cells. Some special
features such as distilling a reaction component out of the reaction mixture for
equilibration shifting are sometimes necessary.
The preferred vessel size is around 2050 mL, it should not be smaller than
5 mL and not larger than 100 mL. The temperature range should be 50 C to
200 C. Sometimes, systems operate at up to 120140 C, which is often not high
enough. An independent temperature control for each reaction vessel would be the
best case, but often this increases apparatus costs exponentially. We regard 612
simultaneous reactions per set as a good throughput, especially when the temper-
ature for all vessels per set is the same. In the case of automated workstations in a
dedicated laboratory, a higher throughput can be realized.
Examples of commercially available automated workstations For standard chemis-

try, the full range of automated organic synthesizers can be considered. Most of
them are based on an automated dispenser or x, y,z robotics. Within the widely
known systems are the Benchmark station from Advanced ChemTech, the Tecan
Genesis ChemSystem Workstation, the Chemspeed workstations ASW 1000 and
2000, Zinssers Sophas, Bohdans Neptune or the Anachem SK 233 (Table 30.2).
For the dierent applications in primary screening and process screening, every
user has to make his/her own decision: which reaction volume, temperature range,
or mixing form is best suited to screened chemistry? The Anachem SK 233 station
is one which has been used for process development purposes to a larger extent
recently. In collaboration with Glaxo, a special reux unit was developed, which is
now commercially available as Reactarray SK 233.
Preferably for late-stage process screening, the Bohdan process development
workstation oers 12 magnetically stirred reaction vessels with independent tem-
perature control per run. The Bohdan process development workstation and the
Reactarray SK 233 are both good options for automated late-stage process screen-
ing. Recently, HEL has oered a system named Chem-Scan, consisting of a com-
pact x, y,z robot with a maximum of three reaction blocks, each with ten stirred
10-mL reactor cells. The reaction blocks are available either with one temperature
control for all cells or with individual temperature control for each cell. (See Fig.
30.6 for examples of apparatus for each process development phase, or visit the
web sites of the companies; for internet addresses, see Tables 30.2 and 30.3.)
Examples of commercially available low-automated multiple reaction stations Ex-

amples of commercially available low-automated multiple reaction stations are
given in Table 30.2. The list in this table is not exhaustive, but it gives a diverse
selection of appliances for parallel screening, which allow syntheses of 0.5100 mL
at temperatures from 80 C to 250 C. An important criterion is whether or not
the system has individual temperature control for each vessel. Equipment without
this feature is roughly an order of magnitude less expensive than the apparatus
with it. The price categories listed in Table 30.2 refer to the basic set-up in mid-
2001, but this information is supplied without liability. Most simple reaction sta-
tions use test tubes as vessels, e.g. H P blocks, Stem blocks, Argonaut FirstMate, or
Radleys Carousel. The stirring is mostly based on magnetically driven stirring bars.
An interesting alternative is given by Argonaut: the stirring bar is moved vertically
by a large pneumatically driven magnetic bar in the middle of the apparatus.
To ll the gap between nonautomated and fully automated stations, Argonaut
has produced a system called Quest. Originally designed for organic solid-phase
synthesis, the Quest 210 (20 10 mL) and the Quest 205 (10 100 mL) are also
suitable for process screening.
Every user has to make his/her own decision as to whether there are additional
requirements for the application under consideration, e.g. an independent inert
gas supply for each vessel. The ease of adding liquids and solids during the reac-
Fig. 30.6. Examples of commercially available equipment.

844
Tab. 30.2. Workstations for route scouting and parallel process screening.
Workstationb Number of simultaneous Vessel size (mL), agitation Temperature control, Price Internet;
reactions individual (yes/no) category a http://www
Advanced ChemTech, Benchmark 8, 16, 40 and 96-well reactors (70)150 C, no E peptide.com

Bohdan, Neptune TM , MiniBlock TM 12 48 4.5 mL, shaker (40)120 C, no E bohdan.com
66 40 mL, shaker
ChemSpeed, MSW500, ASW 2000 112 13 mL, shaker (70)150 C, no E chemspeed.com
28 75 mL, shaker
Reactarray Workstation, Anachem 5 10 25 mL, magnetic 5150 C, no E Reactarray.com
SK 233
Tecan, Genesis 96-well reactors or reactor D Tecan.com
blocks
HEL-Chem-Scan 10 10 mL (80)300 C, no (optional) D Helgroup.co.uk
Bohdan, Process Development 12 25 mL magnetic (20)140 C, yes E Bohdan.com
Workstation
Advanced ChemTech, LabMate 24 160 mL (78)150 C, no B peptide.com
Calypso Reaction Block System 6 50 mL A charybtech.com
STEM Reaction Block System 10 25 mL, magnetic 5150 C, no A stemcorp.com
30 Concepts of Combinatorial Chemistry in Process Development
H P, Variomag 6 or 12 100 mL, magnetic (80)200 C, no A hp-lab.de

H P, 48 er Block 48 10 mL, magnetic (80)200 C, no A hp-lab.de
Bohdan MiniBlock 6 40 mL, shaker (40)120 C, no A Bohdan.com
Radleys, Carousel 12 1015 mL, magnetic RT160 C, no A Radleys.co.uk
Argonaut, Quest 210 20 510 mL magnetic, (40)130 C, no (2 temp. C Argotech.com
vertical parallel)
Argonaut, Quest 205 10 100 mL magnetic, (40)130 C, no (2 temp. C Argotech.com
vertical parallel) magnetic,
vertical
Argonaut FirstMate 12 magnetic, vertical (78)130 C, no A Argotech.com
Radleys, GreenHouse Parallel 24 0.53 mL magnetic, RT160 C, no A Radleys.co.uk
Synthesizer vertical
Radleys, Metz Parallel Reaction Station 6 150 mL, magnetic 5150 C, no A Radleys.co.uk
Hel-Chem-Scan, High-Pressure 8 10 mL, magnetic, 100 bar RT200 C, no D Helgroup.co.uk
Argonaut, Endeavor 8 58 mL, mechanical, 33 RT200 C, yes (max. 20 C D Argotech.com
bar dierence between two
neighbors)
Parr Multiple Reactor System Series 6 75 mL, magnetic 200 bar RT300 C, yes C Parrinst.de
5000
a Price categories: A <10 T@; B 1025 T@; C 2575 T@;
D 75125 T@; E 125175 T@.
b Numerous names of companies and equipment used in this table
are registered trademarks.
30.3 Parallelization in Process Development
845
tion, the option of collecting samples at reux conditions, and the exibility and
connectability to other glassware and equipment need to be taken into account.
Sometimes a system appears to be the best despite oering only a few features;
often, these systems provide a high degree of freedom and exibility for arranging
a personalized and chemistry-oriented set-up. In our laboratories, we have used
one set-up over ten times: a simple block set-up based on a H P block for six or
12 standard 100-mL side-cap bottles. These bottles are available with one or two
additional screw cap arms originally made for enzyme chemistry. These arms are
suitable for liquid and solid addition, sample collection, etc. Instead of a closed
screw cap, we use three-bore Teon caps, which are available with standard screw
threads for Bola ttings. A stop cock for argon/vacuum, a reux condenser, Teon
tubing, for example to connect a dosimeter pump, or an internal thermometer can
be easily attached (Fig. 30.7). This set-up is more like a small vessel than a test
tube. Each system is independent and built from mass-produced inexpensive
equipment. This multiple reaction set-up has exhibited good properties in numer-
ous standard reactions for ne chemical processes, including Grignard and diazo-
nium salt chemistry. Of course, it is not automated, but it enables the bench
chemist to carry out up to 12 experiments in parallel.
For high pressure reactions dierent pieces of apparatus are required. There are
only a few systems available on the market that are suitable for higher pressure
hydrogenation or carbonylation chemistry. Argonaut Technologies oers a work-
station called Endeavor for reactions up to 33 bar. It has individual temperature
control (restricted to 20 C temperature dierence between vessels) from room
temperature to 200 C and mechanical stirring for eight vessels each containing
Fig. 30.7. Nonautomated multiple reactor block.

58 mL. For reactions at these low pressures we regard the Endeavor workstation
as a good system. Parr instruments oers a multiple autoclave system for high-
pressure applications up to 200 bar and 300 C. Six autoclaves, each containing
75 mL, can be run with magnetic stirring at the same temperature. Besides variants
working with inlets for a single autoclave, such as similar systems developed by
SmithKline Beecham, Parr, and others, this multiple reaction station is suitable for
process screening of, for example, asymmetric hydrogenations and reactions that
need very high temperatures (200 C and 300 C). A pressure range up to 100 bar
is oered by the HEL High Pressure Chem-Scan. Here, eight 10-mL reactors for
temperatures up to 200 C can be congured in one row; the stirring is accom-
plished by a specially xed magnetic anchor agitator.
30.3.2.3 Process Optimization
Which parameters are screened? In process optimization, the most promising

route based on the results of the process screening is selected. The yields from
each step should be good at this point. However, there remain many challenges in
developing a process from the chosen synthetic route. To improve process eciency,
the spacetime yield should be optimized, the work-up developed, and the work-
ow streamlined. These eects can be achieved by minimizing in-between isola-
tion steps, using the same solvent for dierent steps, or recycling solvents. In addi-
tion, if the planned process will have conditions that are extreme in some respect,
for example temperature, corrosion, or heat production, it is advisable to have a
specic vessel in mind while optimizing the reaction. Some important parameters
to take into consideration are the kinetics of the reaction, the eects of diering
rates of addition, stirring speed, the eects of heating and cooling ramps on the
reaction rates, and the impurity spectrum.
An ecient work-up sequence often determines the total process performance.
Therefore, during process optimization, the batch size should be sucient to allow
representative extractions, ltrations, or distillations. We have set up a dedicated
laboratory to determine the relevant design parameters from small batches.
What are the requirements for the parallel optimization equipment? The vessel
should have a volume of 50250 mL, a mechanical stirrer, an independent heating/
cooling aggregate as well as an accurate temperature control. Calorimetric analysis
is advantageous at this stage; reux condensers and metering pumps for the re-
actants are necessary as peripheral equipment.
Examples of commercially available multiple reaction stations for process optimiza-

tion Well-known systems for process optimizations are the Auto-Mate from HEL,
the FlexyLab from Systag, the MultiMax from Mettler-Toledo and the Surveyor
from Argonaut (Table 30.3).
The workstations mentioned above have the following features in common: an
independent temperature control for each vessel, a PC-based control, and data anal-
ysis software. For the basic system, they all have a price of between 100,000 and
848
Tab. 30.3. Workstations for parallel process optimization.
Workstationb Number of Vessel size (mL), agitation Temperature Price Internet;

simultaneous control, individual category a http://www
reactions (yes/no)

Systag, FlexyLab 4 (up to 6) 250 mL mechanical Yes (80)280 C D Systag.ch

HEL, auto-MATE 4 (up to 16) 20100 mL mechanical Yes (80)350 C D Helgroup.co.uk

Mettler Toledo, MultiMax System 4 (up to 16) 50 mL magnetic Yes (50)180 C D Mt.com

Argonaut, Surveyor 10 45 mL magnetic, vertical Yes (40)150 C E Argotech.com

HEL, auto-MATE High pressure 4 100 mL, stainless steel, 200 bar Yes (80)350 C E Helgroup.co.uk
a Price categories: A <10 T@; B 1025 T@; C 2575 T@;
D 75125 T@; E 125175 T@.
b Numerous names of companies and equipment used in this table
150,000 euros. At the time of writing, the Auto-mate from HEL has been on the
market for about 2 years and has users in most pharmaceutical and ne chemical
companies. It has four mechanically agitated vessels per unit (volume 50100 mL),
the opportunity to monitor calorimetric data, and a whole set of extension equip-
ment at an additional charge. From the chemists view, the transparent glass set-
up has the advantage that one can recognize color changes or precipitations in the
reaction mixture. Recently, the Automate has become available in combination with
an x, y,z robot for automated sample collection and handling named DUET.
The four FlexyLab reactors are of larger size (volume 250 mL) and can be run
completely independently. They come with two mass-controlled liquid dosage units
with ow inducers for each reactor. The reactor head has two standard NS 14/NS
19 glass joints, convenient for attaching standard laboratory equipment. The tem-
perature dierence between the two reactors can be up to 200 K, depending on the
cooling aggregate.
The MultiMax from Mettler-Toledo is a compact system with four 50-mL reactors
and a dispenser box for one reagent. Three standard glass joints in the reactor head
allow the attachment of additional equipment, and agitation is carried out with a
stirring bar. Additional features such as mechanical stirring and additional dosage
units may be added; the STAVEX program for statistical experimental design and
the possibility of equipping the system with online in situ FT-IR analysis are useful
additional features.
The Surveyor has been developed by Argonaut Technologies for process devel-
opment chemists. It has ten transparent Teon reaction vessels with a volume of
75 mL and an integrated x, y,z robot. The typical magnetic Argonaut agitation sys-
tem provides good mixing even of viscous media and suspensions (although the
transfer quality to common plant stirrers has not been examined). Online sampling
and the integrated HPLC analysis (not included in the basic station price) are in-
teresting for determining reaction kinetics, an important issue during the process
optimization. With ten parallel reactors and a working volume of 45 mL, this sys-
tem could also be useful as a process-screening workstation.
30.3.2.4 Process Characterization and Validation

In process optimization the third screening stage kinetics, online analysis,
work-up, and isolation are investigated. In this step, the process has to be fully
characterized and validated, which means thermodynamic characterization, testing
the stability of the process, and scaling up. Once the last step of process validation
is accomplished successfully, the process can be run in the pilot plant.
Parallelization is not a topic for process validation yet. The typical vessel volume
is about 12 L, and eventually two, three, or more independent systems are set up.
To perform several validation runs at the same time, fully automated laboratory
reactors are helpful, even necessary. But, owing to the signicant costs per auto-
mated reactor, the usefulness of an additional reactor has to be carefully balanced
against its costs. Some commercially available alternatives to fully automated re-
actors for process validation are the RC-1 and the Lab-Max from Mettler-Toledo or
the Auto-Lab and the Simular oered by HEL.
30.3.3
Requirements for Analytical Instruments
Analytical methods used in process development are typically chromatographic

methods such as gasliquid chromatography (GLC) and HPLC, or in some cases
TLC or mass spectrometry. These methods can be used for dierent projects and
can be adapted to new tasks using standard methodology.
The number of samples increases rapidly after introducing parallelization, and
then analysis becomes a likely bottleneck in the complete workow.
In general, two strategies to avoid this may be used:
. Installing an online analysis. The analytical system needs to be fast enough, i.e.
the run time for one sample has to be the 1/nth part of the required time reso-
lution for all reactors. Usually, this requires more than one analytical instrument
(e.g. 24 GLCs) for one multiple reactor, or simplied analytical methods, or both.
Online analysis may give fast data, but it is more dicult to set up and has to
run reliably and stably to oer a real advantage.
. Analyzing the samples o line. This feature provides more exibility and makes the
system less complex to run. Sample preparation may be performed by a robotic
system which additionally transfers the samples to a standard format that may be
directly introduced into the chromatograph.
For every project a new decision has to be made as to whether time and money
should be invested in a better performing high-throughput method or whether
slow standard methods should be applied.
Quality and type of analytical method depends, on one hand, on the analytical
problem, but, on the other hand, they also depend on the stage of development
and the type of information required. Whereas in a process screening a simple
yes/no answer determined by TLC may be all that is required to eliminate 7080%
of inactive catalysts, the requirements will rise with the progress of the develop-
ment until, nally, elaborate, high-precision quantitative methods will be required
to allow the setting up of mass and mole balances and the specication of trace
amounts of side products.
Important contributions in the development of new methods for high-throughput
testing and analysis in the primary screening have been made recently by re-
searchers working in combinatorial catalysis. Maier and coworkers and Reetz and
coworkers showed infrared (IR) thermography to be a feasible screening tool for
analyzing the catalytic activity of heterogeneous catalysts in hydrogenations or
oxidations [25], homogeneous catalysts in enantioselective reactions, ring-closing
metathesis, and even enzyme-catalyzed reactions [26, 27].
Another issue of increasing importance is the high-throughput determination of
enantiomeric excess; here, the adaptation of parallelization techniques from other
disciplines is a tremendously fruitful approach. By parallel capillary electrophoresis,
Reetz et al. were able to analyze the ee values of 7000 samples per day [28]. Mi-
kami et al. combined a synthesis robot with an HPLC circular dichroism system to
screen their library of chiral ligands in the asymmetric addition of diethyl zinc
to aldehydes [29]. In the future, one can expect new methods in this eld to be
developed.
30.4
Planning of Parallel Process Development
30.4.1
Screening Strategies
Working on process development with combinatorial methods adds new dimen-

sions to the feedback loop, which consists of (1) the design of the experiment, (2)
the experiment itself, and (3) the analysis and the design of the experiment that
follows. Traditionally, one cycle is passed through and only one parameter is varied
at a time until the process is optimized (Fig. 30.8) [30]. In contrast, the parallel
approach enables a large number of parameter sets to be tested simultaneously by
changing the screening strategy to fewer, but more diverse and data rich, feedback
loops. The extreme example would be an open loop, where all parameter sets can
be screened at once and only the best are selected.
With the full range of options of parallel process development available, one has
to think about eciency. What is the most advisable ratio between the number of
experiments and the number of loops? Eciency can roughly be represented by
the product of the frequency (loops), the diversity (number of experiments), and
the learning factor (see the formula in Fig. 30.8).
The learning factor includes, for example, the amount of information gained by
a single experiment. The amount of information from a single experiment is in-
versely related to its scale, the complexity of the screening set-up, and its degree of
Fig. 30.8. Classical and parallel approaches in development.

parallelization, meaning that the more you wish to know about a single experi-
ment, the lower the degree of parallelization and the larger the scale. The goal is
that the additional information gained by performing more experiments over-
compensates for the loss of information from each single experiment. But, never-
theless, it may be more ecient to have an approximate look at a huge experi-
mental parameter space with highly parallelized, small-scale reactions with a yes/
no answer and then selecting the most interesting areas for closer investigation on
a larger scale.
For every loop, and for dierent phases of process development, questions have
to be answered, such as: How precise must the answer from the experiment be?
How many experiments have to be analyzed for the next set of experiments?
The determination of some reaction parameters may cause diculties in small-
scale experiments, e.g. the enthalpies of reactions and parameters related to mass
transfer eects (inuence of mixing, inuence of particle size in heterogeneous
catalysis, mass transfer limitations at interfaces, etc.). In critical cases, it has to be
checked in advance whether or not relative statements under standard conditions
can be translated into reliable information on a larger scale. For example, if experi-
ments are performed at very low conversions, data may be extrapolated to higher
conversions if the formation of the desired compound takes place mainly within a
system of parallel reactions; if the desired compound is an intermediate in a con-
secutive reaction, this may not be the case.
30.4.1.1 Experimental Design

There is a real danger of assuming that large numbers of compounds enable
several hundreds or thousands of experiments to be performed at once if only
very shallow gradients over the whole parameter space are applied. The informa-
tion extracted from these experiments may, owing to larger experimental noise in
the simpler set-up, be even less than in a two-step experimental run with a much
larger grid width in a supercial rst run followed by a second run zooming
in on the area of interest.
Tools that congure the loop as a whole as eciently as possible are given by
dierent experimental design approaches. Besides the classical way of varying one
parameter at a time, and the simple way of scanning the whole parameter space by
an exorbitant number of experiments, there are intelligent designs such as statis-
tical experimental design and genetic algorithms.
The statistical design of experiments is a common tool that is used to examine
critical factors at several levels in order to characterize a chosen parameter space.
Statistical analysis of the data enables a so-called response surface model to be set
up, which allows the interactions between the factors to be analyzed. This analysis
can then serve as the basis for further optimization and a good understanding of
the process. Typical designs are factorial or reduced factorial designs, central com-
posite designs, or fractional factorial PlackettBurman designs. Once a design table
for one loop has been set up, the experiments can be run in parallel. Over recent
years, statistical experimental design has been applied in many case studies [3133].
Not as popular as statistically based design is the use of genetic algorithms, which
are copied from nature. For example, in the rst step of optimizing a heteroge-
neous catalyst, the number of components is dened, then a rst generation of
catalysts is initialized and tested in parallel [34]. The results are evaluated, leading
to a selection of catalysts from the population to create the next generation. The
next generation is created by application of evolutionary operators such as crossover,
or qualitative or quantitative mutation. The loop of testing, selection, and mutation
is repeated until the convergence criterion is satised. In heterogeneous catalyst
development, sometimes the question of whether a quaternary will show activity
if all binary and ternary combinations of a given set of elements are completely
inactive must be considered. Here, the application of genetic algorithms seems to
be a promising strategy [34]. A similar approach in which a genetic algorithm is
used increasingly is in directed evolution for the creation of new enzymes display-
ing improved enantioselectivity in a given reaction [35].
30.4.2
Strategies for the Selection of the Equipment
The ultimate goal would be to have each laboratory equipped for parallel working
at all screening stages. Therefore, a complete cascade of screening apparatus (for
process screening, process optimization, process validation) would have to be pur-
chased or developed, which would require signicant investment. Hence, some
moderating decisions have to be made and preliminary questions have to be
answered:
1 Automation versus manual work?

2 What is the right distribution and number of pieces of apparatus for dierent
stages?
3 Buying commercially available systems or performing in-house development?
30.4.2.1 Automation versus Manual Work?

Discussing adequate equipment for parallelization during dierent phases of pro-
cess development raises the question of What is the right degree of automation?
Criteria that play a role in answering this question are wage costs versus invest-
ment costs, at what phase the parallel set-up should be run, and how exible in
terms of chemistry and time the set-up should be.
Our experience is that, on a screening scale of 5100 mL, a technician can handle
around 12 experiments in parallel per day with rather cheap, nonautomated, mul-
tiple reaction block equipment. These racks (for commercial examples, see Table
30.1) are easy to install, and they can be used for most organic chemistry to cover
the developmental stages of process screening and, to a lesser extent, either pro-
cess screening at an earlier phase or process optimization.
We have introduced these racks into our process development laboratories. In
ne chemical synthesis, our statistical evaluation has revealed that the overall e-
ciency of the laboratories, given by the number of experiments performed per day,
has approximately doubled using this equipment.
Fig. 30.9. Expenses versus simultaneous reactions.
If the parallelization is expanded to a degree much higher than tenfold, then a

large increase in eort and expenditure results. This concept is illustrated in Fig.
30.9.
The sigmoid curve shows the increase from manual work to full automation. In-
stead of the hardware, the control software and the data-handling system become
the cost-determining features. Moreover, software installation and adaptation, hard-
ware integration via numerous interfaces, and training of the operating sta have
to be taken into account.
Software plays an increasingly important role in higher degrees of automation.
In our experience, a parallelization signicantly greater than 10 1 can no longer be
handled with standard programs and, especially if larger amounts of raw data have
to be processed, stored and analyzed, special software and databases have to be
used. The same is true for the control system that steers the components, pumps,
mass ow controllers, pressure controllers, temperature monitors, chromatographs,
etc. The more components from dierent suppliers with dierent protocols and
interfaces that have to be integrated, the more complex the system becomes, and, a
priori, the lower is its reliability. A fully integrated system is useless if it cannot
run reliably on a day-to-day basis.
Costs and complexity (e.g. software, logistics) suggest that a dedicated laboratory
with a sta who are experts in automation should operate this equipment. These
activities can eventually be outsourced to central research units or to small re-
search service companies.
Owing to the limited chemical exibility of most workstations, the jump to au-
tomation is particularly rewarding for long-term projects with a specic chemistry-
or technology-based screening. For example, when we test our enantiomerically
pure ligand database in asymmetric hydrogenations, we test up to 96 combinations
per run to see which catalyst system reveals the best enantiomeric excess for a
given substrate. Where trial and error promises success, a large number of experi-
ments is still the best approach, and the eort and expense incurred in setting up
an automated workstation will pay dividends.
In the case of process optimization and validation, the number of experiments
drops to <20, but these experiments require huge data collections and highly accu-
rate processing. The adaptation to dierent chemistry in independently controlled
vessels is easier and faster than in the high-throughput workstations since these
vessels are designed to enable multiple dosing, to have heat ramps over a wide tem-
perature range or reux, and to have joints for special equipment, making their use
worthwhile even for chemists with rapidly changing projects en route to the pilot
plant.
A question arising in this context is the percentage of chemistry covered by the
systems: a 100% perfect solution compared with a 70% standard solution. Sys-
tems covering the total range of possible parameters (temperature range, pressure
range, materials, special safety requirements) are much more expensive and more
dicult to construct. Therefore, we recommend an approximate 70% coverage,
which can be achieved with a number of commercial systems. A broadly applicable
workhorse is better than one sophisticated wonder machine. Supplementary to
these workhorses, we have set up dedicated special equipment for our core tech-
nologies, such as high-pressure reactions and phosgenations.
30.4.2.2 What is the Right Distribution and Number of Pieces of Apparatus for
Dierent Stages?
For a group working in ne chemical synthesis with rather fast-changing organic
chemistry demands, we have had positive experiences in starting with nonauto-
mated multiple reaction blocks for process screening. The advantages are the rather
low costs, the ready-to-go installation, the exibility in chemistry, and the ability to
equip every laboratory (broad introduction) with multiple reaction blocks without
any special training or environment.
The decision of where to expand next with parallel techniques is mostly depen-
dent on the problems and the orientation of the process development group (Fig.
30.10). Either priority is given to a primary screening, which means expanding to
automated workstations and robotics, or priority is given to process optimization
and validation, which means expanding to parallel, independently controlled vessel
stations for scaling up experiments.
In general, it is advantageous to set up and use sophisticated, highly parallelized
equipment in long-running basic chemical projects [4], whereas for the ne chemi-
cal area a more general apparatus with a lower degree of parallelization seems to
be appropriate, reecting the fact that large-scale productions take place in dedi-
cated plants and ne chemicals are produced in multipurpose plants (without tak-
ing into account the quality requirements for dedicated apparatus).
An often underestimated point in the parallelization debate is the generally low
acceptance of new equipment by technicians: expensive workstations often remain
unused (investment ruins). As a consequence, aversion to new developments in the
eld of automation and parallel working increases. Therefore, a stepwise approach
to the introduction and use of new equipment is advisable, e.g. beginning with a
Fig. 30.10. Possible introduction of parallel process development equipment.
low parallelization degree of 48 and simple, Excel-based data processing, which is

an almost standard working routine today, and then upgrading the equipment step
by step with the involvement of the technicians who will use it.
30.4.2.3 Buying Commercially Available Systems or Carrying out In-house

Development?
Many arguments can be found for and against carrying out in-house development,
some of which are listed in a Table 30.4 and are based on recent publications [36].
Using systems that have been developed in house based on existing laboratory
equipment has been discussed by Pollard [36]. It allows one step after another to be
analyzed by looking at the existing workow and checking for bottlenecks, leading
to fast improvement in the performance of the tailor-made solution. Disadvantages
of in-house developments are high development costs, the lack of external or user
group support, and the need for local specialists with skills in programming, elec-
tronics, etc. During the last 5 years, several mainly pharmaceutical companies
have chosen in-house development of automated workstations for process devel-
opment, e.g. SmithKline Beecham, Glaxo Wellcome, Aventis, Schering, and Bayer
among others. Companies chose to move projects in this direction because of the
lack of reasonable commercial alternatives at that time. Today, the situation is dif-
ferent. For all screening stages a host of commercially available systems is on the
market (refer to examples in Tables 30.1 and 30.2), even for high-pressure or low-
temperature reactions. Therefore, we believe that now, for most applications in
Tab. 30.4. Pros and contras for an in-house development [36].
Pro in-house development Contra in-house development

. Tailor-made solution you can . Long development time
design exactly what you need
. Flexible . High development costs
. Cheap to install multiple copies . Hidden development costs? For example,
generating support documentation
. Easier learning curve . Need to source unusual components
glassware, electronics, etc.
. Continuous improvement process . Lack of external support
. Own IP position strengthen . Lack of user group support
. Fits to existing equipment . Local specialists are required, with skills
in programming, etc.
ne chemicals, an acceptable commercial solution is available, which makes it

possible to introduce parallel process development immediately o the shelf.
Even huge primary catalyst-screening projects can be carried out in cooperation
with third-party combinatorial rms, for example Avancium, THE, or Symyx, and
their screening tools can be purchased for in-house research [37].
30.5
Case Studies
Numerous examples using parallelization in process development have been pub-

lished over the last 5 years covering a wide range of chemistry, mainly for the syn-
thesis of intermediates. Often, authors describe a case study as the proof of principle
for their parallelization or automation approach. These are important contributions
in the process development (PD) community, where almost every PD group is set-
ting up its parallelization equipment with high commitment. But after the begin-
ners enthusiasm has subsided, the future will show which solutions will progress
from proof of principle to everyday use.
We have listed some recent examples from literature in Table 30.5 to illustrate
the possibilities of combinatorial chemistry in process development. Some of them
are discussed below in more detail.
Guram and coworkers from Symyx presented the development of an oxida-
tion protocol for 2-butyl-5-hydroxymethyl-imidazole to 2-butyl-5-formylimidazole
(Scheme 30.1) [38, 39]. They developed a catalytic solution in 4 weeks by screening
5000 samples using three platforms of catalysts: POM, zeolites, and transition met-
als on support. Libraries of 96 catalysts were prepared by high-throughput robotic
synthesis and screened using 96-well reactors of dierent sizes for primary and
secondary screening and conventional autoclaves and reux apparatus for tertiary
screening. They were able to nd a proprietary catalyst system with a V-MCM-41
catalyst and air as oxidant which gives >90% yield. This example shows impres-
858
Tab. 30.5. Examples of parallel process development.
Reaction/operation Screened variables Number of DOE e Stage Equipment a Reference

experiments
Acid chloride addition to bis-imine Solvents, bases, equivalents, order of 112 Yes PSg DARTb 23
addition
Alcohol oxidation Catalysts, solvents pressure, oxidants 5000 ? PS In-house platforms 38, 39
Aldol condensation Base, solvent, concentration, temperature, 60 ? PS Bohdan development 41
order of addition workstation
Bredereck reaction, imidazole Temperature, formamide equivalent, 26 Yes POh Gilson 215 Bohdan 19
synthesis workstation
Condensation reaction Cocatalysts, concentration 284 Yes PS/PO In-house workstation 42
Cyclization of 3-chloroamide Water addition, temperature, equiv. NaOH ? ? PS Anachem SK 233 22
Phase transfer catalyst
Deprotection of silyl ether Temperature, concentration equivalents 6 Yes PO DART/PROSPERc 33, 23
Deprotection of TFA groupd Base, equivalent, concentration, volume, 116 Yes PS/PO 43
solvent
FriedelCrafts acylation Lewis acids, equivalent of Lewis acid, 52 Yes PS/PO Bohdan workstation 17
solvents, temperature
Heck reaction Catalyst, Pd/ligand ratio, loading 96 No PS/PO Anachem SK 233, ReactArray 13
Hydrogenation Catalyst, loading, pressure, temperature, 44 Yes PS Argonaut Endeavor 44
equivalent MsOH
Hydrogenation Catalyst, loading, solvent, stoichiometry of 77 No PS Multihydrogenation vessel 22
base, quality of starting material
Imidazolidin-2-one synthesis Reagent, solvent, temperature, concentration, A60 No RSf/PS Argonaut Surveyor 18
stoichiometry
Liquidliquid extraction Solvent, temperature 30 No PS Anachem SK 233 21
Michael Addition Solvent 10 No PS Anachem SK 233, 45
REACTarray
Mitsunobu coupling Temperature, concentration, addition rate, 36 Yes PS/PO DART 12
stoichiometry
Nucleophilic substitution Bases, solvents, temperature prole ? ? PS STEM Block 22
Reductive amination Catalyst, additives, stoichiometry Several Yes PS Multi vial reactor 46
hundred
Silyl enol ether addition Lewis acids, solvents 140 No PS Anachem SK 233, ReactArray 45
Suzuki reaction Concentration, water level, catalyst load, 10 Yes PS Anachem SK 233, 45
boronic acid stoichiometry REACTarray
a Numerous names of companies and equipment used in this table
b DART development automated reaction toolkit.
c PROSPER process research optimization screening parallel
experimentation robot.
d TFA triuoroacetic acid.
e DOE design of experiments.
f RS route scouting.
g PS process screening.
h PO process optimization.
30.5 Case Studies
859
sively how a combination of dierent screens on dierent scales can lead eec-
tively to new catalytic systems in a very short period of time.
Scheme 30.1.
Another example within imidazole chemistry was published by Kirchho et al.

[19], who applied automated experimentation equipment with statistical experi-
mental design to the synthesis of 4(5)-(3-pyridyl)imidazole (Scheme 30.2).
Scheme 30.2.
They consecutively performed two sets of experiments: rst, a three-level facto-

rial design; second, a central composite design to optimize further the reaction
conditions. They found a proprietary parameter set at 160 C and 9 equiv. of for-
mamide, giving 74% in situ yield of 4(5)-(3-pyridyl)imidazole. With only 26 experi-
ments, they succeeded in nding the optimized reaction conditions for the given
transformation. This result demonstrates the potential of a combination of auto-
mation with statistical design of experiments, since for more complex problems
big multivariable statistical design sets are necessary which can only be eciently
handled by automated equipment.
Studies optimizing concentration, temperature, dosing rate, or stirring speed
have been published less frequently than the screening of reagents or catalysts,
reecting the greater degree of diculty in establishing reliable and relevant data.
Evens from Avecia has described ve short case studies for the use of the HEL
AutoMate module to exemplify the power of calorimetry in process development
[21]. For example, in the rst case a mesylation of a benzylic alcohol with mesyl
chloride and triethylamine in tetrahydrofuran (THF) was studied. They simulated
the plant addition times, which were factored along with hold times, temperatures,
and reagent charges in order to dene the robustness of the reaction. In particular,
the PC-controlled syringe pumps were found to be useful in replicating the plant
feed times of 8 and 12 h.
Higginson et al. from Pzer reported an automated two-reactor system built
around a Zymark XP Track Robot which was developed for process optimization
and validation [40]. Two examples were described: the rst one was the optimization
of a crystallization, where the granulation temperature, the concentration, and the
References 861
ratio of the two solvents aected the product quality. The second example included
two prolonged liquid additions and two strictly controlled cooling ramps. In both
cases, excellent product quality and a robust process were reached by using this
automated robotic system together with an experimental design approach.
Summing up the examples, it is evident that most of them involve the combi-
nation of statistical experimental design (DOE) and automation to screen rapidly
the parameter space of interest for the process.
30.6
Summary
Combinatorial chemistry has now moved into process development in the form of
parallelization. Although the degree of parallelization is still moderate compared
with biological assay high-throughput screening, over the last few years this num-
ber has signicantly increased. There are several examples in the literature, includ-
ing some hundreds of experiments during a single development. The probation in
everyday use and the signicant acceleration of process development by parallel-
ization still has to be proven.
In the past, several companies developed individual solutions to transfer parallel
techniques into their process development department, but recently various pieces
of apparatus and workstations for all development phases have become commer-
cially available, making it easier for newcomers to enter the eld of parallelization.
However, signicant nancial outlay and eort are still required for successful im-
plementation. Especially when moving to highly parallel solutions, the expenditure
for automation and software becomes the determining factor and makes interdis-
ciplinary teams necessary.
High-throughput experiments in themselves have no value, thus deliberate ex-
perimental design has to be included to reach the true objective a highly ecient
workow. A well thought out tuning of the design steps, testing, and analysis, as
well as good coordination between the development phases, are necessary to avoid
limiting bottlenecks.
Yet, process development is still carried out in several phases. Even hundreds of
experiments on a small scale cannot replace a pilot run. It will be interesting to see
during the next few years if and how combinatorial chemistry can have an impact
on this problem and is able to shortcut the route from the test tube to the plant.
It is our belief that combinatorial chemistry is not a substitute for experience
and creativity in process development, but an additional powerful tool in the chem-
ists hand.
References
1 G. Agricola, De re metallica libri XII, zung 1557). Deutscher Taschenbuch

1556 (Zwolf Bucher vom Berg und Verlag GmbH & Co Kg, Munchen
Huttenwesen, erste deutsche Uberset- 1994.
2 F. Feigl, Qualitative Analyse mit Hilfe Chemistry in the Pharmaceutical

von Tupfelreaktionen, 2nd edn. Industry. Gadamasetti, K. G. (ed.),
Akademische Verlagsgesellschaft, Marcel Dekker, Inc., New York 1999,
Leipzig 1935. p. 429.
3 J. Kisser, K. Lettmayer, Mikrochemie 20 K. J. Carpenter, Chem. Engin. Sci.
1932, 12, 234. 2001, 56, 305.
4 A. Mittasch, Geschichte der 21 K. J. Carpenter, Entropie 2000, 223, 4.
Ammoniaksynthese. Verlag Chemie, 22 S. Senkan, Angew. Chem. 2001, 113,
Weinheim 1951. 322.
5 M. R. Arnold, K. Atwood, H. M. 23 V. V. Guliants, Catalysis Today 2001,
Baugh, H. D. Smyser, Ind. Eng. 67, 307; and the full volume Catalysis
Chem. 1952, 44, 999. Today 2001, 67, 307409.
6 D. A. Dowden, G. W. Bridger, Adv. 24 InnoCentive, 2001, http://www.
Catal. IX 1957, 669. inocentive.com.
7 M. Harre, U. Tilstam, H. 25 A. Holzwarth, H.-W. Schmidt,
Weinmann, Org. Proc. Res. Dev. 1999, W. F. Maier, Angew. Chem. 1998,
3, 304. 110, 2788.
8 D. F. Emiabata-Smith, D. L. 26 M. T. Reetz, M. H. Becker, K. M.
Crookes, M. R. Owen, Org. Process Kuhling, A. Holzwarth, Angew.
Res. Dev. 1999, 3, 281. Chem. 1998, 110, 2792.
9 J. Hiebl, L. Hsu, L.-J. Ping, S. B. 27 M. T. Reetz, M. H. Becker, M. Liebl,
Shetzline, E. C. Webb, M. A. Furstner, Angew. Chem. 2000, 112,
Armitage, G. Smith, K. Veal, Chim. 1294.
Oggi 2000, 18, 41. 28 M. T. Reetz, K. Kuhling, A. Deege,
10 N. W. Hird, Drug Discovery Today H. Hinrichs, D. Belder, Angew.
1999, 4, 265. Chem. 2000, 112, 4049.
11 A. Orita, Y. Yasui, J. Otera, Org. 29 K. Mikami, K. Ding, A. Ishii, Angew.
Process Res. Dev. 2000, 4, 337. Chem. 1999, 111, 519.
12 A. Orita, Y. Yasui, J. Otera, Org. 30 K. D. Shimizu, M. L. Snapper, A. H.
Process Res. Dev. 2000, 4, 333. Hoveyda, Chem. Eur. J. 1998, 4, 1885.
13 J. Zhang, E. W. Kirchhoff, D. E. 31 D. R. Pilipauskas in: Process
Zembower, N. Jimenez, P. Sen, Z.-Q. Chemistry in the Pharmaceutical
Xu, M. T. Flavin, Org. Process Res. Industry. Gadamasetti, K. G. (ed.),
Dev. 2000, 4, 577. Marcel Dekker, Inc., New York 1999,
14 O. W. Gooding, T. Lindberg, W. p. 411.
Miller, E. Munyak, L. Vo, Org. 32 D. Lendrem, M. Owen, S. Godbert,
Process Res. Dev. 2001, 5, 283. Org. Process Res. Dev. 2001, 5, 324.
15 E. W. Kirchhoff, D. R. Anderson, 33 M. R. Owen, C. Luscombe, L.-W. Lai,
S. Zhang, C. S. Cassidy, M. T. S. Godbert, D. L. Crookes, D.
Flavin, Org. Process Res. Dev. 2001, 5, Emiabata-Smith, Org. Process Res.
50. Dev. 2001, 5, 308.
16 W. Hoyle, Automated Synthetic 34 D. Wolf, O. V. Buyevskaya, M.
Methods for Speciality Chemicals. Royal Baerns, Applied Catalysis A: General
Society of Chemistry, Cambridge 1999. 2000, 200, 63.
17 N. Evens in: Automated Synthetic 35 M. T. Reetz, K.-E. Jaeger, Chem. Eur.
Methods for Specialty Chemicals. J. 2000, 6, 407.
Hoyle, W. (ed.), The Royal Society of 36 M. Pollard, Org. Process Res. Dev.
Chemistry, Cambridge 1999, p. 69. 2001, 5, 273.
18 M. A. Armitage, G. E. Smith in: 37 A. Wood, A. Scott, Chemweek 2001,
Automated Synthetic Methods for July 18, 18.
Specialty Chemicals. Hoyle, W. (ed.), 38 A. Guram, A. Hagemeyer, B.
The Royal Society of Chemistry, Jandeleit, D. Poojary, H. Turner,
Cambridge 1999, p. 83. H. Weinberg, Proceedings of 12th
19 M. R. Owen, S. H. Dewitt in: Process ICC (Granada, Spain) 2000, in Proc.
References 863
Surf. Sci. Catal. Vol 130, Coruia, A., 42 R. W. Wagner, F. Li, H. Du, J. S.
Mel, F. V., Meuioroz, F. J. L. G. Lindsey, Org. Process Res. Dev. 1999, 3,
(eds.), Elsevier, Amsterdam 2000. 2837.
39 P. Desrosiers, A. Guram, A. 43 V. W. Rosso, J. L. Pazdan, J. J. Venit,
Hagemeyer, B. Jandeleit, D. M. Org. Process Res. Dev. 2001, 5, 294
Poojary, H. Turner, H. Weinberg, 298.
Catalysis Today 2001, 67, 397. 44 J. M. Hawkins, T. W. Makowski, Org.
40 P. D. Higginson, N. W. Sach, Org. Process Res. Dev. 2001, 5, 328330.
Process Res. Dev. 2001, 5, 331. 45 M. A. Armitage, G. E. Smith, K. T.
41 M. Harre, H. Neh, C. Schulz, U. Veal, Org. Process Res. Dev. 1999, 3,
Tilstam, T. Wessa, H. Weinmann, 189195.
Org. Process Res. Dev. 2001, 5, 335 46 M. A. Huffman, P. J. Reider,
864
31
High-Throughput Screening Applied to Process
Development
Oliver Brummer, Bernd Jandeleit, Tetsuo Uno, and
W. Henry Weinberg
31.1
Introduction
31.1.1
General
The advent of combinatorial chemistry and high-throughput screening has greatly

changed the landscape of drug development activity within the pharmaceutical in-
dustry. The increase in the number of compounds in the early phase of the drug
development pipeline has created a new bottleneck in the development of cost-
eective, scalable chemical processes. Emphasis on cost reduction and speed to
market has added to the pressures being felt by chemical process development
groups. Even back in 1999, the cost and time to develop a new drug averaged $500
million and 15 years, respectively [1]. In response to these pressures, chemical de-
velopment groups and their suppliers are implementing their own forms of high-
throughput screening [2]. Much has been learned from the high-throughput tech-
niques developed specically for drug discovery. These techniques have been
merged with the laboratory automations that were developed in analytical labo-
ratories and process laboratories [3]. Combinatorial chemistry techniques have also
been applied for the discovery of materials and catalysts [4]. Obviously, combina-
torial and high-throughput catalyst development approaches will be an integral
part of future chemical process development. This chapter reviews recent publica-
tions covering the implementation of high-throughput screening and automation
in chemical process development. For a historical background and earlier develop-
ments in these elds (before 1999), the reader is referred to reviews from Harre et
al. [5], and Owen and Dewitt [6]. The following section summarizes the eorts in
combinatorial high-throughput process development and examples of implementa-
tion of automated process optimization and automations in process characteriza-
tion and validation. Section 31.3 includes a summary and an outlook concerning
the future of combinatorial aspects in process development.
High-throughput screening can be applied to chemical process development in

ISBN: 3-527-30509-2
three phases: (1) route scouting, (2) screening and optimization, and (3) character-
ization and validation. In addition to these phases, the real combinatorial discovery
activity will be necessary to incorporate a totally new process where a novel catalyst
or reaction is required. New process discovery is an important activity that can
provide for the introduction of more environmentally benign processes, the use of
more cost-eective starting materials, or provide a higher purity of an intermediate
or a product. Process hazard evaluation must also be carried out for all new pro-
cesses. Hazard analysis should be considered as early as possible in the process
development to insure that a safely scalable process is being pursued.
Finally, the authors want to point out that they do not comment on any of the
described automation devices and tools. This review only describes the latest devel-
opments in high-throughput techniques for process automation but does not give
any recommendations.
31.1.2
Automation and Experimental Design
Automation is indispensable for high-throughput chemical development. Com-

mercially available automated synthesizers and custom-built instruments, some of
which are also useful for chemical process development, have been recently re-
viewed [7]. Reecting the diverse requirements of process development in dierent
phases, dierent types of high-throughput tools have been developed for a variety
of modes of process development, since no single instrument can cover all activ-
ities. Further information regarding laboratory automation, including commercially
available automated systems for chemical process research as of late 1998, is avail-
able [5]. Although the review of equipment available is already out of date because
of the rapid development in this eld, Weinmann provides many excellent exam-
ples of how automation can be applied to chemical process development. More re-
cent additions to these instruments that are especially aimed toward chemical pro-
cess development will be discussed in the following sections.
Some benets of automation for chemical process development are:
. The time necessary for optimization of the process is shortened, leading to the
faster development of the drug candidate.
. A much wider range of variables can be selected, giving an improved chance of
success in process screening.
. The quality of data will improve by eliminating human operational errors.
. Better yields can be obtained owing to the more precise control of reaction con-
ditions.
. Large amounts of experimental data are eciently collected with minimum op-
erator involvement.
. The sta is released from tedious repetitive tasks, allowing more time for cre-
ative work.
. Researchers will have more exibility so that operations involving monitoring
reactions over extended time periods are possible.
866 31 High-Throughput Screening Applied to Process Development
Automated process development also facilitates the statistical design of experi-

ments (DOE), i.e. full or fractional factorial design of experiments and construc-
tion of mathematical models or response surface models of the reactions. The DOE
approach often helps to identify crucial factors and their interactions that govern
the chemical process. These types of information are useful for developing a ro-
bust chemical process [8]. Indeed, the combination of statistical DOE and high-
throughput automated experimentation has been proven to be a powerful meth-
odology for the development of a robust process. However, it should be noted that
this statistical approach can only be feasible if enough chemical knowledge on the
reaction of interest is available, which should be the case at the optimization stage
of developmental activities.
Owen et al. describe the benets of applying experimental design in process re-
search as follows [9]:
. Powerful mathematical models of the chemical process or procedure are pro-

duced that allow opportunities or constraints to be fully considered.
. The good quality of data allows better strategic decision-making and faster scale-
up of optimized processes into plant.
. The models are obtained for a quantiable amount of resource.
. It is an ecient and eective method of choosing which experiments to perform.
. The strategy is compatible with running automated reactions in parallel.
. If circumstances change (e.g. the price of reagent increases dramatically or work-
up alters), the model can be interrogated in dierent ways to take the new crite-
ria into account.
. The methodology can be used as a framework to capture and share information
between project teams.
31.1.3
High-throughput Process Development
Combinatorial high-throughput process discovery requires the screening of as

many variables as possible. Workows for screening thousands of experiments
must be fully integrated. It is not possible to screen several thousand reaction com-
binations without having fully debottlenecked the system. Small volume, typically
less than 1 mL, multiwell reactors, and liquid-handling robotics are required for
this screening approach. In addition, development of high-throughput analysis is
crucial for process discovery, since conventional high-performance liquid chroma-
tography (HPLC) and gas chromatography (GC) methods are not fast enough to
match the reactor productivity.
When tens of thousands of reaction combinations must be screened for process
discovery because of the lack of sucient chemical knowledge regarding the trans-
formation, the traditional statistical DOE approach is not helpful because the im-
portant reaction parameters are not well dened. In such cases, dierent types of
strategies will be necessary to eciently explore the parameter space. Recently,
Cawse has reviewed these strategies developed in the eld of combinatorial chem-
istry for drug discovery and materials science [10].
Process optimization utilizes parallel reactors of 550 mL volume. The process
parameters, such as reaction temperatures, stirring eciency, and rates of reagent
addition, should be strictly controlled for high-quality data. At this stage, online
(real time) reaction monitoring is essential to obtain information regarding reac-
tion proles. Even when the number of reactions is small, the amount of data can
be large owing to multiple sampling from the same reaction over time. Currently,
high-throughput automated process optimization attracts most developmental ef-
forts in this eld.
Reactors for process characterization and validation should be a good model for
the real pilot plant. Throughput is low for this stage, but these developments have
also been included in this review since automation can accelerate it, thus higher
throughput can be achieved than in the conventional operation. Calorimetry has
emerged as a useful technique because it can provide information on both reaction
kinetics and reaction hazards. Real time in situ infrared technology (FT-IR) has
also been used to assess reaction hazards [11].
In high-throughput process development, the use of software can signicantly
reduce the time required to design combinatorial experiments, can manage data
collection and monitoring during runs, and can analyze data to reach conclusive
insight into the process. Instruments should be controlled by user-friendly inter-
faces. Because high-throughput experiments generate data orders of magnitude
faster than conventional methods, powerful database and data handling will be an
integral part of the system. The resulting database, in eect, becomes an extension
of the laboratory notebook, and, in conjunction with an appropriate database
structure and access tools, this extension becomes a powerful intellectual asset.
31.2
Case Studies
31.2.1
High-throughput Combinatorial Process Discovery
The high-throughput combinatorial approach plays an important role in discover-

ing processes, in searching for reagents and catalysts that use cheaper starting
materials or reduce the number of steps required of a given chemical transforma-
tion, or in providing more environmentally friendly processes.
Early eorts of Symyx Technologies led to the development of an integrated
high-throughput technology screening platform useful for pharmaceuticals and for
ne chemicals process discovery, screening, and optimization.
A proprietary software package is an essential part of the design of combinatorial
libraries [12]. It also controls all robotic functions (such as running liquid han-
dling as well as temperature and pressure manipulations), gathers data from each
reaction entity (spatially addressable format), and automatically stores the process
data in a central database, thus allowing for analysis of the results at the end of the
screening experiments. The technology also uses a variety of 96-well reactor for-
mats equipped with a liquid-handling robot to manage exibly both homogeneous
and heterogeneous liquid-phase reactions under high pressures or reux conditions.
In one example, 2000 high-throughput screening experiments were performed
to discover a novel catalyst system for a homogeneous palladium-catalyzed Suzuki
coupling reaction of 2-chlorobenzonitrile (1) with 4-(methylphenyl)boronic acid (2)
to yield ortho-tolylbenzonitrile (OTBN) (3), an important key intermediate of Du-
Ponts antihypertensive compound Losartan (6) (Scheme 31.1). All 2000 screening
experiments were performed in a custom-made 96-well reactor format within 4
weeks. Multidimensional combination of archived ligands, palladium metal pre-
cursors, various bases, and solvents were screened, leading to the discovery of a
lead catalyst structure. The lead was optimized into a new catalyst system that ex-
hibited 5000 turnovers (TO) with >99.5% selectivity of the desired heterocoupling
product over the undesired homocoupling impurity [13].
Scheme 31.1. Application of high-throughput screening in the

discovery of novel catalysts for the preparation of building
blocks 3 and 5 that are used for the synthesis of antihyper-
tensive compound Losartan (6) (DuPont Pharmaceuticals).
The same group also developed appropriate technology for high-throughput syn-
thesis and screening of metal-doped polyoxometalate (POM) libraries in 96-well
format. Libraries of the heterogeneous POM catalysts were screened to discover se-
lective aerobic oxidation catalyst systems. In this case, the imidazole alcohol 4 was
oxidized to aldehyde 5, which also represents an important key intermediate for the
Losartan (6) synthesis (Scheme 31.1). Within 4 weeks, 5000 experiments had been
performed to screen dierent catalyst compositions, eects of solvents, and addi-
tives under variable reaction conditions. Two classes of catalyst systems that give
more than 90% yield were identied. These results were conrmed and validated
in subsequent scale-up experiments [14].
Symyx Technologies has also extended its high-throughput capabilities to asym-
metric reactions. As an example, hundreds of catalyst compositions were screened
consisting of transition metals and an array of chiral phosphine ligands under a
variety of conditions for asymmetric hydrogenation of a particular substrate, iden-
tifying the optimum composition that provided high enantiomeric excess and cat-
alyst productivity. The hits were then scaled up in a secondary screening cycle
using a system that is capable of running 96 5-mL pressure reactions in parallel
(Fig. 31.1) [15].
31.2.2
Route Scouting, Screening, Optimization, and Validation
Recently, a large body of work was published describing medium-throughput

screening (ten at a time) applied to process development. Not surprisingly, this
approach has prompted much eort because a benet can be obtained from in-
creasing experimental throughput by just one order of magnitude. Therefore, sys-
tems are being developed that allow for the set-up, control, and analysis of ten-
at-a-time reactor modules. Fortunately, true combinatorial exploration of the very
large parameter space is often not necessary for process optimization, therefore
this arena provides greatly improved productivity before encountering the real
issues of high-speed analytical and data management required to advance to high-
throughput screening (100s or 1000s at a time).
Owen and his group at GlaxoSmithKline described a step-by-step approach to
the optimization of a synthetic transformation using a central composite experi-
mental design, in conjunction with a standard Gilson 231XL autosampler and auto-
mated online HPLC [9]. This procedure aids the appropriate decision-making at
each phase from the route scouting to the process validation and nally to the pilot
or real plant production. The reactions specied by the experimental design model
were prepared by hand. Aliquots of reactions were placed in the Peltier block sample
tray of the autosampler, and the progress of each reaction was monitored automati-
cally. The analysis of the data obtained from these semiautomated experiments was
performed by commercially available DOE software package Design-Expert 5 (DX-5)
(http://www.statease.com), resulting in highly predictive models for the reaction after
just 6 days of experimentation. A set of the preferred conditions was rst validated
in traditional glassware in the laboratory and then subsequently at the pilot plant.
Fig. 31.1. Illustration of hard- and software array of 96 pressure reactors; top left, table
package developed by Symyx Technologies for with conversion data for 48 parallel reactions;
scaled up secondary screening of hits top right, graphical representation of
identied in primary screening. Bottom left, conversion data from the table.
This study showed that it was possible to carry out reactions in a reaction station
located within the working envelope of an autosampler. Although adequate for this
study, the Gilson 231XL and the Peltier rack had severe limitations in the feasibil-
ity of other chemistries. The study also showed that having minimized the bottle-
neck of analyzing the samples, reaction preparation and data manipulation became
the labor-intensive task. For all of these reasons, researchers at Glaxo Wellcome
designed the development automated reaction toolkit (DART) and the process re-
search optimization screening parallel experimentation robot (PROSPER) systems,
which are specically designed to accelerate process optimization using automa-
tion and experimental design.
The DART system became commercially available from Anachem as SK233 TM .
The SK233 TM consists of one or two STEM reaction blocks and a Gilson 233XL
Autosampler. Each STEM reaction block allows up to ten reactions at a tempera-
ture of 30 C to 150 C. The SK233 TM was designed to deliver liquids to each re-
action and perform online automated HPLC analysis without attendance [16]. Re-
searchers at SmithKline Beecham extended the ability of the SK233 TM workstation
by improving the performance of the SK233 TM under reux conditions. New glass
reaction vessels with a quick-t female joint and a cold nger-type reux con-
denser with a hollow center were implemented in the SK233 TM [17]. This multiple
condenser arrangement is now known as the REACTarray TM (the REACTarray TM

is available under license form Anachem Ltd; http://www.reactarray.com). The
REACTarray TM allows reactions under reux conditions and inert atmosphere, as
well as reagent additions and sampling under the same conditions.
Researchers at Glaxo Wellcome performed process screening and optimization,
robustness tests, reaction proling, and stability testing using the SK233 in con-
junction with statistical experimental design (i.e. DOE). In order to optimize, for
example, a Mitsunobu reaction, 20 experiments were run based on a two-level fac-
torial design over 5 days, followed by 16 experiments over 4 days. These results
helped to identify an important reaction factor, and the yield was improved from
less than 70% to almost 90% [16].
A group at SmithKline Beecham performed reaction scouting, process screen-
ing, and process optimization using the REACTarray and the SK233. In one exam-
ple, the screening of air-sensitive reagents and solvents for a Lewis acid-catalyzed
reaction between enol ether 7 and b-lactam 8 was carried out (Scheme 31.2). The
screening of 20 Lewis acids and seven solvents provided a number of eective new
catalytic systems. During this study, the large amounts of data generated (420 chro-
matograms) were handled using Excel [17]. Researchers at SmithKline Beecham
described additional applications of multireactor systems in their presentation at
the CombiCat conference 1999 [18]. The catalyst, solvent, amine stoichiometry, and
catalyst loading were optimized for a sensitive hydrogenation in the synthesis of
famciclovir.
Scheme 31.2. Medium-throughput screening in the synthesis of Elanapril (9) (Merck).
Glaxo Wellcomes new PROSPER system has over 50 reactors that are individu-
ally controlled with features to enable rapid process development [19]. One example
is the optimization of a phase transfer-catalyzed alkylation to produce a secondary

amine.
In the process chemistry group at Eisai, the more than 30-step synthesis of an
endotoxin antagonist was carried out by a team of four to six chemists by employ-
ing automation-assisted DOE, which can be a very tedious task using conventional
manual operations. An array reactor that runs 12 parallel reactions with exible
liquid handling, independent temperature control, timed sequences, and an HPLC
interface was used to apply this methodology to optimize carbodiimide-mediated
amide bond formation using very precious starting materials; the amine 10 for
this reaction was prepared in 12 steps and the acid 11 was purchased at $25,000
per kg (Scheme 31.3). Five factors were targeted for DOE and 20 experiments were
run in two batches of ten experiments each. The analysis of data by the statistical
software identied the temperature as the only signicant factor. The verication
runs were also carried out in the array reactor, and the further optimization led to
the successful pilot plant synthesis on a 1-kg scale [20].
Scheme 31.3. Lewis acid-catalyzed reaction using REACTarray and SK233.
The high-throughput process development group at Schering AG has developed a

robotics system that consists of three main parts: a parallel synthesis robot (Bohdan
process development workstation), a second robot for the preparation of analytical
samples (custom-tailored Bohdan sample preparation workstation), and four Dio-
nex HPLC devices [21]. The synthesis robot can perform 12 parallel reactions with
up to 25 mL maximum reaction volume, each reaction can be individually heated
or cooled between 40 C and 140 C and stirred by magnetic stir bars under inert
gas. For all reactions, the block and the inner reaction temperature can be mea-
sured. Both robots have two dierent types of cannulas to transfer air- or moisture-
sensitive reagents and slurries into the reaction vessels. A barcode system facili-
tates the analytical sample handling and data management. The data identied by
the corresponding barcodes are easily exchanged in an automated manner in the
network environment. To achieve a high throughput of the analytical samples, rapid

HPLC analysis methods on short columns are used. Finally, the analytical results
are transferred into Excel spreadsheets.
In the rst 10 months after installation of the automated reaction optimization
system, over 1200 reactions have been performed for the successful optimization
of 26 dierent synthetic steps. One example was the aldol condensation between
m-methoxy-benzaldehyde 13 and acetaldehyde 14 to m-methoxy-cinnamaldehyde
15 (Scheme 31.4). After 60 experiments with the synthesis robot and 480 fast
HPLC analyses, the yield was improved to 65% from 1020%. It took only seven
working days to achieve this result, and the improved yield was smoothly repro-
duced on a 65-kg scale in the pilot plant.
Scheme 31.4. High-throughput carbodiimide-mediated amide bond formation reaction.
Symyx Technologies and Argonaut jointly developed Endeavor TM (http://www.

argotech.com) for performing parallel reactions at elevated pressures and temper-
atures (Fig. 31.2). In addition to traditional solution-phase chemistry, Endeavor TM
can be used to perform reactions such as hydrogenations, carbonylations, and ole-
n polymerization as well as to optimize both homogeneous and heterogeneous
catalysts. Reactors with magnetically coupled overhead impellers, individual con-
trol of temperature and pressure in each vessel, and the monitoring of gas uptake
allow process chemists to track and compare the course of reactions under dier-
ent conditions [22].
Researchers at Pzer employed Endeavor TM for a case study of partial hydro-
genations of 4-nitroacetophenone (Scheme 31.5) [23]. The optimization consisted
of two steps: (1) an initial screen crossing a discontinuous variable (the choice of
catalyst) with a continuous variable (modier stoichiometry), and (2) optimization
for selected catalysts by a full factorial analysis of four continuous variables (cata-
lyst loading, pressure, temperature, and modier stoichiometry). Thus, eight cata-
lysts were rst screened both with and without methanesulfonic acid (MsOH, 1.1
equiv.) at 30 C and 50 psi of H2 . Reductions were run eight at a time on a 500-mg
scale in 5 mL of ethanol. The yields were determined by HPLC. The best con-
Fig. 31.2. Endeavor TM for performing parallel reactions at

elevated pressures and temperatures (jointly developed by
Symyx Technologies and Argonaut).
ditions from this initial screen gave 17 in 85% yield, 18 in 90% yield, and 19 in
96% yield using 5% Pd/CaCO3/Pb with 0 equiv. of MsOH, 10% Pd/C with 0 equiv.
of MsOH, and 10% Pd/C with 1.1 equiv. of MsOH, respectively. These three con-
ditions were then optimized for the two catalysts involved by examining low and
high points for catalyst loading (5% and 20%), pressure (25 and 100 psi), temper-
ature (25 C and 60 C), and, for Pd/C, the amount of MsOH (0 and 1.5 equiv.).
The best conditions from this full factorial screen gave 17 in 97% yield, 18 in 95%
yield, and 19 in 99% yield. The measurement of hydrogen uptake helped to set re-
action times and parameter ranges for the full factorial analysis, allowed for quickly
Scheme 31.5. Partial hydrogenations of 4-nitroacetophenone 16 using Endeavor TM (Pzer).

spotting under- and overreduction, aided predicting robust reaction endpoints, and
provided data for analyzing kinetic behavior. These techniques can be applied to
the rapid optimization of reactivity and selectivity for the hydrogenation of a vari-
ety of polyfunctional molecules.
Researchers at Argonaut have also developed the automated chemical develop-
ment platform Surveyor TM (http://www.argotech.com) especially for conducting
process screening and optimization with a consortium of six companies: Pzer,
Agouron Pharmaceuticals, Aventis Pharmaceuticals, Eli Lilly & Company, and
Rohm & Haas. Surveyor has ten individually controllable reaction vessels with au-
tomated reagent/solvent addition. The system is also capable of sample extraction/
quenching/injection for online HPLC analysis. It uses simple graphical software to
set up experiments and to control temperature, temperature ramp rates, reagent
addition, agitation, sampling, and analysis.
Researchers at Argonaut have demonstrated the automated optimization for the
multistep synthesis of chiral imidazolidinones, useful auxiliaries for the asymmet-
ric synthesis and key intermediates for some human immunodeciency virus (HIV)
protease inhibitors [24]. This study included the initial route scouting, the reaction
condition screening, and the optimization, followed by a scale-up run using the
conventional laboratory set-up. Two routes were compared and variables such as
choice of reagents, time, temperature, and concentration were examined using
Surveyor (Scheme 31.6). Each route was evaluated and compared from a scale-up
standpoint, and the optimized conditions for the selected route were subsequently
applied on a 6-g scale, aording the imidazolidin-2-one 20 in 90% isolated yield.
Scheme 31.6. Automated optimization of the multistep

synthesis of chiral imidazolidinones 20 (Argonaut).
A group at Bristol-Myers Squibb described the deprotection of N 0 -triuoroacetyl-

S-tert-leucine-N-methylamide (21) using their high-throughput discovery and opti-
mization tools [25]. Standard deprotection reaction conditions aorded 22 in only
6266% yield (Scheme 31.7). These studies included three phases: a combinatorial
screen of discrete reaction factors (process discovery), a multivariable screening
DOE of all the continuous factors, and an optimization DOE on the important
factors identied in screening DOE.
Scheme 31.7. Deprotection of N 0 -triuoroacetyl-S-tert-leucine-

N-methylamide 21 (Bristol-Myers Squibb).
The discovery phase of this study was a combinatorial screening of ten bases
and seven 50% aqueous solvents. The reactions were performed by dispensing 100
mL of a stock solution of 21 in methylene chloride into each reactor. The solvent
was evaporated in a Savant SpeedVac, and the appropriate reaction solvent (200 mL)
and the appropriate base (200 mL of 0.5 M aqueous base) were dispensed into each
reactor. The reactors were incubated at 45 C for 3 h on a J-Kem shaker plate. After
the reaction aliquots were taken for HPLC analysis, this combinatorial screening
of the 66 reactions revealed that the best overall combination is lithium hydroxide
and water.
With the selection of aqueous alkoxide solutions for the screening DOE, the fol-
lowing factors were then subjected to the second-phase experiment (a screening
DOE): choice of hydroxide (lithium, sodium, or potassium hydroxide), concentra-
tion, temperature, and the equivalents of base. Thirty reactions were performed
including a full factorial 2 3 experiment with each base, including an additional six
center points distributed among the three bases to measure experimental error. A
Zymark Robot performed the experiments by dispensing the appropriate amount
of water and dilute aqueous hydroxide solution to each reaction. Of the four factors
evaluated, only the equivalent of base had a statistically signicant impact on con-
version of starting material to product. After optimization of the equivalents and
concentration of base, a two-factor central composite design with four center points
was employed. Twenty reactions were prepared on a Gilson 215 liquid handler,
heated for 3 h at 45 C in a reactor block, and sampled for HPLC analysis. A scale-
up of the optimized conditions resulted in an isolated yield of 95% of product. In
conclusion, 116 reactions were performed within 4 days, improving the yield from
63% to more than 95%.
Outsourcing of chemical development is becoming increasingly important. Com-
panies such as MediChem, Johnson Matthey, and Symyx Technologies oer auto-
mated high-throughput or combinatorial process development or both for phar-

maceuticals and ne chemicals.
In one example, Zhang and coworkers at MediChem disclosed that the Friedel
Crafts acylation reaction used in their total synthesis of ()-calanolide A, a poten-
tial anti-HIV agent currently in clinical trials, was successfully optimized with the
use of automated synthesis equipment that was coupled with the statistical DOE
(Scheme 31.8) [26]. At MediChem, a Bohdan RAM automated workstation was
employed for sample weighing and a Gilson 215 liquid handler for liquid transfer.
The reactions were run on a shaker equipped with a thermocontrol unit. Samples
were dried by a Savant speed vacuum dryer. The reaction yields were determined
by HPLC analysis. Out of 24 randomly selected Lewis acids, the best results were
obtained with AlCl3 and AlBr3, and AlCl3 was chosen because of cost considera-
tions. Design Expert software (Stat-Ease) was utilized to generate a series of ex-
periments according to a statistical design to investigate the eects of solvent, reac-
tion temperature, and AlCl3 stoichiometry on product formation. Two sets of 13
experiments followed by 16 experiments proposed by the software were performed
to give useful insights into the transformation for the nal optimization. On a 10-g
scale, the reaction aorded the crude product in 91% yield under the optimized
conditions, compared with 45% prior to optimization. With the use of automated
equipment coupled with statistical DOE, it took 1.5 months for one chemist to
complete the optimization, compared with 6 months for two chemists to deter-
mine optimal reaction conditions using conventional methods [26].
Scheme 31.8. Optimization of a FriedelCrafts acylation and

the synthesis of 26 using automated synthesis equipment
coupled with statistical DOE (MediChem).
In another application of the automated process development technology, re-

searchers at MediChem were able to improve the yields of 4(5)-(3-pyridyl)imidazole
26 from 20% to 74% [27].
Pollard of Avantis CropScience gave a useful and interesting account on issues

related to a stepwise and unied approach to automation across all three phases of
process development, using existing standard laboratory equipment and inexpen-
sive commercial software packages. In addition, a detailed discussion of an auto-
mation system (computer-aided reactor system; CAR) was given that has evolved
and has been developed at Aventis CropScience over the last 10 years. The discus-
sion extends to a variety of examples, including calorimetry, DOE, crystallization
studies, and plant simulation along with equipment and computer issues. The CAR
can be used across all three phases of development activities and also to datalog and
monitor a small pilot plant, presenting a single interface to chemists at all scales.
The system controls a variety of external equipment including Gilson autosam-
plers, HPLC equipment, many types of heater/circulator, as well as traditional lab-
oratory equipment. The CAR provides round-the-clock capabilities of sophisticated
multireaction control and datalogging on reactors ranging from 10 mL to 10 L [28].
The CAR system originated as a single automated laboratory reactor (ALR) which
was used largely for DOE work, but owing to its exibility and power it has been
used in many areas:
. ALRs control multiple automated laboratory reactors, on many scales from 100
mL to 10 L, for optimization, validation, DOE, and kilo-lab work.
. Calorimetry: addition of an internal heater and controllable power supply gives
calorimetric capabilities.
. Plant simulation: multiple independently controlled reactors, hold/feed vessels,
and crystallizers can be used to simulate full-sized plant operation in the laboratory.
. Crystallization studies: using optical sensors to detect the onset of crystallization
and control crystallization processes.
. Optimization, DOE, and kinetics: using an HPLC and autosampler directly from
three small reactors, a fully automated parallel system has been produced.
. Route scouting: the autosampler system combined with a modied Stem-type
heating block allows the study of the inuence of solvent/catalyst/base, etc. of
ten parallel reactions.
Data logged from the system are generally handled in Excel, a suitable graphing
package, or a statistical package.
The latest and most exible version of the CAR system runs a set of three custom-
built jacketed reactors attached to a Gilson analytical autosampler and a high-
throughput HPLC system. Even though the author states that the system has been
used considerably for DOE optimization work, it appears to be most suitable for
process characterization or validation or both. The throughput is rather slow but it
oers a precise reaction control under realistic conditions as well as a high degree
of analytical capability. Each reactor is equipped with an overhead stirrer, reux
condenser, thermopocket and sample port, and two nondedicated ports for addi-
tions, pH probe, etc. The reactor volume is 50150 mL, and each reactor has an
independent heater/circulator to heat the jacket up to 200 C. Any other traditional
laboratory equipment can also be utilized balances, pumps, pH meters, etc. The
autosampler is programmed to collect samples directly from each reactor on com-

mand from the control system. The system can slow or stop the agitation during
sampling and alter the sampling height to sample dierent phases. Samples can
be diluted and then injected automatically onto the HPLC. A standard analytical
LIMS (Laboratory Information Management System) system allows easy visual ex-
amination of stacked chromatograms for qualitative assessment of reaction pro-
les or more sophisticated kinetic analyses. The author also mentions a variation
of the three-reactor optimization system described above that is constructed
around a Gilson autosampler/HPLC and Stem or Variomag heating block with
modied glassware. This system is technically more simple than the optimization
system described above and is still in development.
The Auto-MATE is a miniature computer-controlled multiple reactor system
(25100 mL) that was designed to ll the gap between rapid process screening and
optimization by robotic systems and process characterization and validation by large
automated laboratory reactors (> 1 L). Between four and 16 independent reactors
can be controlled simultaneously from a single computer interface, although the
conguration of four reactors is most common. The system consists of a small con-
tainer that constitutes an oil jacket with a central recess into which a close-tting
miniature reactor is placed. Reactors of dierent sizes and materials can be used
interchangeably with the jacket. The reactor cover has an integral stirrer mounted
on it and has ports for a thermocouple, pH probe, heater, reux condenser, etc.
The electrical heater that is placed within the reactor maintains the temperature
(isothermal or nonisothermal), enabling the precise and rapid control of the reac-
tor temperature and optionally allows calorimetric data to be acquired using the
power compensation technique. Using this information, it is possible to determine
reaction endpoints and to establish a rst-pass screen for hazard assessment in
scale-up. Reactions under elevated pressures, such as hydrogenations, can be car-
ried out with the Auto-MATE using high-pressure reactors. Researchers at HEL
demonstrated that the Auto-MATE was useful for process analysis and for rene-
ment and scale-up in conjunction with calorimetric data [29].
To meet the increasing demands being created by the combinatorial revolution
in drug discovery and the demanding timelines forced on chemical development
departments, Pzer development laboratories were interested in a exible auto-
mated system that mimics a plant reactor with the capability of controlling reaction
conditions very precisely [30]. Since no commercial instruments met their require-
ments, the custom system was built around a Zymark XP Track Robot especially to
accelerate the late-stage process development, i.e. optimization coupled with DOE
and validation. The key features of the system include:
. plant reactor mimics;

. self-cleaning and draining for continuous operation;
. solids dispensing;
. accurate liquid handling;
. online analysis;
. exible software.
Two plant reactormimics of the system consist of cone-bottomed glass reactors

with 50400 mL capacity equipped with a ve-port ange lid incorporated in an
automated addition port, overhead stirring, a condenser, a thermocouple, and a
spare port for probe technology. The triple-jacketed vessel has a temperature range
of 20 C to 150 C, controlled inert gas ow, and automated drain valve for post-
reaction collection and manipulation if necessary.
Throughput limitations of two reactors were resolved by incorporating automated
self-draining/self-cleaning modules into the system to allow continuous operation.
The system is capable of dispensing solids at any time during the reaction, includ-
ing seeding for crystallization studies.
The software was developed internally in LabView, conforming to the evolving
standard of Laboratory Equipment Control Interface Specication (LECIS). The re-
sulting software was extremely exible, functional, and modular. It was demon-
strated that the system performs well when applied to process optimizations and
validations that are time-consuming, tedious, and dicult to control when con-
ducted manually.
31.2.3
Miscellaneous
Sumitomo Chemical in Japan has developed a robotic workstation for automated

organic synthesis. The system consists of a computer, a robot, and several other
devices (including a reaction device, a separation device, dispensing device, etc). The
reaction device has four temperature regulation units, each of which can freely
change the reaction temperature between 30 C and 160 C. Since each of the
four units can handle four reaction containers, 16 reactions under dierent con-
ditions can be performed simultaneously. Reactions beyond the boiling points of
solvents are possible using reux condensers. The separation-processing device
automatically performs solution extraction operations, based on the detected liquid
levels and interface positions. The dispensing device can automatically pump vari-
ous reagents and/or solvents at various speeds into the reaction containers by
switching valves through a digital syringe pump. This system can automate all syn-
thesis and analysis processes and can perform at least 3000 experiments per year
[31].
Lindsey and coworkers investigated the conditions for condensation of mesi-
taldehyde and pyrrole to provide tetramesitylporphyrin (27) (TMP) using an auto-
mated chemistry workstation (Scheme 31.9) [32]. The automated chemistry work-
station consists of a 60-vessel reaction station, a 264-sample vial rack, reagent and
work-up reagent racks, a solvent inlet line, a reagent and sample transfer syringe, a
washing station for syringes, a robotic arm, and an ultraviolet (UV)-visible absorp-
tion spectrophotometer. Each reaction vessel consists of a 10-mL glass vial tted
with a septum cap. The entire station is controlled by thermostats, and a magnetic
stirrer individually stirs each vessel. The workstation also has a space for additional
analytical instruments. Using this workstation and the proprietary algorithm, cata-
lystcocatalyst [BF3 O(Et)2 /alcohol] combinations and concentrations were exam-
ined in 284 reactions over a 10-week period, yielding 1704 data points. Three e-
cient cocatalysts were identied and the rate and reactor volume productivity were
optimized. The authors concluded that the comprehensive set of data accumulated
from the automated experiments establishes the scope of BF3/ethanol cocatalysis
in the synthesis of TMP and should be useful for planning syntheses as well as for
studying the mechanism(s) of catalysis.
Scheme 31.9. Condensation of mesitaldehyde and pyrrole to

provide tetramesitylporphyrin 27 (TMP) using an automated
chemistry workstation.
Otera and coworkers have developed a new type of automated synthesizer with
the ability to conduct a variety of synthetic reactions [33]. Although not intended
for the process development, their results suggest that the system will be useful for
automated process development with some modication. The system consists of
a control unit [automatic reaction system (ARS) and a sequencer], a jacketed glass
reactor (50 or 130 mL), reservoirs, volumetric ceramic valveless piston pumps, a
syringe for quenching the reaction, and a cooling unit. Reactions can be run under
inert atmosphere at reaction temperatures from 78 C to elevated temperatures.
Using the synthesizer, air-sensitive organolithium and Grignard reagents as well
as transition metal catalysts could be handled. Also, the dependence of chemical
yields on the reaction temperature for Peterson alkene synthesis and on the addi-
tion rates of the aldehyde for aldol reactions were examined. Because the order of
reagent addition is programmed and the reaction temperature is quickly tunable,
sequential reactions can be conducted smoothly. An advanced control system was
incorporated that allows a task to start immediately after the preceding one has
nished, minimizing the time for completing the multistep process.
In the current environment of intense market competition, batch process in-
dustries stand to benet from faster process development. Two batch process areas,
operating procedure synthesis (OPS) and process hazards analysis (PHA), are time-
consuming because they are often performed manually. Recently, a Purdue Uni-
versity Group developed two intelligent systems, iTOPS and Batch HAZOPExpert
(BHE), to automate OPS and PHA. Two applications from the specialty chemical
industry are presented to demonstrate the utility of the integrated system [34].
Resolution by forming diastereomeric salts is still an important method for ob-
taining enantiomerically pure chiral compounds. Generally, tedious trial-and-error
experiments are required to identify the satisfactory combination of resolving
agents. Researchers at Roche Discovery Welwyn described the use of dierential
scanning calorimetry (DSC) as a means to identify diastereomeric salts with a clear
eutectic composition that is needed for eective resolution and for forming the
basis of a resolving agent screening process. This work also included automated
salt synthesis using the ACT robot in 96-well microtiter plate format. (ACT refers
to the Advanced ChemTech synthesis robot, which is primarily used for solid-phase
synthesis.) Automation showed good correlation with the nonautomated experi-
ment, and is therefore suitable for future screening of resolving agents. Rapid data
analysis was facilitated using the in-house software package Resolution Compan-
ion, which also enabled identication of the optimum crystallization conditions
following a trial crystallization experiment. This software package enables (1) the
construction of binary-phase diagrams using the Schroedervan Laar equation, (2)
the rapid analysis of data from DSC thermograms, and (3) the construction of
ternary-phase diagrams for evaluation of optimal solution concentrations. The au-
thors also point out that the method has some limitations: (1) a failure to crystal-
lize under multiwell evaporation does not imply crystallization will not occur under
other conditions, (2) polymorphism, degradation, and signal overlap can compli-
cate DSC analysis, and (3) solvate formation can markedly alter the phase diagram.
Nevertheless, the use of DSC to aid in the selection of a resolving agent has been
demonstrated and forms the basis of an automated screening procedure [35].
31.3
Summary and Outlook
Implementation of medium- and high-throughput screening for chemical pro-

cess development is developing rapidly. Several commercial systems have been in-
troduced and publications are beginning to demonstrate the value and return on
investment for such systems. The cases cited here demonstrate that medium
throughput (ten-at-a-time approach) in conjunction with statistical DOE has taken
hold. At the screening/optimization stages, process chemists generally have sig-
nicant insights into the mechanism of the reaction, thus rendering this approach
especially powerful and dramatically accelerating the process development.
References 883
In the case that an entirely novel process has to be developed, where only a mini-
mal level of chemical knowledge exists, the true combinatorial high-throughput
methodology (hundred-at-a-time or thousand-at-a-time approach) needs to be im-
plemented. There will be, however, signicant technical hurdles between the ten-
at-a-time technology and the hundred-at-a-time technology, and it will take con-
siderable eorts to develop these systems [36]. Not only will the close collaboration
between process chemists and combinatorial chemists be necessary, but the involve-
ment of engineers and computer scientists will be likewise indispensable for full
implementation. Nevertheless, the truly high-throughput systems will fundamen-
tally change the way chemical process development is carried out in the future.
Acknowledgments
The authors wish to thank Dr Michael Cannarsa (Synthetech) for his contribution
to the original ideas of this manuscript, Ms Cate Larsen (Symyx Technologies) for
useful help, and Ms Silvia Lee (Symyx Technologies) and Ms Kathryn Boykin
(XenoPort) for their invaluable support in reference and patent searches. The
authors are grateful for Ron Krasnow (Symyx Technologies) for checking the
manuscript.
References
1 C. Littlehales, Modern Drug Discovery 8 For design of experiments (DOE), see:

1999, 2, 21. a) G. E. Box, W. G. Hunter, J. S.
2 M. J. Cannarsa, T. Uno, C. Larsen, Hunter, Statistics for Experimenters.
Curr. Opin. Drug Discovery Dev. 2000, Wiley, New York 1978; b) D. R.
3, 743749. Pilipauskas in: Process Chemistry in
3 T. Laird, Org. Process Res. Dev. 2001, the Pharmaceutical Industry.
5, 272. Gadamasetti, K. G. (ed.), Marcel
4 For recent reviews concerning Dekker, New York 1999, pp. 411428.
combinatorial aspects of materials 9 M. R. Owen, C. Luscombe, L.-W. Lai,
science and catalysis, see previous S. Godbert, D. L. Crookes, D.
chapters or: B. Jandeleit, D. J. Emiabata-Smith, Org. Process Res.
Schaefer, T. S. Powers, H. W. Dev. 2001, 5, 308323.
Turner, W. H. Weinberg, Angew. 10 J. N. Cawse, Acc. Chem. Res. 2001, 34,
Chem. 1999, 111, 26482689; Angew. 213221.
Chem. Int. Ed., 1999, 38, 24952532. 11 D. J. am Ende, P. J. Clifford, D. M.
5 M. Harre, U. Tilstam, H. DeAntonis, C. SantaMaria, S. J.
Weinmann, Org. Process Res. Dev. Brenek, Org. Process Res. Dev. 1999, 3,
1999, 3, 304318. 319329.
6 M. R. Owen, S. H. Dewitt in: Process 12 D. Dorsett in: Proceedings of
Chemistry in the Pharmaceutical CombiCat2000. Lisbon, Portugal,
Industry. Gadamasetti, K. G. (ed.), October 2000. The Catalyst Group,
Marcel Dekker, New York 1999, pp. Inc., 714 N. Bethlehem Pike Spring
429455, and references cited therein. House, PA 19477, USA
7 N. W. Hird, Drug Discovery Today 13 T. S. Powers, T. Uno in: Proceedings
1999, 4, 265274. of the 10th Conference on
Combinatorial Chemistry, Osaka, Org. Process Res. Dev. 2001, 5, 335

Japan, April 2000. Japan 339.
Combinatorial Chemistry Focus 22 K. Andrews, Chimia 2000, 54, 155
Group (JCCF), The Society of 157.
Synthetic Organic Chemistry, Japan, 23 J. M. Hawkins, T. W. Makowski, Org.
Kanda-Surugadai 1-5 Chiyoda-ku, Process Res. Dev. 2001, 5, 328330.
Tokyo 101-0062, Japan. 24 O. W. Gooding, T. Lindberg, W.
14 a) A. Guram, A. Hagemeyer, B. Miller, E. Munyak, L. Vo, Org.
Jandeleit, D. M. Poojary, H. Process Res. Dev. 2001, 5, 283293.
Turner, W. H. Weinberg in: 25 V. W. Rosso, J. L. Pazdan, J. J. Venit,
International Congress on Catalysis Org. Process Res. Dev. 2001, 5, 294298.
12th: 2000: Granada, Spain, 1st ed. 26 J. Zhang, E. W. Kirchhoff, D. E.
(Amsterdam, Elsevier, 2000); Zembower, N. Jimenez, P. Sen, Z.
b) P. Desrosiers, A. Guram, A. Xu, M. T. Flavin, Org. Process Res.
Hagemeyer, B. Jandeleit, D. M. Dev. 2000, 4, 577580.
Poojary, H. Turner, H. Weinberg, 27 E. W. Kirchhoff, D. R. Anderson,
Catalysis Today 2001, 2448, 16. S. Zhang, C. S. Cassidy, M. T.
15 P. Desrosiers, B. Jandeleit, D. M. Flavin, Org. Process Res. Dev. 2001, 5,
Lowe, T. Uno, A. Vimercati, A. 5053.
Volpe Jr, T. Weskamp, J. Zhang in: 28 M. Polland, Org. Process Res. Dev.
Book of Abstracts by the Division of 2001, 5, 273282.
Catalysis and Fine Chemicals of the 29 C. Simms, J. Singh, Org. Process Res.
Catalysis Society of Japan, Tokyo, Dev. 2000, 4, 554562.
Japan. International Symposium on 30 P. D. Higginson, N. W. Sach, Org.
Catalysis and Fine Chemicals. Tokyo, Process Res. Dev. 2001, 5, 331334.
Japan, March, 2001. 31 H. Okamoto, K. Deuchi, Lab. Rob.
16 D. F. Emiabata-Smith, D. L. Autom. 2000, 12, 211.
Crookes, M. R. Owen, Org. Process 32 R. W. Wagner, F. R. Li, H. Du, J. S.
Res. Dev. 1999, 3, 281288. Lindsey, Org. Process Res. Dev. 1999, 3,
17 M. A. Armitage, G. E. Smith, K. T. 2837.
Veal, Org. Process Res. Dev. 1999, 3, 33 a) A. Orita, Y. Yasui, J. Otera, Org.
189195. Process Res. Dev. 2000, 4, 333336;
18 M. J. Cannarsa, Chim. Oggi 2000, 18, b) A. Orita, Y. Yasui, J. Otera, Org.
2224. Process Res. Dev. 2000, 4, 337341.
19 M. Owen, Automation in Process R&D. 34 J. S. Zhao, S. Viswanathan, C. H.
Boston, MA, 2000. Scientic Update, Zhao, F. P. Mu, V.
Maycraft Place Stone Cross Mayeld Venkatasubramanian, Comput.
East-Sussex TN 20 6EW, UK. Chem. Eng. 2000, 24, 15291533.
20 G. S. Proehl in: Proceedings of The 35 U. C. Dyer, D. A. Henderson, M. B.
3rd International Conference on Mitchell, Org. Process Res. Dev. 1999,
Organic Process Research and 3, 161165.
Development, Montreal, Canada, 2000. 36 P. Cohan in: Proceedings of the
Scientic Update Maycraft Place Stone Knowledge Foundation Combi2001
Cross Mayeld East-Sussex TN 20 Conference. San Diego, CA, January,
6EW, UK. 2001. The Knowledge Foundation, Inc.
21 M. Harre, H. Neh, C. Schulz, U. 18 Webster Street Brookline, MA
Tilstam, T. Wessa, H. Weinmann, 02446-4938, USA.
885
32
Combinatorial Methods in Catalysis
Bill Archibald, Oliver Brummer, Martin Devenney, Sasha Gorer,
Bernd Jandeleit, Tetsuo Uno, W. Henry Weinberg, and
Thomas Weskamp
32.1
Introduction
32.1.1
Combinatorial Catalysis
The conventional process used to search for new materials in important areas such
as biopharmaceuticals, materials science, and catalysis has traditionally been long
and expensive, relying on a large number of iterative steps to produce new or op-
timized materials. Increasing competition in the chemical industry demands faster
and more ecient identication and development of improved materials, includ-
ing catalysts. This drive toward increased research productivity was rst encoun-
tered in the pharmaceutical industry, where long development times and high re-
search costs necessitated the introduction of new research and development (R&D)
approaches designed to accelerate the drug discovery process. One approach in-
tended to speed up the discovery process is to develop high-throughput methods
for rapidly synthesizing and screening large numbers of diverse chemical com-
pounds, searching for trends in desired parameters. Virtually every major drug
manufacturer now utilizes this new research technology, called combinatorial
chemistry, as an integral part of its research and development program [110].
The combinatorial process involves the design and synthesis of discovery libraries
aimed at eciently exploring large numbers of structurally or compositionally di-
verse compounds thought to be of interest as a result of a review of their chemical,
biological, physical, and/or structural properties. Rapid, sensitive measurements of
one or more relevant chemical or physical properties of each library member result
in the identication of a family of lead compounds with a desired property. These
compounds are then optimized by continuously varying the stoichiometries or
structures of a more focused set of precursors in a focus library. Compounds with
optimum compositions are then synthesized in quantities sucient for detailed
characterization and evaluation. Finally, with methods of combinatorial chemical

ISBN: 3-527-30509-2
886 32 Combinatorial Methods in Catalysis
synthesis evolving together with rapid analysis and high-throughput screening, data
management is becoming challenging and requires appropriate database technol-
ogy.
The biopharmaceutical industry has levered development of combinatorial tools
from the broad availability of low-cost, high-performance computers, robotics, mo-
lecular modeling, database software tools, and tools created for the clinical diag-
nostics, optics, and semiconductor industries. Adoption of combinatorial methods
has also created novel research areas such as bio- and chemoinformatics to man-
age and mine the large amounts of structural and functional information obtained
from combinatorial investigations [11].
Application of combinatorial methods to nonbiological materials and catalyst
development is still in its infancy. Work initiated by Schultz and coworkers in 1995
has initiated tremendous eorts in this eld [12], although the concepts and their
experimental realizations can be traced back to Hanak in the early 1970s [13]. The
combinatorial paradigm, however, is beginning to be explored increasingly in in-
dustrial and academic laboratories around the world. Combinatorial methods have
been applied to optical and electronic materials, magnets, polymers, and catalysts
for commodity, specialty, and ne chemical applications. Traditional materials de-
sign and screening approaches, which are often based on an a priori mechanistic
approach, typically only lead to structures that were known or expected by the
chemist. This applies even more so to catalysis, where knowledge of the underly-
ing mechanism of the catalytic reaction often drastically limits the number of prob-
able metal/ligand combinations. Combinatorial catalysis methods allow for both
the probable and improbable metal/ligand combinations to be investigated. Fur-
thermore, combinatorial catalysis is rapidly taking advantage of the numerous solid-
and solution-phase synthetic methodologies that exist, including polymer-supported
reagents [1418].
In general, three dierent approaches exist for preparing and testing libraries of
compounds (Fig. 32.1). Conventional research, performed in a one-at-a-time or
serial fashion, provides thorough quality control over samples entering the screen-
ing process. Combinatorial methods that involve, for example, split-and-pool
synthesis are much faster and make the preparation of relatively large numbers of
compounds feasible; however, compounds entering the screening equipment often
lack phase purity. Additional methods that are intermediate to the two extremes
outlined above are based on the parallel synthesis of compounds in a spatially ad-
dressable format with usually one composition per site, which are then coupled to
automated screens. This allows multidimensional problems in the discovery and
optimization of catalysts to be eciently addressed by coupling parallel synthesis
with automated or high-throughput screens.
A SciFinder= reference search performed in February 2001 using the key word
combinatorial resulted in more than 9000 hits. An analysis of the literature
search reveals a tremendous growth in scientic publications and patent applica-
tions in the combinatorial eld. Most contributions deal with combinatorial appli-
cations to pharmaceutical, biological, and medical disciplines; however, signicant
advances in the development of combinatorial approaches to the discovery and
Fig. 32.1. Conventional, parallel array, and combinatorial

approaches to catalyst synthesis and screening.
optimization of new materials and catalysts has occurred in recent years. An in-
creasing number of review articles have been written that address new methods in
combinatorial chemistry and high-throughput screening for chemical process de-
velopment [19] and, of course, combinatorial catalysis [20].
This chapter summarizes applications of combinatorial methodologies to the
discovery and optimization of new catalysts published in the scientic literature
between 1995 and August 2001; patents, patent applications, and conference pro-
ceedings have only been included if they are of the utmost importance.
After this introductory section, the following section introduces combinatorial
approaches to novel metal binders, combinatorially functionalized polymers, and
combinatorially discovered metal complexes as enzyme mimetics. Section 32.3
discusses combinatorial catalysis in asymmetric synthesis. Section 32.4 describes
examples of multidimensional screening in combinatorial catalysis. Section 32.5
summarizes recent eorts in one-pot multisubstrate screening approaches, while
Section 32.6 summarizes some applications of combinatorial methods in the search
for novel polymerization catalysts. Section 32.7 describes combinatorial inorganic
homogeneous catalysis, and Section 32.8 deals with combinatorial approaches in
heterogeneous catalysis. Section 32.9 emphasizes combinatorial electrocatalysis.
Novel high-throughput screening tools are discussed in Section 32.10. Section 32.11
includes a summary and an outlook concerning the future of combinatorial catal-
ysis science.
32.1.2
Combinatorial Organic and Organometallic Catalysis
In homogeneous catalysis [21], the catalytically active species is in most cases a

metal ion stabilized by one or more ligating or chelating organic moieties. The re-
lationship of ligand structure to the chemical and physical properties of derived
metal complexes is a central theme in numerous elds such as selective catalysis,
sensor discovery, and bioorganic chemistry. In an extremely challenging rational
approach, the identication of metalligand complexes with new physical or chem-

ical properties such as well-designed structural, electronic, and/or stereochemical
features typically involves the synthesis of a small number of appropriate ligand
derivatives, and, subsequently, the individual analysis of their metal-binding prop-
erties. This empirical approach often proves to be very labor intensive and not
economical since the potential for optimization is limited by resources and time.
In this context, a systematic methodology for the expedient generation of new
classes of coordination complexes would clearly be of great value. The synthesis of
a library of ligands for the discovery of new or improved catalysts may be carried
out using combinatorial organic synthesis methodologies to overcome a limited
ligand supply, and may subsequently be followed by metal complexation and
screening for catalytic activity in a targeted chemical transformation.
32.2
Metal-binding Ligands, Polymeric Enzyme Mimetics, and Metal Complexes as
Enzyme Mimetics
The application of combinatorial methodologies to the synthesis of metal-binding

agents may be considered as one of the starting points in the development of or-
ganic and organometallic catalysts by combinatorial methods. Since combinatorial
methods have their origin in the eld of peptide library synthesis, it is not sur-
prising that libraries of peptide-based compounds have been studied to identify
new sequences with high anity for transition metals. A traditional approach to
new metal-binding agents is based on core receptors that have already established
binding properties and the modication of their substitution patterns to induce
changes in binding strength and selectivity. In their eorts to identify novel ligand
structures, researchers may as well take advantage of constructing building blocks
that incorporate metal ion coordinating functional groups and link them in a man-
ner such that selective metal binding may result.
32.2.1
Combinatorial Approaches to Metal-binding Ligands
32.2.1.1 Combinatorial Functionalization of Metal-binding Core Structures

Cyclen, a cyclic tetramine, its derivatives, and several other related macrocylic
ligands possess anity to metal ions and have been widely investigated and used
as synthetic transmembrane ionophores and uorescent sensors [22, 23]. Still and
coworkers synthesized libraries of up to 10 5 peptide-modied macrocyclic cyclens
[24]. After attaching one of the ring nitrogen atoms of the cyclen core to a poly-
(ethylene)glycol-grafted polystyrene resin (PEG-PS-resin), the remaining three sec-
ondary nitrogen atoms of the cyclen scaold were then functionalized using a
split-and-pool protocol. Employing uorenylmethoxycarbonyl (Fmoc) solid-phase
peptide synthesis methodology, peptidic side arms derived from a pool of 19 side-
chain-protected amino acids (AA)n , were linked via aminoethyl spacers. Four dif-
32.2 Metal-binding Ligands, Polymeric Enzyme Mimetics, and Metal Complexes as Enzyme Mimetics 889
Fig. 32.2. Libraries of peptidic cyclen-based metal Cu(II)-

binding agents synthesized on solid support. The numbers in
parenthesis represent the appropriate library size. AAi amino
acids.
ferent cyclen libraries were synthesized, diering in both length and nature of the
peptidic side arms (Fig. 32.2).
The side-chain-protected and -deprotected resins were agitated with diluted
aqueous Cu(II) and Co(II) ion solutions. Selective metal binding was screened
visually in a pooled assay identifying binding to Cu(II) and Co(II) by characteris-
tic bright blue and red colors. Deconvolution of the chemically encoded polymer
beads allowed the identication of ligand structures that were responsible for the
selective binding of the metal ions [25]. The peptidic sequences generally diered
for Cu(II) and Co(II) ions, and the length and chemical nature of the peptidic ap-
pendages in both protected and unprotected amino acid forms signicantly inu-
enced the anity of the new peptidic functionalized tetraamines for Cu(II) and
Co(II) ions relative to the corresponding unfunctionalized or alkylated cyclen core.
In a related combinatorial procedure, the development of uorescent sensors for
nanomolar aqueous copper was reported by Sames and coworkers [26]. A library of
ionophoric ligands was generated based on three dierent N-containing macro-
cyclic or tridentate scaold using a split-and-pool strategy and an orthogonal tert-
butyloxycarbonyl (Boc)/Fmoc protecting group protocol. The library was assayed
visually by incubating the solid support-bound ligands with aqueous Cu(II) solu-
tion followed by reaction with a copper-selective staining reagent (blue color). All
identied ionophores contained a carboxylic group as well as an aromatic nitrogen
heterocycle. A pyrazine-containing ligand was selected as a lead structure for fur-
ther development of a uorescent sensor bearing a covalently linked dansyl uo-
rophore (Fig. 32.3).
Fig. 32.3. Pyrazine-containing lead structure obtained from

visual primary screening of the solid-phase-bound ionophore
library. Structure of the identied sensitive and selective copper
ion chemosensor bearing a covalently linked dansyl
uorophore.
After covalent attachment of the uorescent sensor to polymeric microspheres

(3.1 mm), the microsphere sensors were examined in the presence of 50 nM buf-
fered CuCl2 solution using uorescent optical microscopy equipped with a custom
ber optic [27]. Anity (K d 10 nM) and binding selectivity (Cu > Co > Ni > Fe)
were assessed by uorescence quenching and competition experiments.
The X-ray structure of metalloprotein recombinant isopenicillin N synthase
(IPNS), which is involved in the biosynthesis of isopenicillin N, has served as a
lead structure for library design. IPNS possesses at its active site two iron-binding
peptides, IleaHisaArg and TrpaHisaGluaAspaVal, which are linked by a short
peptidic sequence [28]. Hoping to discover potentially new catalysts, Baldwin, Wood,
and coworkers combinatorially explored various versions of resin-bound peptide
libraries of the general structure resinaArgaHisaIlea(AA i )n aValaAspaGluaHisa
TrpaAc (AA i amino acid; n 13), and examined their metal-binding abilities
(Fig. 32.4) [29].
Three dierent peptide libraries with a total of 7240 individual oligomers, each
diering in length and amino acid content, were synthesized using Fmoc peptide-
coupling chemistry in a split-and-pool protocol. Up to three variable amino acids
were incorporated in between the conserved peptide sequences IleaHisaArg and
ValaAspaGluaHisaAcTrp. Selective ion binding was assayed by agitating the resin
beads with aqueous solutions of Cu(II), Fe(II), and Co(II) sources. Signicant metal
binding was accompanied by a color change of the beads. Co(II), for which the
color changed to pink/purple, bound most selectively. No encoding/deconvolution
strategy was implemented in order to characterize the ligand structure that gave
Fig. 32.4. A peptide based on isopenicillin N-synthase.

Schematic diagram of the active site. The wavy lines represent
the remainder of the protein. A peptidic library designed to
mimic the metal-binding region. n 03; AA amino acid;
Ac acetyl.
rise to colored metal complexes from the pooled assay, and catalytic activity of the
new metal complexes in the ring closure of the Arnstein tripeptide (ACV) to iso-
penicilline N was not addressed.
Metalloproteins, synthetically or biosynthetically appended to proteins or other
biomolecules, are nding increasing utility in the biochemical analysis of non-
covalent proteinnucleic acid and proteinprotein interactions. The amino termi-
nal Cu(II)- or Ni(II)-binding (ATCUN) motif is a structural feature of several natu-
rally occurring proteins such as certain types of albumins (e.g. human serum
albumin (HSA), bovine serum albumin (BSA), and rabbit serum albumin (RSA)
and neuromedins C and K, among several others [30]. Generally, this domain is
described as Ni(II)H2 NaAA1 aAA2 aHis. Long and coworkers employed a posi-
tional scanning combinatorial protocol to optimize the desoxyribose-based cleav-
age of B-form DNA by Ni(II)H2 NaAA1 aAA2 aHis metallopeptides [31]. Using a
standard Boc protocol and split-and-mix technique on methylbenzhydrylamine
(mBHA) resin, two libraries were generated from a selection of l-amino acids in
which the rst (AA1 ) and the second position (AA2 ) of the peptide ligand were
varied within the H2 NaAA1 aAA2 aHis sequence. The libraries were assayed after
cleavage from the solid support for increased direct DNA cleavage relative to
Ni(II)H2 NaGlyaGlyaHis after incubation with a Ni(II) source and oxidative acti-
vation of the metal complex with KHSO5 or magnesium monoperoxophthalate
(MMPP). Increased catalytic activity was found when the amino-terminal peptide
position contained a hydrophobic amino acid and the second peptide position con-
tained an ionic or polar amino acid. The optimized and resynthesized metal-
lotripeptide domain Ni(II)HNaProaLysaHis was found to oxidatively cleave DNA
an order of magnitude faster than the reference Ni(II)H2 NaGlyaGlyaHis. DNA-

binding anity was slightly increased relative to Ni(II)H2 NaGlyaGlyaHis, but
metal complexation and the A/T-rich site DNA-binding selectivity were not altered.
Another approach to generate large libraries of metal-binding proteins is to take
advantage of the immune system. Janda and coworkers identied antibodies that
bind unique metals with excellent anity by combining a metallo-panning agent
with the high-throughput screening of a combinatorial antibody library [32]. The
single-chain antibody (scFv) library was constructed from the blood of 50 healthy
volunteers, the resulting phage scFv antibody library was estimated to be 1 10 9
in diversity. This library was then screened against three metal pool mixtures and
an immobilized phosphorodithioate metallo-panning reagent that binds metals,
leaving them coordinatively unsaturated. Two single-chain antibodies were identi-
ed and isolated that bind lanthanum and yttrium in the mM range. Inductively
coupled plasma mass spectroscopy analysis suggests that the selected antibodies
contain a single metal ion binding site.
32.2.1.2 Combinatorial Synthesis of Metal-binding Ligands from Building Blocks

with Metal-coordinating Functionalities
In this approach, selective metal-binding ligand libraries are synthesized de novo
by incorporating building blocks possessing potential metal-coordinating function-
alities. Jacobsen and his group reported the synthesis of a 12,000-member library
using split-and-pool methodology and a chemical-encoding protocol [33]. The
study aimed to discover highly selective metal-binding agents directly on a solid
support. The general ligand structure comprised four variable modules (Fig. 32.5).
It was hoped that the stereochemically dened building blocks were subject to con-
formational restrictions facilitating the formation of potential binding sites in which
both amino acid side-chains interact with metal.
The resin-bound ligands were screened in a pooled assay by agitation in meth-
Fig. 32.5. General structure of a turn-element-containing

metal-binding agent. Specic examples of Ni(II)-binding
ligands synthesized and screened on solid support.
AAi amino acid; Trt trityl.
anolic solutions of Ni(II) and Fe(III) salts. After staining with the appropriate indi-
cators (dimethyglyoxime (DMG) in the case of Ni(II) or KSCN in the case of Fe(III)),
beads containing high concentrations of Ni(II) or Fe(III) were visually identied by
their red or orangered color, respectively, using a light microscope. The chemical
tags on the selected beads were cleaved from the solid support, allowing deconvo-
lution of the chemical synthesis history of an individual selective metal-binding
ligand. Several new ligand structures were disclosed that selectively bind Ni(II) or
Fe(III), each of which consisted of histidine residues, and, in most cases, a set of
two turning elements and/or terminating caps.
Technetium-99m complexed to organic compounds, proteins, peptides, or anti-
bodies plays an important role in the radioimmunodetection (RIAD) of organs and
in tumor imaging because of its low cost, ideal physical properties, and broad avail-
ability. Schneider-Mergener and his group synthesized and screened a cellulose-
bound hexapeptide combinatorial library for the identication of technetium-99m
( 99m Tc)-binding peptides [34]. A combinatorial library of approximately 8000 hex-
apeptides of the general structure B1 aXaB2 aXaB3 aX was synthesized using auto-
mated synthesis on a cellulose platform (spot synthesis) yielding the hexapep-
tide library in a spatially addressable format. The amino acids Bi i 13) were
positioned on the dened positions 1, 3, and 5 within the hexapeptide sequence
and each was one of the 20 naturally occurring l-amino acids. The amino acids Xi
in positions 2, 4, and 6 were systematically randomized. After incubation with an
aqueous pertechnate solution as a 99m Tc source, the library was screened for 99m Tc
anity by phosphorimaging. Besides a variety of cysteine-containing hexapeptides,
known for their strong complexing capability toward 99m Tc, peptidic ligands con-
taining the amino acids His, Lys, Arg, and Met showed signicant anity toward
the radioisotope. In subsequent focused libraries, the three X-positions were dened
by positional scanning and revealed the noncysteine-containing primary se-
quences LysaGlyaHisaSeraHisaVal and LysaAlaaMetaTyraHisaGly as superior
99m
Tc ligands.
Pirrung and Park disclosed the discovery of selective metal-binding peptoids
using 19 F-encoded combinatorial libraries [35]. A method for encoding solid-phase
split-and-mix combinatorial libraries was developed taking advantage of the large
chemical shift dispersion of synthetic uoroarenes (F-tags). Nine uoroarenes ( 19 F-
tags) bearing linkers for attachment to solid support through a photocleavable linker
(Holmes photolinker) were prepared [36]. A 90-member library of N-alkylglycines
bearing substituted succinamides was prepared on solid support from a set of nine
amines, in which the amine was encoded by the uorinated tag, and ten anhydrides
(Fig. 32.6). Bead pools were visually assayed for metal binding by treatment with
a Cu(II) ion source (blue color). Selection of ten blue beads was followed by ir-
radiation to release the tag. Sensitive 19 F-nuclear magnetic resonance (NMR)
was used for decoding. Two compounds, obtained from solution-phase synthesis,
showed high anity either for copper(II) (CuOTf2 ) (K d 44 mM), or iron(III)
[Fe(2-ethylhexanoate)3 ] (K d 31 mM).
Walt and coworkers reported the solution-phase synthesis and characterization
of metal-binding indicators with diverse optical responses on exposure to various
Fig. 32.6. Split-and-mix solid-phase synthesis of a N-

alkylglycine library for the discovery of selective metal binding.
Specic examples of Cu(II)- and Fe(III)-binding ligands
synthesized in solution.
heavy metal ions [37]. A combinatorial approach, based on azo coupling with sub-
sets of either phenolic compounds or aromatic amines, generated a library of azo
dyes. Each reaction mixture containing the product(s) of the azo coupling was in-
cubated with a series of a heavy metal ion sources. Physical parameters such as
absorbance and uorescence spectra of the resulting complexes were measured. Of
the azo dyes prepared, terdentate dyes were particularly useful, providing distinct
spectral responses to three or more metal ions.
Metal-binding agents that are immobilized on appropriate inorganic supports
are important in environmental chemistry, in sensing chemistry, and in bio-
chemistry. Bergbreiter and coworkers prepared a library of surface-bound metal-
complexing hydroxamic acids on silica-coated glass plates as selective and reversible
metal sensors [38]. Aminopropylated silica was reacted with a set of 12 dicarboxylic
acid derivatives as acylation agents to modify the aminopropylated surface into
a carboxylic acid-containing surface. Subsequent attachment of three dierent hy-
droxylamines furnished the immobilized hydroxamic acids (Fig. 32.7). Binding of
the hydroxamic acids to Fe(III) ions resulted in a reddish coloration which was as-
sayed qualitatively or semiquantitatively by either visual inspection or using diuse
reection spectrometry, respectively. The highest yields in the formation of an
Fe(III) complex were obtained when glutaric anhydride or maleic anhydride was
used as an acylation agent. The results were conrmed on bulk samples.
Fig. 32.7. Schematic representation of metal-binding

hydroxamic acids immobilized on silica support.
32.2.1.3 Miscellaneous
Besides the potential utility of a particular class of ligands for a particular catalytic
application, several features must be considered in the selection of ligand libraries.
Reactions that use more than two dierent starting materials are called multi-
component reactions (MCRs) [39]. In the light of chemical productivity and gen-
eration of molecular diversity, an ideal MCR should comprise more than two com-
ponents. High atomic economy (ideally the incorporation of all of the atoms that
build the starting materials into the nal product) is an asset [40], and, further-
more, ligand synthesis and purication procedures must be readily amenable to
parallel synthesis techniques. With respect to their productivity, yield, conversion,
and facile execution, MCRs occupy an outstanding position among other reactions
making them especially interesting for the concept of combinatorial chemistry.
Attempts are now being made to discover new multicomponent reactions by means
of combinatorial technology [39].
In this context, Lapointe reported the parallel synthesis of substituted amino-
methylphosphines of the general structure R1 R 2 PCHR 3 NR 4 R 5 in 1999 [41]. By
combining two secondary phosphines (R1 R 2 PH), a subset of six substituted alde-
hydes (R 3 CHO), and eight secondary amines (HNR 4 R 5 ) in a facile Mannich-type
three-component condensation reaction, a 96-member library of substituted ami-
nomethylphosphines was synthesized (Scheme 32.1). According to their backbone-
building atoms, these ligands were termed PCN ligands. The relatively mild reac-
tion conditions [tetrahydrofuran (THF), room temperature], the large number of
substructures available, and the lack of protection/deprotection steps for the phos-
phine moiety made this protocol an attractive target for parallel synthesis. The
delivery of the reagents and the mixing were performed by an automated liquid
dispenser. The crude condensation products were of sucient purity (@ 95% by
1
H- and 31 P-NMR spectroscopy) for their direct use as ligands. The parallel synthe-
sis of libraries of metal complexes of these PCN ligands and their use as ethylene
polymerization catalysts, for example, is currently being investigated [42]. This ex-
ample is one of the rst reports about parallel syntheses of organophosphines,
and, owing to the broad availability of the appropriate building blocks, large num-
bers of diverse functionalized PCN ligands are accessible.
Scheme 32.1. Parallel synthesis of aminomethylphosphine ligands.
Bidentate phosphorus-containing ligands play a major role in homogeneous

catalysis [21]. Therefore, Li and coworkers at the DuPont Company have developed
a facile and rapid polymer-supported synthesis of novel diphosphane, phosphane
phosphinite, phosphanethiophosphane, and phosphanechlorophosphane ligands
to access a variety of dierent molecular architectures (Scheme 32.2) [43]. The
synthesis starts by treating Merrields resin with excess tert-butylamine to give
the polymer-supported secondary amine A which was then reacted with 1,2-
Scheme 32.2. Polymer-supported synthesis of P/P ligands.

bis-(dichlorophosphanyl)ethane in the presence of triethylamine. The resulting pre-

cursor B was coupled with a variety of Grignards, organolithium reagents, and
metal alkoxides, resulting in the complete substitution of all three PaCl bonds to
give C. Subsequent cleavage of the PaP ligands from the resin proceeded selectively
with PCl3 and with a variety of alcohols and thioalcohols to produce the bidentate
phosphorus-containing ligands D and E in good yields (2675%). In all 15 cases
the crude cleaved products were obtained with a high degree of purity (b 95%).
Functionalized 2,2 0 -bipyridines constitute an interesting class of ligands that
form coordination complexes with a variety of transition metals. Gallop and co-
workers developed a versatile solid-phase adaptation of the classical Hantzsch three-
component condensation reaction for the synthesis of highly functionalized bipy-
ridines (Scheme 32.3) [44]. In one of their approaches, Knoevenagel condensation
of polymer-supported picolinoyl acetate with aromatic aldehydes yielded stable ar-
ylidene intermediates. Subsequent Hantzsch heterocyclization with enamino esters
provided resin-bound 1,4-dihydro-2,2 0 -bipyridines that were oxidized with ceric am-
monium nitrate and cleaved from the support with triuoroacetic acid to give 2,2 0 -
bipyridine carboxylates. In an additional approach, dierent classes of b-ketoesters
were immobilized and the pyridine moiety was introduced via the enamino ester
building block. This methodology was applied to the generation of a library of 500
bipyridines by split-and-pool synthesis from ve b-ketoesters, ten aldehydes, and
ten electron-decient enamines. These compounds were also exploited for their
coordination capacity toward Pt(II).
Scheme 32.3. Solid-phase synthesis of 2,2 0 -bipyridines via Hantzsch condensation.
Wang and Schwabacher reported the synthesis of ve pyridine-containing bi-

dentate ligand building blocks with nucleophilic groups at dierent positions (Fig.
32.8) [45]. Solid-phase alkylation of these building blocks resulted in the construc-
Fig. 32.8. Library of dipeptides each bearing two bidentate pyridine ligands.
tion of a small library of 25 dipeptides, each bearing two bidentate ligands. These
ligands can serve as building blocks for the construction of disparate metal-binding
molecules.
Schmalz and coworkers reported a modular approach to a new class of structur-
ally diverse bidentate P/N, P/P, P/S, and P/Se chelate ligands for transition metal
catalysis [46]. Bis-protected bromohydroquinones that are accessible from hydro-
chinone were used as the central building blocks (Scheme 32.4). The rst donor
functionality (L 1 ) is either introduced by Pd-catalyzed amination, by Suzuki cross-
coupling, or by lithiation and subsequent treatment with electrophiles (e.g. chlor-
ophosphanes, disuldes, or carbamoyl chlorides). In the case of the Suzuki reac-
tion, the bromohydroquinones were rst transformed into the corresponding bor-
onic acid via lithiation and reaction with triisopropylborate and then reacted with
various heteroaryl bromides. After selective deprotection, the second ligand tooth
is introduced via reaction of the phenolic OH moiety with a chlorophosphane, a
chlorophosphite, or a related reagent. Some of the resulting ligands were converted
into the corresponding PdCl2 complexes that were characterized by X-ray crys-
tallography.
Scheme 32.4. Modular approach to structurally diverse

bidentate chelate ligands for transition metal catalysis.
The aforementioned contributions exemplify the successful implementation of

combinatorial methods such as parallel synthesis on solid supports or in solution,
spot synthesis, split-and-mix methodology, and encoding/deconvolution tech-
niques for the identication of potential ligands and their metal organic complexes.
Although the screening tools were in most cases relatively simple, the high grade
of parallelism and the simplicity of these approaches allowed ecient and rapid
screening of literally thousands of ligands.
32.2.2
Combinatorial Libraries of Polymeric Catalysts as Enzyme Mimetics
Enzymes have found widespread use in industry in a multitude of chemical reac-

tions because of their often perfect selectivities and high activities under relatively
mild reaction conditions [47, 48]. For a multitude of the most dierent reasons,
chemists are obviously stimulated to rationally design and synthesize numerous
classes of low- and high-molecular-weight synthetic enzyme catalysts (synzymes)
that mimic, improve, substitute, or exceed a natural enzymatic function or struc-
ture. However, most of them have fallen short of the goal of eciently reproducing
enzymatic catalysis, but, nonetheless, these studies have brought more insights
into enzymatic reactions [49].
Immobilized (polymer supported) catalysts are of increasing importance in syn-
thetic organic chemistry and library synthesis. In this scenario, established (metal)
organic catalysts are anchored to a solid support to facilitate product work-up, sep-
aration, isolation, and catalyst recycling. However, the scope and limitations of
these catalysts are reviewed elsewhere [50].
A novel approach to identify enzyme-like new organic catalysts is by searching
through a multitude of randomly generated polymeric systems [51]. Random
Fig. 32.9. Examples of a combinatorially functionalized

polymeric catalysts based on poly(allylamine) (PAA) or
poly(ethyleneimine)(PEI) facilitating the hydrolysis of
phosphate esters or the reduction of a-keto carboxylates.
compounds are meant to be combinatorially functionalized polymers. Assuming

a proper juxtaposition of multiple functional, catalytically active groups within the
polymer, the groups of Menger and Ford developed synthetic methodology for
combinatorially functionalized polymers hoping to eect catalysis of several target
reactions.
One of the rst applications of this concept in combinatorial catalysis was the
development of phosphatase-like catalysts [52], or a combinatorially developed
polymeric reducing agent (Fig. 32.9) [53]. In these studies, commercially available
poly(allylamine) (PAA) or poly(ethyleneimine) (PEI) was functionalized with vari-
ous combinations and proportions of small diverse sets (three, four, and eight) of
carboxylic acids to aord randomly functionalized polymers bearing variably sub-
stituted amide groups ranging in concentration from 5% to up to 60% and leaving
some amino functions unreacted. Automation facilitated the synthesis of up to

8198 combinatorial variations of the polymeric reducing agents. To introduce redox-
active capabilities into the reducing polymer catalysts, 1,4-dihydropyridine (DHP),
known from NADH models to reduce activated ketones to alcohols, was incorpo-
rated. Depending on the kind of reaction to be catalyzed, metal ions such as
Mg(II), Zn(II), and Fe(III) [52], or Cu(II), Mg(II), and Zn(II) ions were added [53].
In each case, the polymeric mixtures were then screened spectrophotometrically
either in a one-at-a-time fashion [52], or in a parallel 96-at-a-time microtiter plate
format [53].
Analysis of initial hydrolysis rates of the bis-( p-nitrophenyl)phosphate test sub-
strate concluded some compositionactivity relationships (degree and nature of
carboxylic acid content with respect to catalytic activity). Signicant rate accelera-
tions (kcat =kuncat ) of up to 3 10 4 (exceeding that of a catalytic antibody for the
same reaction) [54] were observed for a specic polymer composition in the pres-
ence of Fe(III) ions [52].
About 92% of the polymeric reducing agents were found to be catalytically inac-
tive in the reduction of benzoylformate (a-keto carboxylate) to the mandelate (a-
hydroxy carboxylate) as the test reaction. Among others, two of the most active
polymer compositions could be identied, and, for example, an active PEI-based
polymer had a functional composition of 5% dihydropyridine, 2.5% 2-imidazol-
acetic acid, 15% 2-naphthyl carboxylic acid, 2.5% 3-mercaptopropionic acid, and
5% Zn(II) [53].
A library of 1344 polymeric variations with an amide bond functionalization
ranging up to 20% was obtained by aminolysis of poly(acrylic anhydride) and sets
of mixtures of three to four amines taken from a library of 11 amines and using an
instrumentational set-up for library synthesis similar to that described above (Fig.
32.10) [55].
Assuming that these polymeric catalysts possessing both acid and basic func-
tional groups in proper spatial orientation would likely catalyze the dehydration of
Fig. 32.10. Example of a combinatorially functionalized

polymeric catalyst based on poly(acrylic anhydride) facilitating
the dehydration of b-hydroxyketones.
Fig. 32.11. Representative structural element of a hydrolytically

active trimethylammonium (TMA) functionalized polymer.
b-hydroxy ketones, the researchers spectrometrically monitored the appearance of

the b-aryl-a,b-unsaturated carbonyl chromophore of the product. About 1% of the
polymeric catalysts revealed a signicant rate enhancement kcat =kuncat 920. For
comparison, an antibody-catalyzed dehydration of the test substrate aorded a cat-
alytic rate enhancement of 1200 above background [56]. Several other interesting
features could be assessed rapidly such as the observation of a nonbiological in-
duced t, i.e. a substrate-induced transformation into a catalytically active confor-
mation upon variation of the reaction parameters such as temperature and pH.
Ion exchange latexes, especially those bearing quaternary ammonium anion ex-
change sites, signicantly increase the hydrolysis rate of activated esters such as
the ever-popular p-nitrophenyl diphenyl phosphate [57]. In this context, Miller and
Ford reported the parallel synthesis of a small library of 32 anion exchange alkyl
methacrylate latexes via radical polymerization which contained @20% of quater-
nary ammonium units (Fig. 32.11) [58]. The latexes comprised monomers such as
vinylbenzyl chloride, sets of aliphatic methacrylates, divinylbenzene (crosslinker),
and (m-/ p-vinylbenzyl) trimethylammonium chloride (stabilizer). The number and
combination of the aliphatic monomers were combinatorially varied and additional
anion exchange sites were introduced by quaternization of the benzylchloride resi-
dues with either trimethylamine or tributylamine. Pseudo-rst-order reaction rate
coecients were spectrophotometrically determined. Relative rate enhancements
ranged from 2.3 for a polystyrene-trimethyl ammonium (TMA) latex to 16.5 for a 2-
ethylhexyl methacrylate-tributyl ammonium (TBA) latex. In addition, several other
compositionactivity relationships and performance trends could be rationalized
from the molecular structure.
The random nature of the synthesis of polymeric catalysts leads to a lack of
structural information about catalytically active sites. However, a polymeric system
that serves a useful function, even devoid of detailed structural information, may
be generally of great interest. The obvious ease and practicability of this approach
may allow for a rapid evolution and optimization of polymeric catalysts and may
be useful, especially if reproducibility issues are carefully addressed, to identify
active polymeric catalysts for many other important chemical reactions.
32.2.3
Combinatorial Synthesis Enzyme Mimetics
32.2.3.1 Hydrolytically Active Metal Complexes

Enzyme mimics for activated ester or phosphate hydrolysis remain at the center of
interest. Janda and his group synthesized and screened novel transition metal com-
plexes as enzyme mimics that catalyze the hydrolysis of carboxylic esters [59]. A
hydroxy-substituted azacrown ether was modied in a conventional solution-phase
three-step sequence to give three additional macrocylic ligands (Scheme 32.5). The
ligands were then complexed with ten transition metal ion sources. The 40-member
transition metal complex library was screened in parallel, without prior purica-
tion or isolation of the intermediates, for hydrolytic activity towards p-nitrophenyl
acetate and N-methoxycarbonyl-l-phenylalanine- p-nitrophenyl ester as model sub-
strates. Initial reaction rates were determined by repetitive photometric scanning
of the absorption of the released p-nitrophenolate. Zinc and cobalt complexes gave
only moderate rate enhancements kcat =kuncat @3. The kinetic data implied that
the systems do not behave like hydrolytic enzymes because of their linear depen-
dence on both substrate and metal complex concentration.
Scheme 32.5. General structure of transition metal complexes

of hydroxy or alkoxy azacrown ethers ecient for hydrolysis of
activated carboxylic acid esters.
The researchers extended their methodology towards the synthesis of the corre-
sponding azacrown etherlanthanide complexes that were capable of hydrolyzing
phosphate esters, a crucial chemical transformation in areas such as nucleic acid
chemistry [60]. The lanthanide complexes synthesized catalyzed the cleavage of
phospho di- and triesters and double-stranded DNA as well, which opens up the
possibility of using this class of chemicals as therapeutics. Another important po-
tential application is the hydrolytic decontamination of toxic organophosphates,
phosphonates, and uorophosphates which are widely used as insecticides and are
stockpiled as chemical warfare agents.
A 625-member library of undecapeptides has recently been assayed for cata-
lytic activity in phosphate hydrolysis, using test substances that in the presence of
oxygen form insoluble indigo dyes. Using a split-and-mix approach, Berkessel and
Herault synthesized on solid support sequences PheaXaGlyGlyaXaGlyGlyaXa
GlyGlyaX, where X is one of Arg, His, Tyr, Trp, or Ser [61]. About 2500 beads were
incubated with Cu(II), Zn(II), Fe(III), Co(III), Eu(III), Ce(IV), and Zr(IV) solu-
tions; only in the presence of Zr(IV) did the observation of the blue indigo color
indicate catalytic hydrolysis activity. The most promising candidates were isolated,
identied, and synthesized on solid support and in solution to conrm the library
screening results.
32.2.3.2 Evolutionary Solid-phase Synthesis of Oxygenase Mimics

The catalytic oxygen transfer activity of the enzyme cytochrome P450 oxygenase
inspired Sames and his coworkers to develop polymer-supported diamide com-
plexes of manganese for catalytic oxygenation reactions [62]. The signicant mod-
ular character of the targeted ligand structures allowed for an evolutionary solid-
phase ligand synthesis strategy resulting in the synthesis of three subsequently
improved generations of diamide-based ligands. Upon transformation into the
corresponding manganese(III) complexes, the resulting catalysts were directly
screened on-bead for the epoxidation of vinylbiphenyl (Scheme 32.6). The rst-
Scheme 32.6. Evolution of diamide ligands for Mn(III)-catalyzed oxygenation on solid support.
generation library quickly showed that a number of structural variants led to

respectable yields of the epoxide (74% yield for the rst-generation ligand). The
second round identied a ligand which led to nearly complete consumption of
vinylbiphenyl in 16 h (96% yield). The third generation of ligands provided a cyclic
system that exhibited the highest turnover rate of the entire assay: 5 mol% of this
catalyst yielded 98% of epoxide in 2 min, which translates into two orders of mag-
nitude rate enhancement in comparison with the second-generation catalyst. The
same catalysts were also used for the oxidation of ethyl benzene derivatives.
32.2.3.3 Libraries of Organic Acylation Catalysts

Mimics for acyl transferases require a concerted interplay between tethered func-
tional groups where the catalyst should possess a suitable base that is covalently
tethered in close proximity and the correct orientation relative to a nucleophilic
center. Taylor and Morken reported the preparation of a library of 3150 distinct
nucleophilic acylation catalysts on approximately 7000 encoded polymer beads
prepared by split-and-pool methods [63]. Their trimeric catalysts consisted of
a primary amine, a protected amino acid including the capping agent N-4-
pyridylproline, and functionalized carboxylic acids (Scheme 32.7). Temperature
Scheme 32.7. Solid-phase synthesis of a nucleophilic acylation

catalyst library. On the bottom are shown the structures of the
catalytically most active compounds containing the N-4-
pyridylproline moiety. R1, R2, R3, functionalized organic
residues; Boc, tert-butyloxycarbonyl.
changes due to the exothermic catalytic acetylation of ethanol were monitored di-
rectly on the oating beads by infrared (IR) thermography. The hottest 23 beads
were then manually selected, and decoding revealed three structures as eective
catalysts (Scheme 32.7, bottom). Most of them have N-4-pyridylproline incorpo-
rated as the capping agent and contained either (R)- or (S)-3-aminoquinuclidine as
the primary amine component.
32.3
Combinatorial Catalysis in Asymmetric Synthesis
The importance and practicality of asymmetric synthesis as a tool to obtain opti-

cally pure or enantiomerically enriched compounds have been fully acknowledged
by chemists in the areas of synthetic organic, medicinal, agricultural, and natural
products chemistry and their related industries [64]. Among the asymmetric
transformations, the most desirable and also the most challenging is catalytic
asymmetric synthesis, where one chiral catalyst molecule can create millions of tar-
geted chiral product molecules in a process that has been termed chirality multi-
plication. Thus, asymmetric catalysis represents a signicant economic advantage
over stoichiometric asymmetric synthesis, and, consequently, the development of
new methods for discovering asymmetric catalytic transformations stands as an
important and emerging objective in chemistry. Among others, divergent ligand
synthesis strategies, where the transformation of an advanced ligand intermediate
into a series of dierent chiral ligands is performed, appear to be especially fruitful
in this area. In most cases, the ligand bears the chiral information and, therefore,
creates a discriminating chiral environment in close proximity to the active metal
site of the catalyst. Asymmetric synthesis is an especially suitable area for combi-
natorial catalyst discovery since asymmetric catalysis is often mechanistically very
complex and critical variables in the parameter space to be evaluated for catalyst
development and optimization are mutually dependent. Thus, by rapid parallel
synthesis and metal complexation of chiral ligand libraries, coupled to automated
or high-throughput screening, multidimensional problems in the discovery and in
the optimization of catalysts may be eciently addressed.
32.3.1
Combinatorial Catalyst Libraries in Enantioselective Additions of Dialkyl Zinc
Reagents
The enantioselective addition of dialkyl zinc reagents to aldehydes can be catalyzed

by enantiopure amino alcohols [65]. This ligand class as well as other proline-
based ligands have also been used extensively to prepare asymmetric catalysts for
enantioselective reductions of ketones and asymmetric DielsAlder reactions [66].
Chiral 1,2-amino alcohols attached to polymers have been used to catalyze the
enantioselective addition of organozinc derivatives to aldehydes [67].
In 1995, Liu and Ellman reported the parallel solid-phase synthesis of a small
library of substituted 2-pyrrolidine methanol ligands [68]. To anchor trans-4-

hydroxy-l-proline methyl ester as a ligand scaold to Merrield resin, a parallel
solid-phase synthesis approach involving a cleavable tetrahydropyranol linker was
used [69]. Subsequent nucleophilic addition of various Grignard reagents, followed
by reductive N-alkylations, gave the desired amino alcohols (Scheme 32.8). On-
bead screening of the asymmetric addition of diethyl zinc to a variety of aromatic
(up to 94% ee) and aliphatic aldehydes (up to 85% ee) yielded slightly inferior
enantioselectivity compared with that of the corresponding free ligand in solution
(Scheme 32.8). Further studies revealed that the purication of the ligands was not
necessary to yield catalysts of similar performance with both aromatic and aliphatic
aldehydes.
Scheme 32.8. Parallel solid-phase synthesis of pyrrolidine-type

catalysts and their screening in the enantioselective addition of
diethyl zinc to aldehydes.
In a more recent example, Gennari and coworkers disclosed a new family of

chiral ligands for enantioselective catalysis of the Ti(OiPr)4 -mediated addition of
diethyl zinc to various aliphatic and aromatic aldehydes [70]. The novel ligands
were based on a modular building block strategy to incorporate disulfonamide
moieties as metal chelating units. Related disulfonamide ligands have previously
been shown to facilitate the title reaction as well as asymmetric cyclopropanation
reactions [71].
The 30-compound ligand library was synthesized by coupling the commercially
available vicinal diamine scaolds 1,2-diphenylethylenediamine [(R,R)- and (S,S)-
isomers] and 1,2-diaminocyclohexane [trans-(R,R)-, trans-(S,S)-, cis-(R,S), and
rac-trans-isomers] in the presence of the polymer-bound nucleophilic catalyst
dimethylamino pyridine with ve N-protected b-amino sulfonyl chlorides derived
from the l-amino acids Ala, Val, Ile, Phe, and Pro (Scheme 32.9) [72]. To avoid the
classical aqueous work-up and purication of the ligands, solid-phase extraction

(SPE) was utilized [16a, 73]; excess reagents were scavenged by solid-phase-bound
tris(2-aminoethyl)amine. This methodology also eliminated the need for additional
handles on the scaolds for attachment to a solid support and avoided any interplay
of a solid matrix on the yields and enantiomeric ratios of the catalyzed reactions.
Scheme 32.9. Synthesis of bis-(sulfonamide) ligands with

polymer-supported reagents and solid-phase extraction
technology.
By using this methodology, the same group also synthesized a library of 60 chiral
Schi base ligands that contains a set of dierent metal-binding sites (a phenol, an
imine, and a secondary sulfonamine) [74]. By means of a high-throughput screen-
ing approach, a ligand was identied that catalyzed the copper-mediated, enantio-
selective conjugate addition of diethyl zinc to cyclic enones with up to 90% ee (Fig.
32.12).
In a highly related approach, Liskamp and coworkers developed a solid-phase
synthesis of bis-(sulfonamide) ligands [75]. A library of these ligands was screened
in a simultaneous substrate-screening procedure for the ability to enantioselectively
catalyze the Ti(OiPr)4 -mediated addition of diethyl zinc to aldehydes. The best solid-
phase candidate was resynthesized in solution and gave enantioselectivities up to
66% (Fig. 32.12).
32.3.2
Ligands for the Lewis Acid-catalyzed Asymmetric Aza-DielsAlder Reaction
The asymmetric aza-DielsAlder reaction provides an eective route to optically

active nitrogen-containing heterocycles, as well as to other compounds of funda-
mental importance [76]. Asymmetric catalysis of imine dienophiles has remained
Fig. 32.12. Ligands for enantioselective diethylzinc addition

generated from combinatorial solid-phase synthesis.
elusive, and the successful asymmetric induction in the aza-DielsAlder reaction

heavily relied on auxiliary-based methodology. However, Yamamoto and coworkers
stoichiometric enantiopure triarylborate Lewis acids [77] and Kobayashi and co-
workers ytterbium-based Lewis acid for azadienes represent recent exceptions [78].
Furthermore, aza-DielsAlder reactions of a-imino ester dienophiles with activated
dienes by Johannsen as well as Jrgensen and coworkers merit closer attention [79].
In 1999 Jno and Ghosez disclosed chiral copper(II) complex-catalyzed asymmet-
ric DielsAlder reactions of 2-azadienes to enantiomerically pure piperidones [80].
Kobayashi and coworkers reported a novel class of chiral zirconocene complexes
that catalyze the aza-DielsAlder reaction of aldimines with Danishefskys diene to
aord the corresponding piperidine derivatives in high yields with high enantiose-
lectivities [81]. In a solid-phase approach, polymer-supported (R)-1,1 0 -binaphthols
(BINOLs) have been synthesized and rapid catalyst optimization could be achieved
(Scheme 32.10). A tethered, methoxymethyl (MOM)-protected (R)-BINOL deriva-
tive was brominated and then attached to Merrield resin. Suzuki coupling of a
variety of boronic acids with the immobilized building block and subsequent
MOM deprotection gave a library of polymer-bound BINOLs. The best catalyst was
found by mixing the immobilized ligands with Zr(Ot-Bu)4 and screening the re-
sulting complexes for their performance in a model aza-DielsAlder reaction of an
aldimine with Danishefskys diene. The authors then synthesized the most prom-
ising ligands in solution, further optimized the inorganic precursor, and nally
identied the Zr complex A as the best catalyst, giving 68% yield and 94% ee.
32.3.3
Divergent Ligand Synthesis for Enantioselective Alkylations
In 1998, Burgess and coworkers highlighted in several examples the value of di-
vergent ligand synthesis strategies for the preparation of focused ligand libraries
Scheme 32.10. Solid-phase approach for the identication of a

catalyst for the asymmetric aza-DielsAlder reaction.
and the use of automated ligand screening [82, 83]. By denition, divergent syn-
theses of chiral ligands are characterized by an optically pure material being pro-
duced and then subsequently being used to prepare many ligands of a structurally
similar class of ligands.
Based on l-serine, a chiral building block (chiral synthon chiron) was pre-
pared as a key intermediate that was then converted into a family of 13 novel chiral
phosphine oxazoline ligands using several dierent routes and employing conven-
tional organic solution synthesis [82]. It was shown that the divergent ligand syn-
thesis approach was very suitable for eciently accessing this ligand class with
good diversity in terms of steric bulk and/or electronic pertubation (Fig. 32.13).
The ability of these ligands to asymmetrically catalyze the addition of dimethyl
malonate to 1,3-diphenylprop-2-enyl acetate was investigated [84]. The best of these
ligands gave a palladium complex that catalyzes the allylic alkylation with up to
94% ee.
In a dierent modular approach to generate chiral catalysts for the same trans-
Fig. 32.13. Divergent approach to phosphine oxazoline ligands.

Boc, tert-butyloxycarbonyl; R, alkyl and aryl.
formation, Gilbertson and coworkers synthesized a phosphine oxazoline ligand

library from amino acids and phosphinocarboxylate building blocks (Scheme 32.11)
[85]. Following amide formation between phosphinocarboxylates and amino acids,
the carboxy group of the amino acid was reduced to an alcohol. These molecules
could then be cyclized with the Burgess reagent and reduced in the presence of
Raney Ni to give a 13-member library of phosphine oxazoline ligands. The best of
these ligands gave a palladium complex that catalyzes the addition of dimethylmal-
onate to 1,3-diphenylprop-2-enyl acetate in 99% yield and in 98% enantiomeric
excess.
Scheme 32.11. Divergent synthesis of new phosphino-oxazoline ligands.
Gilbertson and coworkers also used solid-phase chemistry to synthesize a library

of 77 chiral phosphines that contain the b-turn structural motif [86]. Coordination
of palladium gave metal complexes that catalyzed the addition of dimethylmalo-
nate to cyclopentenyl acetate in up to 80% ee.
Kobayashi and coworkers developed a solid-phase strategy to synthesize novel
pentamine ligands for the enantioselective a-alkylation of lithium amide enolates
[87]. The synthesis started with polymer-supported piperazine which was coupled
with three dierent amino acids using standard peptide synthesis protocols fol-
lowed by the addition of N,N-dialkylglycine. At this stage, the resulting compounds
were cleaved o the resin, the terminal secondary amine was methylated, and the
amide moieties were reduced using BH3 THF to give a library of 20 chiral penta-
mines. From this set of ligands, only moderate selectivities were obtained. Through
modication of the N-methylpiperazine moiety, one complex was identied that
catalyzes the alkylation of piperidinepropionamide with good yields and up to
84% ee (Scheme 32.12).
Scheme 32.12. Chiral pentamine ligand for the enantioselective

a-alkylation of lithium amide enolates.
32.3.4
Chiral Phosphine Ligands for Asymmetric Hydrogenation
In homogeneous catalysis, phosphines are particularly important ligands in late-

transition metal-catalyzed processes such as hydrosilylation, hydroformylation,
carbonylation, olen dimerization, and, last but not least, hydrogenation reactions
[88]. For example, industrially important hydrogenations are involved in the syn-
thesis of l-dopa (Monsanto) and Mercks novel HIV protease inhibitor, indinavir,
marketed currently as Crixivan= [89].
Phosphine-containing amino acids were originally synthesized to eect con-
formational states of peptides and to stabilize and control peptide structures upon
metal binding [90]. Their application in catalytic asymmetric hydrogenation was
reported in 1996 by Gilbertson and Wang [91]. Geysens polyethylene pin technique
was used to synthesize a 63-member library of peptidomimetic ligands for the Rh(I)-
catalyzed hydrogenation of methyl 2-acetamidoacrylate to the corresponding amino
acid derivative N-acetyl alanine. The general primary structure of the ligands, best
described as AcaAlaaAibaAlaa[P-containing, internal peptide]aAlaaAibaAlaaNH2 ,
shared terminal AlaaAibaAla sequences to force an overall a-helical secondary
structure and to bring the phosphine groups of the internal peptide sequence into
close proximity with each other (Scheme 32.13). For the internal sequence, three
classes of structurally unique chiral tetra- or pentapeptides were synthesized by
combining the novel amino acids dicyclohexyl- and diphenylphosphane serine (Cps
and Pps respectively) with two or three hydrophobic amino acids. Each ligand was
screened directly on-bead in a parallel 24-vial reactor that was coupled to a gas chro-
matograph (GC) equipped with a chiral stationary phase to determine enantiose-
lectivity and overall conversion. Unfortunately, only modest enantiomeric excesses
up to 18% were observed, but some trends and correlation between peptide se-
quence and selectivity were established. In a more recent publication, the same
group synthesized larger libraries, giving access to ligands that were used for the
catalytic asymmetric hydrogenation of methyl-2-acetamidoacrylate in the presence
of rhodium. Enantiomeric excesses up to 38% were obtained [92].
Scheme 32.13. Screening of a library of support-bound

a-helical peptide/phosphine-Rh(I) catalysts in enantio-
selective hydrogenation reactions of prochiral methyl-2-
acetamidoacrylate to N-acetyl alanine methyl ester.
32.3.5
Asymmetric Reactions Catalyzed by Schi Base-type Ligands the Positional
Scanning Approach
In this section, the successful application of a modular approach based on well-

established functional building blocks to the rapid discovery of novel catalysts is
described [93, 94]. The philosophy of this positional scanning approach for
identifying a chiral catalyst consisting of three modular subunits, for example, is to
optimize each of the three modular subunits while keeping the other two subunits
constant. Common to the positional scanning approach (iterative optimization
approach) of the modules composing the ligand structure are the two assump-
tions of (1) an independent and additive inuence of each of the building blocks,
and (2) the absence of negative cooperative eects during their systematic varia-
tion. In addition, the positional scanning approach, especially when coupled with
automated screening, not only oers unique opportunities for the identication of
substrate-specic catalysts (ne tuning) but also permits the discovery of ligands
that possess unusual properties and which might otherwise elude detection.
In 1992, Hayashi and coworkers reported the addition of trimethylsilyl cyanide
(TMSCN) to epoxides catalyzed by titanium Schi base complexes to yield racemic
b-cyanohydrins [95]. Based on this work, Snapper, Hoyveda, and coworkers dis-
closed a diastereo- and enantioselective version of this reaction in 1996 (Scheme
32.14) [93]. With combinatorially optimized chiral titanium Schi base complexes,
nonracemic b-cyanohydrins were obtained in good chemical and optical yields. Chi-
ral dipeptidic hemisalen ligands of the general structure SBaAA2 aAA1 aGlyOMe
(SB Schi base or hemisalen; AA1 amino acid) were synthesized in a modu-
lar fashion from various amino acid and aldehyde building blocks using parallel
solid-phase synthesis techniques. After cleavage from the solid support, complex-
ation with a titanium alkoxide precursor, and parallel screening of the chiral Lewis
acids for eciency and enantioselectivity, a potent catalytic system for ring open-
ing of cyclohexene oxide in 89% enantiomeric excess was discovered (Scheme
32.14).
Scheme 32.14. Discovery of a new Schi base catalyst for the

Ti-catalyzed enantioselective addition of trimethylsilyl cyanide
(TMSCN) to meso epoxides by an iterative optimization
approach using positional scanning.
Subsequent work by the same group demonstrated that screening did not require
cleaving the Schi base ligand from the solid support, which signicantly accel-
erated the optimization process [96].
Using a closely related approach for their ligand synthesis, Sigman and Jacobsen
disclosed polymer-supported Schi base catalysts of the general structure linker1
amino acidlinker2 diaminephenylidene in 1998 [94]. In this example, the on-
bead iterative optimization of ligands for the asymmetric hydrocyanation of imines
(Strecker reaction) is described. The Strecker reaction constitutes one of the most
direct and viable strategies for the asymmetric synthesis of a-amino acid deriva-
tives [97]. Ligand synthesis was made amenable to solid-phase synthesis techniques
by choosing readily accessible building blocks and reaction conditions (Scheme
32.15). Systematic but non-obvious permutation cycles of their building blocks
(iterative optimization), such as sequential variation of the amino acid compo-
nents, the nature of the linker, or the diamino bridging moiety, revealed a transi-
tion metal-free catalyst after the synthesis of only three ligand generations that
mediated the reaction of both aromatic and aliphatic aldimines in more than 70%
and 83% enantiomeric excess, respectively. Screening was performed sequentially
by gas chromatography using a chiral stationary phase. The best catalyst was re-
synthesized in solution and showed further improved enantioselectivity of 91% ee
for an aromatic aldimine. Meanwhile, independent investigations by the same
group disclosed a very active chiral salen Al(III) complex for the same reaction, re-
sulting in imine hydrocyanation products of enantiomeric excesses as high as 95%
[98].
Scheme 32.15. Combinatorially optimized Schi base ligand

for the asymmetric Strecker reaction (hydrocyanation of
imines). AA, amino acid; TFAA, triuoroacetic anhydride.
Hoveyda, Snapper, and coworkers applied their modular approach to Schi base-
type ligands for identifying catalysts for a variety of asymmetric transformations.
Scheme 32.16 summarizes the novel catalytic systems for enantioselective addi-
tions of cyanide to imines (A) [99], for Cu-catalyzed conjugate addition of alkylzinc
reagents to cyclic enones (B) [100], for Zr-catalyzed addition of diethylzinc to
imines (C) [101], and for Cu-catalyzed allylic substitutions (D) [102].
Scheme 32.16. Novel chiral catalysts containing Schi base ligands.
32.3.6
Identication of Novel Catalysts for the Asymmetric Epoxidations via the Positional
Scanning Approach
In 1999 Francis and Jacobsen disclosed the discovery of a novel catalyst for alkene
epoxidation [103]. Using a solid-phase synthesis protocol on an aminomethyl poly-
styrene resin, ligands bearing potential metal-binding moieties were prepared. The
ligands comprised ve amino acids with donor side arms (Asp, Cys, His, Met, and
Ser), three dierent chiral linking elements each diering in rigidity (1-amino-2-
indanol, trans-1,2-diaminocyclohexane, and Ser), and 12 dierent capping agents
with functionalities such as heterocycles, phosphanes, and salicylimines, which in

turn were attached through imine and amide bonds. Initially, the metal-binding
ability of the resulting 192 ligands was determined in a pooled assay with 30 dif-
ferent transition metal ions to yield 5760 possible metalligand combinations.
Metal binding was visually detected with selective inorganic staining reagents in a
fashion similar to previous studies. The entire pooled catalyst library was screened
for the epoxidation of trans-b-methylstyrene (TBMS) to determine suitable reaction
conditions. Those catalysts prepared from VOSO4 and FeCl2 were most active.
Since VOSO4 also displayed signicant epoxidation activity in the absence of the
ligand library, FeCl2 was chosen for further investigations. The screening of 12
FeCl2 -derived libraries each containing a mixture of 16 basic structures and a dif-
ferent end cap furnished ligands with pyridine-containing end caps as the most
active epoxidation catalysts. Further deconvolution showed that the most active cat-
alytic system comprised FeCl2 , ligand structures exhibiting a pyridine-containing
end cap, a serine linker, and serine or cysteine as the amino acid bound to the
solid support. These systems resulted in high levels of catalytic activity, but only
low enantioselectivities for the epoxidation of TBMS was observed (ee 47%). A
second-generation 96-member optimization library based on the identied epox-
idation catalyst produced moderately enantioselective variants (ee 1520%) for
the target reaction.
Hoshino and Yamamoto have described the vanadium-catalyzed asymmetric
epoxidation of allylic alcohols using a-amino acid-based hydroxamic acid ligands
[104]. In order to optimize the ligands, again the iterative positional optimization
approach was used, which involves screening one compound of a ligand structure
for selectivity, while holding the other units constant (Scheme 32.17). In the rst
step, the source of chirality for the ligand the amino acid moiety was opti-
mized, and the best result in this case was achieved using the tert-leucine-derived
hydroxamic acid. In the second step, the imido group was examined and optimized
to the 1,8-naphthalenedicarbonyl-protected hydroxamic acid (87% ee). Finally, the
aryl groups near the metal coordination site were changed, identifying N-bis-(1-
naphthyl)methyl-substituted hydroxamic acid as the most eective ligand for a
range of disubstituted allylic alcohols. The asymmetric epoxidations were per-
formed in the presence of 1 mol% of VO(OiPr)3 and 1.5 mol% of the best ligand
giving rise to the corresponding chiral epoxy alcohols in 5899% yield and 76
96% ee.
32.4
Multidimensional Combinatorial Screening
Conventional research in a one-at-a-time or serial fashion provides thorough

quality control of the samples entering the screening process to insure that accu-
rate data are obtained. Combinatorial methods that involve, for example, split-
and-pool synthesis are much faster and render the preparation of relatively large
numbers of compounds feasible but often lack control over the purity of the com-
Scheme 32.17. The iterative positional optimization approach

to identify ligands for chiral epoxidations.
pounds entering the assay screen. Methods intermediate between the two extremes
outlined above are based on parallel or array syntheses or screening, in a spatially
addressable format with usually one compound per well, coupled to automated
screens. This approach facilitates a relatively high level of quality control and a sig-
nicantly enhanced throughput compared with sequential methods. Thus, multi-
dimensional problems in the discovery and in the optimization of catalysts may be
eciently addressed by coupling parallel ligand synthesis with automated or high-
throughput multidimensional screens (e.g. metal precursors, ligands, solvents, and
reactant ratios). An integrated instrumental set-up for parallel high-throughput
catalyst screening should encourage researchers to investigate a broader variety of
systems, some of which may be regarded as too unusual to warrant testing in a
sequential fashion.
32.4.1
Catalyst Discovery and Optimization Using Catalyst Arrays
Intramolecular carbonhydrogen insertion of metal carbenes generated by cata-

lytic decomposition of diazocarbonyl compounds is a facile methodology for
carboncarbon bond formation. The reaction involves presumably the insertion
of in situ-generated metallocarbenes, often catalyzed by rhodium complexes, into
CaH bonds [105]. In 1995, Lim and Sulikowski disclosed active copper catalysts
for this type of reaction and used them in the synthesis of chiral indolyl derivatives
from diazoesters [106]. Subsequently, Burgess and colleagues used a highly paral-
lel screening approach for the optimization of ligand/metal/solvent combinations
for the same reaction (Scheme 32.18) [107].
Scheme 32.18. Discovery and optimization of high-throughput catalyst screening. l-Menth,

a new catalyst for the intramolecular CaH l-menthyl; dr, diastereomeric ratio; DDQ,
insertion reaction of Rh carbenes from a-diazo 2,3-dichloro-5,6-dicyano-1,4-benzoquinone.
esters for the synthesis of indolyl derivatives by
A library of 96 catalytic systems was created in a standard microtiter/ltration

plate in order to accommodate incremental variation of the reaction parameters.
Combinations of ve dierent natural or synthetic chiral ligands, seven metal pre-
cursors, and four solvents were evaluated in a high-throughput fashion using an
HPLC device equipped with an autosampler. Subsequent data analysis not only
identied two superior catalyst systems based on a bis-(oxazoline) ligand but also
led to the identication of a novel and unexpected Ag(I)-based catalytic system
with an overall increased diastereoselectivity compared with the original system.
Using the optimized set of reaction conditions (AgSbF6 , THF, 25 C, 24 h), the
desired product was obtained in 75% yield and in a diastereomeric ratio of 3.5:1.
Burgess and coworkers demonstrated in several examples the value of a multi-

dimensional screening for catalyst optimization. Using a small library of a novel
phosphine oxazoline ligand class obtained by a divergent ligand synthesis approach
[82, 85], parallel assaying was employed to evaluate and optimize application of
these ligands. The novel ligands were screened simultaneously in a customized
parallel reaction block bearing a 27- or 34-well format. The asymmetric alkylation
of 1,3-diphenylpropenyl acetate with malonate was chosen as a classical test reac-
tion (Scheme 32.19) [84]. Product evaluation and analysis were performed in an
automated serial fashion by means of a conventional HPLC equipped with a chiral
stationary phase. The parallel screening format allowed for a rapid assessment of
various inuential reaction parameters, including solvent eects, ligand substitu-
tion pattern, presence or absence of ions, ligand-to-metal ratios, and solvent eects
on the enantiomeric excess and absolute conguration.
Scheme 32.19. High-throughput screening of phosphine

oxazoline ligands in Pd-catalyzed asymmetric allylic alkylation
reactions.
Allylic alkylation products with an enantiomeric excess as high as 94% were ob-
served. In a closely related experiment, using the same instrumental set-up, ligands,
metal sources, and additives, but a more dicult to control methyl-substituted
allylic substrate, the best enantiomeric excess was determined to be 74% [83]. The
related divergent ligand synthesis strategy and an identical instrumental set-up for
the high-throughput catalyst screening as described above revealed novel so-called
propeller-shaped, C3 -symmetric triarylphosphines as chiral ligands [108, 109].
The ligands were screened in an allylic amination reaction with phthalimide as the
nucleophilic component, resulting in N-Substituted phthalimide derivatives were
obtained with up to 82% enantiomeric excess.
Taylor and Morken uncovered an eective catalyst for the diastereoselective re-
ductive aldol reaction with the aid of an arrayed catalyst evaluation protocol [110].
An array of 192 experiments in glass 96-well microtiter plates was used to evaluate
the interdependence of a variety of reaction variables such as the metal precursor,
the ligand, and the hydride source in a parallel fashion. The parent test reaction
was the reductive coupling of methyl acrylate and benzaldehyde (Scheme 32.20).
Scheme 32.20. Catalytic stereoselective reductive aldol reaction

by parallel catalyst array evaluation.
Each reaction was analyzed for relative conversion and stereoisomer ratios by
conventional gas chromatography employing chiral stationary phases (GCCSP ). Sev-
eral relationships between reaction condition and yield could be rapidly concluded,
including that catechol borane was a superior reducing agent with the largest
number of catalysts under the reaction conditions. The novel catalyst derived from
[(COD)RhCl]2 , Me-DuPhos, and Cl2 PhSiH provided generally moderate yields (15
69%) for a variety of other substrates but with a high syn stereoselection of up to
23:1 syn/anti. The study demonstrated a rapid assessment of the interdependence
of reaction parameters showing that traditional empirical catalyst development
approaches, where reaction variables are independently optimized, may not have
revealed all active catalyst formulations found within the array.
The metal-catalyzed addition of amines to carbon double bonds, especially of
acrylic acid derivatives yielding b-amino acid derivatives, which are useful in peptide
analogs or as precursors of optically active amino alcohols, diamines, and lactams,
is of utmost importance. Kawatsura and Hartwig uncovered several late transition
metal complexes that catalyze the addition of amines to acrylic acid derivatives using
a novel parallel colorimetric assay to analyze the addition of primary and second-
ary alkyl amines to substrates with CbC bonds [111]. All possible combinations of
seven metal precursors and 11 phosphine ligands were evaluated in a glass 96-well
microtiter plate format for catalytic activity in the addition of piperidine or octyl-
amine to methacrylonitrile as representative experiments (Scheme 32.21).
Scheme 32.21. Transition metal-catalyzed addition of amines to acrylic acid derivatives.
The colorimetric spot test allowed for qualitative evaluation of secondary

amines present in the reaction mixture either by consumption of secondary amine or
by formation of secondary amine products. Catalysts derived from [Rh(COD)2 ]BF4 ,

[Ir(COD)2 ]BF4 , and [Ru( p-cymeneCl2 )]2 and several phosphine ligands were cata-
lytically active in the addition of piperidine to methacrylonitrile, while Pd(OAc)2
showed activity in the addition of octylamine to the substrate. The results were con-
rmed in scale-up experiments and the scope and limitations of the reaction of
alkylamines with acrylic acid derivatives were assessed in more detail.
In 1998, Whiting and colleagues reported a parallel array screening approach to
chiral catalyst discovery in the Lewis acid-catalyzed aza-DielsAlder reaction of an
N-aryl imine with Danishefskys diene [112], a reaction known not to proceed under
normal thermal cycloaddition conditions (Scheme 32.22) [113].
Scheme 32.22. Parallel screen for asymmetric induction

in Lewis-acid catalyzed aza-DielsAlder reaction of a
N-aryliminodienophile with Danishefsky s diene.
Using multiple-well plates, discrete homochiral Lewis acid complexes were indi-
vidually generated in solution from four dierent metal salts, three dierent com-
mon enantiopure ligands, three dierent solvents, and two dierent additives.
Screening was performed sequentially in about 1 week by measuring the enantio-
meric excesses and conversions by means of an automated HPLC equipped with a
chiral stationary phase to result in 144 sets of approximate yields and enantiomeric
excesses. Reproducibility was conrmed and the most ecient chiral Lewis acid
was a combination of MgI2 and (R,R)-1,2-diphenylethylenediamine in acetonitrile
in the presence of 2,6-lutidine to aord the N-arylpiperidinone in 97% enantio-
meric excess.
Hydrosilylation of substrates such as acetophenones with ruthenium catalysts
requires mixed P/N ligands for activity and selectivity; neither pure P/P-chelating
nor pure N/N-chelating ligands show activity and selectivity alone [114]. Based
on that knowledge and adapting Noyori and coworkers concept of mixed ligand
ruthenium complexes as precatalysts [115], Frost and coworkers developed an e-
cient ruthenium-catalyzed asymmetric hydrosilylation of ketones using high-
throughput parallel screening to optimize ligand combinations for the target
reaction [116]. A small 50-member mixed ligand library of ruthenium diamine/
diphosphine complexes (precatalysts) was prepared in situ by addition of enantio-
merically pure tol-BINAP ligands to a ruthenium precursor [RuCl2 (C6 H6 )2 ], fol-
lowed by addition of various monoimine or diamine ligands. Diphenylsilane and
the precatalysts were added to a solution of acetophenone as the substrate to syn-
thesize the corresponding 1-phenyl ethanols (Scheme 32.23).
Scheme 32.23. High-throughput screening of ruthenium

hydrosilylation catalysts to determine the optimal P/P and N/N
ligand combination.
Yield and enantiomeric excesses were assayed by serial high-performance liquid

chromatography (HPLC) and gas chromatography (GC). For various ruthenium
diamine/diphosphine complexes, catalytic performance trends (yield, enantiose-
lectivity, and absolute conguration) could be observed. The results obtained from
parallel screening were conrmed by traditional serial experiments. The most ef-
fective catalyst formulation could be further improved by the addition of catalytic
amounts of AgOTf to yield a catalyst that is active and selective in the hydrosilyla-
tion of a variety of aromatic ketones. For example, 1-phenyl ethanol was obtained
from acetophenone in 53% yield and in 82% enantiomeric excess.
Human and Reider from Merck Research Laboratories reported the discovery
of improved conditions for the diastereoselective reductive amination in the large-
scale synthesis of the angiotensin converting enzyme (ACE) inhibitor elanapril
[117]. Using a multidimensional screening approach, the eects of various hetero-
geneous catalyst formulations and a variety of additives were assayed (Scheme
32.24).
Scheme 32.24. High-throughput screening of the Raney nickel-

catalyzed reductive amination between ketoester and dipeptide
AlaPro for Elanapril synthesis.
Experiments were performed in a hydrogenation reactor in which up to 18

reactions in vials were stirred in a single vessel under 1 atm. of hydrogen pres-
sure. Product yield and diastereomer ratio were determined by standard high-
performance liquid chromatography (HPLC) equipped with an autosampler. Hun-
dreds of reactions were run with four catalyst formulations, including Raney/Ni,
Pt/Al2 O3 , Pd/Al2 O3 , and Pd/C, and one or two additives at 10 wt% against AlaaPro
as the substrate. The additives were chosen from a number of classes, both chiral
and achiral, including amino acid derivatives, carbohydrates, salts, organic acids,
and Lewis acids. Several trends and eects of the reaction parameters (catalyst,
additives) for the selectivity of the reductive amination were observed. It was
found that acetic acid and potassium uoride, which in isolation were detrimental
to the stereochemical outcome of the reaction, worked together to improve the
(S,S,S):(R,S,S) selectivity with Raney nickel in ethanol from 11:1 to 17:1. The value
of simultaneously varying multiple reaction parameters was demonstrated in the
rapidly increased diastereoselectivity, which in turn led to a signicant isolated yield
improvement [90%, (S,S,S) (R,S,S) isomers] of this high-volume, high-value drug
just by the addition of two inexpensive compounds.
The transition metal-catalyzed reaction of enamines derived from b-oxoesters
and a-amino acid amides with Michael acceptors such as methylvinylketone (MVK)
was studied by Christoers and Mann [118]. In the initial reaction step, enami-
noesters were reacted with MVK in the presence of 14 metal salts including transi-
tion metals and main group metals in dichloromethane. The auxiliaries based on
a-amino acid derivatives derived from Val, Leu, Ile, and tert-Leu already gave rise to
enantioselectivities of up to 78% enantiomeric excess in the absence of a metal salt.

This result could be improved by 20% (up to 98% ee) by addition of Cu(OAc)2 H2 O
as catalyst. Variation of solvent and catalyst loading nally led to the discovery of
the catalytic system depicted in Scheme 32.25. Although stoichiometric but readily
available amounts of auxiliary had to be employed, Christoers and Mann demon-
strated the application of combinatorial techniques in auxiliary-controlled catalytic
reaction.
Scheme 32.25. Synthesis of enaminoesters and high-

throughput screening copper(II)-catalyzed reaction with
Michael acceptors.
32.4.2
Parallel Array Screening for Catalyst Optimization Using Discovery and Focused
Ligand Libraries
In analogy to the pharmacological model of drug discovery, a large parent set of

ligands can be screened for lead compounds. After screening of the ligand library
and discovering successful hits, smaller, more focused daughter libraries can be
created based on ligand structureactivity relationships, resulting potentially in a
higher hit rate because of the closer diversity space. This screening approach is use-
ful for the optimization of reaction parameters, especially when essential reaction
parameters of the targeted reaction such as preferred ligand class, mechanism of
the catalytic cycle, or natural metal sources are already known.
A 96-member library of pyridine-containing ligands consisting of both rationally
chosen and randomly selected members was used by Hauptman and her group
from DuPont to screen copper(I)- or copper(II)-catalyzed Ullmann aryl ether-
forming reactions [119, 120]. Aryl ethers are a structural element common to many
agrochemical and pharmaceutical lead compounds. The study aimed to screen

commercially available pyridine and pyridine-like compounds to nd the best
ligand for copper to produce the highest yield with the least amount of arene-
reduction byproduct. The reaction of 2-bromo-4,6-dimethylaniline as test substrate
with a variety of alkoxides, including potassium phenoxide and sodium methoxide,
was investigated under dierent conditions, such as ligand-to-copper ratio or sol-
vent variation with the aid of an automated liquid workstation for library prepara-
tion (Scheme 32.26).
Scheme 32.26. High-throughput screening of copper

pyridine catalysts for the Ullmann aryl ether formation.
Product analysis was performed by serial gas chromatography (GC). The results
of the initial 96-member library screening allowed for assessment of structure
activity proles. 8-Hydroxyquinoline derivatives proved to be outstanding ligands
for the copper-catalyzed phenoxylation of the test substrate, yielding the desired aryl
ether in @80% yield. Among the best ligands for methoxylation in terms of yield
and low arene-reduction byproduct were pyridines bearing amino groups in posi-
tion 2 (60% to >90%). Subsequent smaller focused ligand libraries including 8-
quinolinols (30 member) and 3-hydroxypyridine (23 member) for the phenoxylation
reaction and 2-aminopyridine-type ligands (41 member) for the methoxylation con-
rmed the results obtained. The most eective ligands were found to be generally
useful for alkoxylation of a variety of substrates, including intramolecular ether-
forming reactions.
Parallel solution-phase synthesis techniques and parallel array assaying facili-
tated the identication and optimization of new nonpeptidic chiral dirhodium(II)
carboxylates useful in the enantioselective SiaH insertion reaction of diazoesters
with silanes [121123]. A systematic search through the Available Chemical Direc-
tory (ACD) resulted in a set of 2000 useful alternative chiral carboxylic acid ligands
which were then clustered and the centroid of each of 80 clusters selected as a rep-
resentative acid [124]. The representative chiral carboxylic acid ligand from each
of the 80 clusters then underwent a 20-at-a-time parallel synthesis format ligand
exchange with a dirhodium(II) carbonate precursor to yield the desired chiral dir-
hodium(II) carboxylate catalyst. A total of 69 chiral dirhodium(II) catalysts were
assayed in the targeted enantioselective carbenoid SiaH insertion of methyl 2-
(diazo)phenylethanoate into silanes with varying degrees of steric bulk to yield in-
sertion product (Scheme 32.27).
Scheme 32.27. High-throughput screening of dirhodium

insertion catalysts for the carbenoid insertion of azo esters into
SiH bonds.
Enantioselectivities of the SiaH insertion products were assessed by automated

HPLC after a short parallel purication step. The rst-generation screen revealed
a-hydroxy carboxylic acids and N-arene sulfonyl a-amino acids as promising ligand
candidates. Based on these results, a focused second-generation array was con-
structed from the original 80 clusters to identify N-arene sulfonyl a-amino acids as
superior ligands for the targeted reactions. Up to 76% enantiomeric excess for the
product was obtained with N-(toluene-4-sulfonyl)-l-leucine as a ligand at 78 C.
The use of parallel synthesis and screening techniques has resulted in the rapid
identication of improved catalysts for enantioselective SiaH insertion reactions of
diazoesters with silanes.
32.5
One-pot, Multisubstrate Screening
Hadamard transformation is a mathematical algorithm that can be used to identify

the properties of a particular group of candidates by recording the sum or super-
positions of signals from well-selected groups or pools of single wells, catalysts,
etc. [125]. Subsequent deconvolution of a set of data obtained from an entire group
coupled with computer simulations can provide analytical solutions in various
branches of physical sciences, including homogeneous and heterogeneous cataly-
sis. Many applications and scenarios of Hadamard transformations in combinato-
rial catalysis can be envisioned, including multisubstrate/one-catalyst screening,
one-substrate/multicatalyst (multiple ligands, metals) screening, or simultaneous
screening of a variety of catalysts against multiple substrates.
Consequently, Gao and Kagan investigated a Hamadard-type approach to com-
binatorial catalysis [126]. The researchers checked the validity of the one-catalyst
against the multiple substrate screening in the asymmetric reduction of mixtures

(families) of prochiral aromatic ketones to their corresponding alcohols. Coreys
chiral oxazaborolidine catalyst was chosen as the chiral catalyst (Scheme 32.28)
[127].
Scheme 32.28. One-pot, multisubstrate screening of a chiral

oxazaborolidine catalyst in the enantioselective reduction of a
family of aromatic ketones. DMS, dimethylsulde.
Conversion and enantiomeric excesses of the resulting mixture of alcohols was

monitored by conventional HPLC equipped with a chiral stationary phase (CSP).
Key was the careful calibration of the screening conditions, including baseline
separation of all of the ketones as starting materials from the corresponding alco-
hols, and, in addition, a sucient resolution of the enantiomers of the enantio-
meric alcohols. All ketone reductions were repeated individually in solution, with
most of the discrepancies between the individual asymmetric reductions and the
multisubstrate approach ranging from 1% to 7%. For example, asymmetric reduc-
tion of acetophenone resulted in the formation of (R)-1-phenylethanol with 97%
enantiomeric excess under screening conditions (ketone mixture) and in the iso-
lated ketone reduction.
In another example of an application of a one-pot, multisubstrate screening
approach, Gennari and coworkers disclosed a family of chiral ligands for enantio-
selective catalysis of the Ti(OiPr)4 -mediated addition of diethylzinc to aliphatic and
aromatic aldehydes [70]. A 30-compound ligand library was synthesized based on a
modular building block strategy. The disulfonamide ligands comprised six chiral
and racemic vicinal diamine scaolds which were reacted with a set of ve l-amino
acid-derived N-protected b-amino sulfonyl chlorides [72]. This ligand class has pre-
viously been shown also to facilitate asymmetric cyclopropanation reactions [71].
Modern combinatorial synthesis techniques such as employment of a polymer-
bound nucleophilic acylation catalyst [polymer-bound dimethylaminopyridine
(DMAP)] and the consequent use of solid-phase extraction (SPE) facilitated the
solution-phase ligand synthesis, and also eliminated the need for additional han-
dles on the scaolds for solid support attachment [73].
In analogy to Kagans protocol, the individual ligands were assayed in parallel
and in spatially addressable format on a mixture of four aldehydes (multisubstrate).
After optimization of the analytical conditions, product analysis was performed
sequentially with capillary GC equipped with a chiral stationary phase. Excellent
enantiomeric ratios for aromatic and aliphatic aldehydes in favor of the (R)-
enantiomer [(R)/(S) 9798:32] were obtained. A ligand derived from trans-(S,S)-
diaminocyclohexane and the N-protected b-amino sulfonyl chloride derived from
l-Phe performed the title reaction best (Scheme 32.29). The puried ligand was
subjected to characterization, and the screening results were conrmed by reaction
with the four separate aldehydes.
Scheme 32.29. One-pot screening of bis-sulfonamide ligands

in the enantioselective addition of diethylzinc to aldehydes. dr,
diastereomeric ratio.
A one-catalyst/multiple substrate strategy for the pooled synthesis of libraries

of internal olens via metathesis was reported by Brandli and Ward [128]. It was
hypothesized that cross-metathesis of only two internally disubstituted olens
should produce up to 20 statistically distributed olens including (E )/(Z )-isomers
[NN 1, N number of unequivalent olenic termini]. In this study, biologi-
cally important oleic acid derivatives were subject to cross-metathesis using Grubbs
metathesis catalyst [Ru(bCHPh)Cl2 (Pcy3 )2 , Cy cyclohexyl]. Product analysis and
distribution were conducted by coupled gas chromatography/mass spectrometry
(GC/MS) analysis and further oxidative degradation experiments. The results dem-
onstrated the applicability of the multisubstrate/one-catalyst approach in this reac-
tion for the synthesis of small libraries of organic compounds.
A conceptually related combinatorial, or family approach to the resolution of
racemates, was reported by Vries and coworkers. The simultaneous addition of a
family of resolving agents to a solution of a given racemate caused a very rapid
precipitation of crystalline diastereomeric salts in good to high enantiomeric purity
and yield [129].
The novel concept one-pot, multisubstrate screening in asymmetric catalysis
may suer from intrinsic drawbacks and limitations, such as undesired cooperative/
noncooperative interactions (between chiral catalyst and chiral reaction product,
including autoinduction, or nonlinear behavior of catalytic activity, etc.) and neigh-
boring element eects (cross-talk between library entities). However, the simplicity
of this method makes it convenient for a preliminary evaluation of many dierent
chiral reagents or catalysts in a targeted reaction once the substrate mixture is

standardized.
32.6
Combinatorial Approaches to Olen Polymerization Catalysts
An annual production of approximately 46 million metric tons exemplies the in-

dustrial importance of polyolens [130]. Combinatorial programs for catalysis and
materials can be utilized for both discovery and optimization purposes. The dis-
covery process involves, for example, the identication of catalyst systems for novel
copolymerizations, whereas in the optimization process the inuence of new
ligands, metals, activators, alkylators, solvents, and temperature is tested.
Recent reports have shown that certain late transition metal diimine-based cata-
lyst systems exhibit olen polymerization activities similar to those reported for
commercially employed early-metal single-site metallocene-based systems [131
133]. These new systems have sparked considerable interest in the polyolens in-
dustry because of their high activity, ease of synthesis and handling, and tolerance
toward functionalized olens such as methacrylate and vinyl acetate. Over the past
few years, an increasing eort has been expended, in both academic and industrial
research laboratories, towards the discovery of new olen polymerization catalysts
diering dramatically from the forefront group 4 metallocenes and half-sandwich
titanium amide catalysts [134]. Most commercial-scale polyolen processes employ
high-surface area supports for immobilizing olen polymerization catalysts, and
only few reports have appeared examining the use of polystyrene as a catalyst sup-
port [135].
The researchers Powers, Murphy and colleagues at Symyx Technologies have
developed a parallel synthesis and screening protocol for a polymer-bound 96-
member library of 1,2-diiminetransition metal complexes (Scheme 32.30) [136,
137].
The key intermediate, a resin-bound diketone, was converted in a titanium-
mediated condensation with 48 commercially available anilines with varying steric
and electronic substituents to furnish a 48-member 1,2-diimine library. In these
catalytic systems both substituent topography and electronic perturbation have been
reported to play a dramatic role in catalyst activity, molecular weight, and yield of
the polymer [138]. Splitting of the ligand library followed by conversion into the
corresponding 48 Ni(II) or Pd(II) complexes with (DME)NiBr2 or (COD)PdMeCl,
respectively, aorded a polymer-bound 96-member library of 1,2-diiminetransition
metal complexes. In order to compare performance of the resin-bound catalysts
with that of the corresponding catalysts in solution, a corresponding 1,2-diimine
library based on a related diketone framework was synthesized [136]. To eciently
complex the solution-phase 1,2-diimine library with Ni(II) and Pd(II), metal-delivery
agents (MDAs), a novel class of polymeric reagents, were used as metal ion sources
[139]. After activation of the Ni(II) or Pd(II) catalyst precursors (1,2-diimine com-
plexes) with MAO (methylalumoxane) or sodium tetrakis-(3,5-bistriuoromethyl)
phenyl borate (Na[(3,5-(F3 C)2 C6 H3 )4 B]), respectively, a custom high-pressure par-
32.6 Combinatorial Approaches to Olefin Polymerization Catalysts 931
Scheme 32.30. Synthesis of Brookhart-type heteroaryl, halogen, functional groups; tag,

polymer-bound Ni(II) or Pd(II) 1,2-diimine chemical code; MAO, methylalumoxane; ArF,
complexes and their use in the polymerization 3,5-(F3 C)2 C6 H3 ; dme, dimethoxyethane; cod,
of ethylene. M Ni(II), X Y Br; 1,5-cyclooctadiene.
M Pd(II), X Me, Y Cl; R, alkyl, aryl,
allel polymerization reactor with a modular series of 48 reaction chambers was

used to screen for ethylene polymerization. The device was equipped with individ-
ual ethylene pressure controls, and reactants were loaded using a three-axis liquid-
handling robot (Fig. 32.14) [136].
Compared with the corresponding free complexes screened under identical con-
ditions in solution, catalyst performance consistently proved to be decreased for
the on-bead Ni(II) catalysts and increased for the solid support-bound Pd(II) com-
plexes. For example, assaying the isolated discrete polyethylene granules by rapid
high-temperature gel permeation chromatography, molecular weights (MWs) up to
59,000 g mol1 were found for resin-bound Ni catalysts and up to 213,000 g mol1
for the corresponding diimineNi catalysts in solution. Assuming that catalyst per-
formance is proportional to the growth of the polystyrene support beads (210
times from the initial diameter of 70 mm), visual inspection of the beads allowed a
distinction between Ni(II)- and Pd(II)-derived catalysts in mixed assays (Fig. 32.15).
These results were conrmed by a chemical encoding/deconvolution strategy with
cleavable tertiary amine tags, followed by HPLC analysis.
The present work demonstrates the feasibility of applying a multitude of combi-
natorial techniques, including solid-phase synthesis, on-bead screening, and the
encoding/deconvolution of pooled libraries of catalysts, for the discovery and opti-
mization of new olen polymerization catalysts. Moreover, the technology appears
to be suitable for catalytic processes other than ethylene polymerization. In this
Fig. 32.14. Symyx Technologies Parallel Polymerization Reactor-96.
Fig. 32.15. Representative samples of polymeric products

obtained from a pooled polymerization of ethylene with
polymer-supported 1,2-diimine Ni(II) and Pd(II) catalysts.
respect, Symyx Technologies has developed general methodologies for the combi-
natorial synthesis, high-throughput screening, and characterization of libraries of
supported and unsupported organometallic compounds and catalysts [139a, 140].
For the discovery of novel polymerization catalysts, libraries of ligands in combi-
nation with various metals are screened in the presence of dierent monomers. In
order to optimize the yield and selectivity of a given organometallic complex in a
polymerization reaction, a variety of factors are tested in a high-throughput fashion,
including the form of the ancillary ligand precursor, the choice of the metal pre-
cursor, the reaction conditions (e.g. solvent, temperature, time), and the stability of
the desired product.
Mullen and coworkers tagged silica- or polymer-supported heterogeneous cata-
lysts for industrial olen polymerization with uorescent dyes [141]. Here, direct
detection of the dierent product beads obtained by dierent catalysts is available
through uorescent dyes that exhibit dierent emission wavelengths. The approach
starts with producing the tagged catalysts by supporting various metallocenes with
silica, activating them with MAO, and labeling them with dierent rylene dyes (Fig.
32.16). The dyes were chosen because of their high chemical stability, their high
tendency to physisorb on silica, their high uorescence yield, and because of the
fact that they do not inuence the polymerization. Also, a great variety of rylene
dyes with dierent emission wavelengths covering the entire visible spectrum is
available. These labeled catalysts are then mixed and introduced in a single poly-
merization vessel. During the olen polymerization each catalyst particle forms
only one product granulate through a particular growth process and can be con-
sidered as a microreactor. To assign the dierent compounds of the product mix-
ture to the employed catalyst, the polymer products are exposed to UV light, and
can be directly identied, manually separated, and characterized because of the
dierent emission wavelengths of the labels. The authors could demonstrate the
feasibility of this concept for the polymerization of ethylene as well as for the co-
polymerization of ethylene/hexene.
Fig. 32.16. Catalysts and dyes for the synthesis of tagged, supported catalysts.
Coates and coworkers used a pooled polymerization catalyst strategy to identify

catalysts for the synthesis of syndiotactic polypropylene [142]. The basis of this
concept is that the formed polymer itself serves as a stereochemical recording of
the events of the polymerization catalyst. Assuming that the catalyst species do not
react with one another, then a group of complexes for stereoselective polymeriza-
tion can be screened simultaneously. When the desired polymer product has dis-
tinguishing chemical or physical properties, techniques such as solubility, spec-
troscopy, or chromatography can be used to quickly probe the crude product of a
pooled polymerization reaction to see if a noteworthy catalyst is present. To probe
this concept, a library of 12 salicylaldiminato ligands was synthesized separately
by the condensation of three dierent salicylaldehydes and four amines (Scheme
32.31). Equimolar amounts of these ligands were combined, deprotonated with
Scheme 32.31. Synthesis of a library of salicylaldiminato titanium complexes.

BuLi, and reacted with 0.5 equiv. of TiCl 4 to give a library of 78 possible titanium
species. This complex library was then activated with MAO ([Al]/[Ti] 100] in tol-
uene and the resulting catalyst solution was exposed to propylene (2.7 atm.). Even
though 90% of the formed polymer could be washed away in reuxing diethyl
ether (atactic polypropylene), the remaining 10% of polymer was found to be
syndiotactic polypropylene ( 13 C-NMR microstructural analysis). Deconvolution
methods, i.e. the synthesis and testing of sublibraries, were used to identify suc-
cessfully the most active catalyst.
Hinderling and Chen reported the use of electrospray ionization tandem mass
spectrometry (ESI-MS/MS) and gas-phase ion molecule reactions for the rapid
screening of Brookhart-type Pd(II) olen polymerization catalysts [143]. A test
library of eight catalysts was prepared by reacting eight diimine ligands with
[(cod)Pd(CH3 )(Cl)], washing and drying of the complex, and activation with AgOTf
(Scheme 32.32). An electrospray mass spectrum of the mixture of complexes
showed that all eight catalysts are present in similar concentrations. The mixture
Scheme 32.32. Rapid screening of Brookhart- desolvation conditions to give polymeric ions
type Pd(II) olen polymerization catalysts by (and loss of DMSO); (iv) reject all ions below
ESI-MS/MS. (i) [(cod)Pd(CH3 )(Cl)], then a certain mass and subject the remaining high-
AgSO3 CF3 ; (ii) excess ethylene, then quenching mass ions to collision with Xe to induce b-
with DMSO; (iii) electrospray under mild hydride elimination.
was then dissolved in dichloromethane, saturated with ethylene, reacted for 1 h,

and quenched with dimethyl sulfoxide (DMSO). The electrospray mass spectrum
of the crude reaction mixture was rather complex and showed multiple, overlapping
series of oligomeric and polymeric ions corresponding to each catalyst species with
between 0 and @100 ethylene units added. After selection of ions with m=z > 2200,
these high-mass ions were collided with xenon to induce b-hydride elimination.
From the corresponding daughter ion spectrum the structure of the best catalyst
can be derived. Similarly, the daughter ion spectrum with a lower mass cut-o
shows the next best catalysts. The advantages of this methodology are sensitivity,
speed, direct assay, versatility, and possible automation.
32.7
Combinatorial Inorganic Catalysis
32.7.1
Combinatorial Libraries of Homogeneous Polyoxometalate-based Catalysts
Early transition metal oxygen anion clusters or polyoxometalates (POMs) have a

signicant impact in a variety of dierent research elds. Among catalysis by
heteropolyacids, selective hetero- and homogeneous oxidation processes are of
utmost importance [144]. Of extraordinary interest are POMs of the so-called Keg-
gin type that possess the general formula fH3x [PVx M12x O40 ](aq)g (M Mo,
W; x 05).
Hill and Gall published the combinatorial synthesis of phosphorus-centered
molybdenum and tungsten polyoxometalates of the Keggin structure [145]. The
POM catalysts were evaluated in the selective aerobic oxidation of tetrahydrothio-
phene (THT) to its corresponding sulfoxide (THTO) (Scheme 32.33).
Scheme 32.33. Aerobic oxidation of tetrahydrothiophene (THT)

to tetrahydrothiophene sulfoxide (THTO) by combinatorially
prepared POMs.
Catalyst library synthesis was performed by combinatorially mixing stock so-

lutions of appropriate tungsten, molybdenum, and vanadium precursors under a
constant phosphate concentration. Completion of catalyst formation was achieved
by equilibration at room temperature, which was followed by 51 V-NMR spectros-
copy. Conventional gas chromatography was used to quantify product (THTO)
yields and selectivities. Promising catalysts were selected and subsequently identi-
ed with the aid of 51 V-NMR and IR spectroscopy, revealing the complex [a-1,4-
32.7 Combinatorial Inorganic Catalysis 937
PV2 W10 O40 ] 5 as the most eective among them. All the samples evaluated, in-
cluding the starting materials, exhibited catalytic eciency to a certain degree in the
conversion of THT to THTO, suggesting that Keggin-type polymolybdato- or tung-
stophosphates have the ability to oxidize selectively THT to THTO regardless of
their vanadium content. It was assumed that the catalytically most active species
were primarily Keggin polyoxometalates rather than lower nuclearity polyoxometa-
lates. Several other combinatorial libraries containing boron, silicon, and arsenic
were evaluated under a variety of conditions, but the results were not quantied.
Selective catalytic oxidations that proceed at satisfactory rates at ambient condi-
tions and use oxygen or air as terminal oxidant are of utmost interest [146]. In a
more recent contribution, Hill and his group reported a diversity-based discovery
and mechanistic investigation of selective homogeneous thioether oxidation by
the Au(III)Cl2 NO3 (thioether)/oxygen system [147]. A 150-member library of inor-
ganic complexes was constructed by combinatorially combining polyoxometalate
anions and redox-active cations. The library design comprised POMs with reversible
redox chemistry and redox-active d-block ions or appropriate precursors including
HAuCl 4 , as well as s-block and p-block cations as counterions for the POMs. The
catalyst library included also POM-free control formulations such as the chloride,
nitrate, or perchlorate salts of the appropriate redox-active d-block cations.
Each library member was evaluated for its ability to catalyze the oxidation of the
thioether mustard analog 2-chloroethyl ethyl sulde (CEES) to the corresponding
sulfoxide (CEESO), using only oxygen as the oxidant (Scheme 32.34).
Scheme 32.34. Aerobic oxidation of 2-chloroethyl sulde

(CEES) to 2-chloroethyl sulde sulfoxide (CEESO) by the POM-
free combinatorially discovered catalysts system Au(III)Cl2 NO3
(thioether).
Product analysis and distribution was assessed by conventional serial GC. Most
catalyst preparations showed little or no activity in the target reaction but three cat-
alyst compositions exhibited considerable catalytic activity. The catalytically active
compositions included the POMs [CuPW11 O39 ] 5 and [MnPW11 O39 ] 5 , and the
POM-free system AgNO3 , each of them with ve equivalents of HAuCl 4 . The most
optimized combination of HAuCl 4 and AgNO3 formed a catalyst that exhibited
orders of magnitude higher reaction rates and higher turnover numbers (TONs) at
ambient temperature and at 1 atm. of air or oxygen than previously reported cata-
lysts. Extensive kinetic and mechanistic studies for the oxygen-based oxidation of
thioethers catalyzed by the parent system Au/Ag/NO3 revealed two gold complexes
as the catalytically active species (Fig. 32.17).
Fig. 32.17. Proposed catalytically active gold complexes.
32.7.2
Combinatorial Libraries and High-throughput Screening of Heterogeneous
Polyoxometalate Catalysts
Early eorts by Symyx Technologies led to the development of an fully integrated

high-throughput technology-screening platform useful for pharmaceuticals and
for ne chemicals process discovery, screening, and optimization. The platform
includes a proprietary software package as an essential component in the design of
combinatorial libraries. It also controls all the robotic functions, gathers data from
each spatially addressable reaction entity, and automatically stores the process data
in a central database. The hardware also comprises a variety of 96-well reactors
equipped with a liquid- and slurry-handling robot. In one example, the integrated
screening platform was employed for the high-throughput synthesis and screening
of metal-doped polyoxometalate (POM) libraries in 96-well format [148]. Libraries
of the heterogeneous POM catalysts were screened to discover selective aerobic
oxidation catalyst systems. In this case, an imidazole alcohol was catalytically oxi-
dized to the corresponding aldehyde, which represents an important key interme-
diate for the synthesis of DuPonts antihypertensive compound Losartan (Scheme
32.35).
Scheme 32.35. Application of high-throughput screening in the

discovery of novel catalysts for the POM-catalyzed oxidation of
imidazole alcohol to aldehyde, a key intermediate in the
synthesis of the antihypertensive compound Losartan (DuPont
Pharmaceuticals).
Within 4 weeks, 5000 experiments were performed to screen dierent catalyst

compositions, eects of solvents, and additives under variable reaction conditions.
Two classes of catalyst systems that gave more than 90% yield were identied. These
results were conrmed and validated in subsequent scale-up experiments, but the
proprietary catalyst composition was not disclosed.
32.8
Combinatorial Heterogeneous Catalysis
32.8.1
Introduction
The mechanism of catalytic activity in a heterogeneous system is complex [149].

The distribution of active sites in heterogeneous catalysts as well as the phase in-
tegrity is in general poorly dened. The phase integrity plays a major role because
the extent of deviation from the equilibrium structure under reaction conditions
controls the catalytic function. These types of inherent problems severely hamper
or even prevent the rational design of a heterogeneous catalyst for a particular reac-
tion. Conventional methods of catalyst discovery are primarily trial-and-error pro-
cesses where one catalyst at a time is tested for activity followed by numerous mod-
ications to achieve satisfactory activity. The process is therefore time-consuming
and laborious, and in most cases only local minima in a predened parameter
space (composition, reaction conditions, etc.) have been identied rather than the
absolute minimum. Combinatorial synthesis and screening oer a new dimension
for the quick discovery and optimization of heterogeneous catalysts in terms of
both composition and process conditions. The high-throughput approach allows
rapid exploration of a much larger parameter space than the conventional approach
and therefore leads more likely to the discovery of novel materials with signicant
performance improvements.
In this section, we focus on recent developments in the area of high-throughput
synthesis and screening of heterogeneous catalyst libraries. Special emphasis is
given to some recently published literature on methods of sample preparation and
parallel screening. A number of interesting patents and articles has appeared which
deal mostly with the development of methods for high-throughput synthesis and
screening of heterogeneous libraries. Integrated synthesis and screening of a plu-
rality of catalysts in library format has been recognized as an essential factor [150].
In 2000, Gennari and coworkers summarized inorganic catalysis in a review on
combinatorial technologies for catalyst design and development [20e]. Recently,
Senkan published a more detailed review on combinatorial heterogeneous catalysis
[20c]. Mirodatos and coworkers discussed the application of combinatorial chem-
istry to heterogeneous catalysis in terms of current strategies and perspectives on
the industrial and academic levels [151].
There are basically two techniques to prepare libraries of heterogeneous catalytic
materials: solution-based methods and thin-lm deposition methods. The descrip-
tion of both techniques is omitted in this part since they are described in detail in
Chapter 34. Impregnation of catalyst components onto a preformed solid support,
however, is an important solution-based technique for the preparation of hetero-

geneous catalysts, but is seldom utilized for other material sciences applications.
The solution-based methods are predominant in the eld of combinatorial hetero-
geneous catalysis. The majority of commercial heterogeneous catalysts is manu-
factured by solution-based techniques such as coprecipitation, impregnation, and
their variations [152], and, thus, results from library experiments can be translated
more easily into a bulk catalyst using the solution-based techniques. In addition,
the solution-based methods present fewer scale-up problems. Furthermore, many
liquid-handling robots and inkjet-based liquid-dispensing systems can be employed
to prepare the heterogeneous catalyst libraries of microgram scale to gram scale by
the solution-based methods. On the other hand, the thin-lm deposition methods
are performed on custom-designed and assembled high-vacuum instruments that
generally require high initial investment. Special care should be taken to ascertain
that the phase integrity of each catalyst member is the desired one since the thin-
lm deposition methods rely on the interlayer diusion for mixing and the multi-
component layers occasionally result in phase separation. The thin-lm-based
method will perhaps be of choice for fused catalyst libraries, e.g. metal alloys.
In most cases, the catalyst performance depends on the method of preparation.
Therefore, it is very important to adopt proper methods to obtain catalysts with
expected surface area, uniform metal distribution, and desirable particle size.
Newsam and Schuth have described various routes for combinatorial catalyst syn-
thesis that include hydrothermal synthesis, use of uid precursors, carrier im-
pregnation, precipitation [153]. A number of other research papers have outlined
dierent methods of preparing combinatorial catalyst libraries. These include
computer-controlled inkjet deposition of liquid reactants [154], methods based on
solution precursors [155157], sol-gel techniques [158160], impregnation of solid
supports [161], as well as standard methods such as precipitation and coprecipita-
tion [162, 163]. Table 32.1 summarizes some examples of heterogeneous catalyst
libraries.
With the development of new and ecient technologies for the synthesis of
large catalytic libraries, there is an ongoing eort for inventing fast and parallel
screening tools to identify active and selective catalysts. Several new techniques have
been proposed and demonstrated in the past few years, including the resonance-
enhanced multiphoton ionization (REMPI), time resolved and dierential IR ther-
mography, scanning mass spectrometry, and colorimetry. While IR thermography
and uorescence or colored dye assays are established techniques, a few other new
methods have emerged recently to identify active catalysts in an array. So far, no
screening method oers a general solution to the problem of fast screening of
libraries together with the complexity involved in parallel detection of the reactants,
products, and side products. Therefore, it is very important to develop screening
technologies according to the detection requirements of the reactants, products,
and side products of the reaction. Accordingly, in some cases, it is essential to have
a combination of tools for a better characterization of reaction products. It is also
very important to characterize the time-dependent nature of the catalyst library for
developing a practical catalyst. Some catalysts have a signicant induction period
Tab. 32.1. Examples of combinatorial heterogeneous catalyst libraries.
Catalyst libraries Preparation method Target reaction Screening method Reference
0.5% Ag, Bi, Co, Cr, Cu, Er, Fe, Gd, Ir, Ni, Solution-based impregnation H2 O2 Infrared thermography 164
Pd, Pt, Rh, Ti, V, Zn, on Al2 O3 pellets
37, 110% Co, Cr, Cu, Fe, Ir, Mn, Ni, Pd, Solution-based sol-gel method Hyrogenation of 1-hexyne Infrared thermography 165
Pt, Rh, Ru, V, Zn on Si, Ti oxides
100 Na2 O/Al2 O3/SiO2 zeolites with Li Solution-based hydrothermal a a 166
and Cs zeolite synthesis
37 TiO2/Al2 O3/SiO2/TiO2/ZrO2 zeolites Solution-based hydrothermal a a 167
zeolite synthesis
645 clusters of Pt, Ru, Os, Ir on carbon Solution-based Methanol direct fuel cell Fluorescence acidbase indicator 157
coprecipitation
120 ternary thin lm clusters of Pt, Pd, Thin lm deposition: CO oxidation, CO NO Scanning quadruple mass 168
Rh, and Pd, Rh, Cu sputtering spectrometry
66 ternary combinations of 1% Pt, Pd and Solution-based impregnation Cyclohexane dehydro- REMPI 161
In on Al2 O3 genation to benzene
16 Au/Co3 O4 and Au/TiO2 powders Solution-based CO oxidation Quadruple mass spectrometry 162
coprecipitation
33 16% Ag, Au, Bi, Co, In, Cr, Cu, Fe, Solution-based sol-gel method Propylene oxidation Spatially resolved analysis of an 169
Mo, Ni, Re, Rh, Sb, Ta, Te, V, Y on Si, array of batch microreactors
Ti, Zr oxides
50 ternary and quaternary oxides of Co, Solution-based Ethane and propane Six-parallel gas chromatography 170
Cd, Fe, Ga, Ge, In, Mn, Mo, Ni, Nb, V, coprecipitation dehydrogenation
W, Zn
32.8 Combinatorial Heterogeneous Catalysis
941
942
Catalyst libraries Preparation method Target reaction Screening method Reference
30 binary combinations of Na2 WO4 and Solution-based impregnation, Oxidative coupling of Quadruple mass spectrometry 171
Mn on SiO2 ; Au and In on ZrO2 , TiO2 , deposition, and methane and CO
SiO2 , MgO, ZnO, Nd2 O3 , Y2 O3 , CeO2 , precipitation oxidation
Mn2 O3
66 ternary combinations of oxides of Mo, Solution-based sol-gel Ethane oxidative Scanning quadruple mass 172
V and Nb deposition dehydrogenation spectrometry, photothermal
deection, gas chroma-
tography
32 Combinatorial Methods in Catalysis
144 ternary combinations of oxides of Solution-based sol-gel Ethane oxidative Scanning quadruple mass 173
V/Al/Nb, and Cr/Al/Nb deposition dehydrogenation spectrometry, photothermal
deection
66 ternary combinations of 1% Pt, Pd, Solution-based impregnation Cyclohexane Quadruple mass spectrometry 174
and In on Al2 O3 dehydrogenation to
benzene
45 3- to 5-element combinations of Pt, Solution-based impregnation C3 H8 total oxidation Quadruple mass spectrometry 175
Pd, Rh, Ru, Au, Cu, Ag, and Mn on
TiO2 and Fe 2 O3
56 quaternary combinations of Pt, Pd, In, Solution-based impregnation NO reduction by C3 H6 Quadruple mass spectrometry 176
Na on Al2 O3
V2 O5/TiO2 mixtures Solution-based Oxidation on Laser-induced uorescence 177
coprecipitation naphthalene to imaging (LIFI)
naphthoquinone
36 Pt/Zr/V/Al2 O3 Solution-based impregnation Methane oxidation Scanning quadruple mass 178
Co oxidation spectrometry coupled with
monolith multichannel
reactor
52 Pt/Zr/V/Al2 O3 Solution-based impregnation Oxidative dehydro- Scanning quadruple mass
onto Al2 O3 electro- genation of isobutane spectrometry coupled with 35
chemically formed on parallel microreactors
aluminum plate
715 combinations of Pt, Ru, Os, Ir, Rh Solution-based deposition O2 reduction H2 O Fluorescence acidbase indicator 179
oxidation
280 V2 O5 , MoO3 , MnO2 , Fe 2 O3 , Ga2 O3 , Solution-based impregnation Propane dehydrogenation Quadruple mass spectrometry 180
La2 O3 , B2 O3 , MgO on Al2 O3
32 Ti-silsesquioxanes from 8 RSiCl3 /Ti Solution-based sol-gel method Epoxidation of 1-octene Standard GC equipped with 181
(OiPr)4 ternary composition of with tert-butyl- sampling robot
cyclopentyl, cyclohexyl, and phenyl- hydroperoxide (TBHP)
substituted silanes
65 1 mol% main group, transition, and Solution-based sol-gel method Photooxidation of 4- Standard HPLC equipped with 182
rare earth metal dopands on TiO2 , chlorophenol sampling robot
SnO2 , or WO3
a These publications describe only the synthesis of heterogeneous
catalyst libraries.
32.8 Combinatorial Heterogeneous Catalysis
943
before they become fully active, and most catalysts deactivate over time. These
properties will also vary according to the reaction conditions. Some parallel screen-
ing schemes oer the capability of monitoring the reactions over time. For example,
a multichannel xed bed reactor coupled with parallel GC and an array micro-
reactor equipped with REMPI allow library screening over a prolonged reaction
time. Many techniques such as MS, IR, and other optical detection schemes can be
applied in both homogeneous and heterogeneous catalysis. Each of these emerg-
ing techniques and tools for high-throughput catalyst screening will be described
in detail in the screening section (see Chapter 32.10). Finally, the heterogeneous
catalysis section will be concluded by case studies (see Section 32.8.2).
32.8.2
Case Studies
32.8.2.1 Oxidative Dehydrogenation of Ethane

The development of ecient heterogeneous catalysts for the gas-phase oxidative
dehydrogenation of light parans is of particular interest because of the eco-
nomic benets of using parans directly as raw materials for the production of
important base chemicals [174]. The low-temperature oxidative dehydrogenation
of ethane to ethylene has been a research topic of consistent interest after the
report of catalytic activity in the Mo/V/Nb/O system below 300 C in 1978 [183,
184]. The optimum compositional range for these catalysts was reported to be
Mo0:61 0:77 V0:31 0:19 Nb0:08 0:04 [183, 184]. Researchers at Symyx Technologies have
reported eorts in reproducing and improving these catalyst systems using com-
binatorial methods.
The strategy reported is based on a three-step approach: in the primary screen
thousands of catalyst formulations are generated using automated solution-based
methods as arrays of thick lms on 7.5-cm wafer plates (dispensing volumes on a
nanoliter to microliter scale). The lms themselves were prepared from sol-gel pre-
cursors that were deposited by automated solution deposition methods. The typical
layout of a ternary library is shown in Fig. 32.18. In this case the wafer holds a ter-
nary AaBaC library consisting of two identical triangular matrices with 66 ele-
ments. The three corners in this library correspond to 100% A, 100% B, and 100%
C. Thus, the compositional increments are 10% per matrix element for this kind
of library layout.
The libraries were then screened using simultaneous mass spectrometry and
photothermal deection spectroscopy. The best catalysts were consecutively synthe-
sized on milligram scale (2550 mg) for the secondary screen using parallel xed
bed reactors. The secondary screen provides conversion and selectivity data for the
catalysts under realistic operating conditions. Catalysts that performed well in the
secondary screen are further evaluated in tertiary screens using bench-scale re-
actors with gram quantities of the catalysts.
To demonstrate the reliability of combinatorial methods compared with larger
scale experimentation, Symyx Technologies scientists tried to reproduce Thorstein-
Fig. 32.18. Library design for a 7.5-cm quartz wafer.
sons catalyst formulations on a microgram scale and plotted their primary screen-
ing results versus Thorsteinsons activity diagram [183]. Figure 32.19 shows that
the primary screening data with conversions in the ppm range correlate well with
bulk catalyst activity with percent level conversions.
For greater compositional precision, researchers at Symyx Technologies inves-
tigated additional libraries focusing on the most active area. This ne-tuning of
the catalyst resulted in an ethane conversion of 12.8% and an ethylene selectivity
of 74.4% at an optimal composition of Mo73 V24 Nb3 . Including Sb, Ca, and Li as
dopants improved the catalysts even further. Under identical synthesis and reac-
tion conditions, the optimal composition reported by Thorsteinson, Mo73 V18 Nb9 ,
converts 6.1% at a selectivity of 83.2%.
Considering new mixed metal oxide ternary libraries, for example Cr/Al/Nb/O
systems, researchers at Symyx Technologies were able to identify catalysts that are
signicantly more active than the previously known MoaVaNbaO systems [173,
185, 186].
32.8.2.2 Oxidative Dehydrogenation of Propane

Recently, Baerns, Senkan, and coworkers reported the impregnation method of
catalyst preparation coupled with multitube packed bed reactors [171] and array
microchannel reactors [187] within the framework of genetic algorithms [188] to
nd catalysts for the low-temperature oxidation of propane at low concentrations
[175]. The catalyst libraries were prepared by an automatic liquid-dispensation
system applying the incipient wetness method. A total of eight active compo-
nents were selected as candidates for incorporation into TiO2 or Fe 2 O3 as carrier
materials.
Fig. 32.19. Comparison of the ethylene concentration reported

by Thorsteinson (left) in conventional experimentation (tens of
grams of catalyst) and by Symyx Technologies (right) in their
primary screen (micrograms of catalyst).
In the rst step, a library containing 45 supported catalytic materials consisting

of mixtures of active elements at dierent compositions was prepared in a stochastic
manner in such a way that each catalytic material consisted of up to ve of eight
primary components. The libraries were then tested for their catalytic performance
(conversion of C3 H8 to CO2 ) in both the multitube packed bed reactors [172] and
in array channel microreactors [187].
The creation of the next library based on the results of the previous generation
was accomplished using mutation and crossover operators of the genetic algo-
rithm approach as applied to the previous generation catalysts [188], leading to the
creation of another library also containing 45 supported catalytic materials. The
authors were able to demonstrate that the application of genetic algorithm led to
an improvement in activity. Signicant propane conversions could be achieved
at 50 C. Catalysts providing propane conversions on the order of 90% were also
achievable at higher temperatures. The best catalytic materials were found to be
rich in ruthenium; multimetal combinations were signicantly superior [175].
More recently, the same group disclosed an evolutionary approach to optimize
multimetal oxide (V2 O5 , MoO3 , MnO2 , Fe 2 O3 , Ga2 O3 , La2 O3 , B2 O3 , and MgO) cat-
alysts supported on a-Al2 O3 for the oxidative dehydrogenation of propane to pro-
pene [180]. Thus, 56 catalytic materials were prepared for each generation, and this
process was iterated ve times according to the aforementioned genetic algorithm.
Both manual and robotic synthesis were used for the library preparations, and
these catalytic materials were tested in parallel. For the best materials, propene
yields of 7% (rst generation) to 9% (fth generation) were achieved.
32.8.2.3 Catalytic Oxidation of CO and the Reduction of NO

These two processes were studied at Symyx using catalyst libraries of metal alloys
of Rh, Pd, Pt, and Cu [168]. Triangular libraries 15 15 15 containing approx-
imately 24 mg of 120 independently prepared catalysts were synthesized by deposi-
tion methods using fully automated radiofrequency sputtering techniques. Libraries
with similar catalysts were also prepared by sol-gel-based methods.
The oxidation of CO was carried out in the presence of oxygen and the produc-
tion of CO2 was determined by scanning mass spectroscopy. The amount of CO2
produced followed the trend Rh > Pd > Pt, which is in good agreement with results
from experiments with single crystalline surfaces as well as supported catalysts.
In subsequent libraries, one of the noble metals was replaced by transition met-
als. In the case of a library with Rh/Pd/Cu, the 1:1 composition of Cu/Rh showed
activity very similar to that of pure Rh and the catalyst with 93% Cu and 7% Rh
maintains 40% of the activity of pure Rh. In addition, Pt/Cu and Pd/Cu binaries
show activity enhancements over the respective pure metals, with the enhance-
ment being stronger at low temperatures than at high temperatures.
The oxidation of CO by NO was investigated along the same lines using the above-
mentioned Rh/Pd/Pt library. The reaction was carried out at ambient pressure at
various temperatures. As in the CO oxidation by oxygen, the activity for the oxida-
tion of CO by NO follows the trend Rh > Pd > Pt similar to that reported in the
literature for bulk catalysts.
32.9
Combinatorial Electrocatalysis
Electrochemical reactions play an important role from energy production in fuel

cells and batteries to industrially important processes such as the production of
chlorine and the electrohydrodimerization of acrylonitrile to adiponitrile that is
used in the production of nylon. Electrocatalysis deals with the modication of the
overall rates of electrochemical reactions so that selectivity of these reactions, their
yield, and eciency are maximized. The main focus is on the electron-transfer re-
actions that take place at the electrode/electrolyte interface with electrochemical
parameters such as potential and current being the major driving forces for the
reaction.
32.9.1
Electrocatalysts for Fuel Cells
Fuel cell technology holds the promise of low to zero emission energy for power
plants, backup generators, and in the transportation sector. Fuel cells will also oer
fuel eciency in the order of 50% or more. With the increasing interest in fuel
cells as alternative energy sources for stationary power, portable, and automotive
applications, there is a need to develop new anode and cathode electrocatalysts. The
cost of the current precious metal-based electrocatalysts is a considerable hurdle to
the successful commercialization of fuel cells.
The oxidation of methanol in fuel cells has been extensively studied for several
decades. At present, however, the commercialization of the direct methanol fuel
cell (DMFC) is beset by several problems. Given the lower electrochemical activity
of methanol in comparison with hydrogen, much higher loading levels of noble
metal catalysts must be employed. The most ecient anode systems for the com-
plete electro-oxidation of methanol consist of the platinum metals and mixtures
or alloys thereof. Notwithstanding the high cost issues, presently employed anode
systems suer from complications due to catalyst poisoning by CO, which leads to
both an unacceptable loss in cell voltage and degradation in long-term performance.
Numerous studies have indicated that the most promising anode systems consist
of either a supported or unsupported binary alloy of Pt/Ru [189, 190].
The traditional approach to evaluating anode materials has involved the relatively
time-consuming and laborious practice of synthesizing and characterizing mate-
rials one at a time. Mallouk, Smotkin, and coworkers developed a rapid combina-
torial synthesis and uorescent screening method for the exploration of ternary
and quaternary anode electrocatalysts for the DMFC (Fig. 32.20) [157]. The authors
created libraries of alloys by using automated inkjet deposition of metal precursor
aliquots onto a conducting ber paper, followed by reduction of the metal salts
with a borohydride reagent. The authors created 135 unique ternary compositions
Fig. 32.20. Photo images of the dierent overpotential, identifying the most active
stages of discovery of a ternary alloy in array region of composition space. c) Fluorescence
format using a quinine indicator. a) Image in image at high overpotential, where methanol
white light. b) Fluorescence image at low oxidation occurs at every spot in the array.
on nine exploratory library arrays. These compositions were based on ve transi-

tion metals: Pt, Ru, Os, Rh, and Pd. After treatment, the libraries were immersed
in an aqueous methanolic sodium sulfate electrolyte containing a uorescent pH
indicator. Screening was performed with a typical three-electrode cell (electrode
array as working electrode, Pt counter, and saturated calomel reference electrode)
by conducting a single potential sweep from cathodic to anodic potentials. The
electrocatalysts are all on a common working electrode, and, as a result, it is not
possible to directly measure the electrochemical activity at each electrocatalyst.
However, upon the oxidation of methanol, it is expected that the pH will drop close
to the regions where methanol is being oxidized. The conducting Toray paper was
illuminated with an ultraviolet lamp and observation of the highest uorescent in-
tensities due to local proton release (pH drop) upon electro-oxidation of methanol
determined the catalytically most active spots on a given library. The composition
performances were compared with Pt/Ru (50:50 atom%). The best composition
was given as Pt/Os/Rh (60:25:15 atom%).
Later, these authors prepared, screened, and analyzed a 645-member electrode
array of Pt, Ru, Rh, Ir, and Os consisting of 80 binary, 280 ternary, and 280 quater-
nary combinations [191ac]. The most active catalyst was found to be Pt/Ru/Os/Ir
(47:29:20:4 atom%). Results of these zoom screens are shown in Fig. 32.21. Most
recently, Mallouk and coworkers applied a combinatorial approach to the discovery
Fig. 32.21.Anode polarization curves (V vs. RHE) of NaBH4

reduced catalysts from zoom screens.
Fig. 32.22. Symyx Technologies electrode array consisting of 64

individually addressable electrodes prepared on an insulating
7.5-cm quartz substrate using lithographic techniques.
of bifunctional oxygen reduction/water oxidation electrocatalysts for regenerative

fuel cells [181].
Scientists at Symyx Technologies have developed another combinatorial approach
for the rapid synthesis and screening of fuel cell electrocatalysts. Libraries of alloy
materials are synthesized directly onto an 8 8 electrode array (Fig. 32.22) which
consists of 64 individually addressable electrodes prepared on an insulating 7.5-cm
quartz substrate using lithographic techniques. The electrode material can be
made from gold or titanium. Each electrode is approximately 1.0 mm diameter
and electrical contact is made with each electrode via a contact pad on the edge of
the wafer. Electrocatalysts were synthesized by a combination of magnetron sput-
tering or by parallel electroplating. The electrode array was then sealed to a Teon
cylinder that was lled with aqueous electrolyte. All 64 electrodes were therefore
exposed to the same electrolyte solution. A common reference electrode and work-
ing electrode was immersed in the cell. The array was interfaced to a 64-channel
potentiostat via a PCB interface and the electrocatalytic performance of the result-
ing materials were tested by parallel monitoring of the currentvoltage time be-
havior of each individual electrocatalyst.
The authors tested a number of catalytic concepts for the anodic electrooxida-
tion of methanol (DMFC) as well as the cathodic electroreduction of oxygen in
aqueous acidic electrolytes [192]. The authors demonstrated that for known sys-
tems the electrochemical activity as measured directly on the thin-lm samples on
the addressable electrochemical array correlated with the activity of known powder
samples.
32.9.2
Combinatorial Electrosynthesis
Ward and coworkers applied two dierent combinatorial approaches to study the
electrochemical reduction of 1,4-benzoquinone to hydroquinone at organosulfur-
modied gold electrodes [193]. The authors prepared an array of physically but not
electrically isolated gold electrodes on a glass substrate. Monolayers of organo-
sulfur reagents were prepared on selected electrodes on the 4 7 array by dispens-
ing aliquots of either hexanethiol or hexadecanethiol dissolved in ethanol at the
respective electrodes. The array was subsequently rinsed and housed in a thin-layer
electrochemical cell. The electrolyte contained 1,4-benzoquinone dissolved in 0.5 M
KOH acidied to pH 3.0 and also a uorescent dye, uorescein, which uoresces
green at pH > 6. A potential of 0.1 V (vs. Ag/AgCl) was applied to the array and
the thin-layer cell illuminated with an ultraviolet lamp. Green uorescence was ob-
served in those electrode regions that had not been modied with an organosulfur
reagent as well as on electrode regions that had been modied with a monolayer
of hexanethiol. Benzoquinone is reduced by two electrons at this potential with the
consumption of two protons. It is the decrease in protons at the electrodes where
benzoquinone is reduced that causes the local pH to increase. No uorescence was
observed at the hexadecanethiol-modied electrodes.
In a second approach, the authors created an electrochemically addressable elec-
trode array from which it was possible to measure directly the electrochemical
activity by monitoring the currentvoltage behavior at each individual electrode.
An 8 8 gold electrode array was created on an insulating thermally oxidized sili-
con substrate ensuring physical and electrical isolation of the individual electrodes
using standard lithographic techniques. Electrical contact was made via standard
64-pin connectors with a single channel potentiostat and multiplexer. Selected elec-
trodes were subsequently modied with hexanethiol, hexadecanethiol, or dodeca-
nethiol monolayers through a series of adsorption and electrochemical desorption
steps. An electrochemical cell was created by attaching the electrode array to a Del-
rin cylinder with a Delrin cap congured for a reference and counter electrode.
Electrolyte containing benzoquinone and KOH acidied to pH 3 was added to the
cell, exposing all 64 electrodes to the electrolyte. In a serial manner, the electro-
chemical reduction of benzoquinone was studied at each electrode by cyclic voltam-
metry in which the potential of each electrode was cycled and the current measured.
The authors proposed that this direct measurement of the electrochemical activity
was more sensitive than the uorescent screen in quantifying the benzoquinone re-
duction at the modied electrodes with the results indicating that the activity in the
library increases in the order of hexadecanethiol < dodecanethiol < hexanethiol <
gold, illustrating suppression of current with increasing alkanethiol chain length.
The authors propose that the uorescent screen allows for measurement of active
zones while electrochemical screens can be used to discriminate smaller dier-
ences in activity.
Yudin and coworkers demonstrated how combinatorial electrochemistry could
be used in the electrosynthesis of small organic molecules [194a]. The authors de-
veloped what they term a spatially addressable electrolysis platform (SAEP). Each
electrochemical cell in the 4 4 array was equipped with a stainless-steel cathode
and a graphite rod anode. The cathodes were welded directly onto a stainless-steel
support that provided a common terminal for the current source. The authors ex-
plored the anodic oxidation of carbamates, amides, and sulfonamides leading to
libraries of a-alkoxycarbamates, a-alkoxyamides, and a-alkoxysulfonamides, respec-
tively. The authors have also demonstrated the intramolecular cyclization of hy-
droxyamides yielding heterobicyclic compounds as well as the generation of vicinal
diamines by the reductive hydrocoupling of aldimines.
In another application, Yudin and coworkers generated libraries of catalytic ma-
terials on electrode surfaces by the copolymerization of bithiophene and pyrrole-
containing TEMPO (2,2,6,6-tetramethilpiperidin-1-yloxy) catalysts [194b,c]. Diver-
sity was created by electrochemical copolymerization and by creating surfaces with
dierent ratios of bithiophene/pyrrole. These catalyst lms were utilized in the
electrochemical oxidation of primary alcohols to aldehydes, where cyclic voltamme-
try was used to screen the catalytic activities of the modied electrodes.
Another example of a high-throughput screen for catalyst activity comes from
Hillier and coworkers, who applied a scanning electrochemical microscope to
characterize the hydrogen oxidation reaction on a polycrystalline platinum surface
[195]. This technique utilizes tip-sample feedback and works reliably for determi-
nation of the kinetics of the reaction over a large range of substrate potentials from
the hydrogen adsorption region to the platinum oxidation region.
Hillier explored this technique further and directly demonstrated the measure-
ment of the rate constant for hydrogen oxidation and performed reactivity map-
ping of heterogeneous electrodes consisting of catalytic and noncatalytic domains.
32.10
Novel High-throughput Screening Tools
The process of discovering new catalysts or materials from a large pool of potential
candidates requires a reliable and robust screening process. Traditionally, this pro-
cess presents itself as a bottleneck in the discovery eort, especially if large libraries
of potential catalysts or materials have already been synthesized or prepared. The
rst step in combinatorial catalysis, like all materials design, involves the identi-
cation of a specic chemical transformation of interest. A collection of potential cat-
alysts, prepared from a set of chemically diverse ligand sets and metal precursors,
are combined in a parallel or combinatorial fashion and screened for activity in a
high-throughput primary screen. Although the large volume of potential catalysts
examined in a primary screen typically allows only relative activity to be established,
the goal at this stage of discovery is to identify promising lead catalysts worthy of
further investigation and follow-up. Lead materials are then further examined in
a high-throughput secondary screen designed to screen for specic trends in the
physical and chemical properties in greater detail and typically at a slightly lower
throughput than the primary screen. The information obtained from the second-
ary screen is then used to prepare additional generations of catalysts that can be
optimized into a superior catalyst worthy of commercialization.
Typically, the information necessary to classify new materials cannot be obtained
from a single piece of characterization equipment. Therefore, a series of high-
throughput screening tools is employed at various stages in the combinatorial
process. While a large number of automated commercial systems exist for high-
throughput analysis of microliter quantity samples for medical and pharmaceutical
applications, the vast majority of the screening tools necessary for advanced mate-
rials research are custom-made instruments. Conventional analytical tools such as
mass spectrometry, gas [196] and liquid chromatography, electrophoresis [197, 198],
Raman [199] and nuclear magnetic resonance spectroscopy, X-ray uorescence
microprobe [182], and X-ray diraction [200] have been automated and redesigned
for rapid serial measurements of hundreds of samples per day [201]. A number of
recent reviews of combinatorial catalysis discuss high-throughput screening tech-
niques [20c,d,h, 151, 202204]. Several examples of novel high-throughput screen-
ing systems are discussed below.
32.10.1
Infrared Screening Tools
Infrared detection has become an extremely popular technique for the analysis of
combinatorial libraries because it is generally noncontact, nondestructive, and ame-
nable to very high-throughput screening. Use of the infrared can be divided into
two general categories: thermal imaging (thermography) and infrared spectros-
copy.
32.10.1.1 Infrared Thermography

One of the rst truly parallel high-throughput screens utilized infrared thermog-
raphy to identify catalytic activity. Infrared radiation is emitted by all materials above
0 K according to the StefanBoltzmann Law, W esT 4 , where W is the emitted
power density, e the emissivity (e 1 for a blackbody), s is the StefanBoltzmann
constant, and T is the temperature. Modern infrared cameras utilize a photovoltaic
focal plane array (FPA) detector made of InSb, HgCdTe, or PtSi to convert infrared
radiation into digital images. It is important to note that the infrared cameras
measure emitted or reected intensity, not temperature, and a calibration must be
performed to relate the intensity images to temperature.
Pawlicki and Schmitz rst reported using infrared thermography to monitor the
dynamics of reactions on solid surfaces in 1987 [205], and Sermon and coworkers
applied this technology to the analysis of temperature proles of exothermic reac-
tions on silicon oxide-supported platinum catalysts [206]. Time-resolved infrared
thermographic detection and infrared emission analysis of temperature proles en-
able virtually any reaction to be monitored in a truly parallel fashion [63, 207].
As the eld of combinatorial materials science began to heat up in the late 1990s,
several groups applied infrared thermography to the search for new catalysts. Will-
son and coworkers employed infrared thermographic imaging to identify possible
Fig. 32.23. Schematic of a catalytic reactor for infrared thermography.
formulations of heterogeneous catalysts for the oxidation of hydrogen to water

[164]. The catalyst entities on the array were prepared in a conventional manner by
impregnating g-aluminum oxide pellets as a catalyst support with aqueous stock
solutions of 16 metal salt precursors. After reduction to zero-valency metals by ex-
posure to pure hydrogen, the pellets were manually placed in an aluminum reac-
tor and assayed in a parallel manner in a spatially addressable format. The reactor,
shown schematically in Fig. 32.23, was equipped with an infrared imaging camera
and devices to control reaction conditions such as gas ow, heating rates, and data
collection/analysis. After calibrating the radiation intensity with respect to temper-
ature and equilibrating the reactor at 35 C with hydrogen, a gas stream containing
5 vol% of oxygen was introduced into the hydrogen feed stream. Hydrogen oxida-
tion activity was found for pure Pd, Pt, and Ir within 10 s of oxygen introduction.
Heating the reaction chamber up to 300 C ignited the Rh-loaded pellet at ap-
proximately 82 C and the activity was measured with the camera as an increase
in catalyst temperature (relative to the background) while continuously heating the
reaction chamber. Although basically a proof of concept, the experimental proce-
dure proved useful for parallel screening of new catalyst formulations and evaluat-
ing operational issues such as catalyst lifetime, resistance to poisoning, and re-
generability [208].
Direct thermal imaging of combinatorial libraries for activity is very useful as
a qualitative or semiquantitative tool for determining whether catalytic activity is
present in a particular material. True quantitative determination of the tempera-
ture prole for a given library of materials is complicated by the dierence in
emissivity between members of the library. The emissivity of an opaque material is
related to the reectivity (lower reectivity means higher emissivity), which is dif-
ferent for most elements in a catalyst library. Furthermore, emissivity must be

calibrated as a function of wavelength and temperature. The absolute reectivity
and emissivity characteristics of a new material are not known for most high-
throughput experiments, which means that the proportionality factor used to cal-
culate the temperature prole from the emitted infrared radiation is generally not
available.
Emissivity can be accounted for (to some degree) by the use of linear corrections
to the detector response, and subtraction of a reference image typically taken at
the beginning when the experiment is cold. These corrections minimize emissivity
eects for systems where the emissivity varies slowly with temperature, such as
metals and metal alloys.
In 1998, Maier and coworkers applied emissivity-corrected infrared thermog-
raphy to detect activity in heterogeneously catalyzed gas-phase reactions on a model
library [165]. The researchers chose transition metal-impregnated, amorphous mi-
croporous mixed oxide (AMM) supports, a class of materials previously shown to
possess unusual properties as bulk catalysts or as catalytic membranes in selective
oxidation, hydrocracking, hydrogenation, etherication, and esterication reactions
[209211]. The catalytic hydrogenation of hexyne and the oxidation of isooctane
and toluene were chosen as their test reactions. With automated sol-gel proce-
dures, less then 200 mg of each catalyst was deposited on a low-reection slate
substrate followed by controlled drying, calcination, and reduction to aord a cata-
lyst array.
A high-sensitivity infrared camera with a platinum silicide (PtSi) FPA was used
to monitor the heat evolution upon catalytic conversion. The same catalyst array
was screened in a customized parallel reactor and on a catalyst microgram scale
under appropriate conditions for three test reactions. Several eective catalysts for
each of the targeted conversions were identied.
Further extensions of the technology came in 1998 when Reetz and coworkers
stressed the general usefulness of infrared thermography to the time-resolved
screening of liquid-phase catalytic reactions, such as enantioselective hydrolytic
ring opening of epoxides to nonracemic diols and a lipase-catalyzed acetylation of a
secondary alcohol [207a]. The experiment utilized a modied microtiter plate con-
sisting of a commercial Eppendorf Thermomixer with the top replaced by an alu-
minum plate in which holes were drilled then lled with 8 32 mm glass vials.
As a model reaction, Reetz chose the enantioselective lipase-catalyzed acylation of
(R)-, (S)-, and rac-1-phenylethanol with vinylacetate. The reaction was followed with
the infrared camera, periodically acquiring 250 images of the library, which were
then averaged and visually inspected. To demonstrate the screening capability of
the infrared camera under homogeneous conditions, the activity and selectivity of
three metal catalysts were tested thermographically in the hydrolysis of epichlo-
rhydrin. Finally, relative substrate activity was screened studying the hydrolysis of
three dierent chiral epoxides with the cobalt catalyst that was found to be most
active in the previous screening of epichlorhydrin hydrolysis. In all cases, relative
trends in the activity and selectivity of the catalytic reactions were reproduced from
the available literature.
The same group used IR thermographic screening for thermoneutral or endo-

thermic transformations, in this case ring-closing olen metathesis [207b]. Four
dierent ruthenium-based olen metathesis catalysts were screened for four dif-
ferent types of ring-closing metathesis reactions. Highest catalyst activity is identi-
ed by heat uptake from the surroundings, as monitored by the appearance of
cold spots. The heat of vaporization of one of the reaction products (ethylene or
propylene) plays a crucial role in this process.
Infrared thermography holds promise for more extensive application of this tech-
nology in homogeneous, heterogeneous, organic, and inorganic catalysis research.
However, thermal imaging does not resolve the product composition of the cata-
lyst, an important limitation in chemical catalysis.
32.10.1.2 High-throughput Infrared Spectroscopy

Spectroscopic techniques are extremely popular for the analysis of combinatorial
libraries because of their speed, nondestructive nature, and relative ease of use. In
addition, infrared spectroscopy is very useful for identifying structural properties
of organic solid-phase-supported combinatorial libraries. Indeed, many commer-
cial Fourier transform infrared (FTIR) spectrometers have been equipped with an
automated attachment to allow multiple compounds to be screened in rapid suc-
cession.
Single-bead FTIR microspectroscopy has been utilized by chemists for quite
some time to analyze spectral information of products on solid supports. Exten-
sion of this technique to combinatorial chemistry in the form of a scanned high-
throughput screen has been reported by Jung and coworkers [212]. In Jungs
method, polymer-bound resin beads modied through combinatorial synthesis
were withdrawn from the reaction vessel and embedded in a KBr window. The KBr
window was then placed on the automated x/ y stage of an infrared microscope
and the spectra mapped. Data were presented as a map of the infrared absorption
as a function of position across the KBr plate. Direct identication of resin-bound
molecules is possible by superposition of maps taken at dierent absorption wave-
numbers. Jung and coworkers mapped approximately 300 dierent resin beads at
a rate of approximately 5 h per wavenumber map.
While extremely useful, scanning spectroscopic measurements have a number
of limitations stemming from the relatively slow speed of the x/ y scanning meth-
odology. As combinatorial libraries increase in size, the time necessary to screen
libraries in a serial manner becomes cumbersome; the time being dependent on
the number of scans averaged, the wavenumber resolution, and the number of ele-
ments in the library. Incorporation of the microscope and x/ y scanning stage into
a chemical reaction chamber in which the pressure and temperature can be varied
is also complicated and expensive. Finally, the time needed to scan from point to
point virtually eliminates the ability to derive kinetic information from the mea-
surement.
True parallel spectroscopic measurements rely on the ability of the analytical
technique to simultaneously collect information from multiple samples. Parallel
measurements oer the throughput and temporal resolution necessary to measure
the kinetics of the large number of catalytic reactions possible in combinatorial
Fig. 32.24. Optical layout for an imaging FTIR a bandpass lter (F), a KBr diuser (D), CaF2
spectrometer. The light source is composed of plano-convex lens (L1), reactor (R), and CaF2
an infrared source (S), a KBr beam splitter biconvex lens (L2). The infrared camera with
(BS), a moving mirror (M1), and a stationary Hg/Cd/Te detector array (FPA) acts as the
mirror (M2). The optical set-up is composed of detector.
studies. Lauterbach and coworkers have constructed an imaging FTIR capable of

collecting spatially resolved spectral data for 4096 samples in the 13602720 cm1
spectral range (8 cm1 resolution) in less than 20 s (Fig. 32.24) [213215]. De-
pending on the optics used, the eld of view can be varied from an area of a few
hundred square microns to several square centimeters. The system, shown sche-
matically in Fig. 32.24, consists of an FTIR spectrometer, infrared optics, and a
64 64 element HgCdTe (MCT) infrared camera. A detailed description of the
instrument can be found in elsewhere [215].
Imaging FTIR spectroscopy was utilized by Lauterbach and coworkers to inves-
tigate the eects of adsorbed CO on both Cu-ZSM5 zeolite and silica-supported Pt/
SiO2 catalysts as a function of dierent process conditions [213a, 214]. CO was
preadsorbed onto the catalysts and the temperature increased at a rate of 8 K min1
in owing oxygen. Spectral images collected during the heating ramp identied
distinct spectral bands assigned to CO adsorbed on the Cu oxidation state (2157
cm1 ) and to CO adsorbed on the Cu oxidation state with a water molecule in the
coordination sphere of the Cu ion (2139 cm1 ). As the temperature increased and
the water desorbed, a decrease in the band at 2139 cm1 was observed. The entire
heating process took 11 min and 13 spectral images (4096 spectra per image) were
acquired at a spectral resolution of 4 cm1 . Following a chemical process in a high-
throughput manner demonstrates the ability of imaging techniques to monitor
chemical reactions in situ. Imaging allows kinetic information and spectral data on
reaction components to be gained from a combinatorial high-throughput screen.
The same group also applied the parallel FTIR analysis to determine conversion
during temperature-programmed complete oxidation of propene in the presence of
platinum group metals, a reaction that is important for the automotive three-way
catalyst [213b].
32.10.2
Optical High-throughput Screening Techniques
The eort to create parallel assays for solution-phase catalysis has led to the devel-
opment of a number of optical techniques. Many techniques include probe mole-
cules that change color or uoresce with catalytic behavior. Additional techniques
incorporate ultraviolet or infrared lasers to ionize or heat catalytic products, fol-
lowed by detection with electrodes or probe lasers. Finally, circular dichroism has
been developed to study the eects of chirality on catalysis.
32.10.2.1 Colorimetric Assays

Visual detection remains one of the simplest and most practical methods for mea-
suring catalyst activity. While direct assays such as thermal imaging are fast and
generic to most chemical processes, they lack chemical selectivity and are unable
to identify reaction products. One approach, used extensively in enzymatic assays,
is to use indirect detection of a molecular probe that uoresces upon detection of a
desired reaction product.
Crabtree and coworkers have developed reactive dyes that photobleach as a chem-
ical reaction occurs [216, 217]. Designed for hydrosilation reactions, the probe must
not have any interfering reactive groups, a criteria met by using a ferrocenyl group
as an electron donor and a pyridinium group as an acceptor (Scheme 32.36); a
benzylic tail was added to make the dye more soluble. When the reactive func-
tionality (CbC or CbN bond) is saturated upon reaction with a catalytic species, the
electronic overlap between the donor and acceptor groups is diminished, giving rise
to a loss of the parent dye color. The dye color as a function of time was recorded,
with a hit being indicated by the dye bleaching in a reaction well.
Scheme 32.36. Reactive dyes as a method for rapid screening of homogeneous catalysts.
Crabtree and coworkers assayed a 60-well discovery library of hydrosilation cata-

lysts in parallel using a digital camera. Of the 12 catalysts examined by the authors,
Wilkinsons catalyst, which is a known hydrosilation catalyst, was among the most
active of the catalysts screened. However, a palladacyclic Heck reaction catalyst was
also quite active, a compound not previously reported as a hydrosilation catalyst.
A limitation of the screen is that the dye substrate is a nonstandard alkene with a
higher reactivity than conventional substrates and has a strong tendency to give
competitive hydrogenation instead of hydrosilation. Despite this, relative trends in
activity seem to be well represented.
Hartwig and coworkers utilized resin beads tagged with uorophors in the in-
vestigation of coupling reactions [218]. Their method allows for visual screening of
a large set of parallel chemical reactions in which two molecules are bound by co-
valent interactions. In their study, one substrate (A) is attached to a dye molecule
and the other (B) to a solid support. After a successful coupling reaction, the solid
supports and the dye molecule would be bound together by a covalent interaction
between the two substrates (Scheme 32.37). Analysis under UV illumination fol-
lowing ltering of the reagents allowed the substrate combinations that are capable
of covalent coupling to be identied. In their investigation, an acrylate containing a
tethered coumarin was reacted with an aryl halide supported on a crosslinked poly-
styrene bead. Comparison of the results from the uorescence assay with results
from a standard GC analysis showed that the uorescence assay accurately repre-
sented the trends for the Heck coupling of aryl bromides and chlorides. Two ligands
identied in the assay, tri-(tert-butyl)phosphine and di-(tert-butylphosphino)ferro-
cene, were shown to be the most active systems for the olenation of unactivated
aryl bromides, and di-(tert-butylphosphino)ferrocene the most ecient for olena-
tion of unactivated aryl chlorides.
Scheme 32.37. Visual assay for coupling reactions.
Hartwig and coworkers then focused on the development of solution-phase

assays for homogeneous catalysis that are based on uorescent resonance energy
transfer (FRET) between a substrate with a tethered uorophor and a second mol-
ecule that is attached to a solid support [219]. FRET occurs when two uorophors
within close proximity (2080 A) interact such that the emission band of one mol-
ecule overlaps the excitation band of a second molecule. Excitation of the higher
energy uorophor (donor), followed by resonant energy transfer to the lower en-
ergy uorophor (acceptor), leads to a quenching of the uorescent intensity. With a
constant total concentration of free and bound FRET pairs, the emission at the do-
nor molecule wavelength is inversely proportional to the mole fraction of paired
molecules. Standard plate readers can be used to track the covalent bond forma-
tion uorometrically. In the investigation of Heck reactions, Hartwig and co-
workers chose uorophores that contained functionalities that are compatible with
most cross-coupling chemistries. A dansyl uorophore was tethered to a styrenyl
group, and an azodye quencher tethered to an aryl bromide. Upon covalent link-
ing, the danzyl group was quenched by the diazo compound (Scheme 32.38). The
results of their investigation show that the FRET method is signicantly faster
than standard HPLC techniques, while only one in ten cases showed a yield by
HPLC that was more than 10% dierent from the FRET result. It was suggested
that the FRET pair developed for this study should have application to many dif-
ferent reactions, such as aryl halide amination, aryl halide etherication, carbonyl
a-arylation, Suzuki coupling, and Hiyama coupling with silanes.
Scheme 32.38. Assay for homogeneous catalysis based on

uorescent resonance energy transfer (FRET).
Copeland and Miller developed a similar method for the study of acetic acid
evolution that employs aminomethylanthracenes as pH-sensitive uorophors. Neu-
tral aminomethylanthracenes undergo photoinduced electron transfer (PET) and
uoresce when protonated (Fig. 32.25a) [220]. Attachment of the aminomethylan-
thracenes to partially derivatized resin beads, followed by attachment of peptide
catalysts, created a collection of resin beads related to the structure shown in Fig.
32.25b [221]. Beads functionalized with the most active catalysts appeared bright-
est as a given acylation reaction proceeded. Furthermore, the beads maintained
their relative intensities when examined in separate vessels or pooled together as
catalyst mixtures.
Copeland and Miller have applied the same aminomethylanthracenes as pH
sensors in solution-phase catalyst libraries as well [220]. In this investigation, seven
unique catalysts (Fig. 32.26) were deposited into a standard 96-well plate at three
Fig. 32.25. a) Acetic acid sensor in acyl transfer reactions.

b) Representative polystyrene bead simultaneously
functionalized with a sensor and a catalyst.
Fig. 32.26. Seven dierent acylation catalysts used for the

chemosensor-based approach to catalyst discovery.
Fig. 32.27. Fluorescent gel system for the detection of bead-supported catalysts.
dierent catalyst loadings. The reaction progress was monitored as a function of

time with a standard uorescence plate reader, allowing individual reaction rates to
be determined. The known superacylation catalysts 4-pyrollidimo-pyridine (PPY)
and DMAP were the most active catalysts, producing rapidly growing uorescent
signals. N-methyl-imidazole (NMI) and pyridine gave very low reaction rates. Most
signicantly, the uorescent intensities are consistent with the observation that the
catalytic activity of A is greater than B and NMI.
A sensor-functionalized polymeric gel for screening pooled catalyst libraries has
been developed by Miller and coworkers [222]. The method involves deposition of
resin-bound catalysts onto a polymeric matrix that is designed with sucient per-
meability such that reagents can diuse to the beads. The polymer also incorporates
(by covalent attachment) a uorescent probe that signals the presence of reaction
products. The method (Fig. 32.27) relies on slow diusion of reaction products out
of the bead into the matrix, which triggers the probe and creates a uorescent zone
around the active catalyst. Miller and coworkers used the same aminomethylanth-
racenes as in the previous experiments to investigate acylation reactions of alco-
hols with acetic anhydride; poly(ethylene glycol)dimethylacrylamide (PEGA) was
used for the polymer matrix.
Smotkin, Mallouk, and coworkers have developed an optical screen for electro-
oxidation that utilizes a uorescent pH indicator [157]. In their method, catalyst
compositions were applied to Teon-coated Toray carbon discs such that each 2-
mm-diameter catalyst spot contained the same molar concentration of metal at a
Fig. 32.28. Fluorescent pH indicators used in an optical screen for electro-oxidation.
loading of approximately 1 mg cm2 [179]. The catalyst array was analyzed using
a three-electrode gas diusion cell, with the Toray carbon substrate linking the
catalyst elements as a working electrode, Pt gauze as the counter electrode, and a
reversible hydrogen electrode as a reference. Electrochemical half-cell reactions
either generate or consume ions, creating a change in the pH in the location of
active catalysts. Utilizing an indicator that is uorescent in the presence of an acid
or conjugate base allows the determination of which elements within the library
were most active for a particular anode or cathode reaction. Mallouk and coworkers
have used quinine and Phloxine B as uorescent indicators for neutral pH, and
Ni 2 complexed with 3-pyridine-2-yl-(4,5,6)triazolo-(1,5-a)pyridine (Ni-PTP) (Fig.
32.28) for low pH [157]. Using the uorescence method, Mallouk and coworkers
screened ternary libraries of metal alloys and identied novel electrocatalysts for
methanol and bifunctional oxygen reduction/water oxidation regenerative fuel cells
[157, 179].
Additional optical screening techniques have been developed for a number of
dierent chemical processes. The methods include colorimetric assays where col-
orless 1-naphthol undergoes an electrophilic aromatic substitution with a diazo-
nium salt to give a bright orange azo product [223], indigo [61], and Prussian blue
staining of reaction products [224].
32.10.2.2 Resonance-enhanced Multiphoton Ionization (REMPI)

In a proof of concept experiment, Senkan has described high-throughput screen-
ing technology for combinatorial catalyst libraries that may supply data on both
activity and selectivity for a dehydrogenation reaction [187]. Senkans approach is
Fig. 32.29. Illustration of high-throughput screening of

combinatorial catalyst libraries by resonance-enhanced
multiphoton ionization (REMPI). See text for details.
based on in situ photoionization of the reaction products using tunable UV lasers,

followed by the detection of the photoions or electrons by spatially addressable
microelectrodes placed in the vicinity of the laser beam (Fig. 32.29). When the laser
frequency matches an intermediate electronic state of a molecule, the cross-section
for photoionization is enhanced, resulting in resonance-enhanced multiphotonion-
ization (REMPI).
Senkan and coworkers reported the application of the REMPI technology together
with novel array microreactors to the discovery of an optimal composition in the
ternary Pt/Pd/In metal catalyst system [161]. Preformed cylindrical g-Al2 O3 sup-
ports were treated with aqueous metal precursor stock solutions of H2 PtCl6 , PdCl2 ,
and InCl2 , dried, and calcined. The catalyst library consisted of 66 ternary combi-
nations of Pt, Pd, and In in 0.1% weight increments of each, with 1% total metal
loading on the alumina support. Catalyst screening was performed after condition-
ing the reactor unit and reduction of the metal precursors to metallic form with
hydrogen. Contrary to a previous report [161], the researchers conrmed that
no species other than benzene contributed to the signals measured by the micro-
electrodes. Indium proved to be catalytically inactive in the dehydrogenation and
Pt and Pd individually exhibited catalytic activities, with Pt being more active than
Pd. Most importantly, a ternary mixture (0.8% Pt, 0.1% Pd, 0.1% In) exhibited the
best benzene productivity of all the 66 ternary metal combinations tested. The
screen for the entire catalyst library (66 catalysts) required ve cycles in a time
window of approximately 23 h and the total time for discovery (library preparation
Fig. 32.30. Schematic of a photothermal deection cell for the detection of ethylene.
and screening) took 2.5 days, including additional checks for reproducibility of the
results.
A similar method utilizing laser-induced uorescence has been developed by Su
and Yueng [177]; however, the technique is only applicable to uorescent species,
which limits its use.
32.10.2.3 Photothermal Deection

A photothermal deection method has been developed by Cong and coworkers at
Symyx Technologies for the purpose of screening potential catalysts for the oxida-
tive dehydrogenation of ethane to ethylene [172]. The experimental set-up (Fig.
32.30) utilizes a CO2 laser operating at a single line (10P14) as a pump in resonance
with an ethylene mode at 949.48 cm1 . Absorption by the ethylene creates a local
hot spot in the gas, which causes a change in the index of refraction (a mirage). A
10-mW HeNe laser is used to detect changes in the index of refraction through a
slight deection in the probe beam, which can be detected using a position-sensitive
photodiode. In their studies, Cong and coworkers used a scanning probe (described
with the scanning mass spectrometer later in this chapter) that sampled gaseous
products into a small measurement chamber. The instruments sensitivity for eth-
ylene is better than 0.1 ppm and has a very high discrimination factor (@ 10 6 )
against ethane and other species present in the reaction.
32.10.2.4 Enantiomeric Excess by Circular Dichroism

A number of reports have appeared utilizing combinatorial strategies to facilitate
the discovery and optimization of chiral catalysts. These reports have successfully
addressed the synthetic combinatorial aspects of chiral catalyst discovery. How-
ever, they still rely solely on conventional means determining the enantioselectivity
using HPLC or GC with chiral columns, a time-consuming process that creates a
potential bottleneck in any combinatorial discovery eort. Mikami and coworkers
have developed a new screening strategy employing circular dichroism (CD) detec-
tion added to HPLC on nonchiral stationary phases for the rapid determination
of enantiomeric excesses (ee values) of a reaction product without separation of
the chiral products [225, 226]. Circular dichroism is observed when optically active
matter absorbs left- and right-hand circular polarized light dierently. The dier-
ence in left- and right-hand absorbance is very small, resulting in a small CD sig-
nal De. The absorption e provides a dissymmetry factor g De=e, which is inde-
pendent of product concentration and is linearly related to the ee.
In order to validate the approach, diethyl zinc was added to prochiral aldehydes
in the presence of chiral diol ligands (L1*, L2*, . . .) and chiral nitrogen-based acti-
vators (A1*, A2*, . . .). Reactions were screened in 1-mL polypropylene microtubes
and the crude reaction products were then autosampled with a HPLC instrument
equipped with CD detection. Combining diethyl zinc with an assortment of chiral
ligands and activators led the researchers to identify an extremely eective ligand/
activator combination that gave excellent ee values in high overall yield with a vari-
ety of aldehydes. Although the authors dubbed the above technique as super high-
throughput screening, the technique may still be somewhat limiting in terms of
its overall throughput (@ 3 min per sample) and it is probably best described as a
rapid serial technique.
32.10.3
High-throughput Screening Using Mass Spectrometry
Mass spectrometry is an established technique used to analyze complex gaseous

mixtures. The technique allows for the direct determination of many reaction prod-
ucts; however, it has been limited in application because of its serial nature and be-
cause it requires sample withdrawal. Several groups have created scanning probes
to extract product gases from combinatorial experiments, and new techniques have
been developed to extend the throughput of mass spectrometry.
32.10.3.1 Scanning Mass Spectrometry

Cong, Guan, and coworkers have developed an instrument for the rapid screening
of heterogeneous catalysts using a scanning mass spectrometer (Fig. 32.31) [168,
227]. The instrument is divided into two parts: a reaction chamber where each
library element is examined for catalytic activity, and an analysis chamber where
Fig. 32.31. Schematic of the scanning mass spectrometer for

screening catalyst libraries for catalytic activity. See text for
details.
the products from the catalytic process are snied from the reaction chamber
and analyzed by a mass spectrometer. In addition to the two chambers, ancillary
equipment is used to control the positioning of the library and to maintain vari-
ables such as the ow rate of reactant gases, temperature, and reaction pressures.
In a typical experiment, a catalyst library is placed onto a platform capable of
translation in three orthogonal directions. Gas ows to and from the library through
a cylindrical delivery tube containing a second concentric internal tube. A reactant
gas ows down the annular region of the tube onto the quartz substrate. Product
gas ows from an element in the library to the analysis chamber through the inner
tube via a capillary connection between the two chambers. Product gas exits the
capillary in the ionization zone of the quadruple mass spectrometer. The tempera-
ture of the individual library elements is controlled using a CO2 laser, an infrared
sensor, and a feedback control loop.
Analysis of the data collected from the entire library (approximately one library
element per minute) allows the relevant parameters associated with the reaction,
such as catalyst activity and selectivity, to be determined for each element in the
library.
Cong and coworkers reported a systematic and integrated approach for the syn-
thesis and screening of libraries of mixed metal alloys containing rhodium, palla-
dium, platinum, and copper [168]. Fully automated gas-phase thin-lm deposition
techniques (RF sputtering) were used to synthesize three unique 120-member li-
braries of Rh/Pt/Cu, Rh/Pd/Cu, and Rh/Pt/Pd alloys. The metal alloy combinato-
rial libraries were screened in the scanning mass spectrometer as described pre-
viously for the gas-phase oxidation of carbon monoxide and the reduction of nitric
oxide. In accordance with the literature and despite some discontinuities, rhodium-
rich regions in the Rh/Pt/Pd ternary generally showed enhanced activity for car-
bon monoxide oxidation with oxygen and, interestingly, Rh/Cu binaries such as
Rh/Cu (50:50 atom%) showed promising oxidation activity.
A similar scanning mass spectrometer has been constructed by Maier and co-
workers [169]. This spectrometer incorporated a similar concentric capillary gas
feed and sensing design, but utilized simpler scanning robotics and an open-air
environment.
32.10.3.2 Mass Tags as Chirality Probes

High-throughput screening of enantioselective catalysts using electrospray mass
spectrometry has recently been addressed by Siuzdak, Finn, and coworkers and
by Reetz and coworkers [228, 229]. Two dierent stereochemical processes were
addressed including the kinetic resolution of racemates and asymmetric transfor-
mation of prochiral substrates due to the presence of enantiotropic groups. Both
groups utilized a similar method based on the use of an equimolar mixture of
pseudoenantiomeric mass-tagged compounds (Scheme 32.39), such that the
mass of the molecule is correlated to its absolute conguration. The relative
amounts of the products and/or reactants are detected by electrospray mass spec-
trometry.
Scheme 32.39. a) Asymmetric transformation pseudoenantiomers involving either cleavage

of a mixture of pseudoenantiomers involving or bond formation at the functional group FG;
cleavage of the functional group FG and isotopic labeling at R2 is indicated by the
labeled functional group FG*. b) Asymmetric asterisk.
transformation of a mixture of
Kinetic resolution of racemates was investigated by preparing enantiomerically

pure compounds A and B, which dier in absolute conguration and in labeling at
the functional group FG*, and then mixing them in a 1:1 manner to simulate a
racemate. True enantiomers C and D were formed following asymmetric functional
group transformation, as well as labeled and nonlabeled achiral products E and F.
The ratios of the total intensities of A/B and E/F in the mass spectra allow for the
determination of enantioselectivity. Kinetic resolution of pseudoenantiomers A and
G, in which mass labeling occurs at the residue R2, created a new pair of pseu-
doenantiomers C and H (Scheme 32.39b). The ratios of mass intensities A/G and
C/H allow the conversion, enantioselectivity, and the selectivity factor to be ob-
tained [229].
32.10.4
Electronic High-throughput Methods
A new group of electronic high-throughput assays has been developed to screen

for catalytic behavior that utilize multiplexed arrays of electrodes or solid-state elec-
tronic devices. A majority of the new screens are for electrochemical measurements,
although a novel thermal sensor for activity and solid-state gas sensors have also
been reported.
32.10.4.1 Electrochemical Analysis with Electrode Arrays

A number of high-throughput screens have been developed to screen for electro-
chemical activity of modied electrode surfaces. Smotkin, Mallouk, and coworkers,
for example, have developed an indirect uorescent screen for pH changes already
described in this article [157].
Ward and coworkers have constructed a computer-controlled electrode array ca-
pable of rapid serial measurements of electrode kinetics for 64-element libraries
[193]. Utilizing standard photolithographic techniques, the researchers created
an 8 8 patterned array of 1 mm 2 Au contact pads and connections on a 100-mm-
diameter thermally oxidized silicon wafer. The wafer was then coated with an in-
sulating silicon nitride layer using plasma-enhanced chemical vapor deposition,
followed by reactive ion etching to remove the silicon nitride from the contact pads.
A Delrin cylinder was then glued to the wafer to provide an electrolyte reservoir
with the electrode array in the center, and the electrode array was attached to a
standard potentiostat through a computer-controlled multiplexer. A schematic of
the electrode array and the set-up are shown in Fig. 32.32.
The time required to cycle through all 64 electrodes depends on the cyclic vol-
tammetry sweep rate (typically 100 mV s1 here), the voltage range of the sweep,
and the number of sweeps. A typical dataset takes 23 h to complete. Unlike uo-
rescent screens, direct electrochemical measurements are capable of detecting small
variations in current at dierently modied electrodes.
Matsumoto and coworkers have developed a high-throughput technique to screen
libraries of potential photocatalysts that involves a silicon nitride-covered silicon
sensor to image changes in pH [230]. The instrument, shown schematically in Fig.
32.33, sandwiches an electrolyte between the combinatorial library and the sensor
array. A scanning laser provides a light source for photocatalysis. As an example,
Matsumoto and coworkers investigated a library of doped TiO2 compounds as po-
tential water cleavage catalysts. Reaction between the water and Fe 3 ions on the
TiO2 surface produced Fe 2 ions, oxygen, and protons as the water decomposed.
The resulting pH change was detected by the FET array, allowing for the rapid
assay of large numbers of potential photocatalysts in library format.
Yudin and coworkers have reviewed a number of electrochemical devices with
Fig. 32.32. The computer-controlled 64-element electrode array

and control electronics used to record cyclic voltammograms.
application to combinatorial electrosynthesis and high-throughput screening. Of

particular interest is the review of electrochemical biosensors that may have poten-
tial application to combinatorial catalysis research [194ac].
32.10.4.2 Solid-state Temperature Sensors

Connolly and Sutherland reported the use of a multiplexed array of 96 thermis-
tors as temperature probes for catalytic reactions [231]. Thermistors, a term de-
rived from thermally sensitive resistor, are passive semiconductors that produce
resistance values dependent on temperature. The researchers immersed an 8 12
array of thermistors in solutions such that the temperature change associated with
catalytic activity could be detected as a change in the electrical resistance of the
multiplexed thermistors. The method has the disadvantage, relative to thermal
imaging, that the sensor must make contact with the catalytic reaction, oering
Fig. 32.33. Schematic of a library and electrochemical cell for

high-throughput investigation of photocatalysts.
the potential for chemical interference. Advantages of this method include the
elimination of expensive thermal imaging cameras and infrared optics, and a po-
tential increase in the temperature sensitivity.
32.10.4.3 Solid-state Gas Sensors

Yamada and coworkers have incorporated solid-state gas sensors into the eu-
ent stream of a parallel eight-channel microreactor to measure the total oxidation,
oxidative dehydrogenation, and selective oxidation of metal oxide catalysts [232].
Although gas sensors are not as selective as gas chromatographs or other research
tools, they respond quickly and allow continuous observation of reaction products.
In their investigation, Yamada and coworkers used several types of solid-state sen-
sors that incorporate hot-wire resistance, semiconductor, potentiometric, and non-
dispersive infrared (NDIR) detection mechanisms.
The rst type of sensor, used to detect CO, was constructed from an alumina
bead approximately 0.5 mm in diameter covered with platinum. A coiled wire of
a Pt/Rh alloy was placed inside of the alumina bead as a heater/thermometer to
maintain the element temperature at approximately 500 C. Catalytic combustion
of CO increased the temperature of the sensing element, which was measured as a
change in the resistance of the Pt/Rh wire. While there is no gas selectivity, i.e.
any combustible gas will increase the sensor temperature, the detectable gas con-
centration range is between 0.01% and 10% in air.
Semiconductor gas sensors were utilized to analyze catalytic euents for olens
or oxygenates. Flammable gases change the temperature, and therefore the free
carrier density, of an SnO2 semiconductor deposited on an alumina plate held at
600 C. To improve the selectivity, dierent semiconductor layers were deposited
on seven SnO2 sensors. They included 13 wt% SiO2/Al2 O3 , 28 wt% SiO2/Al2 O3 , 28
wt% SiO2/ZnO, 28 wt% SiO2/TiO2 , 28 wt% SiO2/ZrO2 , 3 wt% Mo/SiO2 , and 3 wt%
V/SiO2 . A preliminary investigation revealed that the SnO2 covered with 28 wt%
SiO2/Al2 O3 was most selective for olens, and SnO2 covered with 28 wt% SiO2/
TiO2 or 13 wt% SiO2/Al2 O3 the most selective for oxygenates. A NDIR sensor,
which measures infrared absorption at specic wavelengths, and two SnO2 semi-
conductor sensors sensitized by TiO2 or by 13 wt% SiO2/Al2 O3 were used to eval-
uate catalysts for selective propane oxidation.
The sensors were in a multichannel parallel sensor array for the CO oxidation
and oxidative dehydrogenation studies, and in a serial conguration for the selec-
tive oxidation of propane (Fig. 32.34). Although the accuracy of the gas analysis by
the sensor system was lower than a conventional gas chromatograph, the gas sen-
sors have the advantage of rapid response, continuous measurements, small size,
and lower cost. Furthermore, Yamada and coworkers are investigating new two-
dimensional miniaturized reactors where the solid-state sensor is integrated into
the library.
Fig. 32.34. Schematic showing the gas sensor system for the
evaluation of selective propane oxidation.
32.10.5
Array Reactors
The activity and selectivity of catalysts can change signicantly during extended
exposure to product feedstock, creating the need for a system of high-throughput
secondary screens capable of addressing reaction kinetics. Kinetic studies are indis-
pensable to the catalytic rate as a function of the process variables, such as tem-
perature, pressure, spacetime, and composition of the reaction mixture. Stability
studies that test the catalyst over an extended time period need to be conducted
before a scale-up is initiated. Typically, these extended kinetic studies are performed
in pilot plants with real feed and recycle streams and with the catalyst in its prac-
tical shape. The increased number of potential catalysts generated in a combinato-
rial program has led to the development of a new generation of array reactors that
are capable of testing a larger number of catalysts in parallel for extended periods
of time. Array reactors share common design features, diering primarily in their
construction materials, and in their ow geometries.
32.10.5.1 Array Microreactors

Measuring the intrinsic properties of a group of catalysts requires a microreactor
that maintains sucient contact between the reactants and the catalyst, while
avoiding limitations to the mass and heat transport around the catalyst. In general,
these requirements are met in xed bed reactors operating in a plugow format.
In addition, the design is ideal for high-throughput screening because of the small
sample requirements and because it supports both gas- and liquid-phase systems.
The drawbacks are that a plugow reactor yields conversions rather than rates,
low ow rates can lead to temperature and concentration gradients around the
catalyst, and care must be taken to maintain the plugow behavior [233].
A reactor can be divided into three dierent sections: the gas or liquid mixing
section, reactor section, and analysis section. Computer-controlled mass ow con-
trollers for both liquid and gas streams provide stable molar ow rates necessary
for kinetic studies. Products are typically mixed in a manifold and then introduced
to a reaction block containing the reaction wells and cartridge heaters designed
to keep the entire block at a constant temperature. Analysis typically involves
multiplexing the product gases into a standard gas chromatograph, or mass spec-
trometer.
Schuth and coworkers used a custom array microreactor to identify and optimize
gold-based catalysts for the room temperature oxidation of CO [162]. Automated
solution-phase synthesis, followed by calcination, was used to prepare 16 Au/Co3 O4
and Au/TiO2 catalyst compositions. The array reactor, shown schematically in
Fig. 32.35, consisted of a brass block with 16 1-cm-diameter holes. The block was
equipped with nine heating cartridges to ensure that the temperature would be
uniform within 1 K across the block. The catalysts were placed on a plate with 16
small wells, which was then sealed against the brass body. The plate divided the
gas introduction manifold from a series of capillaries that were equipped with
three-way valves to switch an individual euent stream to the analytical equip-
Fig. 32.35. Cross-sectional drawing of a reactor for the parallel

testing of 16 catalysts under nearly conventional conditions.
ment. Capillaries placed in the euent stream present the major ow resistance in
the system, which means that the largest pressure drop is not over the catalyst bed
but through the capillaries, meaning that dierences in the catalyst packing do
not signicantly inuence the ow through the individual wells. A nondispersive
infrared sensor was used to determine CO and CO2 concentrations, and the au-
thors report a factor of 15 increase in throughput relative to traditional methods.
Senkan and coworkers have applied an array microreactor to a number of cata-
lytic systems including a 66-element Pd/Pt/In library for the catalytic dehydroge-
nation of cyclohexane to benzene. The library consisted of 66 ternary combinations
of Pt, Pd, and In prepared in 0.1 wt% increments, for a total metal loading of
1 wt% that was impregnated on 4-mm-diameter by 1-mm-long alumina supports
[161, 176]. The catalyst library was prepared from solution-phase metal salt pre-
cursors using an automated liquid-handling robot. The compositions were slowly
evaporated, dried, and nally calcined at 500 C for 2 h. The catalyst pellets were
placed in a reactor array consisting of 20 rectangular channels that were micro-
machined on a at nonporous silica slab. The 1-mm-wide, 1-mm-deep, and 20-mm-
long channels had a 4 2 mm cylindrical well to hold the catalyst pellets. A simi-
lar silica slab was micromachined to t onto the top, forming a silica block with
cylindrical channels leading to and from the catalyst sample. Four microarray re-
actor blocks, each containing 20 samples, were stacked and placed into an alumi-
num heating block, making it possible to test up to 80 samples in parallel.
The entire reactor system was mounted on a stand that could be moved in three
dimensions by a computer. The test samples were heated in Ar gas up to 350 C,
then reduced under hydrogen gas, cooled to the desired reaction temperature, and
nally exposed to a feed stream of 10% cyclohexane in Ar. The contact time be-
tween the sample and the feed gas was approximately 4 ms. The level of reactants,
products, and inert carrier gas were determined by withdrawing a small sample
from each microreactor channel using a capillary sampling probe (50 mm diam-
eter) inserted 2 mm into the channels. The gas was analyzed by a quadruple mass
spectrometer. The capillary was inserted into each channel for approximately 5 s via
a computer-controlled positioning system. In this manner, the entire 80-element
array could be screened in approximately 10 min.
Building on an earlier microreactor design that used 15 quartz reactors [234],
Claus and coworkers designed a ceramic monolith reactor with 2.2-mm-square
channels, 150-mm long, that were arranged in a 16 16 array [178]. Each channel
in the monolith represents a single xed bed reactor, which allowed up to 256 cata-
lysts to be tested in parallel up to 600 C. Product gases were analyzed using a cap-
illary mounted on an x/ y/z scanning stage, and attached to a quadruple mass spec-
trometer (Fig. 32.36). A series of control experiments demonstrated that the axial
and radial temperature proles between channels (as measured without catalysts)
was not in excess of 5 K, and the ow rates did not dier more than 10%. The
performance of the monolithic reactor was evaluated using a 36-element library of
Pt/Zr/V/Al2 O3 catalysts for methanol oxidation. The results showed that the reactor
was valuable as a primary screen, distinguishing between poor and good catalysts
at a rate of about 1 min per sample. The accuracy was lowered owing to diculties
in generating equal ows in all channels of the monolith, and, in certain cases,
owing to diusion of exhaust gases from adjacent catalysts into the end of a chan-
nel containing the catalyst currently under investigation.
Fig. 32.36. Monolithic reactor system for the parallel screening of heterogeneous catalysts.
32.10.5.2 Micromachined Array Reactors

Advancements in microfabrication have led to a new generation of microchannel
reactors, allowing very large heat and mass transfer rates, and enabling safe inves-
tigations into explosive and dangerous reactions. Claus and coworkers describe a
microchannel reactor that consists of a very large number of parallel microchannels
having a square cross-section of approximately 500 mm on a side [178]. The reactor
module consists of a stack of metallic frames with micromachined inlays. Each
microstructured inlay contains a catalyst as an active coating on top of its micro-
channels; stacking the frames creates a system of catalyst-coated microchannels
(Fig. 32.37). The reactants ow through a diuser, through the microchannels and
over the catalysts, and nally to a product outlet where products are detected by a
scanning mass spectrometer. The reactor module design allows for interchangeable
catalyst inlays made of dierent materials such as metals, silicon, ceramics, and
glass, allowing many dierent catalysts and channel geometries to be investigated
rapidly. Channel-to-channel cross-talk was tested by placing an active catalyst next
to an inactive one and then measuring both product streams with a mass spec-
Fig. 32.37. Reactor module consisting of stacked metallic

frames. The catalyst inlays are mounted and removed in the
directions indicated by the arrow.
Fig. 32.38. Chip module for the catalysis-on-a-chip approach.
trometer. The detected amount of catalytic product in the noncatalytic zone was
less than 2% of that found in the active position. A 52-catalyst methanol oxidation
library used for further verication of the microreactor demonstrated excellent
sensitivity and reproducibility.
32.10.5.3 Catalysis on a Chip

Claus and coworkers have created a set of microreactors for enabling catalysis on
a chip [178]. The chip-based system allows for ecient thermal control and short
response time (Fig. 32.38). Preliminary investigations of this new technology uti-
lized parallel microchannels etched into silicon and glass with cross-sectional di-
mensions of 500 200 m. Similar to the micromachined metal reactors, each
microchannel contains a dierent catalyst, which is micropipetted into the chips.
Reactants are introduced through a single inlet in the chip, owing through a pre-
fabricated manifold to each of the catalyst-lled microchannels. The products are
analyzed as they leave the chip at a series of outlets. The prototype chip modules
contain eight or 16 parallel channels having dierent cross-sections and channel
lengths.
32.10.6
Capillary Array Electrophoresis
Recently, capillary electrophoresis (CE) has taken a key role in the parallel screen-
ing of homogeneous catalysts, in addition to the classical methods such as GC
or HPLC. Yeung and coworkers have used multiplexed capillary electrophoresis for
the combinatorial screening of enzyme activity [197a] and homogeneous catalysis
[197b]. In the latter case, this methodology was successfully implemented to opti-
mize, in a multidimensional screening approach, the regiochemistry of a Pd-cata-

lyzed annulation reaction.
Reetz and coworkers have adapted a commercial 96-well capillary electrophoresis
system for the determination of enantiomeric excess [198]. In their initial study,
chiral amines, which are potentially accessible by catalytic reductive ammonation
of ketones, Markovnikov addition of ammonia to olens, or enzymatic hydrolysis
of acetamides, were used as model substrates (Scheme 32.40). Various a- and b-
cyclodextrin derivatives were used as chiral selectors, which were then modied
with uorescent compounds to enable laser-induced uorescence (LIF) to be em-
ployed as a detection mechanism. Known enantiomeric mixtures of the amines
(with the uorescent tag added) were then analyzed by a commercial instrument
and by a capillary array electrophoresis (CAE) system. Results from the CAE sys-
tem initially suered from unstable runs, but results improved with the addi-
tion of a higher viscosity electrolyte composed of 40 mM 2-(N-cyclohexylamino)-
ethanesulfonic acid and 6.25 mM g-cyclodextrin diluted with a buer containing
polyacrylamide. The agreement between the ee values of the mixtures of the (R)-
and (S)-amines measured with the conventional capillary electrophoresis system,
the CAE system, and a conventional GC was excellent. Enantiomeric separation
with these systems requires approximately 19 min.
Scheme 32.40. Test system for the high-throughput screening

of enantioselective catalysts using capillary array
electrophoresis (CAE).
32.11
Summary and Outlook
It is virtually certain that we nd ourselves at the dawn of a new age of applying

combinatorial methodologies to catalysts discovery and optimization. As this chap-
ter demonstrates, signicant rst steps in that direction have been taken in the
area of catalyst research, and a multitude of tools are now available using combi-
natorial technologies to appropriately accommodate the new tasks and require-
ments for combinatorially accelerated materials and catalyst research. A common
underlying theme associated with these technologies is miniaturization, parallel-
References 979
ization, and automation so that large numbers of samples can be synthesized and
screened eciently. Rapid serial and parallelized adaptations of conventional ana-
lytical techniques will become increasingly important in the assay of materials
properties, as will the development and implementation of new and unconven-
tional high-throughput screening tools. Software development and engineering
support in the construction and design of synthesis and screening tools are as
crucial as further advances in chemistry, even when appropriate tools or robots for
synthesis and screening automation are commercially available. Finally, the com-
binatorial methodology generates data much faster than the conventional research
employing empirical and rational approaches to materials discovery, and, inevi-
tably, the proper data handling and storage should accompany the high-throughput
synthesis and screening to maintain the integrity of research and development ef-
forts. Full realization of the combinatorial methodology will require the integration
of chemistry, physics, engineering, and informatics to greatly enhance the proba-
bility of nding a global reaction optimum of a catalyst for a targeted reaction or
materials with desired properties. In the future, the scientists intuition may be
shifted, at least to some degree, toward optimally programming and setting up ap-
propriate experiments and screens, as well as for the analysis of the obtained data
and materials. All these eorts will require an enormous initial investment in all
of these areas [235].
Acknowledgements
The authors are deeply indebted to Ms Silvia Lee (Symyx Technologies) and Ms
Kathryn Boykin (XenoPort) for their invaluable support in reference and patent
searches. The authors thank Mr Ron Krasnow (Symyx Technologies) for checking
the manuscript.
References
1 a) G. Jung (ed.), Combinatorial 4 S. R. Wilson, A. W. Czarnik (eds),

Chemistry: Synthesis, Analysis, Combinatorial Chemistry. John Wiley &
Screening. Wiley-VCH, Weinheim Sons, New York 1997.
1999; b) G. Jung (ed.), Combinatorial 5 a) B. A. Bunin (ed.), The
Peptide and Nonpeptide Libraries. VCH, Combinatorial Index. Academic Press,
Weinheim 1996. San Diego 1998; b) A. W. Czarnik, S.
2 E. M. Gordon, J. F. Kerwin (eds), H. DeWitt (eds), A Practical Guide to
Combinatorial Chemistry and Molecular Combinatorial Chemistry. American
Diversity in Drug Discovery. John Wiley Chemical Society, Washington 1997.
& Sons, New York 1998. 6 I. M. Chaiken, K. D. Janda (eds),
3 a) N. K. Terret, Combinatorial Molecular Diversity and Combinatorial
Chemistry, Oxford University Press, Chemistry. American Chemical Society,
Oxford 1998; b) N. K. Terret, N. Washington 1996.
Terret, Combinatorial Chemistry. 7 a) R. Dagani, Chem. Eng. News 1999,
Oxford University Press, Oxford 1998. 77, 5160; b) S. Borman, Chem. Eng.
News 1998, 76, 4767; c) R. Baum, S. Rees, Tetrahedron 1997, 53, 5643
Borman, A. M. Thayer, J. H. 5678; c) P. H. H. Hermkens, H. C. J.
Krieger, Chem. Eng. News 1996, 74, Ottenheijm, D. Rees, Tetrahedron
2973. 1996, 52, 45274554; d) N. K.
8 a) J. McNeal, Todays Chemist at Work Terrett, M. Gardner, D. W.
1998, 7, 3438; b) J. K. Borchardt, Gordon, R. J. Kobylecki, J. Steele,
Todays Chemist at Work 1998, 7, 35 Tetrahedron 1995, 51, 81358173.
41. 16 For classical reviews about solid-
9 I. Sucholeiki (ed.), High-throughput phase organic synthesis (SPOS), see
synthesis. Marcel Dekker, Inc., New for example: a) J. S. Fruchtel, G.
York, 2001. Jung, Angew. Chem. 1996, 108, 1946;
10 For landmark review articles about the Angew. Chem. Int. Ed. Engl. 1996, 35,
application of combinatorial technol- 1742; b) F. Balkenhohl, C. von
ogies to drug discovery, see: a) M. A. dem Busche-Hunnefeld, A. Lansky,
Gallop, R. W. Barrett, W. J. Dower, C. Zechel, Angew. Chem. 1996, 108,
S. P. A. Fodor, E. M. Gordon, J. Med. 24362488; Angew. Chem. Int. Ed.
Chem. 1994, 37, 12331251; b) E. M. Engl. 1996, 35, 22882337; c) L. A.
Gordon, R. W. Barrett, W. J. Dower, Thompson, J. A. Ellman, Chem. Rev.
S. P. A. Fodor, M. A. Gallop, J. Med. 1996, 96, 555600.
Chem. 1994, 37, 13851401. 17 For accounts and special techniques
11 For chemoinformatics, see: M. Hann, used in combinatorial chemistry, see
R. Green, Curr. Opin. Chem. Biol. for example: a) K. S. Lam, M. Lebl, V.
1999, 3, 379383, and references cited Krchzak, Chem. Rev. 1997, 97, 411
therein. 448; b) A. Nefzi, J. M. Ostreh, R. A.
12 X.-D. Xiang, X.-D. Sun, G. Briceno, Houghten, Chem. Rev. 1997, 97, 449
Y. Lou, K. A. Wang, H. Chang, W. 472; c) M. C. Pirrung, Chem. Rev.
G. Wallace-Freedman, S.-W. Chen, 1997, 97, 473488; d) D. J. Gravert,
P. G. Schultz, Science 1995, 268, K. D. Janda, Chem. Rev. 1997, 97,
17381740. 489509; e) A. W. Czarnik, J. A.
13 a) J. J. Hanak, J. Mater. Sci. 1970, 5, Ellman, Acc. Chem. Res. 1996, 29,
964971; b) J. J. Hanak, Proc. 1er 111170.
Colloq. Int. Pulverisation Cathodiques 18 For a review on recent developments
Ses Appl. 1973, 165, 177197; c) J. J. and applications of polymer-supported
Hanak, J. Vac. Sci. Technol. 1971, 8, reagents and scavangers in synthetic
172175. organic chemistry, see: a) O.
14 F. Zaragoza Dorwald (ed.), Organic Brummer, B. Clapham, K. D. Janda,
Synthesis on Solid Phase, Wiley-VCH, Curr. Opin. Drug Discovery Dev. 2000,
Weinheim 2000. For periodical 3, 462473; b) S. V. Ley, I. R.
selection of signicant papers Baxendale, R. N. Bream, P. S.
published in the recent literature Jackson, A. G. Leach, D. A.
covering the broad area of solid-phase Longbottom, M. Nesi, J. S. Scott,
organic synthesis (SPOS) and R. I. Storer, S. J. Taylor, J. Chem.
advances in linker chemistry, see for Soc., Perkin Trans. 1 2000, 23, 3815
example: C. McCusker, T. Wildman, 4195. For further information about
F. McKerlie, A. Gunn, H. Mandani, polymer-supported reagents, see: c) S.
J. Dalaney, S. Anizon, J. Chem. Soc., W. Kaldor, M. G. Siegel, Curr. Opin.
Perkin Trans. 1 2001, 3, ixxii. Chem. Biol. 1997, 1, 101106; d) S. J.
15 For periodical reviews of recent Shuttleworth, S. M. Allin, P. K.
literature about solid-phase organic Sharma, Synthesis 1997, 12171239;
reactions, see for example: a) S. e) P. Hodge, Chem. Soc. Rev. 1997, 26,
Booth, P. H. H. Hermkens, H. C. J. 417424; f ) D. H. Drewry, D. M.
Ottenheijm, D. Rees, Tetrahedron Coe, S. Poon, Med. Res. Rev. 1999, 19,
1998, 54, 1538515443; b) P. H. H. 97157. For delivery and scavenging
Hermkens, H. C. J. Ottenheijm, D. agents for the synthesis of compounds
References 981
and catalysts, see: T. R. Boussie, K. 425432; b) E. Kimura in: Crown

Hall, A. M. LaPointe, V. Murphy, T. Ethers and Analoguous Compounds,
S. Powers, J. A. M. van Beek (Symyx Studies in Organic Chemistry. Elsevier
Technologies), PCT Int. Appl. WO 98/ Science Publishers B.V., New York
56796. 1992, vol. 45, pp 381478; c) R. M.
19 M. J. Cannarsa, T. Uno, C. Larsen, Izatt, K. Pawlak, J. S. Bradshaw,
Curr. Opin. Drug Discov. Dev. 2000, 3, Chem. Rev. 1991, 91, 17212085.
743749. 23 A. W. Czarnik (ed.), Fluorescent
20 For reviews on combinatorial methods Chemosensors for Ion and Molecule
of combinatorial catalyst development Recognition. ACS Symposium Series
and high-throughput screening in 538, ACS, Washington, DC 1992.
catalysis, see: a) S. Dahmen, S. Brase, 24 M. T. Burger, W. C. Still, J. Org.
Synthesis 2001, 14311449; b) R. C. Chem. 1995, 60, 73827383.
Willson, D. R. Hill, P. R. Gibbs in: 25 a) C. Barnes, S. Balasubramanian,
High-Throughput Synthesis. Curr. Opin. Chem. Biol. 2000, 4, 346
Sucholeiki, I. (ed.), Marcel Dekker, 350; b) A. Czarnik, Curr. Opin. Chem.
New York 2001, pp. 271281; c) S. Biol. 1997, 1, 6066; c) M. H. J.
Senkan, Angew. Chem. 2001, 113, Ohlmeyer, R. N. Swanson, L. W.
322341; Angew. Chem. Int. Ed. 2001, Dillard, J. C. Reader, G. Asouline,
40, 312329, and references cited R. Kobayashi, M. Wigler, W. C.
therein; d) M. T. Reetz, Angew. Chem. Still, Proc. Natl. Acad. Sci. USA 1993,
2001, 113, 292320; Angew. Chem. Int. 90, 1092210926.
Ed. 2001, 40, 285310, and references 26 A. Singh, Q. Yao, L. Tong, W. C.
cited therein; e) F. Gennari, P. Still, D. Sames, Tetrahedron Lett.
Seneci, S. Miertus, Catal. Rev. Sci. 2000, 41, 96019605.
2000, 42, 385402, and references 27 a) K. J. Albert, N. S. Lewis, C. L.
cited therein; f ) M. L. Snapper, A. H. Schauer, G. A. Sontzig, S. E.
Hoveyda in: Combinatorial Stitzel, T. P. Vaid, D. R. Walt,
Chemistry. Fenneri, H. (ed.), Oxford Chem. Rev. 2000, 100, 15951616;
University Press, Oxford 2000, p. 433; b) D. R. Walt, Acc. Chem. Res. 1998,
g) B. Jandeleit, D. J. Schaefer, T. S. 31, 267278.
Powers, H. W. Turner, W. H. 28 P. L. Roach, I. J. Clifton, V. Fulop,
Weinberg, Angew. Chem. 1999, 111, K. Harlos, G. J. Barton, J. Hadju, I.
26482689; Angew. Chem. Int. Ed. Andersson, C. J. Schoeld, J. E.
1999, 38, 24952532, and references Baldwin, Nature 1995, 375, 700704.
cited therein; h) D. R. Liu, P. G. 29 N. Shibita, J. E. Baldwin, M. E.
Schultz, Angew. Chem. 1999, 111, 36 Wood, Bioorg. Med. Chem. Lett. 1997,
56; Angew. Chem. Int. Ed. Engl. 1999, 7, 413416.
38, 3654, and references cited 30 For a review about the ATCUN motif,
therein. see: C. Harford, B. Sarkar, Acc.
21 For a comprehensive overview, see: Chem. Res. 1997, 30, 123130, and
a) B. Cornils, W. A. Herrmann, references cited therein.
Applied Homogeneous Catalysis with 31 X. Huang, M. E. Pieczko, E. C.
Organometallic Compounds. Wiley- Long, Biochemistry 1999, 38, 2160
VCH, Weinheim 2000; b) B. Cornils, 2166.
W. A. Herrmann (eds), Applied 32 C. Gao, O. Brummer, S. Mao, K. D.
Homogeneous Catalysis with Janda, J. Am. Chem. Soc. 1999, 121,
Organometallic Compounds. VCH, 65176518.
Weinheim 1996; c) G. W. Parshall, 33 M. B. Francis, N. S. Finney, E. N.
S. D. Ittel, Homogeneous Catalysis. Jacobsen, J. Am. Chem. Soc. 1996,
Wiley, New York 1992. 118, 89838984.
22 For reviews on cyclens and related 34 R. Malin, R. Steinbrecher, J.
ionophores, see: a) G. W. Gokel, O. Jannsen, W. Semmler, B. Noll, B.
Murillo, Acc. Chem. Res. 1996, 29, Johannsen, C. Frommel, W. Hohne,
J. Schneider-Mergener, J. Am. Kobayashi, Curr. Opin. Chem. Biol.

Chem. Soc. 1995, 117, 1182111822. 2000, 4, 338345; c) Y. R. de Miguel,
35 M. C. Pirrung, K. Park, Bioorg. Med. J. Chem. Soc. Perkin Trans. 1 2000,
Chem. Lett. 2000, 10, 21152118. 42134221.
36 C. P. Holmes, D. G. Jones, J. Org. 51 a) F. M. Menger, Angew. Chem. 1991,
Chem. 1995, 60, 23182319. 101, 11041117; Angew. Chem. Int Ed.
37 F. Szurdoki, D. Ren, D. R. Walt, Engl. 1991, 30, 10861099; b) F. M.
Anal. Chem. 2000, 72, 52505257. Menger, Z. X. Fei, Angew. Chem.
38 D. E. Bergbreiter, V. N. Zaitsev, 1994, 106, 329331; Angew. Chem. Int
E. Y. Gorlova, A. Khodakovsky, Ed. Engl. 1994, 33, 346348.
Spec. Publ. R. Soc. Chem. (Fundamental 52 F. M. Menger, A. V. Eliseev, V. A.
and Applied Aspects of Chemically Migulin, J. Org. Chem. 1995, 60,
Modied Surfaces) 1999, 235, 353360. 66666667.
39 For a review on the discovery of new 53 F. M. Menger, C. A. West, J. Ding,
multicomponent reactions with Chem. Commun. 1997, 633634.
combinatorial methods, see: L. Weber, 54 T. S. Scanlan, J. R. Prudent, P. G.
K. Illgen, M. Almstetter, Synlett Schultz, J. Am. Chem. Soc. 1991, 113,
1999, 366374, and references cited 93979398.
therein. 55 F. M. Menger, J. Ding, V. Barragan,
40 For a review on atom economic J. Org. Chem. 1998, 63, 75787579.
reactions, see: B. M. Trost, Angew. 56 T. Uno, P. G. Schultz, J. Am. Chem.
Chem. 1995, 107, 285317; Angew. Soc. 1992, 114, 65736574.
Chem. Int. Ed. Engl. 1995, 34, 259 57 J.-J. Lee, W. T. Ford, J. Am. Chem.
281, and references cited therein. Soc. 1994, 116, 37533759.
41 A. M. Lapointe, J. Comb. Chem. 1999, 58 P. D. Miller, W. T. Ford, Chem.
1, 101104. Commun. 1998, 11511152.
42 A. M. LaPointe, A. Guram, T. S. 59 T. Berg, A. M. Vandersteen, K. D.
Powers, B. Jandeleit, T. Boussie, Janda, Bioorg. Med. Chem. Lett. 1998,
C. Lund (Symyx Technologies), US 8, 12211224.
Patent no. 00/6043363A. 60 T. Berg, A. Simeonov, K. D. Janda, J.
43 G. Y. Li, P. J. Fagan, P. L. Watson, Comb. Chem. 1999, 1, 96100.
Angew. Chem. 2001, 113, 11401143; 61 A. Berkessel, D. A. Herault, Angew.
Angew. Chem. Int. Ed. Engl. 2001, 40, Chem. 1999, 111, 99102; Angew. Chem.
11061109. Int. Ed. Engl. 1999, 38, 102105.
44 S. Tadesse, A. Bhandari, M. A. Gallop, 62 M. Havranek, A. Singh, D. Sames,
J. Comb. Chem. 1999, 1, 184187. J. Am. Chem. Soc. 1999, 121, 8965
45 F. Wang, A. W. Schwabacher, 8966.
Tetrahedron Lett. 1999, 40, 47794782. 63 S. J. Taylor, J. P. Morken, Science
46 R. Kranich, K. Eis, O. Geis, S. 1998, 280, 267270.
Muhle, J. W. Bats, H.-G. Schmalz, 64 For some monographs, see: a) I.
Chem. Eur. J. 2000, 6, 28742894. Ojima (ed.), Catalytic Asymmetric
47 C. J. Suckling (ed.), Enzyme Synthesis. VCH, Weinheim 2000;
Chemistry: Impact and Applications. b) A. N. Collins, G. N. Sheldrake, J.
Chapman and Hall, New York 1990. Crosby (eds), Chirality in Industry I.
48 W. Gerhartz (ed.), Enzymes in John Wiley & Sons, Chicester 1992;
Industry. VCH, Weinheim 1990. c) A. N. Collins, G. N. Sheldrake, J.
49 For a review on enzyme mimics, see: Crosby (eds), Chirality in Industry II.
A. J. Kirby, Angew. Chem. 1996, 108, John Wiley & Sons, Chicester 1997;
770790; Angew. Chem. Int. Ed. Engl. d) R. A. Sheldon (ed.), Chirotechnology:
1996, 35, 705724. Industrial Synthesis of Optically Active
50 For reviews about immobilized Compounds. Marcel Dekker, New York
catalysts in combinatorial chemistry, 1993; e) R. Noyori, Asymmetric
see: a) L. A. Thompson, Curr. Opin. Catalysis in Organic Synthesis. John
Chem. Biol. 2000, 4, 324337; b) S. Wiley & Sons, New York 1994.
References 983
65 For a review see: K. Soai, S. Niwa, 37, 85898592; b) M. Gude, U.

Chem. Rev. 1992, 92, 833856. Piarulli, D. Potenza, C. Gennari,
66 J. Seyden-Penne, Chiral Auxiliaries Chem. Eur. J. 1998, 4, 24372449; c) A.
and Ligands in Asymmetric Synthesis. J. Brouwer, M. C. F. Monnee, R. M.
John Wiley & Sons, New York 1995. J. Liskamp, Synthesis 2000, 11, 1579
67 A. Vidal-Ferran, N. Bampos, A. 1584.
Moyano, M. A. Pericas, A. Riera, J. 73 For reviews on polymer-supported
K. M. Sanders, J. Org. Chem. 1998, reagents, see: a) S. W. Kaldor, M. G.
63, 63096318, and references cited Siegel, Curr. Opin. Chem. Biol. 1997,
therein. 1, 101106; b) G. Bhalay, A.
68 G. Liu, J. A. Ellman, J. Org. Chem. Dunstan, A. Glen, Synlett 2000,
1995, 60, 77127713. 18461859; for a review on polymer-
69 L. A. Thompson, J. A. Ellman, assisted purication techniques see:
Tetrahedron Lett. 1994, 35, 93339336. c) J. J. Parlow, R. V. Devraj, M. S.
70 C. Gennari, S. Ceccarelli, U. South, Curr. Opin. Chem. Biol. 1999,
Piarulli, C. A. G. N. Montalbetti, 3, 320336; for a review on polymeric
R. F. W. Jackson, J. Org. Chem. 1998, scavenger reagents, see: d) J. Eames,
63, 53125313. M. Watkinson, Eur. J. Org. Chem.
71 For applications of related disulfon- 2001, 12131224.
amides as metal chelating units in 74 I. Chataigner, C. Gennari, U.
Et2 Zn additions to aldehydes and Piarulli, S. Ceccarelli, Angew.
for cyclopronation reactions, see: Chem. 2000, 112, 953956; Angew.
a) H. Takahashi, T. Kawakita, M. Chem. Int. Ed. 2000, 39, 916918.
Yoshioka, S. Kobayashi, M. Ohno, 75 A. J. Brouwer, H. J. van der Linden,
Tetrahedron Lett. 1989, 30, 70957098; R. M. J. Liskamp, J. Org. Chem. 2000,
b) X. Zhang, C. Guo, Tetrahedron Lett. 65, 17501757.
1995, 36, 49474950; c) N. Imai, K. 76 For a review on hetero-DielsAlder
Sakamoto, M. Maeda, K. Kouge, K. methodology, see: a) K. A. Jorgensen,
Yoshizane, J. Nokami, Tetrahedron Angew. Chem. 2000, 112, 37023733;
Lett. 1997, 38, 14231426; d) H. Angew. Chem. Int. Ed. 2000, 39, 3558
Takahashi, T. Kawakita, M. Ohno, 3588; b) L. F. Tietze, G. Kettschau
M. Yoshioka, S. Kobayashi, in: Stereoselective Heterocyclic
Tetrahedron 1992, 48, 56915700; e) H. Synthesis I, vol. 189. Metz, P. (ed.),
Takahashi, M. Yoshioka, M. Springer, Berlin 1997, p. 1; c) S. M.
Shibasaki, M. Ohno, N. Imai, S. Weinreb in: Comprehensive Organic
Kobayashi, Tetrahedron 1995, 51, Synthesis, vol. 5. Trost, B. M.,
1201312026; f ) C. Lutz, P. Flemming, I., Semmelhack, M. F.
Knochel, J. Org. Chem. 1997, 62, (eds), Pergamon, Oxford 1991, p. 401;
78957898; g) S. E. Denmark, S. P. d) D. L. Boger, S. M. Weinreb,
OConnor, J. Org. Chem. 1997, 62, Hetero Diels-Alder Methodology in
584594; h) S. E. Denmark, S. P. Organic Synthesis. Academic Press,
OConnor, J. Org. Chem. 1997, 62, New York 1987, Chapters 2 and 9.
33903401; i) D. J. Ramon, M. Yus, 77 For a review on asymmetric synthesis
Tetrahedron: Asymmetry 1997, 8, 2479 with chiral Lewis acid catalysts and
2496; j) M. Cernerud, A. Skrinning, representative examples in hetero-
I. Bergere, C. Moberg, Tetrahedron: DielsAlder reactions, see: a) K.
Asymmetry 1997, 8, 34373441; k) C. Ishihara, H. Yamamoto, CatTech
Halm, M. J. Kurth, Angew. Chem. 1997, 1, 5161; b) K. Hattori, H.
1998, 110, 523525; Angew. Chem. Int. Yamamoto, Tetrahedron 1993, 49,
Ed. Engl. 1998, 37, 510512. 17491760; c) K. Hattori, H.
72 For the synthesis of N-protected b- Yamamoto, Synlett 1993, 129130.
amino sulfonyl chlorides: a) M. Gude, 78 For representative examples, see: a) H.
U. Piarulli, D. Potenza, B. Salom, Ishitani, S. Kobayashi, Tetrahedron
C. Gennari, Tetrahedron Lett. 1996, 1997, 53, 73577360; b) S. Kobayashi,
S. Komiyama, H. Ishitani, Angew. 93 B. M. Cole, K. D. Shimizu, C. A.

Chem. 1998, 110, 10261028; Angew. Krueger, J. P. A. Harrity, M. L.
Chem. Int. Ed. Engl. 1998, 37, 979 Snapper, A. H. Hoveyda, Angew.
981. Chem. 1996, 108, 17761779; Angew.
79 S. Yao, M. Johannsen, R. G. Hazell, Chem. Int. Ed. Engl. 1996, 35, 1668
K. A. Jrgensen, Angew. Chem. 1998, 1671.
110, 33183321; Angew. Chem. Int. Ed. 94 M. S. Sigman, E. N. Jacobsen, J. Am.
Engl. 1998, 37, 31213124. Chem. Soc. 1998, 110, 49014902.
80 E. Jnoff, L. Ghosez, J. Am. Chem. 95 a) M. Hayashi, M. Tamura, N.
Soc. 1999, 121, 26172618. Oguni, Synlett. 1992, 663664; for
81 S. Kobayashi, K. Kusakabe, H. asymmetric desymmetrizations see:
Ishitani, Org. Lett. 2000, 2, 1225 b) Katsuki, Chem. Coord. Rev. 1995,
1227. 140, 189214; c) D. M. Hodgson,
82 A. M. Porte, J. Reibenspiess, K. A. R. Gibbs, G. P. Lee, Tetrahedron
Burgess, J. Am. Chem. Soc. 1998, 120, 1996, 52, 1436114384; d) T. L. Ho,
98109187. Symmetry: A Basis for Synthesis Design.
83 K. Burgess, A. M. Porte, Tetrahedron: John Wiley & Sons, New York 1995.
Asymmetry 1998, 9, 24652469. 96 K. D. Shimizu, B. M. Cole, C. A.
84 For a review on transition metal- Krueger, K. W. Kuntz, M. L.
catalyzed asymmetric allylic alkylation, Snapper, A. H. Hoveyda, Angew.
see: B. M. Trost, D. L. V. Vranken, Chem. 1997, 109, 17821785; Angew.
Chem. Rev. 1996, 96, 395422. Chem. Int. Ed. Engl. 1997, 36, 1704
85 a) S. R. Gilbertson, C.-W. T. Chang, 1707.
J. Org. Chem. 1998, 63, 84248431; for 97 For a review on a-amino acid
additional ligand syntheses by synthesis, see: R. O. Duthaler,
divergent modular approaches and Tetrahedron 1994, 50, 15391650.
screening in asymmetric allylic 98 M. S. Sigman, E. N. Jacobsen, J. Am.
alkylation, see: b) S. R. Gilbertson, Chem. Soc. 1998, 110, 53155316.
C.-W. T. Chang, Chem. Commun. 99 a) C. A. Krueger, K. W. Kuntz, C. D.
1997, 975976; c) B. M. Trost, D. L. Dzierba, W. G. Wirschun, J. D.
Van Vranken, C. Bingel, J. Am. Gleason, M. L. Snapper, A. H.
Chem. Soc. 1992, 114, 92379343. Hoveyda, J. Am. Chem. Soc. 1999, 121,
86 S. R. Gilbertson, S. E. Collibee, A. 42844285; b) J. R. Porter, W. G.
Agarkov, J. Am. Chem. Soc. 2000, Wirschun, K. W. Kuntz, M. L.
122, 65226523. Snapper, A. H. Hoveyda, J. Am.
87 J. Matsuo, K. Odashima, S. Chem. Soc. 2000, 122, 26572658.
Kobayashi, Org. Lett. 1999, 1, 345 100 S. J. Degrado, H. Mizutani, A. H.
347. Hoveyda, J. Am. Chem. Soc. 2001, 123,
88 L. S. Hegedus, Transition Metals in the 755756.
Synthesis of Complex Organic Molecules. 101 J. R. Porter, J. F. Traverse, A. H.
University Science Books, Mill Valley Hoveyda, M. L. Snapper, J. Am.
1999. Chem. Soc. 2001, 123, 984985.
89 D. G. Blackmond, CatTech 1998, 2, 102 C. A. Luchaco-Cullis, H. Mizutani,
1731. K. E. Murphy, A. H. Hoveyda, Angew.
90 a) S. R. Gilbertson, G. Chen, M. Chem. 2001, 113, 15041508; Angew.
McLoughlin, J. Am. Chem. Soc. 1994, Chem. Int. Ed. 2001, 40, 14561460.
116, 44814482; b) S. R. Gilbertson, 103 M. B. Francis, E. N. Jacobsen, Angew.
X. Wang, J. Org. Chem. 1996, 61, 434 Chem. 1999, 111, 987991; Angew.
435. Chem. Int. Ed. 1999, 38, 937941.
91 S. R. Gilbertson, X. Wang, 104 Y. Hoshino, H. Yamamoto, J. Am.
Tetrahedron Lett. 1996, 37, 6475 Chem. Soc. 2000, 122, 1045210453.
6478. 105 For reviews on metallocarbene CH
92 S. R. Gilbertson, X. Wang, insertions, see: a) T. S. Ye, M. A.
Tetrahedron 1999, 55, 1160911618. McKervey, Chem. Rev. 1994, 94,
References 985
10911160; b) A. Padwa, K. E. Riermeier in: Transition Metals for

Krumpe, Tetrahedron 1992, 48, 5385 Organic Synthesis. Beller, M., Bolm,
5453; c) J. Adams, D. M. Spero, C. (eds), Wiley-VCH, Weinheim 1998,
Tetrahedron 1991, 47, 17651808; Chapter 2:11.
d) M. P. Doyle, Chem. Rev. 1986, 86, 121 R. T. Buck, D. M. Coe, M. J.
919939. Drysdale, C. J. Moody, N. D.
106 H.-J. Lim, G. A. Sulikowski, J. Org. Pearson, Tetrahedron Lett. 1998, 39,
Chem. 1995, 60, 23262327. 71817184.
107 K. Burgess, H.-J. Lim, A. M. Porte, 122 For other work on SiH insertion
G. A. Sulikowski, Angew. Chem. 1996, reactions, see: a) R. T. Buck, M. P.
108, 192194; Angew. Chem. Int. Ed. Doyle, M. J. Drysdale, L. Ferris,
Engl. 1996, 35, 220222. D. C. Forbes, D. Haigh, C. J. Moody,
108 M. T. Powell, A. M. Porte, K. N. D. Pearson, Q.-L. Zhou, Tetra-
Burgess, Chem. Commun. 1998, hedron Lett. 1996, 37, 76317634,
21612162. and references cited therein;
109 For a review on C3 -symmetry in b) P. Bulugahapitiya, Y. Landais,
asymmetric catalysis and chiral L. ParraRapado, D. Planchenault,
recognition, see: C. Moberg, Angew. V. Weber, J. Org. Chem. 1997, 62,
Chem. 1998, 110, 260281; Angew. 16301641; c) Y. Landais,
Chem. Int. Ed. Engl. 1998, 37, 248 L. ParraRapado, D. Planchenault,
268. V. Weber, Tetrahedron Lett. 1997, 38,
110 S. J. Taylor, J. P. Morken, J. Am. 229232; d) Y. Landais,
Chem. Soc. 1999, 121, 1220212203. D. Planchenault, Tetrahedron 1997,
111 M. Kawatsura, J. F. Hartwig, 53, 28552870.
Organometallics 2001, 20, 19601964. 123 a) M. P. Doyle, M. A. McKervey, T.
112 S. Bromidge, P. C. Wilson, A. Ye, Modern Catalytic Methods for
Whiting, Tetrahedron Lett. 1998, 39, Organic Synthesis with Diazo
89058908. Compounds. John-Wiley, New York
113 For a review on reactions of 1998; b) M. P. Doyle, D. C. Forbes,
Danishefskys diene, see: T. Kitahara Chem. Rev. 1998, 98, 911935.
in: Encyclopedia of Reagents for 124 Available Chemical Directory (ACD) is
Organic Synthesis. Paquette, L. A. a product of MDL, Information
(ed.), John Wiley & Sons, Chicester Systems, Inc., San Leandro, 14600
1995, vol. 5, 33953402. Catalina Street, CA 94577, USA,
114 G. Zhu, M. Terry, X. Zhang, J. www.mdli.com.
Organomet. Chem. 1997, 547, 97101. 125 A. Marshall (ed.), Fourier, Hadamard
115 H. Doucet, T. Ohkuma, K. Murata, and Hilbert Transforms in Chemistry.
T. Yokozawa, M. Kozawa, E. Plenum Press Corp., New York
Katayama, A. F. England, T. Ikariya, 1982.
R. Noyori, Angew. Chem. 1998, 110, 126 X. Gao, H. B. Kagan, Chirality 1998,
17921796; Angew. Chem. Int. Ed. 10, 120124.
1998, 37, 17031707. 127 For a review on on the reduction of
116 C. Moreau, C. G. Frost, B. Murrer, carbonyl compounds with chiral
Tetrahedron Lett. 1999, 40, 56175620. oxazaborolidine catalysts, see: E. J.
117 M. A. Huffmann, P. J. Reider, Corey, C. J. Helal, Angew. Chem.
Tetrahedron Lett. 1999, 40, 831834. 1998, 110, 20922118; Angew. Chem.
118 J. Christoffers, A. Mann, Angew. Int. Ed. Engl. 1998, 37, 19872012.
Chem. 2000, 112, 28712874; Angew. 128 C. Brandli, T. R. Ward, Helv. Chim.
Chem. Int. Ed. 2000, 39, 27522754. Acta, 1998, 81, 16161621.
119 P. J. Fagan, E. Hauptman, R. 129 T. Vries, H. Wynberg, E. van
Shapiro, A. Casalnuovo, J. Am. Echten, J. Koek, W. ten Hoeve, R.
Chem. Soc. 2000, 122, 50435051. M. Kellogg, Q. B. Broxterman, A.
120 For a recent review on CX (X N, Minnaard, B. Kaptein, S. van der
O) couplings, see: M. Beller, T. H. Sluis, L. Hulshof, J. Kooistra,
Angew. Chem. 1998, 110, 24912496; 136 T. R. Boussie, C. Coutard, H. W.

Angew. Chem. Int. Ed. Engl. 1998, 37, Turner, V. Murphy, T. S. Powers,
23492353. Angew. Chem. 1998, 110, 34723475;
130 N. Kashiwa, J. Imuta, Cat. Surv. Jpn. Angew. Chem. Int. Ed. Engl. 1998, 37,
1997, 1, 125142. 32723275.
131 a) L. K. Johnson, C. M. Killian, M. 137 T. R. Boussie, V. Murphy, K. A.
Brookhart, J. Am. Chem. Soc. 1995, Hall, C. Coutard, C. Dales, M.
117, 64146415; b) B. L. Small, M. Petro, E. Carlson, H. W. Turner,
Brookhart, A. M. Bennett, J. Am. T. S. Powers, Tetrahedron 1999, 55,
Chem. Soc. 1998, 120, 40494050; 1169911710.
c) C. M. Killian, M. Brookhart, 138 T. Schleis, T. P. Spaniol, J. Okuda,
Organometallics 1997, 16, 20052007; J. Heinemann, R. Mulhaupt, J.
for an application of 1,2-diimine Organomet. Chem. 1998, 569, 159167.
ligands in copolymerization see: 139 a) W. H. Weinberg, E. W.
d) L. K. Johnson, S. Mecking, M. McFarland, I. Goldwasser, T.
Brookhart, J. Am. Chem. Soc. 1996, Boussie, H. W. Turner, J. A. M. van
118, 267268. Beek, V. Murphy, T. S. Powers
132 For a related class of olen poly- (Symyx Technologies), Combinatorial
merization catalysts, see: G. J. P. Synthesis and Analysis of Organometallic
Britovsek, V. C. Gibson, B. S. Compounds and Catalysts, Patent WO
Kimberley, P. J. Maddox, S. J. 98/03521; b) T. Boussie, V. Murphy,
McTavish, G. A. Solan, A. J. P. J. A. M. van Beek, M. Devenny, H.
White, D. J. Williams, Chem. W. Turner, T. S. Powers (Symyx
Commun. 1998, 849850. Technologies), Encoding of Organo-
133 For a review on metallocene catalysis, metallic Libraries, patent pending;
see: M. Hackmann, B. Rieger, c) J. A. M. van Beek, G. C. Dales,
CatTech 1997, 1, 7992. D. Hajduk, R. B. Nielsen,
134 For a review on new-generation P. Mansky, E. W. McFarland (Symyx
olen polymerization catalysts, see: Technologies), Parallel Reactor with
a) G. J. P. Britovsek, V. C. Gibson, Internal Sensing and Method of Using
D. F. Wass, Angew. Chem. 1999, 111, Same, patent pending; d) T. R.
448468; Angew. Chem. Int. Ed. 1999, Boussie, K. Hall, A. M. LaPointe,
38, 428447; b) S. D. Ittel, L. K. V. Murphy, T. S. Powers, J. A. M.
Johnson, M. Brookhart, Chem. Rev. van Beek (Symyx Technologies),
2000, 100, 11691203; c) M. C. Baird, Delivery and Scavenging Agents for the
Chem. Rev. 2000, 100, 14711478; Synthesis of Compounds and Catalysts,
d) L. S. Boffa, B. M. Novak, Chem. Patent WO A98/56796.
Rev. 2000, 100, 14791493. 140 a) C. Lund, K. Hall, T. Boussie,
135 For some examples of polystyrene- V. Murphy (Symyx Technologies),
supported olen polymerization Polymerization Catalyst Ligands,
catalysts, see: a) S. B. Roscoe, J. M. J. Catalytic Metal Complexes and
Frechet, J. F. Walzer, A. J. Diaz, Compositions and Processes Using and
Science 1998, 280, 270273; b) M. C. Methods of Making Same, Patent WO
W. Chan, K. C. Chew, C. I. Dalby, 00/59961; b) A. S. Guram, A. M.
V. C. Gibson, A. Kohlmann, I. R. LaPointe, H. W. Turner, T. Uno,
Little, W. Reed, Chem. Commun. Catalyst Ligands, Catalytic Metal
1998, 16731674; c) A. G. M. Barrett, Complexes and Processes Using Same,
Y. R. de Miguel, Chem. Commun. Patent WO 00/20377; c) T. Boussie,
1998, 20792080; d) L. Sun, A. V. Murphy, J. A. M. van Beek,
Shariati, J. C. Hsu, D. W. Bacon, Compositions and Metal Complexes
Stud. Surf. Sci. Catal. 1994, 89, 8189; Having Ancillary Ligands, Patent WO
e) L. Sun, J. C. Hsu, D. W. Bacon, J. 99/05154.
Polym. Sci. Part A 1994, 32, 2127 141 M. Stork, A. Herrmann, T.
2134. Nemnich, M. Klapper, K. Mullen,
References 987
Angew. Chem. 2000, 112, 45444547; 154 G. M. Nashioka, US Patent No.

Angew. Chem. Int. Ed. 2000, 39, 4367 5,449,754.
4369. 155 W. H. Weinberg, B. Jandeleit, K.
142 J. Tian, G. W. Coates, Angew. Chem. Self, H. W. Turner, Curr. Opin. Solid
2000, 112, 37723775; Angew. Chem. State Mater. Sci. 1998, 3, 104110.
Int. Ed. 2000, 39, 36263629. 156 B. E. Baker, N. J. Kline, P. J. Treado,
143 C. Hinderling, P. Chen, Angew. M. J. Natan, J. Am. Chem. Soc. 1996,
Chem. 1999, 111, 23932396; Angew. 118, 87218722.
Chem. Int. Ed. 1999, 38, 22532256. 157 E. Reddington, A. Sapienza, B.
144 For an overview on the chemistry of Gurau, R. Viswanathan, S.
polyoxometalates, see: C. L. Hill (ed.), Sarangapani, E. S. Smotkin, T. E.
Special Thematic Issue: Polyoxo- Mallouk, Science 1998, 280, 1735
metalates, Chem. Rev. 1998, 98, 1390. 1737.
145 C. L. Hill, R. D. Gall, J. Mol. Cat. A: 158 P. G. Schultz, X.-D. Xiang, I.
Chem. 1996, 114, 103111. Goldwasser, Symyx Technologies,
146 For a monograph, see: K. Inc., USA Patent No. WO 96/11878,
Weissermel, H. J. Arpe, Industrial 1996.
Organic Chemistry, 3rd edn. Wiley- 159 E. Danielson, J. H. Golden, E. W.
VCH, Weinheim 1997. McFarland, C. M. Reaves, W. H.
147 E. Boring, Y. V. Geletti, C. L. Hill, Weinberg, X. D. Wu, Nature 1997,
J. Am. Chem. Soc. 2001, 123, 1625 389, 944948.
1635. 160 E. Danielson, M. Devenney, D. M.
148 a) A. Guram, A. Hagemeyer, B. Giaquinta, J. H. Golden, R. C.
Jandeleit, D. M. Poojary, H. Haushalter, E. W. McFarland,
Turner, W. H. Weinberg, D. M. Poojary, C. M. Reaves, W. H.
Proceedings of The 12th International Weinberg, X. D. Wu, Science 1998,
Congress on Catalysis, Granada, Spain, 279, 837839.
2000; Elsevier, Amsterdam; b) P. 161 S. M. Senkan, S. O zturk, Angew.
Desrosiers, A. Guram, A. Chem. 1999, 111, 867871; Angew.
Hagemeyer, B. Jandeleit, D. M. Chem. Int. Ed. 1999, 38, 791795.
Poojary, H. Turner, H. Weinberg, 162 C. Hoffmann, A. Wolf, F. Schuth,
Catal. Today 2001, 67, 397402. Angew. Chem. 1999, 111, 29712975;
149 For a comprehensive overview on Angew Chem. Int. Ed. 1999, 38, 2800
heterogeneous catalysis, see: G. Ertl, 2803.
H. Knozinger, J. Weitkamp (eds), 163 K. E. Simons, Topics in Catalysis 2000,
Handbook of Heterogeneous Catalysis. 13, 201203.
VCH, Weinheim 1997, vol. 15. 164 a) F. C. Moates, M. Somani, M.
150 P. G. Schultz, X.-D. Xiang, I. Annamalai, J. T. Richardson, D.
Goldwasser, US Patent No. Luss, R. C. Willson, Ind. Eng. Chem.
5,985,356, 1999. Res. 1996, 34, 4801; b) R. C. Willson
151 a) A. Holzwarth, P. Denton, H. (Technology Licensing Co.), Catalyst
Zanthoff, C. Mirodatos, Catal. Testing Process and Apparatus, PCT Int.
Today 2001, 67, 309318; b) for a Appl. WO 97/32208; c) E. W.
critical discussion of combinatorial McFarland, W. Archibald, (Symyx
approaches in heterogeneous catalysis, Technologies), Infrared Spectroscopy
see: R. Schlogl, Angew. Chem. 1998, and Imaging of Libraries, PCT Int.
110, 24672470; Angew. Chem. Int. Ed. Appl. WO 98/15813.
Engl. 1998, 37, 23332336. 165 A. Holzwarth, P. W. Schmidt, W. E.
152 G. Ertl, H. Knozinger, J. Weitkamp Maier, Angew. Chem. 1998, 110, 2788
(eds), Preparation of Solid Catalysts. 2792; Angew. Chem. Int. Ed. 1998, 37,
Wiley-VCH, Weinheim 1999. 26442647.
153 J. M. Newsam, F. Schuth, Comb. 166 D. E. Akporiaye, I. M. Dahl, A.
Chem. Biotechnol. Bioeng. 1999, 61, Karlsson, R. Wendelbo, Angew.
203216. Chem. 1998, 110, 629631; Angew.
Chem. Int. Ed. 1998, 37, 609 Angew. Chem. 2001, 113, 762765;
611. Angew. Chem. Int. Ed. 2001, 40, 740
167 J. Klein, C. W. Lehmann, H. W. 743.
Schmidt, W. F. Maier, Angew. Chem. 182 C. Lettmann, H. Hinrichs, W. F.
1998, 110, 35573561; Angew. Chem. Maier, Angew. Chem. 2001, 113, 3258
Int. Ed. 1998, 37, 33693372. 3262; Angew. Chem. Int. Ed. 2001, 40,
168 P. Cong, R. D. Doolen, Q. Fan, 31603164.
D. M. Giaquinta, S. Guan, E. W. 183 E. M. Thorsteinson, T. P. Wilson,
McFarland, D. M. Poojary, K. Self, F. G. Young, P. H. Kasai, J. Catal.
H. W. Turner, W. H. Weinberg, 1978, 52, 116.
Angew. Chem. 1999, 111, 507512; 184 F. G. Young, E. M. Thorsteinson,
Angew. Chem. Int. Ed. 1999, 38, 484 US Patent No. 4250346, 1981.
488. 185 Y. Liu, P. Cong, R. Doolen, S. Guan,
169 M. Orschel, J. Klein, H. W. D. M. Poojary, H. W. Turner, W. H.
Schmidt, W. F. Maier, Angew. Chem. Weinberg, Innovation in Selective
1999, 111, 29612965; Angew. Chem. Oxidation by Solid Catalysts, Rimini,
Int. Ed. 1999, 38, 27912803. Italy, 1999, p. 117, Book of Abstracts.
170 O. Buyevskaya, D. Wolf, M. Baerns, 186 Y. Liu, P. Cong, R. Doolen, S. Guan,
Catal. Today 2000, 62, 9199. D. M. Poojary, H. W. Turner, W. H.
171 U. Rodemerck, P. Ignaszewski, M. Weinberg, 4th European Congress on
Lucas, P. Claus, M. Baerns, Chem. Catalysis, Rimini, Italy, 1999, p. 41:
Ing. Tech. 1999, 71, 872. Book of Abstracts.
172 P. Cong, A. Dehestani, R. Doolen, 187 S. Senkan, Nature 1998, 394, 350
D. M. Giaquinta, S. Guan, V. 352.
Markov, D. Poojary, K. Self, H. W. 188 D. Wolf, O. V. Buyevskaya, M.
Turner, W. H. Weinberg, Proc. Natl. Baerns, Appl. Catal. A 2000, 200,
Acad. Sci. USA 1999, 96, 11077. 63.
173 Y. Liu, P. Cong, R. D. Doolen, H. W. 189 K. L. Ley, R. Liu, C. Pu, Q. Fan, N.
Turner, W. H. Weinberg, Catal. Leyarovska, C. Segre, E. S. Smotkin,
Today 2000, 61, 8792. J. Electrochem. Soc. 1997, 144, 1543
174 S. Senkan, K. Krantz, S. O zturk, V. 1548.
Zengin, I. Onal, Angew. Chem. 1999, 190 T. E. Mallouk, E. Reddington, C.
111, 29652971; Angew. Chem. Int. Ed. Pu, K. L. Ley, E. S. Smotkin,
1999, 38, 27942799. Proceedings of the Extended Abstracts
175 U. Rodemerck, D. Wolf, O. V. Fuel Cell Seminar, Orlando, Florida,
Buyevskaya, P. Claus, S. Senkan, M. 1996, 686689.
Baerns, Chem. Eng. J. 2001, 82, 3. 191 a) B. Gurau, R. Viswanathan, R.
176 K. Krantz, S. O zturk, S. Senkan, Liu, T. J. Lafrenz, K. L. Ley, E. S.
Catal. Today 2000, 62, 281289. Smotkin, E. Reddington, A.
177 a) H. Su, E. S. Yeung, J. Am. Chem. Sapienza, B. C. Chan, T. E.
Soc. 2000, 122, 74227423; b) H. Su, Mallouk, S. Sarangapani, J. Phys.
Y. Hou, R. S. Houk, G. L. Schrader, Chem. B 1998, 102, 999710003; b) L.
E. S. Yeung, Anal. Chem. 2001, 73, Liu, R. Viswanathan, R. Liu, E. S.
44344440. Smotkin, Electrochem. Solid State Lett.
178 P. Claus, D. Honicke, T. Zech, 1998, 1, 123125; c) E. Reddington,
Catal. Today 2001, 67, 319339. J.-S. Yu, B. C. Chan, A. Sapienza, G.
179 G. Chen, D. A. Delafuente, S. Chen, T. E. Mallouk, B. Gurau, R.
Sarangapani, T. E. Mallouk, Catal. Viswanathan, R. Liu, E. S. Smotkin,
Today 2001, 67, 341355. S. Sarangapani, Comb. Chem. 2000,
180 O. V. Buyevskaya, A. Bruckner, E. V. 401420; d) Y. Sun, H. Buck, T. E.
Kondratenko, D. Wolf, M. Baerns, Mallouk, Anal. Chem. 2001, 73,
Catal. Today 2001, 67, 369378. 15991604.
181 P. P. Pescarmona, J. C. van der 192 a) P. Strasser, S. Gorer, M.
Waal, I. E. Maxwell, T. Maschmeyer, Devenney, Proceedings of the
References 989
International Symposium on Fuel Eng. 2000, 3941 (Combinatorial

Cells for Vehicles, 41st Battery Composition Spread Techniques in
Symposium, The Electrochemical Materials and Device Development),
Society of Japan, Nagoya 2000, p. 153; 8491.
b) P. Strasser, S. Gorer, M. 203 T. Bein, Angew. Chem. 1999, 111,
Devenney, Proceedings of the 335338; Angew. Chem. Int. Ed. 1999,
Electrochemical Society Meeting, DMFC 38, 323326.
Symposium, Washington, March 2001. 204 R. H. Crabtree, Chem. Commun.
193 M. G. Sullivan, H. Utomo, P. J. 1999, 16111616.
Fagan, M. D. Ward, Anal. Chem. 205 P. C. Pawlicki, R. A. Schmitz, Chem.
1999, 71, 43694375. Eng. Prog. 1987, 2, 4045.
194 a) T. Siu, W. Li, A. K. Yudin, J. 206 G. Georgiades, V. A. Self, P. A.
Comb. Chem. 2000, 2, 545549; b) T. Sermon, Angew. Chem. 1987, 99,
Siu, S. Yekta, A. K. Yudin, J. Am. 10501052; Angew. Chem. Int. Ed.
Chem. Soc. 2000, 122, 1178711790; Engl. 1987, 26, 10421044.
c) A. K. Yudin, T. Siu, Curr. Opin. 207 a) M. T. Reetz, M. H. Becker, K. M.
Chem. Biol. 2001, 5, 267272. Kuhling, A. Holzwarth, Angew.
195 K. Jambunathan, B. C. Shah, J. L. Chem. 1998, 110, 27922795; Angew.
Hudson, A. C. Hillier, J. Electroanal. Chem. Int. Ed. 1998, 37, 26472650;
Chem. 2001, 500, 279289; b) B. C. b) M. T. Reetz, M. H. Becker, M.
Shah, A. C. Hillier, J. Electrochem. Liebl, A. Furstner, Angew. Chem.
Soc. 2000, 147, 30433048. 2000, 112, 12941301; Angew. Chem.
196 M. T. Reetz, K. M. Kuhling, S. Int. Ed. 2000, 39, 12361239.
Wilensek, H. Husmann, U. W. 208 D. E. Bergbreiter, Chemtracts: Org.
Hausig, M. Hermes, Catal. Today Chem. 1997, 10, 683686.
2001, 67, 389396. 209 S. Klein, S. Thorimbert, W. F.
197 a) L. Ma, X. Gong, E. S. Yeung, Anal. Meier, J. Catal. 1996, 163, 476488.
Chem. 2000, 72, 33833387; b) Y. 210 S. Bukeikhanova, H. Orzsek, U.
Zhang, X. Gong, H. Zhang, R. Kolb, K. Kuhlein, W. F. Meier,
Larock, E. S. Yeung, J. Comb. Chem. Catal. Lett. 1998, 50, 93105.
2000, 2, 450452. 211 S. Storck, W. F. Meier, I. M.
198 M. T. Reetz, K. M. Kuhling, A. Miranda Salvado, J. M. F. Ferreira,
Deege, H. Hinrichs, D. Belder, D. Guhl, W. Souverijns, J. A.
Angew. Chem. 2000, 112, 40494052; Martens, J. Catal. 1997, 172, 414426.
Angew. Chem. Int. Ed. 2000, 39, 3891 212 W. J. Haap, T. B. Walk, G. Jung,
3893. Angew. Chem. 1998, 110, 35063509;
199 S. A. Holmes, J. A. Saeedi, V. V. Angew. Chem. Int. Ed. 1998, 37, 3311
Buliants, P. Boolchand, D. 3314.
Georgiev, U. Hacker, E. Sabkow, 213 a) C. M. Snively, G. Oskarsdottir, J.
Catal. Today 2001, 67, 403409. Lauterbach, J. Comb. Chem. 2000, 2,
200 E. D. Isaacs, M. Marcus, G. Aeppli, 243245; b) C. M. Snively, G.
X.-D. Xiang, X.-D. Sun, P. G. Oskarsdottir, J. Lauterbach, Angew.
Schultz, M. Kao, G. S. Cargill III, Chem. 2001, 113, 31173120; Angew.
R. Haushalter, Appl. Phys. Lett. 1998, Chem. Int. Ed. 2001, 40, 30283030.
73, 18201822. 214 C. M. Snively, S. Katzenberger, G.
201 C. E. Kibbey in: A Practical Guide to Oskarsdottir, J. Lauterbach, Optics
Combinatorial Chemistry. Czarnick, Lett. 1999, 24, 18411843.
A. W., DeWitt, S. H. (eds), American 215 a) C. M. Snively, G. Oskarsdottir, J.
Chemical Society, Washington, DC Lauterbach, Catal. Today 2001, 67,
1997, pp. 123151. 357368.
202 K. Omote, T. Kikuchi, J. Harada, 216 A. C. Cooper, L. H. McAlexander,
M. Kawasaki, A. Ohtomo, M. Ohtani, D.-H. Lee, M. T. Torres, R. H.
T. Ohnishi, D. Komiyama, H. Crabtree, J. Am. Chem. Soc. 1998,
Koinuma, Proc. SPIE-Int. Soc. Opt. 120, 99719972.
217 R. H. Crabtree, J. A. Loch, K. 228 J. Gao, J. Wu, G. Siuzdak, M. G.

Gruet, D.-H. Lee, C. Borgmann, J. Finn, Angew. Chem. 1999, 111, 1868
Organomet. Chem. 2000, 600, 711. 1871; Angew. Chem. Int. Ed. 1999, 38,
218 K. H. Shaughnessy, P. Kim, J. F. 17551757.
Hartwig, J. Am. Chem. Soc. 1999, 229 M. T. Reetz, M. H. Becker, H.-W.
121, 21232132. Klein, D. Stockigt, Angew. Chem.
219 J. P. Stambuli, S. R. Stauffer, K. H. 1999, 111, 18721875; Angew. Chem.
Shaughnessy, J. F. Hartwig, J. Am. Int. Ed. 1999, 38, 17581761.
Chem. Soc. 2001, 123, 26772678. 230 Y. Matsumoto, M. Murakami, Z. Jin,
220 G. T. Copeland, S. J. Miller, J. Am. A. Nakayama, T. Yamaguchi, T.
Chem. Soc. 1999, 121, 43064307. Ohmori, E. Suzuki, S. Nomura, M.
221 A. H. Hoveyda, Chem. Biol. 1999, 6, Kawasaki, H. Koinuma, Proc. SPIE-
R305R308. Int. Soc. Opt. Eng. 2000, 3941, 1927.
222 R. F. Harris, A. J. Nation, G. T. 231 A. R. Connolly, J. D. Sutherland,
Copeland, S. J. Miller, J. Am. Chem. Angew. Chem. 2000, 112, 44384441;
Soc. 2000, 122, 1127011271. Angew. Chem. Int. Ed. 2000, 39, 4268
223 O. Lavastre, J. P. Morken, Angew. 4271.
Chem. 1999, 111, 33573359; Angew. 232 Y. Yamada, A. Ueda, Z. Zhao, T.
Chem. Int. Ed. 1999, 38, 31633165. Maekawa, K. Suzuki, T. Takada, T.
224 A. Berkessel, R. Riedl, J. Comb. Kobayashi, Catal. Today 2001, 67,
Chem. 2000, 2, 215219. 379387.
225 K. Ding, A. Ishii, K. Mikami, Angew. 233 J. P. Ramirez, R. J. Berger, G. Mul,
Chem. 1999, 111, 519522; Angew. F. Kapteijn, J. A. Moulijn, Catal.
Chem. Int. Ed. 1999, 38, 497501. Today 2000, 60, 93109.
226 K. Mikami, R. Angelaud, K. Ding, A. 234 U. Rodemerck, P. Ignaszewski, M.
Ishii, A. Tanaka, N. Sawada, K. Lucas, P. Claus, M. Baerns, Top.
Kudo, M. Senda, Chem. Eur. J. 2001, Catal. 2000, 13, 249252.
7, 730737. 235 Note added in proof. The follwing
227 a) R. F. Service, Science 1997, 277, contribution to high-throughput
474475; b) W. H. Weinberg, E. W. screening was published after
McFarland, P. Cong, S. Guan submission of the manuscript: A.
(Symyx Technologies), Mass Spectro- Ross, G. Schlotterbeck, H. Senn,
meters and Methods for Rapid Screening M. von Kienlin, Angew. Chem. 2001,
of Libraries of Dierent Materials, PCT 113, 33433345; Angew. Chem. Int. Ed.
Int. Appl. WO 98/15969. 2001, 40, 32423245.
991
33
Diversity-Based Identication of Ecient
Homochiral Organometallic Catalysts for
Enantioselective Synthesis
Amir H. Hoveyda
33.1
Introduction
The discovery and identication of an eective chiral catalyst that promotes a

chemical reaction with desirable levels of eciency and selectivity is a dicult
business [1]. Because only small energy gaps separate an inactive or nonselective
catalyst from one that is potent and selective (@ 12 kcal mol variance in transi-
tion-state energy), variations in reactivity and selectivity often arise unpredictably.
Seemingly insignicant variations in the catalyst or substrate structure and reac-
tion conditions (solvent polarity, temperature, etc.) can lead to entirely unexpected
swings in yield, ee (enantiomeric excess), or both. To outline a new transformation
and achieve maximum levels of reactivity and selectivity, myriad reaction param-
eters must therefore be explored and adjusted. In cases where an eective metal-
catalyzed enantioselective process is the goal, the choice of an appropriate chiral
ligand and metal salt is perhaps most crucial. In such instances, a blend of mech-
anistic knowledge and human intuition are typically used to identify a desirable
metalligand combination.
Mechanistic knowledge is useful in allowing chemists to appreciate the general
contours of a reaction pathway. Such information is critical in catalyst discovery; it
aids us in deciding what class or classes of chiral ligands and what type of metal
salts should be included in a study. However, mechanistic data alone cannot pro-
vide us with sucient information to fully design [2] a catalyst, without requir-
ing any degree of trial and error. That is, a set of mechanistic data collected
through examination of a single substrate under a particular set of conditions with
a specic metal center and chiral ligand is often less general than one might like.
Similar to mechanistic data, chiral catalysts are often not general. Once we do come
across an attractive catalyst, it is seldom eective for a wide range of substrates.
This result is not surprising; a selective catalyst that recognizes a certain structural
type with great delity cannot by nature recognize and associate with a gamut
of substrates and promote reactions selectively.
To address the above general uncertainties and fundamental diculties, chem-
ists have recently turned their attention to advances in combinatorial and high-

ISBN: 3-527-30509-2
992 33 Diversity-Based Identification of Efficient Homochiral Organometallic Catalysts
throughput strategies [3]. This movement arises from the realization that if the
study of a large number of potential catalysts leads to a discovery, then why not
perform the investigation systematically and more eciently by covering a broad
range of catalyst candidates? Another factor that supports the adoption of diversity-
based approaches is that screening of a large number of compounds may allow
chemists to identify an optimal catalyst for each particular substrate and thus
overcome the problem of generality that often looms large when a small number
of catalyst candidates are available. High-throughput screening can give rise to
new mechanistic scenarios that are by nature more comprehensive, derived from a
more extensive collection of data points. It would be idle to assume that screening
is carried out at random or that diversity approaches to catalyst discovery are devoid
of any mechanistic basis. Mechanistic information gained through examination
of a large set of data can serve as the driving force behind additional investigations;
it can lead to the blossoming of a symbiotic relationship between mechanistic in-
quiry and diversity-based screening that results in the discovery of more powerful
and ecient catalysts of all types, and a deeper and more mature appreciation of the
inner workings of various classes of catalysts.
33.2
Factors Critical to the Success of Diversity-based Reaction Development
Three important issues need to be addressed for the successful implementation of

diversity-based catalytic asymmetric reaction development: (1) sources of diversity,
(2) high-throughput synthesis of catalysts, and (3) high-throughput catalyst screen-
ing.
1 Sources of diversity. Variation of the ligand structures can generate an exponential

number of catalysts with dierent steric and electronic attributes. When organo-
metallic complexes are intended for use as catalysts, metal centers can be modi-
ed as well. Reaction conditions represent another dimension of diversity. Co-
catalysts, additives, solvent, concentration, temperature, and reaction times are
potential parameters that can be altered. It must be noted that the above proto-
cols toward enhancing diversity are not mutually exclusive.
2 Catalyst candidates that lend themselves to diversity-based screening. To employ
diversity-based strategies in an ecient and productive manner, the basic struc-
tural features of the targeted class of catalysts must lend themselves to such an
approach. Accordingly, the following fundamental catalyst attributes are critical:
Facile modularity. Depending on the nature of the metal salts involved and the
type of transformation that is being developed, it should be possible to alter
ligand structures readily so that reactivity and selectivity levels are rapidly im-
proved. The modularity of the chiral ligands has been critical to acceleration
of their preparation by making the fabrication of each catalyst identical, re-
gardless of structural variations. It must be noted that, in principle, all chiral
ligands can be modied and thus labeled modular. Some classes of chiral li-
gands are, however, more easily modied because their structural components
33.2 Factors Critical to the Success of Diversity-based Reaction Development 993
are joined by bonds that are readily formed. These ligands are therefore most
suitable for parallel library synthesis. Schi bases and peptide linkages are
among disconnections that fall into the latter category. If CaC, CaP, or CaN
(nonpeptide linkage) bonds are to be modied to alter a ligand (e.g. binol- or
biphen-based systems), then these constructs should be viewed as less readily
modular.
Symmetry. One of the more established dogma in the eld of metal-catalyzed
asymmetric catalysis is that symmetric, particularly C2 -symmetric, chiral li-
gands are preferred so that the number of energetically dierentiable modes
of catalystsubstrate association can be minimized and stereoselectivity can
be more logically designed. Many useful, ecient, and selective transform-
ations have indeed been developed based on C2 -symmetric chiral ligands [1];
it is likely that many more chiral ligands of this type will be developed in the
future. However, recent studies from a number of laboratories indicate that
non-C2 -symmetric chiral ligands can also give rise to outstanding levels of se-
lectivity and eciency in a variety of synthetically important transformations
[4].
As far as diversity-based approaches are concerned, the less symmetric class
of chiral ligands provides a more attractive option. With C2 -symmetric systems,
any structural alteration must be mirrored at the complementary region of the
ligand structure, thus reducing the degree of available diversity.
Multiple binding sites. Another common perception in the eld of asymmetric
catalysis is that the number of binding sites for the metal center within the
chiral ligand should be minimized (often limited to a single point of bind-
ing). As such, chiral ligands have often served a single function in a particular
transformation. The metalligand complex either serves as a Lewis acidic
activator or as a nucleophilic agent. In a limited number of instances, both
functions are delivered by two distinct molecules of the chiral catalyst
(second order in catalyst) [5]. Incorporation of multiple binding sites raises
the intriguing possibility of multimetal systems and multifunctional catalysts
[6]. Care must be taken, however, that dierent sites possess suciently di-
verse coordination properties so that, through association with various metal
salts, chiral ligands give rise to complementary rather than competing eects
[7]. Multiple binding sites are attractive from the point of view of high-
throughput screening studies: they incorporate additional elements of struc-
tural modication and open the possibility of multimetal systems, which, in
itself, represents a critical dimension in diversity.
3 High-throughput catalyst screening. This aspect is often the greatest bottleneck in
assaying each catalyst for asymmetric induction. Although in combinatorial ap-
proaches to biological activity, mixtures of compounds can be analyzed simulta-
neously, such a strategy is by nature problematic in studies that pertain to iden-
tication of eective homochiral catalysts. Because subtle structural variations
can lead to unexpected changes, or even reversal of enantioselectivity, examina-
tion of mixtures of catalysts can lead to conclusions that are misleading (low net
selectivity by two eective catalysts that aord high ee values but in the opposite
sense). Accordingly, recent reports generally involve testing individual systems.
It merits mention that the parallel screening strategy has also been applied in
therapeutic discovery eorts because of the diculties involved in the accurate
deconvolution of various mixtures and because of the synergism that may exist
between several active compounds. As such, combinatorial chemistry does not
necessarily involve the generation of mixtures of compounds; it may be better
characterized by the modular nature of the constituent compounds that in dif-
ferent combinations provide large numbers of molecular ensembles. Analysis of
mixtures of candidates for activity (vs. selectivity) can be feasible however and
may be accomplished eectively [3f ].
33.3
Peptidic Schi Bases as Chiral Ligands
In search of a class of chiral ligands that satises the above-mentioned attributes

(facile modularity, nonsymmetry, and multiple binding sites) and can promote a
variety of CaC bond-forming reactions enantioselectively, we took note of Schi
base peptide ligand 1. In 1992, Inoue and coworkers reported that in the presence
of 10 mol% Ti(OEt)4 and 10 mol% 1, addition of trimethylsilyl cyanide (TMSCN)
to various aldehydes occurs with appreciable enantioselectivity [8]. There are sev-
eral characteristics that are represented by a ligand such as 1: (1) the ease of Schi
base and amide bond synthesis renders these entities as potential readily modular
chiral ligands for a wide range of metal salts; (2) the requisite building blocks, ar-
omatic aldehydes, and optically pure amino acids, are readily available; (3) peptidic
structures can be prepared on solid support, allowing simultaneous synthesis and
examination of a sizeable collection of catalyst candidates in an expeditious man-
ner (see Figure 33.2).
Scheme 33.1. Ti-catalyzed enantioselective addition of cyanide

to aldehydes in the presence of a dipeptide Schi base.
33.3 Peptidic Schiff Bases as Chiral Ligands 995
33.3.1
Ti-Catalyzed Enantioselective Addition of Cyanide to Meso Epoxides
In 1995, we initiated a program wherein we utilized diversity-based protocols to

introduce variations within a modular peptide-based ligand as the means to iden-
tify eective chiral ligands for enantioselective TMSCN addition to meso epoxides
(Scheme 33.2) [9]. In principle, 8000 (20 3 ) dierent chiral catalysts could be made
from the 20 natural amino acids and 20 dierent aldehydes. To circumvent such a
daunting requirement and control the numbers of compounds synthesized and
screened, a representational search strategy was employed (concept illustrated in
Fig. 33.1).
Scheme 33.2. Peptidic Schi bases may be screened for

identication of an eective chiral ligand for catalytic
enantioselective addition of TMSCN to meso epoxides.
First, as shown in Scheme 33.3, we established that in the presence of 10 mol%

ligand 4 and 10 mol% Ti(OiPr)4 the addition of TMSCN to cyclohexene oxide 5
proceeds smoothly to aord 6 in @25% ee (<10% reaction in the absence of 4). To
Fig. 33.1. Representational search strategy adopted for catalyst

screening allows identication of eective ligands without
examination of all possibilities.
improve the observed enantioselectivity, each of the three subunits in the modular
ligand was successively optimized (see Fig. 33.2), such that the rst amino acid 1
(AA1 in box) was varied and the other two subunits were kept constant (with
5 as the substrate). Tert-leucine was found to be optimal at AA1 position and this
structural element was retained in successive generations. The second position
(AA2) was then altered, and O-tert-butyl-threonine was identied as the best AA2.
Finally, from a pool of salicylic aldehydes, 3-uorosalicylaldehyde was selected as
the best Schi base (SB). In the end, only a representative sampling of 60 20 3
catalysts was necessary to identify one (see 10 in Table 33.1) that aords nearly a
95:5 ratio of enantiomers (89% ee). The initial catalyst provided the addition prod-
uct with only 26% ee (cyclohexene oxide as substrate). Successive modications of
the ligand structure led us to identify in three steps a chiral ligand that delivers a
synthetically attractive level of enantioselectivity. It is unlikely that any mechanistic
considerations would have pointed to this specic peptidic complex as a more
suitable one.
Scheme 33.3. Schi base dipeptides promote the Ti-catalyzed

enantioselective addition of cyanide to meso epoxides.
The above strategy for catalyst screening raises an intriguing question: Is the
optimal catalyst identied by this process truly the very best catalyst? And if it is
not, does the attendant improvement in enantioselectivity (> 99% ee), assuming
there will be no notable dierence in eciency, justify the additional eort that
would be required to achieve it? In the approach described above, we have made
certain assumptions about the additivity and absence of cooperativity between the
three subunits of the ligand structure. At least for this small sampling, these assump-
tions seem to hold true, but without testing every combination we cannot deni-
tively answer this question. Examination of every possibility would be taxing and
detract from the efciency of the general screening method. An important practical
advantage of the above approach is that, in a relatively short amount of time, it al-
lowed us to identify a selective catalyst for an entirely new asymmetric process.
That is, the search strategy is not an open-ended odyssey but a well-structured
Fig. 33.2. Screening by positional optimization of various
peptide Schi base ligands for enantioselectivity in the addition
of TMSCN to cyclohexane oxide (5).
33.3 Peptidic Schiff Bases as Chiral Ligands
997
Fig. 33.2. (continued)

Tab. 33.1. Optimized ligands for catalytic enantioselective addition of TMSCN to meso epoxides.
Entry Substrate Product ee (%) Yield (%) Optimized ligand
1 83 72
2 89 65
3 84 68
4 78 69
Conditions: 20 mol% Ti(OiPr)4 , 20 mol% ligand, TMSCN, 4 C, toluene, 620 h.
program that allows a fairly comprehensive assessment of a ligand framework

with respect to a specic asymmetric reaction in a nite and predictable period of
time.
When we applied the above search strategy to various other meso epoxide sub-
strates, a number of crucial observations were made (see Table 33.1) [10]. One sig-
nicant trend that emerged from these studies was that, for each epoxide substrate,
a similar but unique chiral catalyst was identied. This type of catalyst/substrate
selectivity is akin to that observed in Nature where many reactions have their own
unique enzymes. The high levels of selectivity observed with enzymatic reactions
is often accompanied by the lack of substrate generality. In this instance, however,
because ligand modication is relatively straightforward, substrate specicity does
not necessarily imply lack of generality. Another noteworthy issue raised by the
data in Table 33.1 is that the search for a truly general catalyst is perhaps unre-
alistic: catalysts that aord exceptional selectivity do so because they associate with
specic structures with great delity. To expect high specicity and broad range
generality may be somewhat contradictory.
Our studies indicate that the above method of catalyst identication increases the
frequency with which unexpected observations are made. For example, as illustrated
in Scheme 33.4, a subtle alteration in the structure and not the stereochemical
identity of the peptide ligand leads to inversion of stereochemistry in the epoxide-
opening reaction (compare reaction with ligands 9 and 17). These observations vali-
date our choice of individually synthesizing and testing each catalyst, as mixtures
of catalysts can lead to racemic products.
Scheme 33.4. Subtle modications in the structure of a

peptide ligand may unexpectedly lead to signicant variations
in selectivity.
33.3.2
Ti-Catalyzed Enantioselective Addition of Cyanide to Imines
In the second phase of our program, we applied the above screening technology
to identify specic Tipeptide complexes that catalyze the addition of cyanide to
imines [11, 12]. As the representative cases in Scheme 33.5 illustrate, the reactions
proceed eciently and with outstanding enantioselectivity. In addition to arylimines
(e.g. formation of 19 and 22 in Scheme 33.5), acyclic a,b-unsaturated imines are
eective substrates for these asymmetric CaC bond-forming reactions (cf. forma-
tion of 25 and 28 in Scheme 33.5). Initially, our catalyst-screening approach led
us to identify catalysts that deliver amino nitriles with 9097% ee, but in low
conversion (< 25% conversion in 18 h) [13]. Based on certain mechanistic consid-
erations, which ironically later proved to be incorrect, we argued that addition of
protic additives may lead to an enhancement in reactivity. The latter hypothesis
was based on the fact that when reactions are carried out in relatively large scale,
where adventitious water is more easily avoided, conversions are lower. Thus, the
eect of a variety of alcohols and amines on reaction eciency and selectivity were
systematically screened. These studies led us to establish that the Ti-catalyzed cya-
nide additions are signicantly more ecient if one equivalent of iPrOH is added
to the reaction mixture slowly (see below for mechanistic details). Accordingly, re-
actions of arylimines and unsaturated aliphatic imines were eected with high
enantioselectivity and in good yield, as represented by the examples in Scheme
33.5. It is important to note that in the course of these studies we established that
an NnBu amide terminus provides the same levels of reactivity and eciency as
when Gly occupies the AA3 site.
Scheme 33.5. Ti-catalyzed enantioselective addition of cyanide

to imines promoted by modular peptidic Schi base ligands.
The majority of the optically enriched amino nitrile intermediates can be easily
recrystallized to enantiopurity. The Ti-catalyzed asymmetric process is of notable
utility in organic synthesis, since after a single hydrolysis/deprotection step optically
pure amino acids can be obtained; the example shown in Scheme 33.6 is illustra-
tive. It is worth noting that such amino acids cannot be accessed by the celebrated
catalytic asymmetric hydrogenation protocols [14].
With eective and highly enantioselective catalytic Strecker reactions in hand,
we set out to explore the mechanistic details of these important transformations
[15]. It is our conviction that a better mechanistic appreciation, along with the
ability to prepare and screen large collections of catalyst candidates, will allow us
to extend the scope of this versatile class of chiral ligands to include a number of
other critical catalytic enantioselective processes. Thus, kinetic, structural, and ster-
eochemical studies of Ti-catalyzed addition of cyanide to imines in the presence of

Schi base peptides were carried out. Noteworthy among our ndings is that it
is likely HCN (not TMSCN) which serves as the active nucleophile; the slow addi-
tion of iPrOH leads to the formation of the reactive HCN. Moreover, detailed
kinetic studies suggest the reaction is rst order only in the Tiligand com-
plex. These studies also reveal a DSz 45:6 G 4:1 cal K1 mol1 , indicating a
highly organized transition structure for the turnover-limiting step of the catalytic
cycle.
Scheme 33.6. Synthesis of nonproteinogenic a-amino acids by Ti-catalyzed Strecker reaction.
Various structural features of the chiral peptide ligand were systematically altered
and the corresponding relative rates and enantioselectivities were measured. These
studies, summarized in Scheme 33.7, led to several important ndings: (1) not
only is the presence of the AA2 moiety critical to reactivity and enantioselectivity
(compare reaction of 33 with that of 34), its stereochemical identity is of notable
signicance as well (compare reaction of 33 with those of 35 and 36); (2) the pres-
ence of a more Lewis basic amide carbonyl (vs. a carboxylic ester) has an inuence
on the rate of asymmetric CN addition, e.g. the initial rate of reaction (90 min)
with ligand 7 is 2.3 times faster than that for the derived methyl ester 37.
The importance of AA2 and the inuence of local chirality suggest that the
peptide segment of the ligand actively participates in the asymmetric CaC bond-
forming reaction. That is, the TiSchi base coordinates with the substrate while
an amide moiety within the neighboring peptide segment associates and delivers
HCN to the activated imine. A mechanistic model consistent with the kinetic and
stereochemical data is presented in Fig. 33.3. These ndings thus underline the
signicance of the peptidic moiety of this class of chiral ligands not as passive
providers of a chiral environment, but as active participants in the asymmetric
CaC bond formation. These data provide a solid mechanistic basis regarding the
importance of available diversity at the two peptidic sites and the practical utility of
the non-C2 -symmetric structure of these chiral ligands. The above ndings are
signicant, since they demonstrate that, by virtue of their structural and stereo-
chemical identity, peptidic Schi bases may serve as bifunctional catalysts to de-
liver appreciable reactivity and high enantioselectivity. The above mechanistic par-
Scheme 33.7. Eect of the AA2 moiety on reactivity and

enantioselectivity in the Ti-catalyzed addition of cyanide to
imines.
adigm thus suggests that, in addition to HCN, other reagents such as various alkyl
metals may be delivered eectively and enantioselectively to the bound imine sub-
strate. Such a hypothesis led us to the following aspects of our program.
Fig. 33.3. Delivery of HCN by the AA2 moiety of the peptide ligand.
33.3.3
Zr-Catalyzed Enantioselective Addition of Dialkyl Zincs to Imines
To determine whether the above mechanistic paradigms can be employed to deliver

alkyl metals to imines in an enantioselective fashion, we set out to examine the
possibility of developing a catalytic asymmetric alkylation of imines. Such a pro-
cess would deliver optically enriched or pure amines, a class of compounds that is
of great signicance to medicine and biology. Screening of parallel libraries was
used to establish conditions for an eective set of protocols, including the optimal
metal center, solvent, reaction temperature, and amine protecting group [16, 17].
Interestingly, as the representative examples in Scheme 33.8 illustrate, these screen-
ing studies indicated that Zr(OiPr)4 is the most appropriate metal center with
dipeptide Schi base 41 serving as the chiral ligand that delivers excellent reactiv-
ity and enantioselectivity; the previously employed Ti salt leads to signicantly
less reactive and enantioselective reactions. An ecient Zr-catalyzed alkylation of
arylimines in the presence of 0.110 mol% chiral peptidic ligands and Et2 Zn was
thus established (see 38 ! 39 in Scheme 33.8). These transformations aord the
derived amines in >90% ee and >66% isolated yield. As illustrated in Scheme 33.8,
oxidative removal of the o-anisyl protecting group delivers the derived optically en-
riched arylamines (e.g. 40).
Scheme 33.8. Parallel screening points to Zr as the optimal

transition metal for enantioselective addition of Et2 Zn to
imines.
With aryl imines that contain electron-withdrawing or electron-releasing sub-

stituents, the Schi base dipeptides such as 41 are ineective (amine formation
with electron-withdrawing groups and <10% conversion with electron-rich units).
When Et2 Zn is used in such cases, the imine substrate is simply reduced to aord
the achiral amine product; when other dialkyl zinc reagents are employed (e.g.
Me 2 Zn), <2% conversion is detected. The facile reduction of substrates with Et2 Zn
may be due to b-H elimination of the metalEt complexes that generate active
metal hydrides that in turn promote amine reduction. The observed ineciency of
alkyl zinc reagents that do not bear a b-H (Me 2 Zn) or carry one that is less active
(n-alkyl2 Zn) support this hypothesis. Therefore, we speculated that the correspond-
ing amine-based peptide ligand (e.g. 44) may be the active catalyst. Thus, only in
cases where it can be eciently generated (i.e. in the presence of Et2 Zn) does the
asymmetric alkylation proceed smoothly. Once again, based on a mechanistic hy-
pothesis and because of the modularity of the chiral Schi base peptide structure,
a variety of ligand candidates were screened. As the data in Scheme 33.9 illustrate,
we established that the amine-based chiral ligands provide appreciable eciency as
well as enantioselectivity in the presence of all dialkyl zincs, regardless of whether
they bear an active b-H or not. It must also be noted that, as was found with the Ti-
catalyzed addition of cyanide to imines (Scheme 33.7), initial studies indicate that
the AA2 moiety is crucial for achievement of both high reactivity and enantio-
selectivity.
Scheme 33.9. With the peptide-based amine ligand a variety of

alkyl zincs can be added to imines in an enantioselective and
catalytic manner.
The Zr-catalyzed asymmetric alkylation shown in Eq. 1 (48 49 ! 50) illustrates

two important principles [18]: (1) the catalytic asymmetric protocol can be readily
applied to the synthesis of nonaryl imines to generate homochiral amines that
cannot be prepared by any of the alternative imine or enamine hydrogenation pro-
tocols; (2) the catalytic amine synthesis involves a three-component process that
includes the in situ formation of the imine substrate, followed by its asymmetric
alkylation. This possibility, also readily applied to the preparation of arylamines, not
only provides an eective solution to the problems associated with the instability of
aliphatic imines, but also suggests that such a procedure may be used to synthe-
size libraries of homochiral amines in a highly ecient and convenient fashion.
33.3.4
Cu-Catalyzed Enantioselective Addition of Dialkyl Zincs to Allylic Phosphates:
Pyridyl Dipeptides as Chiral Ligands
Catalytic enantioselective addition of alkyl metals to olens has been one of the key
problems that our research group had been interested in for the past 10 years [19].
With the success of the peptide-based ligands in promoting the addition of alkyl
zinc reagents to imines, we set out to examine whether a similar process may be
eected with olenic starting materials. One class of principal interest is the allylic
substitution reactions. Within this context, largely due to the scarcity of related pro-
tocols, we are particularly interested in transformations that utilize the less explored
hard alkylating agents which can enantioselectively deliver the problematic qua-
ternary carbon centers [20]. Recently, we have identied a new class of Schi base
peptides that accomplishes part of the above objective [21].
We initiated our search for the optimal conditions by using the more reactive and
readily accessible disubstituted olens (vs. trisubstituted alkenes described below).
Since CuCN has been demonstrated to exhibit a preference for SN 2 0 mode of ad-
dition in related processes with Grignard reagents, it was selected for the prelimi-
nary optimization studies [22]. Examination of potential substrates indicated that
allylic phosphates are the most suitable starting materials (see 51 ! 52 in Scheme
33.10) [23, 24]. The corresponding chlorides react smoothly with Et2 Zn in CH2 Cl2 ,
toluene, or Et2 O (30 C, 18 h, without ligand and Cu salt) and the derived ace-
tates, phenyl ethers, and phenyl carbamates aord < 10% conversion. Since the
previously mentioned mechanistic work suggested that the Schi base portion of
the peptidic ligands is likely a metal-ligation site that is critical to reactivity and
selectivity, we decided to perform catalyst optimization in the following systematic
Scheme 33.10. Screening studies for optimization of ligand

and Cu salt in catalytic allylic substitution of 51 with Et2 Zn (all
conversions > 98%).
order: (1) identify optimal Schi base type; (2) ascertain the identity of the most
desirable Cu salt; (3) determine the optimal peptidic construct (e.g. di- or tripep-
tide); (4) further enhance enantioselectivity through identication of optimal Schi
base and the amino acid moieties.
As shown in Scheme 33.10 (rst-phase screening), treatment of phosphate 51
(Scheme 33.10) with Et2 Zn in the presence of 10 mol% CuCN and chiral ligands
5356 in tetrahydrofuran (THF) at 30 C leads to >98% conversion within 6 h.
Pyridine dipeptide 56 delivers the highest level of enantioselectivity (34% ee), fol-
lowed by phosphine 55 (26% ee). To ascertain the identity of the most ecient and
selective ligand/Cu salt combination, formation of 52 was examined in two sets of
experiments involving ligands 55 and 56 and a collection of Cu salts (see Scheme
33.10, second-phase screening). This study established that 56 and CuCN, overall,
provide the most ecient regio- and enantioselective process. Next, we secured the
following additional ligand attributes (third-phase screening, Scheme 33.10): (1) an
amide terminus is critical to the enantioselectivity replacement of the NnBu in
56 with an OMe group (57, Scheme 33.10) leads to signicant reduction of ee; (ii)
incorporation of a third amino acid (58, Scheme 33.10) or removal of one (59) is
detrimental to enantioselectivity [25]. The stereochemical outcome from the reac-
tion with 59 (14% ee) once again underlines the importance of the AA2 moiety
and indicates that simple attachment of a chiral group to the pyridyl ligation site is
not alone sucient for high asymmetric induction.
We then prepared chiral ligands 6067 (Scheme 33.10) and examined their abil-
ity to initiate the enantioselective alkylation of 51 under the same conditions men-
tioned above. Thus, the catalytic ability of the derived amine (60), amide (61), and
various a-substituted pyridyl systems (6265) were investigated; in addition, the
related indole-based 66 and C2 -symmetric 67 were probed. All reactions proceed to
>98% conversion and exhibit high degrees of SN 2 0 /SN 2 selectivity, but it is the o-
substituted ligand 64 that generates the highest ee. We thus selected o-OiPr pyridyl
as the Schi base moiety, and continued with the optimization of the AA1 and AA2
segments according to methods reported previously in the context of our work on
the enantioselective addition of cyanide to meso epoxides and imines [3]. These
studies uniformly suggest that l-Phe is the AA2 of choice, and that ligands which
bear l-Val (56), l-t Leu (68, Scheme 33.11) and l-Chg (69, Scheme 33.11) at the
AA1 position oer similarly superior enantioselection. When d-Val is used as AA1,
the sense of enantioselection is reversed, indicating that the stereochemical iden-
tity of AA1 is critical to the sense of induction and that the d,l-ligand may deliver
lower levels of enantioselectivity than the l,l isomer. The above chiral ligands were
subsequently used in catalytic alkylation of a range of aryl olens in the presence
of Et2 Zn and 10 mol% CuCN in THF.
The results shown in Scheme 33.11 are representative and point out which
ligand provides the highest selectivity for a particular substrate (< 2% SN 2 product
in all cases). The selectivity and reactivity levels for the disubstituted alkenes are
competitive with the recently reported catalytic alkylations of allylic chlorides [26],
in which sterically demanding dialkyl zinc reagents (e.g. dineopentyl zinc) are re-
quired for high enantioselectivity (a 50% ee with n-alkyl zinc reagents). The cata-
Scheme 33.11. Parallel screening of ligand libraries indicates

that pyridyl dipeptides can serve as eective ligands for Cu-
catalyzed allylic substitution reactions that aord quaternary
carbon centers enantioselectively.
lytic enantioselective synthesis of quaternary carbons (e.g. formation of 73 and 75 in

Scheme 33.9), however, represents a new and eective method for the regio- and
enantioselective preparation of this important class of homochiral compounds.
The signicance of the new technology was demonstrated in the context of a
brief enantioselective total synthesis of sh deterrent sporochnol (Scheme 33.12)
[27, 28].
33.3.5
Cu-Catalyzed Enantioselective Conjugate Addition of Dialkyl Zincs to Unsaturated
Ketones: Peptidic Phosphines as Chiral Ligands
Another important class of transformations is the catalytic asymmetric conjugate

additions of unsaturated carbonyls [29]. We have examined the possibility of using
the modular Schi base polypeptides as ligands that promote this important class
Scheme 33.12. Cu-catalyzed asymmetric allylic substitution

with longer chain alkyl zinc reagents and total synthesis of
sporochnol.
of transformations [30]. Screening of ligand, Cu salt, and solvent libraries, carried

out in a similar manner as described above, indicated that phoshine-based dipep-
tides, such as 55 shown in Scheme 33.13, promote various conjugate addition re-
actions with excellent reactivity and eciency in the presence of CuOTf. Use of a
hydroxyl-containing ligand such as 53 (see Scheme 33.10) or even a pyridyl ligand
such as 56 leads to the formation of racemic products. Thus, once again, the modu-
lar character of this class of chiral ligands allows facile examination of a dierent
subset of potential ligand structures that provides access to high levels of eciency
and asymmetric induction. The Cu-catalyzed CaC bond-forming reactions require
only 2 mol% (CuOTf )2 C6 H6 and 2.4 mol% of the peptidic phosphine and can be
eected with a wide range of dialkyl zinc reagents. Most importantly, as depicted
in Scheme 33.13 and in contrast to the previously reported protocols, the present
method provides for the rst time an ecient and highly enantioselective
conjugate addition protocol for cyclopentenones.
Unlike the alkyl zinc reagents shown in Scheme 33.13, use of iPr2 Zn leads to
moderate levels of asymmetric induction (e.g. 62% ee with cycloheptenone 84 as the
substrate). To address this selectivity problem, we set out to identify an improved
chiral ligand through the positional optimization strategy, with cyclohexenone 82
serving as the substrate. As illustrated in Scheme 33.14, we established that reac-
tions promoted by 86 (t-Leu at AA1, tBu-Tyr at AA2, and Gly at AA3) deliver 88
in 91% ee (vs. 72% ee with 55). Chiral phosphine ligand 86 also provides a better
selectivity in reaction of cycloheptenone 84 with iPr2 Zn (81% ee vs. 62% ee with
55). In contrast, with cyclopentenone 78 as the substrate, 90 is obtained in 65% ee
when 86 is used (vs. 79% ee with 55). When phosphine 87 (Gly replaced by nBu) is
employed in the reaction of 78, however, cyclopentanone 90 is isolated in 85% ee
(94%) [31]. The above observations once again demonstrate the utility of facile
modularity and its attendant parallel screening. These data imply that if complete
ligand screening is carried out specically for each substrate, a dierent optimal
chiral phosphine construct may emerge for each particular enone.
Scheme 33.13. Cu-catalyzed asymmetric conjugate additions of

cyclic enones with peptidic phosphines as the chiral ligand.
Scheme 33.14. Cu-catalyzed asymmetric conjugate additions of

cyclic enones with peptidic phosphines as the chiral ligand.
Conditions: 1.0 mol% (CuOTf )2 C6 H6 , 2.4 mol% chiral ligand,
3 equiv. (iPr)2 Zn, 30 C.
This last enantioselective transformation catalyzed by peptide-based ligands is also

of notable potential synthetic utility. The sequential catalytic addition/alkylation of
84 provides 91 in 97% ee, 80% yield, and with >15:1 diastereoselectivity (Scheme
33.15). Pd-mediated regioselective oxidation (! 92), followed by Wacker oxidation,
completes a four-step enantioselective synthesis of the anticancer agent clavularin
B (42% overall from commercially available 84) [32].
Scheme 33.15. Application of Cu-catalyzed asymmetric

conjugate additions to the enantioselective total synthesis of
anticancer agent clavularin B.
33.4
Conclusions and Outlook
The studies summarized in this article represent our research groups attempts
in the past 5 years to establish a reasonably general protocol for the identication
and discovery of chiral catalysts that eect a range of important bond formations
enantioselectively and eciently. By selecting an appropriate class of chiral ligands
that satises the important criteria of modularity, lack of high symmetry, and avail-
ability of multiple but dierentiated binding sites, we have been able to develop cat-
alytic asymmetric CaC bond-forming reactions that involve both early (Ti and Zr)
and late (Cu and Zn) transition metals. Although optimal ligands, metal centers,
protecting groups, and solvents have been typically determined through systematic
screening of parallel libraries, mechanistic knowledge along with basic chemical
intuition are also critical ingredients along the way. These research activities are
the result of the appreciation of the principle that a priori rational design of a
catalyst may be near impossible since highly detailed mechanistic principles are
often not general; such principles can vary with subtle changes in reaction con-
ditions or substrate structure so that, even within a single class of substrates, the
identity of the optimum catalyst may change. These studies are based on the
premise that although the design of a specic catalyst may be impossible, general
mechanistic principles can be utilized to outline a systematic screening protocol
for catalyst identication.
The research described above bears testimony to the fact that this line of research
does not advocate that we abandon rational or rigorous investigations of detailed
mechanisms of important processes. Elements of design and a priori decisions are
still required in determining what collections of catalysts need to be prepared; the
framework is simply broader and thus initial bias that may be based on a few ini-
tial observations has less of a chance to point us in the wrong direction.
A diversity-based strategy allows us to base our mechanistic hypotheses on a
much wider pool of data points it discourages us from making naive generalities,
which are more than often revised soon after a few additional experiments. As
demonstrated in the above studies, mechanistic studies based on data that are col-
lected from parallel libraries can provide additional logic and impetus for future
eorts in reaction development.
Acknowledgments
First and foremost, I thank my friend, colleague, and collaborator Professor Marc
Snapper. I am grateful to Dr Joseph Harrity, Dr Ken Shimizu, Dr Bridget Cole, Dr
Clinton Krueger, Mr Kevin Kuntz, Dr Carolyn Dzierba, Mr James Porter, Mr John
Traverse, Ms Courtney Luchaco-Cullis, Dr Hirotake Mizutani, Ms Sylvia Degrado,
Dr Wolfgang Wirschun, Ms Kerry Murphy, Mr Nathan Josephsohn, and Mr John
Gleason for making numerous invaluable intellectual and experimental contribu-
tions to the projects discussed in this article. Research in our laboratories is gen-
erously supported by the National Institutes of Health (GM-47480, GM-57212, and
postdoctoral fellowships F32-GM-17821 and F32-GM-18209). Additional support
has been provided by the National Science Foundation (CHE-9632278), Johnson
and Johnson, Pzer, DuPont, AstraZeneca, Albemarle, ArQule, Dreyfus Founda-
tion, Sloan Foundation, and Deutsche Forschungsgemeinschaft (postdoctoral fel-
lowship to W.W.).
Endnotes and References
1 Jacobsen, E. N., Pfaltz, A., is implied (as is often the case) that
Yamamoto, H. (eds), Comprehensive numerous catalysts are prepared, and
Asymmetric Catalysis. Springer, Berlin then after a period of trial and error a
1999. catalyst is determined to be optimal,
2 The word design is described in the such an excercise should be referred
Unabridged Webster English Dictionary to as a linear screening. In such a
in the following manner: To conceive case, the plan for the direction of
and plan out in mind. Based on such screening and not the catalyst itself
a denition, it is unlikely that a is conceived based on the existing
chemist can, in general, consider mechanistic data.
mechanistic data and directly design a 3 a) K. D. Shimizu, M. L. Snapper, A.
catalyst that proves to be optimal in H. Hoveyda, Chem., Eur. J. 1998, 4,
selectivity and reactivity. If by design it 18851889; b) M. B. Francis, T. F.
Jamison, E. N. Jacobsen, Curr. Opin. Chem., Int. Ed. Engl. 1997, 36, 1704
Chem. Biol. 1998, 2, 422428; c) H. B. 1707.
Kagan, J. Organomet. Chem. 1998, 11 a) C. A. Krueger, K. W. Kuntz, C. D.
567, 36; d) K. W. Kuntz, M. L. Dzierba, W. G. Wirschun, J. D.
Snapper, A. H. Hoveyda, Curr. Opin. Gleason, M. L. Snapper, A. H.
Chem. Biol. 1999, 3, 313319; e) B. Hoveyda, J. Am. Chem. Soc. 1999, 121,
Jandeleit, D. J. Schaefer, T. S. 42844285; b) J. R. Porter, W. G.
Powers, H. W. Turner, W. H. Wirschun, K. W. Kuntz, M. L.
Weinberg, Angew. Chem. 1999, 111, Snapper, A. H. Hoveyda, J. Am.
26482689; Angew. Chem. Int. Ed. Chem. Soc. 2000, 122, 26572658.
Engl. 1999, 38, 24942532; f ) M. L. 12 For a review on catalytic asymmetric
Snapper, A. H. Hoveyda in: additions to imines, see: S.
Combinatorial Chemistry. Fenniri, H. Kobayashi, H. Ishitani, Chem. Rev.
(ed.), Oxford University Press, Oxford 1999, 99, 10691094.
2000, pp. 433455. 13 For related studies on catalytic
4 For a recent review regarding the use asymmetric cyanide addition to
of some non-C2 -symmetric chiral imines, see: a) M. S. Iyer, K. M.
ligands in metal-catalyzed enantio- Gigstad, N. D. Namdev, M. Lipton,
selective reactions, see: a) A. Pfaltz J. Am. Chem. Soc. 1996, 118, 4910
in: Stimulating Topics in Organic 4911; b) M. S. Sigman, E. N.
Chemistry. Shibasaki, M., Stoddard, Jacobsen, J. Am. Chem. Soc. 1998,
J. F., Vogtle, F. (eds), VCH-Wiley, 120, 49014902; c) M. S. Sigman,
Weinheim 2000, pp. 89103; b) G. E. N. Jacobsen, J. Am. Chem. Soc.
Helmchen, A. Pfaltz, Acc. Chem. 1998, 120, 53155316; d) H. Ishitani,
Res. 2000, 33, 336345. S. Komiyama, S. Kobayashi, Angew.
5 For example, see: K. B. Hansen, Chem., Int. Ed. Engl. 1998, 37, 3186
J. L. Leighton, E. N. Jacobsen, J. 3188; e) E. J. Corey, M. J. Grogan,
Am. Chem. Soc. 1996, 118, 10924 Org. Lett. 1999, 1, 157160; f ) H.
10925. Ishitani, S. Komiyama, Y. Hasegawa,
6 a) H. Steinhagen, G. Helmchen, S. Kobayashi, J. Am. Chem. Soc.
Angew. Chem., Int. Ed. Engl. 1996, 35, 2000, 122, 762766; g) M. Takamura,
23392342; b) M. Shibasaki, H. Y. Hamashima, H. Usuda, M. Kanai,
Sasai, T. Arai, Angew. Chem., Int. Ed. M. Shibasaki, Angew. Chem., Int. Ed.
Engl. 1997, 36, 12361256. Engl. 2000, 39, 16501652.
7 For an example, see: M. Sawamura, 14 a) See reference 12; b) M. C. Hansen,
H. Nagata, H. Sakamoto, Y. Ito, S. L. Buchwald, Org. Lett. 2000, 2,
J. Am. Chem. Soc. 1992, 114, 2586 713715, and references cited
2592. therein.
8 a) H. Nitta, D. Yu, M. Kudo, A. 15 N. S. Josephsohn, K. W. Kuntz, M.
Mori, S. Inoue, J. Am. Chem. Soc. L. Snapper, A. H. Hoveyda, J. Am.
1992, 114, 79697975; b) A. Mori, H. Chem. Soc. 2001, 123, 1159411599.
Abe, S. Inoue, App. Organomet. Chem. 16 J. R. Porter, J. F. Traverse, A. H.
1995, 9, 189197. Hoveyda, M. L. Snapper, J. Am.
9 B. M. Cole, K. D. Shimizu, C. A. Chem. Soc. 2001, 123, 984985.
Krueger, J. P. A. Harrity, M. L. 17 For other catalytic asymmetric
Snapper, A. H. Hoveyda, Angew. alkylations of imines, see: a) S. E.
Chem. 1996, 108, 17761779; Angew. Denmark, C. M. Stiff, J. Org. Chem.
Chem., Int. Ed. Engl. 1996, 35, 1668 2000, 65, 58755878; b) S. E.
1671. Denmark, N. Nakajima, O. J.-C.
10 K. D. Shimizu, B. M. Cole, C. A. Nicaise, J. Am. Chem. Soc. 1994, 116,
Krueger, K. W. Kuntz, M. L. 87978798; c) H. Fujihara, K. Nagai,
Snapper, A. H. Hoveyda, Angew. K. Tomioka, J. Am. Chem. Soc. 2000,
Chem. 1997, 109, 17811785; Angew. 122, 1205512056; for a related review,
see: d) S. E. Denmark, O. J.-C. phosphates with soft nucleophiles,

Nicaise, Chem. Commun. 1996, 999 see: b) G. C. Lloyd-Jones, A. Pfaltz,
1004. Angew. Chem. 1995, 107, 534; Angew.
18 J. R. Porter, J. F. Traverse, A. H. Chem. Int. Ed. Engl. 1995, 34, 462
Hoveyda, M. L. Snapper, J. Am. 464.
Chem. Soc. 2001, 123, 1040910410. 25 Tripeptide 57 and its derived Me ester
19 For previous work from these aord similar results.
laboratories in connection to catalytic 26 a) F. Dubner, P. Knochel, Angew.
asymmetric allylic substitutions with Chem. 1999, 111, 391393; Angew.
hard alkylmetals and other related Chem. Int. Ed. Engl. 1999, 38, 379
studies, see: a) A. H. Hoveyda, N. M. 381; b) F. Dubner, P. Knochel,
Heron in: Comprehensive Asym- Tetrahedron Lett. 2000, 41, 92339237;
metric Catalysis. Jacobsen, E. N., moreover, in referene 24b, a catalytic
Pfaltz, A., Yamamoto, H. (eds), alkylation of 1a with nBuMgCl to
Springer, Berlin 1999, pp. 431454; aord 2a is reported to proceed in
for a review concerning catalytic 10% ee (92% SN 2 0 ).
asymmetric addition of soft 27 For previous enantioselective total
nucleophiles to olens, see: b) B. M. syntheses of sporochnol, see: a) M.
Trost, V. L. van Vranken, Chem. Rev. Takahashi, Y. Shioura, T.
1996, 96, 395422. Murakami, K. Ogasawara,
20 For a review of catalytic enantio- Tetrahedron: Asymmetry 1997, 8, 1235
selective methods for the synthesis of 1242; b) T. Kambikubo, M. Shimizu,
quaternary carbon stereogenic centers, K. Ogasawara, Enantiomer, 1997, 2,
see: E. J. Corey, A. Guzman-Perez, 297301; c) A. Fadel, L. Vandromme,
Angew. Chem. 1998, 110, 402405; Tetrahedron: Asymmetry 1999, 10,
Angew. Chem. Int. Ed. Engl. 1998, 37, 11531162.
388401. 28 For a review on asymmetric catalysis
21 C. A. Luchaco-Cullis, H. Mizutani, in target-oriented synthesis, see: A. H.
K. E. Murphy, A. H. Hoveyda, Angew. Hoveyda in: Stimulating Topics in
Chem., Int. Ed. Engl. 2001, 40, 1456 Organic Chemistry. Vogtle, F.,
1460. Stoddart, J. F., Shibasaki, M. (eds),
22 a) C. C. Tseng, S. D. Paisley, H. L. VCH-Wiley, Weinheim 2000, pp. 145
Goering, J. Org. Chem. 1986, 51, 162.
28842891; b) J.-E. Backvall, M. 29 For previous studies on the catalytic
Sellen, B. Grant, J. Am. Chem. Soc. asymmetric conjugate additions, see:
1990, 112, 66156621. a) B. L. Feringa, M. Pineschi, L. A.
23 For Cu-catalyzed (nonasymmetric) Arnold, R. Imbos, A. H. M. de Vries,
addition of organotitanium and Angew. Chem., Int. Ed. Engl. 1997, 36,
organozirconium reagents to allylic 26202623; b) E. L. Strangeland, T.
phosphates, see: a) A. Masayuki, E. Sammakia, Tetrahedron 1997, 53,
Nakamura, B. H. Lipschutz, J. Org. 1650316510; c) R. Naasz, L. A.
Chem. 1991, 56, 54895491; b) L. M. Arnold, M. Pineschi, E. Keller,
Venanzi, R. Lehmann, R. Keil, B. H. B. L. Feringa, J. Am. Chem. Soc. 1999,
Lipschutz, Tetrahedron Lett. 1992, 33, 121, 11041105; d) A. Alexakis, C.
58575860. Benhaim, X. Fournioux, A. van den
24 For Cu-catalyzed asymmetric Heuvel, J.-M. Leveque, S. March, S.
alkylation of allylic phosphates with Rosset, Synlett 1999, 18111813; e) X.
Grignard reagents, see: a) M. van Hu, H. Chen, X. Zhang, Angew.
Klaveren, E. S. M. Persson, A. del Chem., Int. Ed. Engl. 1999, 38, 3518
Villar, D. M. Grove, J-E. Backvall, 3521; f ) Y. Yamanoi, T. Imamoto, J.
G. van Koten, Tetrahedron Lett. 1995, Am. Chem. Soc. 1999, 64, 29882989;
36, 30593062; for W-catalyzed g) I. H. Escher, A. Pfaltz, Tetra-
asymmetric alkylation of allylic hedron 2000, 56, 28792888; h) I.
Chataigner, C. Gennari, U. thus involved variations at AA1 and

Piarulli, S. Ceccarelli, Angew. Chem., AA2. Further details will be disclosed
Int. Ed. Engl. 2000, 39, 916918. in the full account of this work.
30 S. J. Degrado, H. Mizutani, A. H. 32 For previous total syntheses of
Hoveyda, J. Am. Chem. Soc. 2001, 123, clavularin B, see: a) R. Tamura, K.
755756. Watabe, N. Ono, Y. Yamamoto, J.
31 In all screenings, two sets of ligands Org. Chem. 1993, 58, 44714472; b)
involving Gly and nBu as AA3 were K. Hiroya, H. Zhang, K. Ogasawara,
examined. Structural modications Synlett 1999, 592532.
1017
34
Combinatorial Aspects of Materials Science
Bill Archibald, Oliver Brummer, Martin Devenney,
Daniel M. Giaquinta, Bernd Jandeleit, W. Henry Weinberg, and
Thomas Weskamp
Abstract
Combinatorial chemistry, coupled with high-throughput screening and integrated

data management systems, has forever changed the drug discovery process, prom-
ising to bring to the marketplace more drug entities per unit time than ever before.
With rising economic demands to increase eciency in other areas of research
and development, it is not surprising that a similar paradigm is taking hold in the
chemical industry as a whole. In particular, combinatorial synthesis and sophisti-
cated screening technologies are now being applied to the discovery of more e-
cient materials, and with these new technologies come the promise of faster com-
mercialization rates and reduced research and development costs.
The combinatorial process aims at eciently exploring the large parameter
space that controls the properties of a material through the application of rapid
parallel or combinatorial synthesis and subsequent high-throughput characteriza-
tion for a given application. Certain synthesis and screening protocols developed in
the pharmaceutical industry can be adapted to the new areas of research, whereas,
in other areas, a completely new set of techniques must be developed. Unlike in
the pharmaceutical industry where aspects such as solvent, temperature, and addi-
tives are held constant to eliminate assay variability, the examination of processing
conditions in the search for new materials is a critical component of the combina-
torial search. The variation of process and reaction conditions, combined with par-
allel synthesis, results in an exponential increase in the total number of experi-
ments, dramatically increasing the chances of identifying a new material.
Over the past 6 years, since the initial application of combinatorial methods to
materials science discovery research, tremendous advances in this rapidly grow-
ing eld have been made in the academic, private, and public sectors. The goal
of this review is to examine the contributions made during this time period and
to provide insight as to what the future may hold for combinatorial materials
research.

ISBN: 3-527-30509-2
1018 34 Combinatorial Aspects of Materials Science
34.1
Introduction
With increasing competition in the chemical industry, new products must be

brought to the market place rapidly. Global market pressures are driving the chem-
icals and advanced materials industries to improve research and development
(R & D) productivity as measured by return on investment. Principal drivers in-
clude reduced cycle times and higher quality at lower cost, with reduced environ-
mental impact.
This dilemma was rst encountered in the pharmaceutical industry, where long
development times and high research costs necessitated the introduction of new
research approaches to accelerate the drug discovery process. Virtually every major
drug manufacturer now applies this new research technology, combinatorial
chemistry, as the cornerstone of its research and development program; routinely,
libraries of up to 1,000,000 distinct compounds are synthesized and screened for
biological activity. This approach is feasible both because of the fact that technol-
ogy challenges have been addressed, as well as because of the broad availability of
low-cost computers, reliable robotics, molecular modeling, experimental design
strategies, and database software tools [110]. The advent of combinatorial chem-
istry thus created novel research areas such as chemoinformatics to manage the
huge amount of structural and functional information obtained from library-based
research [11].
This new paradigm is now taking hold in the R & D centers of American, Euro-
pean, and Japanese advanced materials industries where combinatorial method-
ologies are being increasingly applied. Among others, advanced materials comprise
optical and electronic materials, polymers, and catalysts for commodity, specialty,
and ne chemical application. Combinatorial techniques represent a powerful re-
search strategy when applied to problems where complex interactions within an ex-
tensive parameter space dictate the properties of a material, and these techniques
will unquestionably inuence the way materials research is carried out in these
elds in the future.
For example, in the case of heterogeneous catalysis, where active sites exist on the
exterior and/or interior surface of a porous solid-state inorganic material, library
synthesis can be carried out by a variety of deposition methods. In the case of
homogeneous catalysis, where the active site is most often a metal ion stabilized
by organic ligands, library synthesis may be carried out using combinatorial ligand
synthesis. This process allows combinatorial homogeneous catalysis to rapidly take
advantage of the numerous solid- and solution-phase synthetic combinatorial
methodologies, including polymer-supported reagents [1217].
Three dierent approaches to the task of preparing and testing libraries of com-
pounds exist (Fig. 34.1). Conventional research provides thorough quality control
at the expense of throughput in a one-at-a-time or serial manner of synthesis
and characterization. Truly combinatorial methods involving split-and-pool syn-
theses are much faster and allow for the preparation of large numbers of com-
pounds, but often lack control over the purity of the compounds entering the assay
Fig. 34.1. Conventional, parallel, and pooled approaches to synthesis and screening.
screen. Methods intermediate between these two extremes are based on parallel or
array syntheses, in a spatially addressable format with usually one compound per
well or region, coupled to automated screens.
A SciFinder9 reference search performed in February 2001 using the key word
combinatorial resulted in more than 9000 hits. An analysis of the literature
search demonstrates the tremendous growth of scientic publications and patent
applications in the combinatorial eld. Although most contributions deal with com-
binatorial applications within pharmaceutical, biological, and medical disciplines,
recent years have witnessed signicant advances in the development of combina-
torial approaches to the discovery and optimization of new materials and catalysts,
as is clearly shown by the increasing number of scientic publications and patent
applications during the last few years within these areas. Additionally, an increas-
ing number of review articles on the application of combinatorial methods to cata-
lyst discovery and optimization, a process dubbed combinatorial catalysis, has
appeared in the recent literature [18]. Furthermore, recent advances of combinato-
rial chemistry and high-throughput screening for chemical process development
have been reviewed [19, 20]. Consequently, several recent reviews address combi-
natorial high-throughput methodologies and experimental strategies in further de-
tail [2132].
This chapter, covering the years 1995 to 2001, summarizes the latest develop-
ments in the application of combinatorial methodologies to the discovery of new
solid-state and organic polymeric materials. Patents, patent applications, and con-
ference proceedings have generally not been included but are well appreciated and
acknowledged. Combinatorial approaches to catalyst discovery and process opti-
mization will be treated in a subsequent chapter.
After this introductory section, the following section, Section 34.2, summarizes
the eorts in combinatorial materials science beginning with a general overview
of combinatorial materials synthesis techniques. Section 34.3 describes examples
of novel high-throughput screening technologies, while Section 34.4 summarizes
some applications of combinatorial methods in the search for novel or improved
electronic, magnetic, and optical properties. Section 34.5 describes case studies
showing the application of combinatorial techniques to the discovery of a new
phosphor and an example of the application of combinatorial methodologies ap-

plied to the optimization of thin-lm layers in an organic light-emitting device
(LED) device. Combinatorial methods in polymers are described in Section 34.6.
Section 34.7 includes a summary and an outlook concerning the future of combi-
natorial materials science.
34.2
Combinatorial Solid-state Materials Science
The properties of solid-state materials often arise from complex interactions involv-
ing the host structure, dopants, defects, and interfaces. Therefore, they depend sen-
sitively on both composition and processing conditions. Few general principles
have emerged that allow the prediction of structure beyond binary systems and the
resulting properties of such solid-state compounds. Conventional one-at-a-time
synthesis and characterization can be a long and expensive process, and combina-
torial materials science holds great promise in facilitating the materials discovery
and optimization enterprises.
Conventional materials research typically begins with a decision on a general-
phase space which targets a property of interest and which is based on a set of
physical or chemical constraints, many of which may be empirically or intuitively
grounded. This parameter space is then divided into discrete compositions that
must be synthesized and screened for properties of interest. Chemical additions,
substitutions, and modications of synthesis and processing conditions allow the
researcher to optimize the properties of a given system. This process is typically
long and laborious, and may or may not lead to a promising material. The inte-
grated application of rapid synthesis, high-throughput screening, and sophisticated
data analysis allows for a promising alternative to the time-consuming classical
methodology. However, a well thought-through experimental design of the experi-
ments (DOE) is required to reduce the number of samples that will be necessary to
dene sample spaces within the experimental universe or to direct screening to
other spaces (feedback loop).
The combinatorial process relies on the implementation and coupling of high-
speed synthesis and high-throughput screening techniques. These methods facili-
tate more ecient explorations of a given composition space and oer a valuable
tool for the investigation of ternary and higher order systems. However, it is often
impossible to rapidly synthesize materials the physical characteristics of which (e.g.
composition, microstructure, grain size, and density) are exactly the same as mate-
rials made using the nal production process. Similarly, screening of desired prop-
erties is often very slow. Thus, combinatorial studies are based on the predictive
capabilities of synthesis and screening tools, and the challenge of the combinatorial
process is to implement appropriate synthesis and screening techniques. Rather
than comparing the properties of a few specic compositions within a phase space,
entire phase spaces can now be examined in a single experiment. The rst library
of compounds is often a broad compositional search covering an entire phase space,
Fig. 34.2. Schematic process of the combinatorial materials

discovery and optimization paradigm. Large numbers of
diverse compounds are rapidly synthesized and screened for
desired properties.
e.g. an entire ternary composition diagram (Fig. 34.2). A primary screen speci-
cally developed to evaluate the very large number of compositions within that li-
brary identies a particular composition or range of compositions that is of further
interest. Primary screens are typically designed to eliminate a large fraction of the
compositions studied in the rst library, while secondary and follow-up libraries
examine a more narrow range of compositions as well as additional chemical sub-
stitutions and processing conditions. Optical and electronic properties such as
capacitance or luminescence are examples of physical properties that may be e-
ciently examined in high-throughput primary screens.
At the follow-up level, more detailed information can be obtained from high-
throughput secondary screens because the number of compounds that must be
screened has been greatly reduced. This process of synthesis, screening, and opti-
mization continues until a manageable number of compositions has been reached.
These selected compositions, all of which have passed previous screens, can now be
studied using conventional methods to obtain the more precise chemical and phys-
ical data necessary to characterize a material completely. Combinatorial methods
can thus act as an ecient lter for conventional methods by selecting only the best
candidates for further, more detailed study.
34.2.1
Materials Library Synthesis
Several synthesis techniques have been developed for combinatorial materials li-
brary formation. Some materials can be made using solution deposition methods,
while others are more suited for thin-lm deposition [3338]. By modifying tech-
nologies similar to those used to make integrated circuit (IC) chips, materials
libraries or integrated materials (IM) chips were rst developed and utilized by
Schultz and coworkers [39]. The choice of synthesis technique is based on both the
material being prepared as well as the primary screen employed after synthesis.
Unlike the case of drug discovery, however, the synthesis of solid-state materials
often relies on processing temperatures in excess of 400 C. High-temperature re-
action conditions have been addressed through the creation of two-dimensional,
spatially addressable arrays of samples deposited on thermally stable substrates.
34.2.2
Vapor Deposition Techniques
Vapor deposition is commonly used in the semiconductor industry to deposit thin

lms of material onto a substrate. Vapor deposition techniques that have been uti-
lized in combinatorial library synthesis include sputtering [21, 22, 40, 41] and ther-
mal evaporation [23, 4246], electron-beam evaporation [29], pulsed laser ablation
[21, 47, 48], ion-beam implantation [4952], molecular-beam epitaxy [24, 5356],
and chemical vapor deposition [57].
One of the most straightforward thin-lm approaches is the continuous compo-
sition spread (CCS) technique, which utilizes two or three o-axis sources to co-
deposit material on a substrate [41]. This technique relies on the nonuniform depo-
sition of materials formed by the geometric arrangement between the sources and
the substrate. The relative concentration of each component at a specic location
on the substrate decreases with the distance from the source. As materials spread
from the sources, they mix in the vapor and are deposited on the substrate creating
atomic-level mixing that reduces or eliminates the need for high-temperature post-
processing of the library. This technique is also amenable to the isolation of meta-
stable or low-temperature phases that are crystalline on deposition. The lack of pre-
cise stoichiometric control and limited compositional range have relegated this
technique primarily to optimization and exploration of systems with only two inde-
pendent variables.
A typical vacuum deposition system for combinatorial materials science has sev-
eral source materials and is used in conjunction with masking techniques (physi-
cal or shadow masks, movable shutters, or photolithography) to deposit dierent
Fig. 34.3. Binary and quaternary masking strategies for

combinatorial material library synthesis. See text for details.
materials, sequentially or simultaneously, in particular areas of the substrate. The

design of the masks and the sequence in which they are employed determine
which materials are deposited at any given location on the substrate. By altering the
sequence, time, and rate of deposition, it is possible to control the exact chemical
composition of each element in the library.
The eciency with which a particular compositional landscape may be exam-
ined is dictated by the masking strategy employed [58]. Simple binary and gradient
masks are useful for optimizing the composition of a known material. In the
binary masking strategy, half of the substrate is exposed to dierent masking pat-
terns (1, 2, 4, . . . strips oriented in two dierent directions) in each step (Fig. 34.3).
After N steps, the number of dierent compositions is 2 N , including all possible
combinations of N elements. Gradient or x/ y shutter masking utilizes movable
masks that either expose or block certain areas of the substrate, allowing for con-
trolled concentration and/or thickness variations in the deposited lms.
Quaternary masking strategies have been developed to enable ecient genera-
tion of diverse libraries containing materials with very dierent compositions [30].
In the quaternary masking scheme, deposition is carried out using a series of N
dierent masks that successively subdivide the substrate into a series of nested
quadrant patterns (Fig. 34.3 and Fig. 34.4). Each mask is used for up to four deposi-
tions, but after each deposition the mask is rotated by 90 . With N dierent masks,
this process will generate up to 4 N dierent compositions in just 4N deposition
steps. The r th 1 a r a N mask contains 4 r1 windows, where each window ex-
poses one-quarter of the area deposited using the preceding r 1 th mask. Within
each window is an array of 4 Nr openings, which can be provided by means of an
underlying contact mask or created directly on the substrate by photolithographic
techniques [33, 34, 5961]. Each section of the substrate is thus exposed to a dier-
ent combination of precursors by depositing each layer through a dierent mask.
Fig. 34.4. The quaternary masking system uses six fractal

masks, each of which can be rotated 90 to allow four choices
of materials at each level.
Thin-lm deposition methods are synthetically quite versatile; they have pro-
gressed to enable atomic- and molecular-layer epitaxy and oer the ability to con-
struct articial lattices, epitaxial overlayers, and patterned lms of a variety of
materials. Dopants are usually sandwiched between layers of the host material to
avoid evaporation and to assure proper interdiusion. Subsequent thermal pro-
cessing results in a library of materials or devices the physical properties of which
can be screened with either contact or noncontact screening probes. The number
of compounds that can be simultaneously synthesized by this technique is limited
by the spatial resolution of the masks and by the degree to which synthesis can be
carried out on a microscale.
One can use either physical shadow masks [39] or photolithographic lift-os [61]
to carry out masking. Photolithography, a standard process in the semiconductor
industry, has a high level of spatial resolution and accuracy and can generate chips
with a high density of diverse compositions (up to 10 6 per square inch). The mul-
tilayer thin-lm deposition may result in the synthesis of multiple binary phases
rather than the desired multielement single-phase material, a result that may be
avoided through the use of an eective two-step annealing process [33]. Early nu-
cleation and thus binary-phase formation is avoided by deposition at relatively low
temperatures. If the thickness of the deposited layer is less than a critical value
(material dependent) of typically 110 nm, diusion is dominant over nucleation
for sequential precursor layers. Johnson and coworkers have advanced this elegant
technique based on the sequential controlled deposition of thin lms [62]. Using
Johnsons method, an extended period of low-temperature (100400 C) annealing is
performed for proper interdiusion of thin-lm precursors. Subsequently, crystalli-
zation of the intermediate, amorphous material is induced by a high-temperature
annealing process allowing growth of entire integrated materials chips [63]. Grow-
ing entire integrated materials chips in this fashion is crucial for many materials,
where the material properties are closely tied to the crystalline quality of the lms.
Reection high-energy electron diraction (RHEED) has been proposed for in
situ monitoring of molecular beam epitaxial (MBE) deposition [35].
Pessaud and coworkers utilized pulsed laser ablation of two compound targets
made of superconducting YBa2 Cu3 O7 (YBCO) and the double-chain insulator
MCuO2 (M Ca, Sr) in an attempt to create new metastable superconducting
compounds [47]. The goal of this exploration was to deposit m consecutive layers
of YBCO with n layers of MCuO2 in an attempt to use the two-dimensional struc-
ture of YBCO as a structural template so that MCuO2 would form additional con-
ducting CuO2 planes upon deposition. The technique has led to the identication
of a number of new phases with enhanced critical temperatures and extends the
multilayer deposition concept from elemental targets to compound targets.
Combinatorial thin-lm methods are also being used to optimize the per-
formance of multiwavelength emitting chips that show potential applications in
wavelength-divisible multiplexing (WDM). Multiwavelength emission has been
achieved using selective area epitaxy and postgrowth selective region intermix-
ing. Layer intermixing techniques have achieved wavelength shifting through
implantation-induced intermixing, which is dicult to control.
Liu and coworkers used arsenic and proton implantation to create a multi-
wavelength-emitting library of doses and species-dependent intermixing,
which they analyzed by microphotoluminescence at room temperature [50].
Al0:35 Ga 0:65 As/GaAs single quantum wells were grown on GaAs (001) substrates
by MBE. Ion implantation was accomplished using four dierent pattern masks
on an 8 8 hollow circle-patterned blank mask in sequence. Four rows of ele-
ments implanted with dierent As doses at an ion energy of 90 keV were obtained.
The four masks were then rotated 90 for proton implantation at an ion energy of
40 keV. The fth column and the fth row were implanted with protons only and
As only. The implanted chip was annealed in a rapid thermal annealer (RTA) at
950 C, and the microphotoluminescence measured at room temperature. Using
this technique Liu and coworkers were able to generate more than 20 dierent
wavelengths from a single chip.
Amorphous materials have been investigated in a combinatorial optimization of
hydrogenated amorphous silicon (a-Si:H)-based thin-lm transistor (TFT) devices
by Koinuma and coworkers using plasma-enhanced chemical vapor deposition
[57b]. A contact mask placed over the indiumtin oxide substrate and sequential
depositions were carried out through a moving slit mask. A 90 substrate rotation
followed by deposition of hydrogenated amorphous silicon nitride (a-SiN:H) allows
for systematic investigation of the eects of thickness and compositional variation
across the library. Source and drain contacts were deposited on the top of the bi-
layers by aluminum evaporation to allow the currentvoltage characteristics of the

devices to be characterized.
34.2.3
Alternative Library Synthesis Techniques
Synthesis for many materials, e.g. zeolites, polymers, polycrystalline phosphors,

and many other oxides and suldes is best accomplished using solution-phase
methods. When applicable, solution-phase methods provide a large number of li-
braries at a signicantly lower capital investment relative to automated vapor depo-
sition equipment. Solution-phase methods may result in improved compositional
control. One signicant complication associated with materials discovery in thin-
lm format is the occasional lack of correlation with bulk properties owing to dif-
ferences caused by lm microstructure, strain, and so on. Physical and chemical
properties of compounds prepared using solution techniques generally show excel-
lent correlation with bulk properties regardless of the quantity of material pre-
pared. Thus, library-based data may be easily conrmed in bulk.
Solution techniques allow mixing at the molecular level, reducing the need for
high-temperature interdiusion and also facilitating the isolation of metastable
phases. Xiang, Schultz, and coworkers have demonstrated that a scanning multi-
head inkjet delivery system can be used to perform automated microsynthesis of
solid-state libraries, enabling rapid delivery and accurate control of nanoliter depo-
sition volumes [34, 64]. Droplets are delivered sequentially to single reaction wells;
the droplet size is on the order of 500 pL with reproducibility better than 1% and a
maximum delivery speed of 2000 droplets s1 . The system has been successfully
used to generate libraries of 100 members per inch 2 (100 members per 6.49 cm 2 ),
and a system to generate 1000 members per inch 2 (1000 members per 6.49 cm 2 )
is under development.
Sol-gel processing of glasses and ceramics provides an eective method for fab-
ricating inorganic nanostructured materials that is amenable to combinatorial
methods. Molecular precursors, such as metal alkoxides, are typically used as
starting materials [65, 66]. The process begins with the formation of arrays of
homogeneous sols with desired compositions through the use of automated
liquid-dispensing robots. The sol is then converted to a gel, while maintaining
its homogeneity and purity. A solid network is obtained through hydrolysis and
condensation reactions. The technique has been applied in the investigation of
phosphors [65] and oxide semiconductors [66], and in the synthesis of polymer/
vanadium oxide nanocomposites [67].
Multicomponent zeolite synthesis is another area of advanced solid-state mate-
rials research in which combinatorial discovery and optimization can be successfully
applied. A multiautoclave system capable of performing at least 100 crystalliza-
tions under hydrothermal conditions has been reported by Akporiaye and col-
leagues [68]. In its simplest form, the reactor consists of a Teon block with cylin-
drical holes, designed to accommodate Teon-coated septa, which is sandwiched
between two steel plates. The capability to stack identical synthesis blocks allows
for the parallel synthesis of in the order of 1000 combinations in one experiment.
The system was tested by reproducing the phase diagram of the intensively studied
ternary phase system Na2 O/Al2 O3/SiO2/H2 O in a single experiment and under
identical reaction conditions. With a total volume of each sample gel of not more
than 0.5 mL, crystalline phases of zeolite A, faujasite, and gmelinite were obtained,
with the region of zeolite A coinciding almost perfectly with earlier results for bulk
materials. Good agreement was also obtained in the case of faujasite. The forma-
tion of sodalite was only observed in a more recent investigation. This partial agree-
ment was attributed to better control of the water content in the parallel autoclave.
The attractiveness of combinatorial methods for hydrothermal synthesis was
also realized by Klein et al., who claim that the advantage of their reactor over the
one described above is their much smaller reaction volume, in the order of 2 mL, as
well as the direct preparation of a library of materials the components of which
can be identied automatically on the library substrate by X-ray microdiraction
(Fig. 34.5) [69]. The central feature of Kleins reactor is a silicon wafer that, after
hydrothermal synthesis and calcination, contains the sintered reaction products and
represents the library. The identication of the individual products may be directly
performed with a GADDS (General Area Detector Diraction System) micro-
diractometer. Choi and coworkers designed a centrifuge apparatus that allows
quantitative product recovery onto lter paper for X-ray microdiraction without
manipulation of the individual samples [70]. Furthermore, Lai and coworkers
demonstrated parallel synthesis of zeolite lms in a 21-well reactor using a vertical
substrate conguration to provide uniform wetting that favored heterogeneous
lm growth in an organic-free clear solution [71]. The results of the synthesis of
Fig. 34.5. Schematic cross-section of the multireactor autoclave.

template molecules and metal components, followed by a qualitative indication

showing that the materials formed are amorphous or crystalline, conrm that
zeolite synthesis on a microgram scale is possible and justied.
A solution-based combinatorial strategy has been described by Baker and co-
workers for synthesis of surfaces exhibiting nanometer-scale variation in mixed-
metal compositions and architecture [72]. Continuous or stepped gradients in the
size and number density of surface features can be generated simultaneously
over dierent regions of a single substrate. Baker et al. and Kneipp et al. prepared
libraries of Ag-clad colloidal Au arrays in which the coverage of colloidal Au and the
extent of the reductively deposited Ag coating were varied in an attempt to opti-
mize the enhancement factor for surface-enhanced Raman scattering (SERS)
[72, 73]. A sulde-functionalized glass slide was immersed at a constant rate into
an aqueous solution of colloidal gold, and the plate was then rotated by 90 and
lowered at a xed rate into a solution of Ag . As a result, a library was generated
containing approximately 10 8 colloids that diered in their particle size and Ag
coverage. Para-nitrosodimethylaniline was adsorbed onto this surface and the sur-
face-enhancement factor of the Raman scattering of this compound was measured.
The values spanned approximately three orders of magnitude across the library
and allowed for identication of a region of the library that gave the greatest en-
hancement. Atomic force microscopy was then used to determine the nanometer
scale morphologies of these regions of interest. The availability of dispersible
metal-containing nanoparticles and the numerous routes to metal deposition from
complexed metal cations should allow for extension of this method to a variety of
other metals.
A scheme for generating complex, spatially separated patterns of multiple types
of semiconducting and/or metallic nanocrystals has been presented by Vossmeyer
and colleagues [38]. Nanocrystals may play an important role in future technologies
such as photovoltaics, switches, phosphors, light-emitting diodes, electronic data
storage systems, and sensors. Most of the photonics and electronics applications
will eventually require parallel schemes for the control of spatial positioning of the
nanocrystals. Standard patterning techniques such as laser ablation of the material
and deposition through a shadow mask do not work well for nanocrystals since
most metal and semiconductor nanocrystals have covalently bound organic surfac-
tants that tend to desorb at temperatures above 100 C. Consequently, any pattern-
ing approach must be carried out at low temperatures. The stepwise preparation of
multiple particle arrays is based on lithographic patterning of amino-functionalized
organic monolayers that contain a photolabile protecting group covalently bound
to SiO2 surfaces. The photosensitive substrate is irradiated through a mask in the
near UV, removing the protecting group in the areas exposed to the radiation. To
prepare binary micropatterns consisting of Pt or Au and highly luminescent CdSe/
CdS core/shell nanocrystals, the substrate is treated with a solution of amine-
stabilized metal-containing nanoparticles, which assemble in the area of depro-
tected amino groups. Changing the orientation of the mask, the deprotection step
is repeated and the amine-stabilized CdSe/CdS nanoparticles are assembled onto
areas of freshly deprotected amino groups, yielding a binary nanoparticle array.
Fig. 34.6. Representation of protonated peptide ligand

framework depicting both the variable spacer residues (X, Y,
and Z ) and the individual regions used in informatic analysis.
[X, Y, and, Z a-Glu, g-Glu, a-aminobutyric acid (GABA),
SerGly, e-aminohexanoic acid (e-Ahx)].
Nanocrystal assembly occurs with high selectivity on just one type of the spatially
and chemically distinct sites. The production of binary, ternary, and quaternary
patterns of nanocrystals has been reported, and the procedure appears applicable
for the preparation of multicolored nanocrystal-based color pixels. Moreover, the
technique should be compatible with other lithographic patterning steps, such as
those involved in the formation of electrical contacts, capacitors, and other device
components of the photonics and microelectronics industries. Furthermore, the
procedure has been demonstrated on a variety of substrates.
A novel approach by Wright and coworkers has shown that combinatorially
derived peptide and peptidomimetic ligands based on phytochelatins can stabilize
CdS nanoclusters [7476]. Using the 7-mer sequence XaCysaYaCysaZaCysaGly
of n3 -phytochelatin as a lead structure, Wright and coworkers employed standard
Fmoc protocols (Fmoc 9-uorenylmethoxycarbonyl) for combinatorial peptide
library synthesis. In their study, the cysteine residues are held constant while the
spacer residues X, Y, and Z are varied over all combinations of the selected spacer
amino acids a-Glu, g-Glu, g-amino butyric acid (GABA), SerGly, and e-Ahx (Fig.
34.6). This approach limits the number of peptides to 125, as opposed to the over
one billion potential ligands obtained if all seven positions are varied over all 20
naturally occurring amino acids. The ve selected spacer residues chosen have be-
tween three and seven atoms in the backbone and can span an idealized extended
C a aC a distance between the cysteines. Using commercial software, quantitative
structureactivity relationship (QSAR) methods were employed to calculate the
molecular numerical properties (descriptors) of the combinatorial peptide library.
The positional analysis of individual amino acids allows the correlation between
the properties of the stabilizing (iso)peptidic ligand and the resultant peptide-
encapsulated CdS nanocluster to be determined.
Many new advanced materials ranging from magnetic materials to bulk metallic
glasses involve alloying multiple elements to control both intrinsic and extrinsic
properties. Permanent magnets, for example, may have a dozen or more elements
included to control grain boundaries and domain wall movement. Cohen-Adad
and coworkers utilized a melting zone technique to investigate AlCo and AlCoFe
alloys [77]. In their method, source materials are cut into wedges and then welded
together into a bar. The bar is then placed in an alumina crucible and drawn
through a horizontal zone furnace to facilitate mixing. The resulting bar is diced
into pieces and the composition at each point along its length measured with
microprobe analysis. The morphology and crystal structure of the materials were
investigated with optical microscopy, dierential thermal analysis, and X-ray dif-
fraction. Inuoe has reviewed similar techniques used to search for new glasses,
which typically have ve or more elements present to inhibit crystallization [25].
34.3
High-throughput Screening
The large numbers of compounds and the speed with which they may be prepared
using the combinatorial synthesis methods described above require automated
high-throughput screening techniques that are capable of equally rapid character-
ization. Typically, the information necessary to classify new materials cannot be
obtained from a single piece of characterization equipment. Therefore, a series of
high-throughput screening tools is employed at various stages in the combinatorial
process to create a screening hierarchy. While a large number of automated com-
mercial systems exist for the high-throughput analysis of microliter samples for
medical and pharmaceutical applications, the vast majority of the screening tools
necessary for advanced materials research are custom-made instruments. Conven-
tional analytical tools such as mass spectrometry, gas and liquid chromatography,
optical and nuclear magnetic resonance spectroscopy, X-ray uorescence micro-
probe [78], and X-ray diraction have been automated and redesigned for rapid
serial measurements of hundreds of samples per day [79, 80]. Several examples of
custom-made high-throughput screening systems are discussed below.
34.3.1
Optical Screening
Optical screening methods, where applicable, oer high-throughput noncontact

screening for combinatorial libraries. Optical screens typically involve either a laser
or ber optic probe that is serially scanned across a library or cameras capable of
imaging library elements in parallel. In studies of luminescent materials, high-
throughput screens have been developed using UV-excited photoluminescence
[81, 82]. A quantitative measure of chromaticity was calculated from three
images obtained using red (602 nm), green (553 nm), and blue (461 nm) band-
pass tristimulus emission lters. The color was quantied by calculating the nor-
malized CIE (Commission Internationale de lEclairage) chromaticity coordinates,
and the relative extrinsic eciencies were estimated from the ratio of the mea-
sured output of the compounds to commercial standards.
Optical transmission and reection measurements have also been utilized to
34.3 High-throughput Screening 1031
determine the band gap of various oxide thin lms. Jin and coworkers [56] and
Makino and coworkers [83] calculated the optical band-gap from the measured
optical absorbance of 81 elements in a library of ZnO thin lms doped with nine
independent 3d-metal ions. Similar transmission and reection methods have been
used in the infrared to estimate band-gaps for thermoelectric and photovoltaic
materials.
Furthermore, Xiang describes an apparatus for the measurement of electro-optic
coecients of thin-lm samples that functions by measuring the polarization mod-
ulation of light passing through a sample [21]. The variation in the index of refrac-
tion upon application of an electric eld is typically small, approximately 0.1%,
making thin-lm measurements dicult. The electro-optic measurements are con-
ducted using the library, a compensator, and a quarter-wave plate which are located
between two crossed polarizers and are illuminated by a HeNe laser. An electric
eld is applied to the sample at 45 to the incident polarization. Given the index of
refraction and some geometric factors, the electro-optic coecients can be deter-
mined.
34.3.2
X-ray Characterization
Structural characterization presents an important issue in high-throughput char-

acterization of solid-state materials. Several groups have created machines capable
of carrying out X-ray microdiraction [78, 79] through the use of intense sources
(rotating anode or synchrotron), and focusing mirrors resulting in an X-ray beam
collimated onto a small spot capable of measuring diraction of thin-lm libraries
(Fig. 34.7). The data collection times are still suciently long that the measure-
ment of a signicant number of library elements takes hours instead of minutes.
Furthermore, exploratory libraries are typically mixed phase, resulting in a com-
plicated analysis that has yet to be dealt with eciently.
Fig. 34.7. Schematic representation of an X-ray microprobe

synchrotron beamline capable of producing a 3 20 mm 2 X-ray
spot on the sample on the library array.
34.4
Applications
34.4.1
Superconductivity
One of the rst demonstrations of combinatorial thin-lm materials exploration

by Schultz and coworkers involved the preparation of libraries of superconducting
copper oxide thin lms by sputtering several metal oxides in sequence onto an in-
ert single-crystal support of either MgO or LaAlO3 [39, 84]. In their initial experi-
ments, arrays containing dierent combinations, stoichiometries, and deposition
sequences of BaCO3 , Bi 2 O3 , CaO, CuO, PbO, SrCO3 , and Y2 O3 were generated
using a series of four and seven binary masks and primary masks having either 16
or 128 openings, respectively, yielding a spatially addressable library of 16 (2 4 ) 2
mm 2 mm and 128 (2 7 ) 1 mm 2 mm samples distributed over a chip with a
surface area of 1 inch 2 . After annealing the entire library at 840 C in an oxidizing
atmosphere, the superconductivity of each sample was evaluated by measuring its
resistance as a function of temperature with an array of small four-point probes
that analyze 64 samples at a time [34]. Superconducting lms of BiSrCaCuOx ,
BiPbCaSrCuOx , and YBa2 Cu3 Ox were identied having critical temperatures in
the range of 8090 K.
Xiang and coworkers have developed a novel scanning evanescent microwave
microscope (SEMM) capable of nondestructive and quantitative mapping of elec-
trical impedance with submicron resolution [21, 85]. Unlike conventional four-
probe methods, the SEMM is a noncontact method, which eliminates dependence
on contact resistance and interfacial eects. The SEMM, shown schematically in
Fig. 34.8, is based on a coaxial microwave resonator with a sharpened tip that
extends through an aperture outside of the resonant cavity. When the probe tip is
near a sample, the interaction of the evanescent eld and the sample changes the
resonant frequency and the ratio between the energy stored in the cavity and the
energy dissipated in the sample, resulting in a measurable change in the electrical
impedance. The microscope is routinely used for characterization of linear and
nonlinear dielectric constants of ferroelectrics and dielectrics. A low-temperature
version has also been developed to characterize superconducting materials.
High-throughput methods are not new to high-TC superconductor research and
several groups utilized pooled samples as a means to increase the throughput of a
conventional magnetometer [86, 87]. Superconductivity is one of the few electronic
properties that can be measured when samples are pooled (mixed together) in a
single vial. In this method, several compositions are synthesized separately and
then mixed together (without heating) to form a single sample. Measurements
of the low-temperature magnetization are performed on the mixture with a Squid
magnetometer searching for a measurable Meissner fraction indicative of super-
conductivity. The presence of a Meissner fraction indicates the presence of super-
conductivity in at least one of the compounds in the mix, the identity of which
must be determined by individually measuring each of the components in that
Fig. 34.8. Schematic representation of a scanning evanescent microwave microscope.
particular mixed sample. In this manner, a slow, serial measurement technique is

converted into a fast parallel tool capable of measuring large numbers of potential
superconducting phases.
Bozovic and coworkers at Oxxel utilized a sophisticated composition spread MBE
system equipped with 16 metal sources, an ozone source, an electron microscope
(LEEM/LEED/PEEM system), time-of-ight ion scattering and recoil spectroscopy,
and scanning quartz microbalances in a search for new materials for oxide elec-
tronics [24].
34.4.2
Ferromagnetic Semiconductors
Ferromagnetic semiconductors are important materials for spin-based electro-

nics in which the correlation between charge and spin is used to generate spin-
dependent electronic functionality such as giant magnetoresistance and spin eld
eect transistors. A majority of the materials currently being investigated are IIIV
and IIVI compounds. Among known materials, Mn-doped GaAs is the most
promising for practical applications because it has the highest magnetic ordering
(Curie) temperature TC @ 100 K. The search for new ferromagnetic semiconductors
has led to the investigation of dilute magnetic oxides, where small concentrations
of 3d ions are added to wide band-gap oxides such as ZnO. Kionuma et al. have
applied a combinatorial approach to the search for new ferromagnetic semicon-
ductors by adding dilute amounts of cobalt to the anatase form of TiO2 [88]. Ana-
tase TiO2 was chosen as a candidate semiconductor because of its high electron
carrier mobility at room temperature.
TiO2 and Ti 0:5 Co0:5 O2 ceramic targets were ablated using a KrF exicmer laser
in a combinatorial laser molecular beam epitaxy system [55]. Anatase lms of
Tix Co1x O2 were grown on LaAlO3 (001) and SrTiO3 (001) substrates and the com-
position mapped by microprobe analysis. X-ray diraction studies show that the Co-
doped anatase compositions obey Vegards law up to a solubility limit of x 0:08.
Magnetic images obtained by a scanning Squid microscope at 3 K showed do-
mains of around 20 mm in size for the Co-doped compositions. The spontaneous
magnetization systematically increases with increasing Co content to 0.32 mB (Bohr
magnetron) observed for the x 0:07 sample. The ferromagnetic ordering tem-
perature was estimated to be in excess of 400 K, a substantial increase over the
Mn-doped GaAs compounds.
34.4.3
Magnetoresistant Materials
The preparative combination of thin-lm deposition and physical masking tech-

niques was subsequently used by Xiang and coworkers in the discovery of new co-
balt oxide magnetoresistance materials [89, 90]. Magnetoresistance is the variation of
electrical resistance with an applied magnetic eld. Materials with particularly large
magnetoresistance properties are useful in high-density magnetic storage technol-
ogy such as read heads for computer hard drives [91]. Colossal magnetoresistance
(CMR) was rst discovered in Mn-based perovskites (La,R)1x Ax MnO3e , where R
is a rare earth element, and A is Ca, Sr, or Ba. Magnetoresistance ratios DR=R0
RH 0 RH=RH 0 as large as 99.0%, 99.9%, and 99.99% have been re-
ported for polycrystalline samples of La 0:6 Y0:07 Ca 0:33 MnO3 and epitaxial thin lms
of La 0:67 Ca 0:33 MnO3 and Nd 0:7 Sr0:3 MnO3e respectively. Two identical 128-member
libraries of composition Lnx My CoOz (1 mm 2 mm) were synthesized on LaAlO3
single crystals to examine the magnetoresistivity of materials that contain cobalt
rather than manganese in simple perovskite, LnCoO3 , and related Ln2 CoO4 or
Lnn1 Con O3n1 structures, where Ln (La, Y) 3 , partially substituted with dier-
ent stoichiometries of M (Ca, Sr, Ba, Pb) 2 . The two libraries were annealed and
sintered under dierent conditions, and one showed an overall decrease in mag-
netoresistivity, highlighting that in combinatorial materials synthesis, postdeposi-
tion processing conditions represent important variables. Using a four-point probe
method with a multichannel switching system in a liquid helium cryostat with
a superconducting 12 T magnet, large magnetoresistance (DR=R0 > 5%) was
measured in La x (Ba,Sr,Ca)y CoOz samples, while Y-based samples exhibited much
smaller magnetoresistive eects. The magnetoresistance of the Co-containing com-
pounds was found to increase as the size of the alkaline earth metal increases, in
sharp contrast to Mn-containing compounds, in which the MR eect increases
as the size of the alkaline earth metal decreases. The MR ratio DR=R0 of a sub-
sequently synthesized bulk sample of the lead compound La 0:58 (Ba,Sr,Ca)0:41 CoOz
was measured to be signicantly higher than that of the corresponding thin-lm

sample in the combinatorial library (DR=R0 60% compared with DR=R0
30%). This nding again illustrates that, in combinatorial materials discovery,
libraries are screened to point the direction to a promising lead; synthesis and
characterization of a bulk sample is then performed to determine the bulk proper-
ties which can dier considerably from the properties of the thin-lm compound.
34.4.4
Dielectric and Ferroelectric Materials
Driven by the current trend toward the continued miniaturization of electronic

devices, improved thin-lm insulators are needed in, for example, dynamic random
access memory (DRAM) computer chips. Using the composition spread technique
(CCS), van Dover and coworkers from Lucent Technologies have reported new di-
electric thin-lm materials that have higher dielectric coecients than amorphous
silicon dioxide (a-SiOx ), the insulating material most commonly used today [41, 85,
9294]. The CCS technique (see above) involves the co-deposition of three dier-
ent reagents onto a substrate from a triangular arrangement of targets. van Dover
and coworkers used o-axis RF magnetron sputtering guns positioned at 90 in-
tervals around a rectangular TiN-coated Si wafer (66 mm 63 mm) to co-deposit a
continuous ternary composition variation of Zr, Ti, and Sn. The three sputter guns
operated simultaneously to create intimate reactant mixing. A continuous thin lm
was obtained and the position-related composition was inferred using Rutherford
backscattering spectroscopy. To isolate the optimum thin-lm transistor candidate
(Zr0:15 Sn 0:3 Ti 0:55 O2e ), more than 30 combinatorial libraries were synthesized and
evaluated at a rate of approximately one per day.
The critical electrical properties, capacitance C (per unit area C/A) and break-
down voltage Vbr, were evaluated with a scanning Hg-probe instrument as a func-
tion of position at approximately 4000 points in the 66 mm 63 mm rectangle,
and the gure of merit data (CVbr =A) were mapped onto a conventional ternary-
phase diagram. It was found that the properties of the Zrx Sn y Tiz O2e thin lms
depend strongly on the deposition conditions, as does the region of composition
that yields the highest values for the gure of merit. Full compositional scans for
lms prepared under various processing conditions thus proved essential. In their
choice of elements, van Dover and coworkers have focused on deposition at sub-
strate temperatures below 300 C to maintain compatibility with back-end Si IC
fabrication technology, and did not apply any postdeposition annealing treatment.
In contrast to the application of combinatorial materials synthesis for supercon-
ducting and magnetoresistant materials, in this application reproduction of the
thin lm results by bulk materials samples is not essential, since in the nal pro-
duction process the materials will be manufactured by thin-lm deposition tech-
niques.
Combinatorial approaches have also recently been applied by Xiang and co-
workers to ferroelectric materials in which the eects of transition metal dopants on
the dielectric coecient and tangent loss of a library of thin lms of (Ba x Sr1x )TiO3
a
Fig. 34.9. a) Dopant map for the materials. A quaternary masking scheme with
(Ba 0:8 Sr0:2 )TiO3 quadrant of a ferroelectric four masks was used to deposit 256 dierently
thin-lm library; the same map applies to the doped thin lms of Ba x Sr1x TiO3 0:5 < x < 1
other three quadrants containing dierent host on a 2.54 cm 2.54 cm LaAlO3 substrate.
(BST) were determined [63, 95]. Ferroelectric materials are being widely used in
the development of new microwave devices such as frequency agile lters, phase
shifters, and tunable resonators, and (Ba x Sr1x )TiO3 compounds have been inten-
sely studied for such applications owing to their low loss and high dielectric co-
ecients. Four libraries of 256 dierently doped thin lms of (Ba x Sr1x )TiO3 ,
where x 1, 0.8, 0.7, and 0.5, were generated on a 2.5 cm 2.5 cm LaAlO3 sub-
strate using multistep thin-lm RF sputtering together with a quaternary masking
strategy with four physical shadow masks. These four hosts were then doped with
dierent combinations of up to three out of nine dierent metallic elements with
each dopant added in excess of 1 mol% with respect to the BST host; the resultant
dopant map for the (Ba 0:8 Sr0:2 )TiO3 quadrant is shown in Fig. 34.9a. The same map
applies to the other three quadrants of the library with the three other host mate-
rials, BaTiO3 , (Ba 0:7 Sr0:3 )TiO3 , and (Ba 0:5 Sr0:5 )TiO3 .
Appropriate postannealing aorded high-quality epitaxial thin lms, similar to
those made by conventional in situ methods from stoichiometric targets on hot
substrates. The rapid, quantitative and nondestructive characterization of the mi-
crowave dielectric properties, the dielectric coecient, and loss tangent of samples
in the library was achieved with a scanning-tip microwave near-eld microscope,
as shown in Fig. 34.8, at 1 GHz, and the results were found to be consistent with
measurements made with interdigital electrodes [21, 33, 34, 59, 96]. In Fig. 34.9b
the averaged dielectric coecient and tangent loss data are displayed for the BaTiO3
(BTO) quadrant; each square corresponds to a dierent thin-lm sample site, and
darker shades represent lower dielectric coecient. Specic dopants were found to
b
Fig. 34.9. b) Dielectric coecient and loss submicron spatial resolution. Each square
tangent images of doped BaTiO3 lms, corresponds to a dierent thin-lm sample site
measured using a scanning-tip microwave as given in the composition map above.
near-eld microscope (STMNM) with
signicantly aect the dielectric coecient and the tangent loss, with La (sample 2)
and Ce (sample 3) increasing the dielectric coecient, whereas most dopants result
in decreased values when compared with the undoped material. In the tangent
loss data, a lighter shade implies a lower loss tangent. In the case of microwave
applications, where the values of the dielectric coecient are considered to be high,
a minor reduction may be tolerable as long as there is a noticeable improvement
in the tangent loss, which is especially important for the microwave application of
tunable dielectric materials. Possible applications include radar, which steers the
beam and quickly locates objects electrically rather than mechanically, and cellular
phones, which instantaneously tune into the incoming signals.
Subsequently, Xiang and coworkers evaluated the eects of dopants on device
performance by incorporating a layer of the doped dielectric (Ba x Sr1x )TiO3 in a
parallel-plate capacitor library between Pt and La 0:5 Sr0:5 CoO3 electrodes [97]. Like
van Dovers work on thin-lm dielectrics, this investigation aims to aid in the iden-
tication of optimal dielectric materials for integrated capacitors in dynamic ran-

dom access memory (DRAM) chips.
Multilayer device structure libraries of 240 dierent host/dopant combinations
were epitaxially synthesized with sharp interfaces from amorphous layers on a
LaAlO3 substrate. Addition of 1.5 mol% W was found to increase the gure of merit,
the ratio of the eective dielectric current, and the leakage current density 220-fold
and to reduce the high-frequency tangent loss fourfold. The epitaxial growth of het-
erostructures in thin-lm device libraries is necessary in order to explore the in-
trinsic eects of compositional variations in the absence of polycrystalline micro-
structural eects which can provide sites for charge traps and other defects. Since
the conventional techniques of high-temperature in situ epitaxial thin-lm growth
cannot be used for combinatorial library synthesis, Xiang and colleagues developed
a synthesis method to form epitaxial multilayers from amorphous layers deposited
at room temperature using pulsed laser deposition (PLD). The capacitor library
consisted of a 100- to 200-nm-thick amorphous layer of La 0:5 Sr0:5 CoO3 (LSCO) on
LaAlO3 ; the substrate is then annealed at 850 C for 1.5 h. Using two-dimensional
shutters, the three dierent hosts BaTiO3 , Ba 0:7 Sr0:3 TiO3 , and Ba 0:5 Sr0:5 TiO3 were
deposited from stoichiometric targets in the x-direction of the substrate, whereas
in the y-direction typically up to four dopants were added to each host as a gradi-
ent from 0 to 3 mol%. Two-step annealing then ensured uniform interdiusion of
dopants and epitaxial crystal growth with sharp interfaces between the BST and the
LSCO layer. To complete the device structure, individual Pt electrodes (50 nm) were
deposited using a photolithographic mask. Approximately 5500 capacitors, each
50 mm 50 mm in size, were formed with 240 dierent host/dopant concentra-
tion combinations, aording about 23 capacitors for each host/dopant concentra-
tion and providing a test of the reproducibility of each device.
34.4.5
Luminescent Materials
The combinatorial methodology of thin-lm deposition and masking techniques

to create materials chip libraries has quickly found applications in the discovery
and optimization of luminescent materials. Despite many years of intensive re-
search, fewer than 100 useful commercial phosphor materials have been dis-
covered through conventional one-at-a-time synthesis and testing. Phosphor mate-
rials with high quantum eciencies nd application in display technologies such
as cathode ray tubes (CRTs) and are of great importance for developing improved
plasma, eld emission, and electroluminescent at panel displays and lighting [98].
Phosphors are typically inorganic powders that consist of a polycrystalline host
doped with ions of a rare earth and/or a transition metal. The dopants may act as
a center for luminescence that generates visible light when excited by ultraviolet
light, or as a sensitizer that absorbs and transfers the ultraviolet energy to the lumi-
nescent center. Although the photophysical processes leading to luminescence are
relatively well understood, the specic spectral properties, luminescence ecien-
cies, and operational lifetimes depend on complex interactions between the excita-
tion source, host lattice, sensitizer, and luminescent center. Two groups reported
application of combinatorial methods to the discovery and optimization of several
luminescent metal oxide materials. Oxides are attractive host materials for the de-
velopment of advanced phosphors owing to their ease of synthesis and stability. For
example, the ecient refractive oxide phosphors Y2 O3 :Eu 3 (red), Y3 Al5 O12 :Tb 3
(green), and BaMgAl10 O17 :Eu 2 (blue), have found applications in tricolor lamps,
projection TVs, and plasma displays.
Symyx Technologies red phosphor, Y0:845Al0:07 La 0:06 VO4 :Eu 0:025 , with a quantum
eciency approaching those of existing commercial red phosphors, was discovered
in a library of 25,000 dierent compositions produced using electron-beam evapo-
ration to deposit thin lms onto a 7.5-cm silicon wafer [81]. In this discovery library,
four constant thickness columns were rst deposited consisting of SnO2 (480 nm),
V2 O5 (160 nm), Al2 O3 V2 O5 (150 nm 80 nm), or Al2 O3 (300 nm). On top of
these layers were deposited four rows of linearly varying thickness of La2 O3 , Y2 O3 ,
MgO, and SrCO3 to create 16 host lattice subregions. Finally, within each of the 16
subregions linearly varying thicknesses of the rare earths Eu2 O3 , Tb4 O7 , Tm2 O3 ,
and CeO2 were deposited, resulting in approximately 600 dierent chemical com-
positions per square centimeter, see Fig. 34.10. A stainless-steel primary mask con-
sisting of 230-mm 2 elements spaced 420 mm apart was attached to the substrate to
separate individual library elements. The spatial variation of materials deposited
on the library was created using stationary and movable physical masks to control
the thickness of specic evaporants in selected regions of the substrate. Because
the constituents of each library element were deposited in layers, oxidative thermal
processing at various temperatures was needed to mix the layers and create the
desired chemical compounds. High-throughput screening for UV-excited photo-
luminescence was performed by photographing the visible emission of the library
with a charge-coupled device (CCD) camera while exciting with a 254-nm broad-
band source. A quantitative measure of the chromaticity relative to calibration stan-
dards was calculated from three images obtained using, respectively, red, green,
and blue tristimulus emission lters. To optimize the best host compositions of
the Eu-doped red phosphors, Y1m Alm VO4 , identied in the initial high-density
exploration library, a second library was deposited on a triangular grid, including
La as a third host component. First, Eu2 O3 and V2 O5 were deposited uniformly
over the entire substrate, followed by linearly varying the amount of Y2 O3 , Al2 O3 ,
and La2 O3 along three axes oset by a rotation of 120 , thus exploring all possible
Y0:95mn Aln Lam VO4 :Eu 0:05 compounds. The maximum intensity with red chro-
maticity suitable for a commercial material corresponds to the phosphor composi-
tion Y0:82Al0:07 La 0:06 VO4 :Eu 0:05 . The activator concentration in this lead host was
subsequently optimized with a third library in which the Eu 3 concentration was
varied between 0% and 20% using a single movable mask, probing the composi-
tions Y0:87m Al0:07 La 0:06 VO4 :Eu m . Screening of this optimization library identied
2.5% Eu as the most ecient dopant, resulting in the nal optimized composition
Y0:845Al0:07 La 0:06 VO4 :Eu 0:025 with improved red chromaticity (x 0:67, y 0:32)
compared with the more orange standard commercial red phosphor Y1:95 O3 :Eu 0:05
(x 0:64, y 0:35). Synthesis of bulk samples by conventional methods produced
1040
34 Combinatorial Aspects of Materials Science
Fig. 34.10. a) Deposition map of diverse library containing approximately 25,000

phosphor discovery library with thicknesses of dierent compositions. In this library, novel
the various materials deposited on a 7.62-cm ecient red and blue phosphor compositions
silicon wafer shown. b) Photograph of the UV- were identied and subsequently optimized in
excited photoluminescence of the discovery focus libraries.
materials indistinguishable from the thin-lm library samples and conrmed the
performance of the newly identied phosphor composition.
Xiang and coworkers prepared several 128-member libraries of aluminates of
the formula Gd(La,Sr)AlOx doped with rare earth activators, and have evaluated the
phosphorescence of all the samples simultaneously by photographing the entire
library under broad wavelength UV light (254 nm) [99]. The resulting color photo-
graph allowed a convenient qualitative evaluation of the library. The combinatorial
libraries were used to survey a wide range of oxide compositions under a variety of
processing conditions, facilitated by the simultaneous deposition of seven identical
libraries on LaAlO3 , MgO, and Si single-crystalline substrates followed by dierent
annealing and sintering conditions.
Subsequently, Xiang and coworkers demonstrated that a scanning multi-inkjet
delivery system (see above) can be used to achieve results identical to the vapor
deposited libraries [64].
Multicomposition materials libraries of thin-lm phosphors
(Gd,La,Y)m (Ta,Zr,W,Mo,Zn)n (Al,Mg,Sr)k Ox :(Tm,Eu,Tb,Ce)y (with 0 a m; n; k a 1,
0:005 a y a 0:1) were generated by Sun and Xiang using sequential RF to create
three identical libraries simultaneously on LaAlO3 [100]. Dierent annealing con-
ditions and atmospheres completed the synthesis of the phosphor libraries, and
photoluminescence images were acquired under 254-nm centered broad wave-
length UV radiation of a Hg lamp using color photography. A new red phosphor
with the composition (Gd1:54 Zn 0:46 )O3d :Eu 30:06 is claimed, and reported to have
characteristics similar to the state-of-the-art orangered phosphor Y2 O3 :Eu 3 and
also to possess excellent X-ray and cathodoluminesent properties.
Schultz and coworkers used RF/DC sputtering to prepare three 1024-member
libraries of silicate and gallate host materials on Si substrates, each library entity
containing a number of dierent dopants [61]. After annealing, a parallel imaging
system and a scanning spectrophotometer were used to identify and characterize
compositions in the library. Few blue phosphor were identied by their emission
and excitation spectra, but neither bulk nor thin lm samples on LaAlO3 sub-
strates exhibited blue luminescence. Subsequently, gradient libraries of
Gd x Ga1x Oz :(SiO2 )y on LaAlO3 substrates were generated using pulsed laser de-
position (PLD) and broadband blue emission was observed from these libraries.
34.5
Case Studies
34.5.1
Materials Discovery
The group from Symyx Technologies followed the red vanadate phosphor with a
report on a novel luminescent oxide, Sr2 CeO4 , with a bluish white emission [82].
Whereas previous studies of luminescent materials had primarily focused on the
synthesis of compositional variants within classes of materials with known struc-
ture types, the discovery of this fundamentally new bluewhite phosphor in an

unexpected region of composition space exemplies and validates the combinato-
rial methodology of materials science and discovery. The new luminescent phase
Sr2 CeO4 was identied by automated high-throughput screening of the discovery
library shown in Fig. 34.10, which suggested the possibility of a new phosphor
with bluewhite emission in the region of the library containing Sr, Sn, and Ce. A
subsequent ternary focus library containing combinations of these three elements
revealed that Sn was not needed for the observed emissive properties, and that
maximum luminance was observed at Sr/Ce ratios greater than 1. A bulk sample
with a 2:1 ratio of Sr/Ce was prepared from the reaction of CeO2 with SrCO3 in
order to study the optical and other physical properties. The excitation and emis-
sion spectra of Sr2 CeO4 displayed broad maxima at 310 and 485 nm, with the emis-
sion appearing bluewhite to the eye (x 0:198, y 0:292) having a quantum
yield of 0.48. The phosphor is eectively excited by X-rays and exhibits ecient
cathodoluminescence. The structure, determined by powder X-ray diraction, is
highly anistropic and reveals one-dimensional chains of edge-sharing distorted
CeO6 octahedra that are linked together by Sr 2 cations (Fig. 34.11) [101]. This un-
usual structure has not previously been found for rare earth-based oxide phosphors,
and it is believed that the structure is critical in the observation of luminescence in
Sr2 CeO4 . Strong evidence suggests the mechanism of luminescence to be based on
ligand-to-metal charge transfer, from O 2 to Ce 4 , and not from isolated valence
transitions (daf ) from Ce 3 defect centers as in all known cerium-based phosphors.
To determine whether there were other luminescent phases within the M2 CeO4
(M Ba, Sr, Ca) composition space, a follow-up library was prepared with the com-
positions Ba2 CeO4 , Sr2 CeO4 , and Ca2 CeO4 at each corner of a triangular library.
The library was prepared by automated liquid dispensing of sol-gel precursors and
followed by heating to 900 C. Under 254-nm excitation the Sr-containing region
was observed to have the brightest emission while no appreciable luminescence
was observed from the pure Ba and Ca regions. Additionally, no evidence of solid
solution formation was seen by X-ray diraction. This work shows that the combi-
natorial materials synthesis approach can identify fundamentally new and unex-
pected structures with properties that arise from unusual mechanisms.
34.5.2
Device Optimization
Thin-layer organic light-emitting devices (OLEDs) are an emerging technology that

is beginning to be commercialized in at panel displays. To develop this technology
further, it is important to optimize dierent materials properties, layer thicknesses,
deposition parameters, and layer compositions under similar and reproducible con-
ditions. A combinatorial approach has been developed to create libraries of dierent
OLEDs in order to screen and optimize device parameters with respect to power
eciency, photometric eciency, and currentvoltage characteristics [4245, 102,
103]. Schmitz and coworkers used a combinatorial approach to optimize the Alq3
[8-hyroxyquinolinlato-Al(III)] layer thickness on top of a constant thickness hole
Fig. 34.11. The crystal structure of the blue phosphor Sr2 CeO4
consists of linear chains of trans edge-sharing distorted CeO6
octahedra with four equatorial O atoms and two terminal CeaO
bonds per octahedron, separated by interchain Sr 2 cations.
transport layer (HTL) to resolve whether an additional electron transport layer

(ETL) can further enhance device performance [45]. Libraries of devices were pre-
pared using a movable sledge developed to carry dierent types of masks or shut-
ters in a vacuum deposition chamber. In addition, a substrate holder that can be
rotated stepwise is positioned above the movable sledge. In this experiment (Fig.
34.12) a uniform layer of N,N 0 -bis-(4-dimethoxyphenyl)-N,N 0 -diphenylbenzidine
(DMeOTPD) which is 40 nm in thickness is deposited on an unpatterned indium
tin oxide (ITO) glass substrate. Continuous movement of the shutter creates a gra-
dient of Alq3 that varies from 0 to 130 nm. The substrate is then rotated 90 and a
linear gradient of spiroquinoxaline ether (spiro-Qux) is deposited over two-thirds of
the substrate. Finally, 400 nm of aluminum is deposited through a mask with 49
holes to create a cathode array. The currentvoltageluminance characteristics were
measured with a computerized set-up consisting of a programmable power supply,
multimeter, and luminometer. Results from this optimization experiment show
that the additional spiro-Qux layer improves the photometric eciency in certain
Fig. 34.12. The preparation of three-layer evaporation of ETL by simultaneous shutter

OLEDs with orthogonal linear gradients of Alq3 movement. Step 4, evaporation of aluminum
and a hole-blocking electron transport layer through a mask with 49 holes. ITO, indiumtin
(ETL). Step 1, evaporation of HTL with oxide; HTL, N,N 0 -bis(4-dimethoxyphenyl)-
constant thickness on an ITO substrate. Step N,N 0 -diphenylbenzidine (DMeOTPD); tris(8-
2, preparation of an Alq3 gradient by vapor hydroxyquinolinato)aluminum(III) (Alq3 );
deposition and simultaneous shutter move- spiroquinoxaline (spiro-Qux).
ment. Step 3, rotation of substrate by 90 and
combinations of Alq3 /spiro-Qux layer thicknesses, which is attributed to better

hole-blocking properties of spiro-Qux. The power eciency, however, could not be
improved by using an additional spiro-Qux layer because of the less ecient elec-
tron injection.
34.6
Organic Materials and Polymers
The application of combinatorial chemistry holds great promise in the discovery of

novel functional organic materials. The current emphasis is on nding materials
that either selectively bind small organic molecules or have improved physical and
mechanical properties.
34.6.1
Schi Bases for Nonlinear Optical (NLO) Materials
An investigation of the combinatorial synthesis procedures needed for the rapid

formation of large libraries of polar compounds for the preparation of nonlinear
optical (NLO) materials has been described by Nesterov and coworkers [104]. The
structural characteristics of the Schi base products (i.e. donor and acceptor groups
connected to a p-conjugated chain) are believed to have potential as NLO or electro-
optical materials. Nesterov and coworkers created a test library using four amines
and two aldehydes as the building blocks for eight potential polar Schi bases.
Figure 34.13 illustrates the acid-catalyzed condensation of a set of electron-rich
cinnamaldehydes with four electron-poor anilines intended to generate a small
library of eight Schi bases. The color of the product compared with that of the
starting material was used as an indication that a chemical reaction had taken place.
Crystalline precipitates were observed in every reaction, and crystals suitable for X-
ray diraction were obtained from all but one of the reactions, where the crystals
were too small. Their results demonstrate that a targeted library of Schi base
Fig. 34.13. Structures of various aniline and cinnamaldehyde

building blocks and their corresponding Schi base library as
new materials for nonlinear optics.
compounds can be synthesized and screened. Five crystal structures were deter-
mined, all with centrosymmetric space groups that preclude the compounds from
being NLO candidates.
34.6.2
Articial Receptors for Small Organic Molecules
Since the rational design of nanoporous materials and their inclusion cavities based
on molecular structures is dicult, combinatorial methods were implemented to
nd superior lattice inclusion compounds [105]. When screened against a guest
molecule (iPrOH), seventeen new ammonium carboxylate host compounds were
discovered from a combinatorial library of 100 salts formed by mixing ten commer-
cially available amines and ten carboxylic acids. One host compound was identied
that forms inclusion compounds with 25 dierent organic solvents. Application to
chiral recognition by the proper choice of amines and carboxylic acids to form a
variety of host compounds is under investigation.
Leblanc and coworkers applied combinatorial principles to surface chemistry by
synthesizing and screening libraries of amphiphilic lipid molecules [106]. At the
airwater interface, the hydrophilic polar moiety of these molecules is embedded
into the water phase and the hydrophobic alkyl chain is oriented toward the air
phase. When compressed at the interface, the amphiphilic molecule will move and
assemble into organized supramolecular structures, known as Langmuir mono-
layers. The polar moiety was functionalized with a peptide library such that the self-
assembly of these functional lipids formed protein-like supramolecular structures
(Fig. 34.14). One library with 250 members and three sublibraries of 54 members
each were assayed for molecular recognition of maltose as well as other sugar mol-
ecules. One sublibrary, containing both polar charged (Glu) and aromatic (Tyr)
amino acid residues, was identied that selectively bound maltose but not d-glucose
and sucrose. This selectivity can be explained by the three-dimensional combina-
tion of those two amino acids in the binding site with Tyr playing a more signi-
cant role for the binding activity.
34.6.3
New Materials for the Separation of Enantiomers
Given the enormous demand of enantiomerically pure compounds in the phar-

maceutical eld, novel chiral stationary phases (CSPs) for high-performance liquid
Fig. 34.14. The structure of a combinatorial peptide lipid library (AA i amino acid).
chromatography (HPLC) were developed by combinatorial means [107]. Frechet

and coworkers prepared a model library of chiral stationary phases (selectors) 1 for
HPLC by attaching a small model library of 36 chiral compounds that were ob-
tained from three l-amino acids and 12 aromatic amines to synthetic polymer beads
(Scheme 34.1) [108]. After the entire on-bead library 1 was packed into a HPLC col-
umn, selectivity was assayed by injecting various racemates of chiral targets. De-
spite the presence of 36 mixed selectors, racemic d,l-(3,5-dinitrobenzoyl)leucine
diallylamide was separated. A deconvolution process was used to determine which
of the 36 selectors in the HPLC column was the most powerful. In contrast to the
one column, one selector approach, which would require the preparation and
testing of 36 chiral stationary phases, this combinatorial scheme requires the prep-
aration of only 11 columns for the discovery of the most selective material. Apply-
ing the same approach, a library of 240 selectors could be deconvoluted using only
17 columns.
Scheme 34.1. Preparation of a model library of chiral stationary

phases (selectors) 1 for HPLC by coupling a small model
library of 36 chiral compounds to synthetic polymer beads.
The same group also applied the principle of reciprocity to the identication of
new CSPs [109]. This approach is based on the following assumption: if a ligand of
the stationary phase is selective toward an analyte, then the same analyte immobi-
lized onto the proper support should result in a stationary phase that is very likely
to be selective toward the original ligand [110]. Following this principle, the chiral
substrate (S)-(3,5-dinitrobenzoyl)leucine acted as an inverse selector and was im-
mobilized on synthetic polymer beads to give CSP 2 (Fig. 34.15). Three-component
Fig. 34.15. Inverse selector CSP 2, library of racemic 4-aryl-

1,4-dihydropyrimidines (DHPM) 3, and the most ecient CSP 4.
Biginelli condensation was utilized to prepare a parallel library of 108 racemic 4-

aryl-1,4-dihydropyrimidines (DHPM) (3) which were then screened against the
inverse selector CSP 2 by observing the enantioselectivity for resolution. The
best candidate was then attached to monodisperse macroporous beads to prepare
the new polymer-based chiral stationary phase 4, which proved ecient in the res-
olution of several analytes.
Li and coworkers also utilized the principle of reciprocity to identify novel chiral
selectors [111]. In order to study the chiral resolution of racemic (1-naphthyl)leucine
ester 5, the l-enantiomer of 5 was immobilized onto silica gel (Scheme 34.2). A
small (4 4) peptide library was synthesized in its d- and l-form, respectively, and
the chromatograms of these two libraries on stationary phase 6 were compared.
The visible dierence between the two chromatograms indicates that immobilized
5 interacts dierently with the enantiomers of at least one library component. De-
convolution methods were used to identify the most potent selector. The same
group also turned the principle around in preparing two stationary phases (l-6,
S-6), one immobilized with the R enantiomer of 5 and the other immobilized with
the S enantiomer of 5 [112]. Potential chiral selectors were identied again by sub-
sequent screening of the racemic (4 4) peptide library against the two stationary
phases and comparison of the chromatograms.
A dierent approach is to synthesize parallel combinatorial CSP libraries with
up to 200 members and screen them for their ability to resolve a racemate of the
analyte [113]. These libraries of potential selectors typically consist of immobilized
dipeptides and a capping group. Racemic analyte is then added to each member of
Scheme 34.2. Immobilized analyte 5 utilized in the reciprocity approach.
the library and allowed to equilibrate. The enantiomeric ratio of the analyte in the
supernatant is analyzed after the equilibration period using circular dichroism
measurements or other methods. A selective absorption of one of the two en-
antiomers to the resin is indicative of a chiral selector.
Welch and coworkers introduced an improved method for rapid liquid chroma-
tography/mass spectrometry (LC/MS) screening of chiral stationary phases based
on the use of isotopically labeled enantiomers [114]. Pseudoracemates made up of
a pair of isotopically dierentiated pseudoenantiomers were prepared and screened
against dierent CSPs. The enantioenrichment of the supernatants can be rapidly
estimated by comparing the MS abundance of the ions corresponding to each of
the pseudoenantiomers.
A visual screen for identifying chiral selectors was introduced by Still and co-
workers [115]. The idea was to treat an equimolar mixture of a blue l-amino acid L-7
and a red d-amino acid D-7 with a library of chiral selectors on synthesis beads
in which each bead carries a dierent selector (Fig. 34.16). Highly enantioselec-
tive binding results in red or blue beads, whereas unspecic binding yields brown
Fig. 34.16. Enantiomeric probe molecules 7 labeled with dierent dyes.

beads. The reddest and the bluest beads found in the assay were picked and de-
coded to determine the structure of the bound chiral selector.
34.6.4
Molecular Imprinting
Molecularly imprinted polymers (MIPs) are another class of articial receptors for
small organic molecules. Their binding performances give these materials great
potential in combinatorial approaches as recognition matrices for the screening
and rapid selection of ligands from a combinatorial library [116]. Molecular im-
printing is a technology where recognition sites can be generated within a macro-
molecular matrix by use of a molecular template in a casting procedure [117]. The
selected ligand (print molecule) is rst allowed to interact freely in solution via
bond formation with one or more functional monomers. The resulting adducts are
subsequently copolymerized with a large excess of crosslinker to give a rigid, in-
soluble polymer. Following extraction of the print molecule, specic recognition
sites are left in the polymer. The technique has been applied to the screening of
a combinatorial steroid library [116a], and a combinatorial library of molecularly
imprinted polymers has been tested in chiral separations [116c]. Combinatorial
methods proved to be advantageous since the preparation and evaluation of MIPs
is usually very tedious and time-consuming.
In 1999, Takeuchi and coworkers reported a rapid combinatorial approach to
synthesize and evaluate articial receptors [118]. The preparation of the MIPs was
automatically performed using programmable liquid-handling equipment with a
new in situ molecular imprinting protocol. The freshly synthesized MIP library
(polymer lms) was then subjected to a primary screening to estimate the anity
of the template to the resultant polymer. A secondary screening on puried MIPs
then allows for a more precise evaluation of the anities and selectivities of the
new materials. MIPs that are articial receptors for triazine herbicides ametryn 8
and atrazine 9 were prepared by the combinatorial molecular imprinting approach
using variable amounts of two functional monomers, methacrylic acid (MAA) 10
and 2-(triuoromethyl)acrylic acid (TFMAA) 11, as well as ethylene glycol dime-
thacrylate as a crosslinker and 2,2 0 -Azo-bis-isobutyryl-nitrile (AIBN) as the poly-
merization initiator (Fig. 34.17). On examination of the 49-member MIP library, it
appears that, depending on the functional monomer used, the imprinting e-
ciency is dierent for each triazine herbicide. This result suggests that high-
throughput synthesis and screening of large sets of polymers will provide the most
ecient molecularly imprinted receptors for given target molecules.
34.6.5
Polymers with Novel Topologies and Functionalization
Combinatorial approaches have also been applied to polymer chemistry. For ex-
ample, a small library of polyarylates (0.2 g per sample) (14) was prepared from 14
distinct tyrosine-derived diphenols (12) and eight aliphatic diacids (13), resulting in
Fig. 34.17. Structures of the template molecules ametryn 8

and atrazine 9 as well as the functional monomers MAA 10 and
TFMAA 11.
112 structurally related strictly alternating copolymers (Scheme 34.3) [119]. These
copolymers are biodegradable and potentially useful as medical implant materials.
The structural variations provided incremental dierences in polymer free volume,
bulkiness, exibility, and hydrophobicity. Up to 32 polymers were synthesized in
parallel under identical reaction conditions and conventional methods were used
to measure the molecular weight by GPC (gel permeation chromatography), Tg by
DSC (dierential scanning calorimetry), and the airwater contact angle (sessile
drop) on a sample-by-sample basis, providing structureproperty correlations. Di-
verse and focused combinatorial libraries of synthetic biodegradable polymers
could also be designed by using molecular topology and genetic algorithm opti-
mized quantitative structureproperty relationships (QSPR) [120].
Scheme 34.3. Library of polyarylates 14 derived from diphenols 12 and diacids 13.
In a dierent approach, polymerization reactions between dierent combinations

of two starting materials have been found to lead to many new, uniquely respond-
ing sensors with responses not simply related to the proportions of the starting
materials [121]. Discrete polymer-sensing cone arrays or gradient sensors show
diverse shifts in uorescence emission wavelength in response to organic vapor

pulses. Combinatorial polymer synthesis from a limited number of starting mate-
rials thus presents an attractive approach to generate large sets of unique and di-
verse polymer sensors for analyte detection rapidly.
Radical polymerizations have been the focus of a variety of combinatorial ap-
proaches due mainly to the fact that a greater number of monomers are amenable
to radical polymerizations than either anionic or cationic methods, and therefore a
higher diversity of polymers may be obtained through free radical polymerizations
[122]. Additional structural variation can be achieved through the synthesis of pol-
ymers based on either one monomer (homopolymer) or multiple monomers (co-
polymers). Block and graft polymerizations oer the possibility of a controlled al-
teration of physical properties by varying polymer block and graft length and
composition [123]. Janda and coworkers applied a sequence of normal and liv-
ing free radical polymerizations to generate a library of 20 block copolymers pos-
sessing either block or graft architecture with initiators 15 and 16 and a diverse set
of vinyl monomers 1721 (Fig. 34.18) [124]. The principle of the combinatorial
approach is outlined in Scheme 34.4. Diazene and TEMPO (2,2,6,6-tetrame-
thilpiperidin-1-yloxy) moieties are known to initiate/mediate free radical polymer-
izations at 70 C and 130 C, respectively. Therefore, bifunctional free radical ini-
Fig. 34.18. Free radical initiators 15, 16 and vinylic monomers

1721 for the construction of a library of block polymers.
tiators of the type 15 were prepared that provide for two independent rounds of po-
lymerization. Block copolymers 22 could be obtained in a temperature-controlled
manner through sequential normal and living polymerizations. To add another
dimension to the combinatorial diversity, initiator 16 participates as a monomer in
the rst polymerization with monomer A, resulting in statistic copolymers of
type 23. The TEMPO-functionalized residues then mediate the living poly-
merization at 130 C, giving access to combinatorial polymers of type 24. The
members of the block copolymer library were then screened for their ability to
serve as a soluble polymer support for organic reactions. One block copolymer
could be identied that has a solubility prole that is complementary to the cur-
rent soluble polymer of choice in liquid-phase organic synthesis (LPOS) poly-
ethylene glycol (PEG). R1 and the nitrile groups in block copolymers of type 22
could be used to functionalize these molecules.
Scheme 34.4. Parallel polymer synthesis via sequential normal/living free radical process.
Hawker and coworkers used combinatorial means to identify novel nitroxide-

based mediators for living free radical polymerizations [125]. Nitroxide-mediated
processes are potentially simpler systems then atom transfer radical processes
(ATRP) since no metal complex needs to be added; thus, more functional groups
are tolerated and purication is simplied. However, nitroxide-mediated processes
are limited by their incompatibility with numerous vinyl monomer families. Since
the structure of the nitroxide moiety plays an important role in the success of
living free radical polymerizations, a structurally diverse, a-hydrogen-bearing
nitroxide library was prepared and screened for the ability to control the polymer-
ization of a variety of functionalized monomers (Scheme 34.5). The a-hydrido al-
koxyamine 25 was identied as the most promising candidate to eect the living
free radical polymerizations of a wide variety of monomers, e.g. styrenes, acrylates,
acrylamides, and acrylonitrile-based monomers.
Scheme 34.5. Synthesis of a diverse alkoxyamine mediator

library for living free radical polymerizations.
Very recently, Frechet, Hawker, and researchers at Symyx Technologies pre-

sented a new technology to synthesize multiarm star polymers using nitroxide-
mediated living free radical polymerizations, giving access to well-dened mac-
romolecules with three-dimensional architecture [125a]. Combinatorial techniques
were used to rapidly evaluate the scope and limitations of this general methodol-
ogy.
Sar, Petro, and colleagues at Symyx Technologies have focused on combining

rapid synthesis and rapid characterization techniques with full automation to reap
the maximum benet of combinatorial chemistry in the area of polymer science
[126]. To demonstrate this integration of fully automated synthesis and character-
ization, living free radical polymerizations, which allow for molecular weight con-
trol, were studied [127]. In particular, for atom transfer radical polymerizations
(ATRP), which have been shown to polymerize a variety of monomers successfully,
the eects of dierent initiators (organohalides) and catalyst/control agents (low
oxidation state organometallic reagents) were studied. A 45-member library con-
sisting of the combinations of ve CuI initiators and nine organohalide control
agents was screened for controlled styrene polymerization using 4,4 0 -di-(5-nonyl)-
2,2 0 -bipyridine (dNbpy) as the ligand [128]. To produce molecular weight diversity
in an 80-member styrene ATRP library, the monomer-to-initiator ratio (M/I), the
rate of propagation, the initiators, the solvents, and the concentrations were varied.
Finally, in a 55-member library, structural and molecular weight diversity was
introduced by using one initiator with ve M/I ratios (100 to 500 in steps of 100)
in the copolymerization of styrene and butylacrylate, creating a gradient in the
polymer composition from 0% to 100% butylacrylate with 10% increments. Utiliz-
ing the standard microtiter plate format equipped with a Teon-faced sealing
mechanism, a 96-well, glass-lined, aluminum reactor was developed to conduct
organic reactions above the boiling point of the reagents without loss of pres-
sure. Two methods of rapid molecular weight determination, i.e. precipitation
redissolution chromatography (PRC) and rapid-re light scattering (RFLS), were
used to screen the resulting polystyrene samples [129]. Combinatorial approaches
were also employed to produce p-conjugated polymers with novel electrical and/or
photofunctional properties. The photoluminescence of p-conjugated polymer thin
lms makes them interesting materials for at panel displays. Since lm prepara-
tion parameters are numerous, combinatorial concepts have been applied for the
synthesis of p-conjugated polymer thin lms [130]. A variety of p-conjugated poly-
mer building blocks was used for this study (Fig. 34.19). In addition, the diversity
of the building blocks was increased by combinatorial copolymerization of PP
(para-phenylene) and MP (meta-phenylene). This goal was achieved by copolymeriz-
ing dierent ratios of the two monomers in the presence of magnesium and nickel
complexes to form poly-(PP-co-MP). Target disks of p-conjugated polymer building
blocks were then evaporated by either vacuum evaporation (VE) or pulsed laser
deposition (PLD) and the lm was deposited on silica and/or Si substrates that were
kept at room temperature. Combinatorial lm preparation was achieved using a
movable mask. Various mixed component and multilayer lms can be fabricated
by employing appropriate mask shapes and the substrate rotation synchronized
with the target exchange. A variety of p-conjugated polymer lms with interesting
photoluminescent properties could be discovered by this method. Especially co-
polymers of PP and MP, poly-(PP-co-MP), showed a very high photoluminescence.
The same group also identied novel p-conjugated polymers with high-quality pan
junctions from a dierent thin-lm library [131].
Fig. 34.19. p-Conjugated polymers utilized for poly-(thiophene-2,5-diyl); PPh2BPV, poly-

the combinatorial fabrication of thin lms: (diphenylene biphenylene vinylene); Poly(PP-
PPP, poly-(para-phenylene); PMP, poly-(meta- co-PM), poly-(para-phenylene-co-meta-
phenylene); Ppy, poly-(pyridine-2,5-diyl), PTh, phenylene).
34.7
Summary and Outlook
We nd ourselves at the dawn of a new age of materials discovery and optimiza-

tion. As this review demonstrates, signicant rst steps in that direction have been
taken in various areas of materials science, and a multitude of tools are now avail-
able using combinatorial technologies to accommodate the new tasks and require-
ments for combinatorially accelerated materials research. A common underlying
theme associated with these technologies is miniaturization, parallelization, and
automation so that large numbers of samples can be synthesized and screened ef-
ciently. Rapid serial and parallel adaptations of conventional analytical techniques
will become increasingly important in the characterization of materials properties,
as will the development and implementation of new and unconventional high-
throughput screening tools. Software development and engineering support in
the construction and design of synthesis and screening tools are as crucial as fur-
ther advances in chemistry, even when appropriate tools or robots for synthesis
and screening automation are commercially available. Finally, the combinatorial
methodology generates data much faster than conventional research employing
empirical and rational approaches to materials discovery, and, inevitably, data
handling and storage advances must accompany the high-throughput synthesis
and screening to maintain the integrity of research and development eorts. Full
realization of the combinatorial methodology will require the integration of chem-
istry, physics, engineering, and informatics, enhancing the probability of nding
materials with desired properties. In the future, the scientists eorts may be
shifted, at least to some degree, toward programming and experimental design in
addition to the already existing analysis of synthesis and data analysis.
References 1057
Acknowledgments
The authors wish to thank Ms Silvia Lee (Symyx Technologies) and Ms Kathryn
Boykin (XenoPort) for their kind and prompt support in reference and patent
searches. The authors thank Ron Krasnow (Symyx Technologies) for checking the
manuscript.
References
1 a) G. Jung (ed.), Combinatorial application of combinatorial techno-

Chemistry-Synthesis, Analysis, Screening. logies to drug discovery, see: a) M. A.
Wiley-VCH, Weinheim 1999; b) G. Gallop, R. W. Barrett, W. J. Dower,
Jung (ed.), Combinatorial Peptide and S. P. A. Fodor, E. M. Gordon, J.
Nonpeptide Libraries, (VCH, Weinheim Med. Chem. 1994, 37, 12331251;
1996.) b) E. M. Gordon, R. W. Barrett,
2 E. M. Gordon, J. F. Kerwin (eds), W. J. Dower, S. P. A. Fodor,
Combinatorial Chemistry and Molecular M. A. Gallop, J. Med. Chem. 1994, 37,
Diversity in Drug Discovery. John Wiley 13851401.
& Sons, New York 1998. 11 M. Hann, R. Green, Curr. Opin.
3 a) N. K. Terret, Combinatorial Chem. Biol. 1999, 3, 379383, and
Chemistry, Oxford University Press, references cited therein.
Oxford 1998; b) N. K. Terret, N. 12 a) F. Zaragoza Dorwald (ed.),
Terret, Combinatorial Chemistry, Organic Synthesis on Solid Phase.
Oxford University Press, Oxford 1998. Wiley-VCH, Weinheim 2000; for
4 S. R. Wilson, A. W. Czarnik (eds), periodical selection of signicant
Combinatorial Chemistry. John Wiley & papers published in the recent
Sons, New York 1997. literature covering the broad area of
5 a) B. A. Bunin (ed.), The Combi- solid-phase organic synthesis (SPOS)
natorial Index. Academic Press, San and advances in linker chemistry, see
Diego 1998; b) A. W. Czarnik, S. H. for example: C. McCusker, T.
DeWitt (eds), A Practical Guide to Wildman, F. McKerlie, A. Gunn, H.
Combinatorial Chemistry. American Mandani, J. Dalaney, S. Anizon, J.
Chemical Society, Washington, DC Chem. Soc., Perkin Trans. 1 2001, 3,
1997. ixxii.
6 I. M. Chaiken, K. D. Janda (eds), 13 For periodical reviews of recent
Molecular Diversity and Combinatorial literature about solid-phase organic
Chemistry. American Chemical Society, reactions, see for example: a) S.
Washington, DC 1996. Booth, P. H. H. Hermkens, H. C. J.
7 a) R. Dagani, Chem. Eng. News 1999, Ottenheijm, D. Rees, Tetrahedron
77, 5160; b) S. Borman, Chem. Eng. 1998, 54, 1538515443; b) P. H. H.
News 1998, 76, 4767; c) R. Baum, S. Hermkens, H. C. J. Ottenheijm, D.
Borman, A. M. Thayer, J. H. Krieger, Rees, Tetrahedron 1997, 53, 5643
Special Report: Combinatorial Chemistry, 5678; c) P. H. H. Hermkens, H. C. J.
Chem. Eng. News 1996, 74, 2973. Ottenheijm, D. Rees, Tetrahedron
8 a) J. McNeal, Todays Chemist at Work 1996, 52, 45274554; d) N. K.
1998, 7, 3438; b) J. K. Borchardt, Terrett, M. Gardner, D. W.
Todays Chemist at Work 1998, 7, 35 Gordon, R. J. Kobylecki, J. Steele,
41. Tetrahedron 1995, 51, 81358173.
9. I. Sucholeiki (ed.), High-Throughput 14 For classical reviews about solid-
Synthesis, Marcel Dekker, Inc., New phase organic synthesis (SPOS), see
York, 2001. for example: a) J. S. Fruchtel, G.
10 For landmark review articles about the Jung, Angew. Chem. 1996, 108, 1946;
Angew. Chem. Int. Ed. Engl. 1996, 35, Reetz, Angew. Chem. 2001, 113, 292
1742; b) F. Balkenhohl, C. von 320; Angew. Chem. Int. Ed. 2001, 40,
dem Busche-Hunnefeld, A. Lansky, 285310, and references cited therein;
C. Zechel, Angew. Chem. 1996, 108, c) F. Gennari, P. Seneci, S. Miertus,
24362488; Angew. Chem. Int. Ed. Catal. Rev.-Sci. 2000, 42, 385402, and
Engl. 1996, 35, 22882337; c) L. A. references cited therein; d) B.
Thompson, J. A. Ellman, Chem. Rev. Jandeleit, D. J. Schaefer, T. S.
1996, 96, 555600. Powers, H. W. Turner, W. H.
15 For accounts and special techniques Weinberg, Angew. Chem. 1999, 111,
used in combinatorial chemistry, see 26482689; Angew. Chem. Int. Ed.
for example: a) K. S. Lam, M. Lebl, V. 1999, 38, 24952532, and references
Krchzak, Chem. Rev. 1997, 97, 411 cited therein.
448; b) A. Nefzi, J. M. Ostreh, R. A. 19 M. J. Cannarsa, T. Uno, C. Larsen,
Houghten, Chem. Rev. 1997, 97, 449 Curr. Opin. Drug Discov. Dev. 2000, 3,
472. c) M. C. Pirrung, Chem. Rev. 743749.
1997, 97, 473488. d) D. J. Gravert, 20 H. Weinmann, Nachr. Tech. Chem.
K. D. Janda, Chem. Rev. 1997, 97, 2001, 49, 150154.
489509; e) A. W. Czarnik, J. A. 21 a) X.-D. Xiang, Biotechnol Bioeng.
Ellman (eds), Special Issue on 1999, 61, 227241; b) X.-D. Xiang,
Combinatorial Chemistry, Acc. Chem. Annu. Rev. Mater. Sci. 1999, 29, 149
Res. 1996, 29, 111170. 171; c) D. R. Liu, P. G. Schultz,
16 For a review on recent developments Angew. Chem. 1999, 111, 3656;
and applications of polymer-supported Angew. Chem. Int. Ed. 1999, 38, 36
reagents and scavangers in synthetic 54.
organic chemistry, see: a) O. 22 a) X.-D. Xiang, Chem. Ind. 1998, 19,
Brummer, B. Clapham, K. D. Janda, 800802; b) X.-D. Xiang, Materials
Curr. Opin. Drug Discovery Dev. 2000, Today 1998, 1, 2326; c) I. Takeuchi,
3, 462473; b) S. V. Ley, I. R. X.-D. Xiang, Gendai Kagaku 1998,
Baxendale, R. N. Bream, P. S. 332, 2430; d) P. G. Schultz, X.-D.
Jackson, A. G. Leach, D. A. Xiang, Curr. Opin. Sol. State Mat. Sci.
Longbottom, M. Nesi, J. S. Scott, R. 1998, 3, 153158.
I. Storer, S. J. Taylor, Special Issue: J. 23 C. Schmitz, P. Poesch, M.
Chem. Soc., Perkin Trans. 1 2000, 23, Thelakkat, H.-W. Schmidt, Polym.
38154195; for further information Prep. 1999, 40, 11821183.
about polymer-supported reagents, 24 I. Bozovic, V. Matijasevic, Mat. Sci.
see: c) S. W. Kaldor, M. G. Siegel, Forum 2000, 352 (Trends in Advanced
Curr. Opin. Chem. Biol. 1997, 1, 101 Materials and Processes), 18.
106; d) S. J. Shuttleworth, S. M. 25 S. Inoue, Kagaku Kogyo 2000, 51,
Allin, P. K. Sharma, Synthesis 1997, 128133.
12171239; e) P. Hodge, Chem. Soc. 26 J. N. Cawse, Acc. Chem. Res. 2001, 34,
Rev. 1997, 26, 417424. 213221.
17 T. R. Boussie, K. Hall, A. M. 27 J. D. Hewes, SPIE-Int. Soc. Opt. Eng.
LaPointe, V. Murphy, T. S. Powers, 2000, 3941 (Combinatorial Composi-
J. A. M. van Beek (Symyx Techno- tion Spread Techniques in Materials
logies), Delivery and scavenging and Device Development), 4661.
agents for the synthesis of compounds 28 a) W. F. Maier, Nachr. Chem. Tech.
and catalysts, PCT Int. Appl. WO Lab. 1999, 47, 12071210; b) W. F.
98/56796. Meier, Angew. Chem. 1999, 111, 1294
18 For reviews on combinatorial methods 1296; Angew. Chem. Int. Ed. 1999, 38,
of combinatorial catalyst development 12611218.
and high-throughput screening in 29 a) E. W. McFarland, W. H.
catalysis, see: a) S. Senkan, Angew. Weinberg, Trends Biotechnol. 1999, 17,
Chem. 2001, 113, 322341; Angew. 107115; b) E. W. McFarland, W. H.
Chem. Int. Ed. 2001, 40, 312329, and Weinberg, Mater. Technol. 1998, 3,
references cited therein; b) M. T. 153158.
References 1059
30 J. D. Hewes, Chim. Oggi 2000, 18, 20 47 S. Pessaud, F. Gervais, C.

24. Champeaux, P. Marchet, A.
31 a) J. R. Engstrom, W. H. Weinberg, Catherinot, M. Licheron, J. L.
AIChE J. 2000, 46, 25; b) X. D. Wu, Longuet, F. Ravel, Mat. Sci. Eng. B
W. H. Weinberg, Vacuum Solutions 1999, B60, 205211.
1997, November. 48 J. Letteri, Y. Jia, S. J. Fulk, D. G.
32 R. L. Bedard, AIChE J. 1999, 45, Schlom, M. E. Hawley, G. W.
24742476. Brown, Thin Solid Films 2000, 379,
33 X.-D. Xiang, Mater. Sci. Eng. B 1998, 6471.
56, 246250. 49 C.-M. Chen, H. C. Pan, D. Z. Zhu, J.
34 X.-D. Xiang, P. G. Schultz, Physica Hu, M. Q. Li, Nucl. Instrum. Methods
C 1997, 282287, 428430. Phys. Res. Sect. B 1999, 159, 8188.
35 H. Koinuma, Solid State Ionics 1998, 50 X. Q. Liu, Z. F. Li, W. Lu, S. C.
108, 17. Chen, C. M. Chen, D. Z. Zhu, J. Hu,
36 X.-D. Sun, K.-A. Wang, Y. Yoo, W. G. M. Q. Li, Appl. Phys. Lett. 1999, 75,
Wallace-Freedman, C. Gao, X.-D. 26112613.
Xiang, P. G. Schultz, Adv. Mater. 51 C. Chen, H. Pan, D. Zhu, J. Hu, M.
1997, 9, 10461049. Li, Gaojishu Tongxun 1999, 9, 4144.
37 B. E. Baker, N. J. Kline, P. J. Treado, 52 C. Chen, H. Pan, D. Zhu, J. Hu, M.
M. J. Natan, J. Am. Chem. Soc. 1998, Li, Mater. Sci. Eng. B 2000, B72, 113
118, 87218722. 116.
38 T. Vossmeyer, S. Jia, E. DeIonno, 53 H. Koinuma, T. Koida, T. Ohnishi,
M. R. Diehl, S.-H. Kin, X. Peng, A. P. D. Komiyama, M. Lippmaa, M.
Alivisatos, J. R. Heath, J. Appl. Phys. Kawasaki, Appl. Phys. A.: Mater, Sci.
1998, 84, 36643670. Process 1999, 69 (Suppl.), S29S31.
39 X.-D. Xiang, X.-D. Sun, G. Briceno, 54 A. Ohtomo, T. Makino, K. Tamura,
Y. Lou, K. A. Wang, H. Chang, Y. Matsumoto, Y. Segawa, Z. Tang,
W. G. Wallace-Freedman, S.-W. G. K. L. Wong, H. Kionuma, M.
Chen, P. G. Schultz, Science 1995, Kawasaki, Proc. SPIE-Int. Soc. Opt.
268, 17381740. Eng. 2000, 3941 (Combinatorial
40 T. X. Sun, Biotechnol Bioeng. 1999, 61, Composition Spread Techniques in
193201. Materials and Device Development),
41 R. B. van Dover, L. F. Schneemeyer, 7081.
R. M. Fleming, H. A. Huggins, 55 Y. Matsumoto, M. Murakami, Z. Jin,
Biotechnol. Bioeng. 1999, 61, 217225. A. Nakayama, T. Yamaguchi, T.
42 C. Schmitz, P. Poesch, M. Ohmori, E. Suzuki, S. Nomura, M.
Thelakkat, H.-W. Schmidt, Proc. Kawasaki, H. Koinuma, Proc. SPIE-
SPIE-Int. Soc. Opt. Eng. 1999, 3797 Int. Soc. Opt. Eng. 2000, 3941
(Organic Light-Emitting Materials and (Combinatorial Composition Spread
Devices III), 423431. Techniques in Materials and Device
43 H.-W. Schmidt, C. Schmitz, P. Development), 1927.
Poesch, M. Thelakkat, Proc. SPIE- 56 Z. Jin, M. Murakami, T. Fukumura,
Int. Soc. Opt. Eng. 1999, 3797 (Organic Y. Matsumoto, A. Ohtomo, M.
Light-Emitting Materials and Devices Kawasaki, H. Koinuma, J. Cryst.
III), 5865. Growth 2000, 214/215, 5558.
44 C. Schmitz, M. Thelakkat, H.-W. 57 a) Q. Wang, G. Yue, J. Li, D. Han,
Schmidt, Adv. Mater. 1999, 11, 821 Solid State Commun. 1999, 113, 175
826. 178; b) H. Aiyer, D. Nishioka, R.
45 C. Schmitz. P. Posch, M. Maruyama, H. Shinno, N. Matsuki,
Thelakkat, H.-W. Schmidt, Phys. K. Miyazaki, H. Fujioka, H.
Chem. Chem. Phys. 1999, 1, 17771781. Koinuma, Jpn. J. Appl. Phys. 2001, 40,
46 C. Schmitz, P. Posch, M. L81L83.
Thelakkat, H.-W. Schmidt, 58 E. W. McFarland, E. Danielson, M.
Macromol. Symp. 2000, 154 (Polymers Devenney, C. Warren (Symyx
in Display Applications), 209221. Technologies), Potential Masking
Systems and Methods for Combinatorial 72 B. E. Baker, N. J. Kline, P. J. Treado,

Library Synthesis, WO-A 98/14641, M. J. Natan, J. Am. Chem. Soc. 1996,
1998. 118, 87218722.
59 E. W. McFarland, W. H. Weinberg, 73 K. Kneipp, H. Kneipp, R.
Mater. Technol. 1998, 13, 107120. Manoharan, E. B. Hanlon, I.
60 X.-D. Xiang, Chem. Ind. 1998, 19, Itzkan, R. R. Dasari, M. S. Field,
800802. Appl. Spectrosc. 1998, 52, 14931497.
61 J. Wang, Y. Yoo, C. Gao, I. 74 J. M. Whitling, G. Spreitzer, D. W.
Takeuchi, X.-D. Sun, H. Chang, Wright, Adv. Mater. 2000, 12, 1377
X.-D. Xiang, P. G. Schultz, Science 1380.
1998, 279, 17121714. 75 G. Spreitzer, J. M. Whitling, D. W.
62 For a review, see: a) M. Noh, C. D. Wright, Mater. Res. Soc. Symp. Proc.
Johnson, M. D. Hornbostel, J. 2000, 599 (Mineralization in Natural
Thiel, D. C. Johnson, Chem. Mater. and Synthetic Biomaterials), 201
1996, 8, 16251635, and references 206.
therein; b) C. D. Johnson, Chem. 76 G. Spreitzer, J. M. Whitling, J. D.
Mater. 1998, 10, 10961101, and Madura, D. W. Wright, Chem.
references therein. Commun. 2000, 209210.
63 H. Chang, C. Gao, I. Takeuchi, Y. 77 M. Cohen-Adad, M. Gharbi, C.
Yoo, J. Wang, P. G. Schultz, X.-D. Goutaudier, R. Cohen-Adad, J.
Xiang, R. P. Sharma, M. Downes, T. Alloys Compd. 1999, 289, 185195.
Venkatesan, Appl. Phys. Lett. 1998, 72, 78 E. D. Isaacs, M. Marcus, G. Aeppli,
21852187. X.-D. Xiang, X.-D. Sun, P. G.
64 X.-D. Sun, K.-A. Wang, Y. Yoo, W. G. Schultz, M. Kao, G. S. Cargill III,
Wallace-Freedman, C. Gao, X.-D. R. Haushalter, Appl. Phys. Lett. 1998,
Xiang, P. G. Schultz, Adv. Mater. 73, 18201822.
1997, 9, 10461049. 79 K. Omote, T. Kikuchi, J. Harada, M.
65 J. L. Wu, M. Devenney, E. Kawasaki, A. Ohtomo, M. Ohtani, T.
Danielson, D. Poojary, W. H. Ohnishi, D. Komiyama, H.
Weinberg, Mater. Res. Soc. Symp. Koinuma, Proc. SPIE-Int. Soc. Opt.
Proc. 1999, 560 (Luminescent Eng. 2000, 3941 (Combinatorial
Materials), 6570. Composition Spread Techniques in
66 J. T. Rantala, T. Kololuma, L. Materials and Device Development),
Kivimaki, SPIE-Int. Soc. Opt. Eng. 8491.
2000, 3941 (Combinatorial Composi- 80 C. E. Kibbey in: A Practical Guide to
tion Spread Techniques in Materials Combinatorial Chemistry. Czarnick,
and Device Development), 1118. A. W., DeWitt, S. H. (eds), American
67 J. Wang, K. E. Gonsalves, J. Comb. Chemical Society, Washington, DC.
Chem. 1999, 1, 216222. 1997, pp. 123151.
68 D. E. Akporiaye, I. M. Dahl, A. 81 E. Danielson, J. H. Golden, E. W.
Karlsson, R. Wendlbo, Angew. Chem. McFarland, C. M. Reaves, W. H.
1998, 110, 629631; Angew. Chem. Int. Weinberg, X. D. Wu, Nature 1997,
Ed. 1998, 37, 609611. 389, 944948.
69 J. Klein, C. W. Lehmann, H.-W. 82 E. Danielson, M. Devenney, D. M.
Schmidt, W. F. Maier, Angew. Chem. Giaquinta, J. H. Golden, R. C.
1998, 110, 35573561; Angew. Chem. Haushalter, E. W. McFarland,
Int. Ed. 1998, 37, 33693372. D. M. Poojary, C. M. Reaves, W. H.
70 K. Choi, D. Gardner, N. Hilbrandt, Weinberg, X. D. Wu, Science 1998,
T. Bein, Angew. Chem. 1999, 111, 279, 837839.
30703073; Angew. Chem. Int. Ed. 83 T. Makino, G. Isoya, Y. Segawa, C.
1999, 38, 28912894. Chia, T. Yasuda, M. Kawasaki, A.
71 R. Lai, B. S. Kang, G. Gavalas, Angew. Ohtomo, K. Tamura, Y. Matsumoto,
Chem. 2001, 113, 422425; Angew. H. Koinuma, SPIE-Int. Soc. Opt. Eng.
Chem. Int. Ed. 2001, 40, 408411. 2000, 3941 (Combinatorial Composi-
References 1061
tion Spread Techniques in Materials Xiang, Science 1997, 276, 20042006;

and Device Development), 2835. b) T. Wei, W. G. Wallace-Freedman,
84 a) J. G. Bednorz, K. A. Muller, Z. P. G. Schultz, X.-D. Xiang, Appl.
Phys. B. 1986, 64, 189193; b) J. G. Phys. Lett. 1996, 68, 35063508; c) C.
Bednorz, M. Takashige, K. A. Gao, T. Wei, F. Duewer, Y. Lu, X.-D.
Muller, Europhys. Lett. 1987, 3, 379 Xiang, Appl. Phys. 1997, 71, 1872
385. 1874; d) I. Takeuchi, F. Duewer,
85 C. Gao, T. Wei. F. Duewer, X.-D. X.-D. Xiang, Appl. Phys. 1997, 71,
Xiang, Appl. Phys. Lett. 1997, 71, 20262028.
18171821. 97 I. Takeushi, H. Chang, C. Gao, P. G.
86 A. W. Webb, E. F. Skelton, S. B. Schultz, X.-D. Xiang, R. P. Sharma,
Quadri, V. Browning, E. R. M. J. Downes, T. Venkatsan, Appl.
Carpenter, Physical Rev. B 1992, 45, Phys. Lett. 1998, 73, 894896.
24802483. 98 T. Justel, H. Nikol, C. Ronda,
87 A. W. Webb, E. F. Skelton, S. B. Angew. Chem. 1998, 110, 32503271;
Quadri, E. R. Carpenter, J. Solid Angew. Chem. Int. Ed. 1998, 37, 3084
State Chem. 1993, 102, 519533. 3103.
88 H. Kionuma, Y. Matsumoto, M. 99 X.-D. Sun, C. Gao, J. Wang, X.-D.
Murakami, T. Shono, T. Hasegawa, Xiang, Appl. Phys. Lett. 1997, 70,
T. Fukumura, M. Kawasaki, P. 33533355.
Ahmet, T. Chikyow, S.-Y. 100 X.-D. Sun, X.-D. Xiang, Appl. Phys.
Kioshihara, Science 2001, 201, 854 Lett. 1998, 72, 525527.
856. 101 E. Danielson, M. Devenney, D. M.
89 G. Briceno, H. Chang, X.-D. Sun, Giaquinta, J. H. Golden, R. C.
P. G. Schultz, X.-D. Xiang, Science Haushalter, E. W. McFarland,
1995, 270, 273275. D. M. Poojary, C. M. Reaves, W. H.
90 a) P. G. Schultz, X.-D. Xiang, I. Weinberg, X.-D. Wu, J. Mol. Struct.
Goldwasser (The Regents of the 1998, 469, 229235.
University of California, Symyx 102 M. Thelakkat, C. Schmitz, H.-W.
Technologies), Giant Magnetoresistive Schmidt, Polym. Prep. 1999, 40,
Cobalt Oxide Compounds, US Patent 12301231.
5,776,359, 1998; b) P. G. Schultz, 103 C. Schmitz, H.-W. Schmidt, M.
X.-D. Xiang, I. Goldwasser (The Thelakkat, Chem. Mater. 2000, 12,
Regents of the University of 30123019.
California, Symyx Technologies), The 104 V. N. Nesterov, T. V. Timofeeva,
Combinatorial Synthesis of Novel O. Y. Borbulevych, M. Y. Antipin,
Materials, PCT Int. Appl. WO 96/ R. D. Clark, Acta Cryst. 2000, C56,
11878. 971975.
91 K. Seeger, Semiconductor Physics. 105 K. Sada, K. Yoshikawa, M. Miyata,
Springer, Berlin 1991. Chem. Commun. 1998, 17631764.
92 a) J. J. Hanak, J. Mater. Sci. 1970, 5, 106 Q. Huo, G. Sui, P. Kele, R. M.
964971; b) J. J. Hanak, Proc. 1er Leblanc, Angew. Chem. 2000, 112,
Colloq. Int. Pulverisation Cathodiques 19341936; Angew. Chem. Int. Ed.
Ses Appl. 1973, 165 (Suppl.), 177197. 2000, 39, 18541857.
93 J. J. Hanak, J. Vac. Sci. Technol. 1971, 107 For reviews about new chiral selectors,
8, 172175. see: a) F. Svec, D. Wulff, J. M. J.
94 R. B. van Dover, L. F. Schneemeyer, Frechet in: Chiral Separation
R. M. Fleming, Nature 1998, 392, Techniques. Subramanian, G. (ed.),
162164. Wiley-VCH, Weinheim 2001, pp. 55
95 J. Li, F. Duewer, C. Gao, H. Chang, 93; b) N. M. Maier, P. Franco, W.
X.-D. Xiang, Y. Lu, Appl. Phys. Lett. Lindner, J. Chromatogr. A 2001, 906,
2000, 76, 769771. 333.
96 a) Y. Lu, T. Wei, F. Duewer, Y. Lu, 108 a) P. Murer, K. Lewandoski, F. Svec,
N.-B. Ming, P. G. Schultz, X.-D. J. M. J. Frechet, Chem. Commun.
1998, 25592560; b) P. Murer, K. see: a) R. J. Ceresa (ed.), Block and

Lewandoski, F. Svec, J. M. J. Frechet, Graft Copolymerization. Wiley, New
Anal. Chem. 1999, 71, 12781284. York 1972; b) A. Noshay, J. E.
109 K. Lewandowski, P. Murer, F. Svec, McGrath, Block Polymers. Academic
J. M. J. Frechet, J. Comb. Chem. Press, New York 1977; c) S. L.
1999, 1, 105112. Aggarwal (ed.), Block Polymers.
110 a) W. H. Pickle, C. J. Welch, B. Plenum Press, New York 1979.
Lamm, J. Org. Chem. 1992, 57, 3857 124 D. J. Gravert, A. Datta, P.
3860; b) C. J. Welch, J. Chromatogr. A Wentworth Jr, K. D. Janda, J. Am.
1994, 666, 326. Chem. Soc. 1998, 120, 94819495.
111 Y. Wu, Y. Wang, A. Yang, T. Li, 125 a) A. W. Bosman, A. Heuman, G.
Anal. Chem. 1999, 71, 16881691. Klarner, D. Benoit, J. M. J.
112 L. H. Bluhm, Y. Wang, T. Li, Anal. Frechet, C. J. Hawker, J. Am. Chem.
Chem. 2000, 72, 52015205. Soc. 2001, 123, 64616462; b) C. J.
113 a) C. J. Welch, G. Bhat, M. N. Hawker, D. Benoit, F. Rivera Jr, V.
Protopopova, J. Combi. Chem. 1999, Chaplinski, A. Nilsen, R. Braslau,
1, 364367; b) Y. Wang, T. Li, Anal. Polym. Mater. Sci. Eng. 1999, 80, 90
Chem. 1999, 71, 41784182; c) Y. 91.
Wang, L. H. Bluhm, T. Li, Anal. 126 a) R. B. Nielsen, A. L. Sar, M.
Chem. 2000, 72, 54595465. Petro, T. S. Lee, P. Huefner, Polym.
114 C. J. Welch, S. D. Pollard, D. J. Mater. Sci. Eng. 1999, 80, 92; b) G.
Mathre, P. J. Reider, Org. Lett. 2000, Klarner, A. L. Sar, H.-T. Chang,
3, 9598. M. Petro, R. B. Nielsen, Polym. Prepr.
115 M. D. Weingarten, K. Sekanina, (Am. Chem. Soc. Div. Polym. Chem.)
W. C. Still, J. Am. Chem. Soc. 1998, 1999, 40, 469.
120, 91129113. 127 For a review, see: a) K. Matyjaszewski
116 a) O. Ramstrom, L. Ye, M. Krook, K. (ed.), Controlled Radical Polymerization.
Mosbach, Anal. Comm. 1998, 35, 9 American Chemical Society,
11; b) O. Ramstrom, L. Ye, M. Krook, Washington, DC 1998; b) G. Moad, D.
K. Mosbach, Chromatographia 1998, Solomon, The Chemistry of Free-
47, 465469; c) L. Sabourin, R. J. Radical Polymerization. Pergamon,
Ansell, K. Mosbach, I. A. Nicholls, Oxford 1995.
Anal. Comm. 1998, 35, 285287. 128 K. Matyjaszewski, T. E. Patten, J.
117 For a review on molecular imprinting Xia, J. Am. Chem. Soc. 1997, 119, 674
see: G. Wulff, Angew. Chem. 1995, 680.
107, 19581979; Angew. Chem. Int. Ed. 129 M. Petro, F. Svec, I. Gitsov, J. M. J.
Engl. 1995, 34, 18121832 and Frechet, Anal. Chem. 1996, 68, 315
references cited therein. 321.
118 T. Takeuchi, D. Fukuma, J. Matsui, 130 T. Hashimoto, Y. Muramatsu, T.
Anal. Chem. 1999, 71, 285290. Hayakawa, H. Fukumoto, T.
119 S. Brocchini, K. James, V. Yamamoto, H. Koinuma, Proc. SPIE-
Tangpasuthadol, J. Kohn, J. Am. Int. Soc. Opt. Eng. 2000, 3941
Chem. Soc. 1997, 119, 45534554. (Combinatorial and Composition
120 C. H. Reynolds, J. Combi. Chem. Spread Techniques in Materials and
1999, 1, 297306. Device Development), 3644.
121 T. A. Dickinson, D. R. Walt, J. 131 T. Hashimoto, Y. Muramatsu, T.
White, J. S. Kauer, Anal. Chem. 1997, Hayakawa, H. Fukumoto, T.
69, 34133418. Yamamoto, H. Koinuma, Proc. SPIE-
122 G. Odian, Principles of Polymerization Int. Soc. Opt. Eng. 2000, 3941
2nd edn. John Wiley & Sons, New (Combinatorial and Composition
York 1981. Spread Techniques in Materials and
123 For block and graft copolymerizations, Device Development), 92100.
1063
35
Reprogramming Combinatorial Biology for
Combinatorial Chemistry*
Sean V. Taylor
35.1
Introduction
As the other chapters in this book have nicely illustrated, combinatorial chemistry
has made dramatic technical advances since its inception, with signicant im-
provements in the design, synthesis, purication, and evaluation of combinatorial
libraries. It is now commonplace for companies focusing on drug discovery to
have 0.51.5 million compounds arrayed throughout their combinatorial libraries,
which can be screened in a matter of weeks or months for activity against any
number of biological targets. The potential success of this strategy is underscored
by reports from numerous pharmaceutical companies of compounds that were
identied or optimized using combinatorial chemistry and that have now entered
clinical drug trials. It is quite likely that, over the next 100 years, a signicant per-
centage of pharmaceuticals will be derived in some manner from combinatorial
libraries.
If we expand our denition of combinatorial libraries, however, the current im-
portance of the combinatorial approach to drug discovery, as well as to most life
processes, is more immediately clear. For instance, eight of the 20 top-selling
pharmaceuticals are natural products or derived from natural products [13]. It is
not a large leap in logic to consider these compounds as already being derived
from combinatorial libraries biological, or perhaps evolutionary combinatorial
libraries. In contrast to combinatorial libraries produced by synthetic means, the
combinatorial libraries that give rise to natural products are not produced at the
compound level, but at the genetic level during the process of evolution, through
mutation, gene duplication, and interspecies genetic transfer. The evaluation of
these biological combinatorial libraries is simply the process of natural selection.
Those compounds that provide some value toward the survival of the producing
organism will be propagated and further improved upon through additional evo-
lutionary rounds.
*Portions of this article were previously published (Angew. Chem. 113 (2001) 34083436; Angew.
Chem. Int. Ed. 40 (2001) 33103335). [Ref. 100]

ISBN: 3-527-30509-2
1064 35 Reprogramming Combinatorial Biology for Combinatorial Chemistry
Nature has utilized such evolutionary libraries over billions of years, but mo-
lecular biologists, biochemists, and chemists have only recently learned how to
harness this combinatorial power, and for a number of dierent uses. In this
chapter, the various eorts to engineer and apply biological combinatorial libraries
for use in enzymology, drug discovery, bioprocessing, and also for addressing fun-
damental issues in chemistry and biology will be explored. Instead of an exhaus-
tive review, specic examples will be used to highlight various combinatorial as-
pects of biology. In addition to asking the question Where are we now?, I also
hope to ask Where are we (or where could we be) going?
35.2
Combinatorial Biosynthesis: Creation of Novel Small-molecule Natural Products
Many secondary metabolites are composed of polyketides, nonribosomally pro-

duced peptides, carbohydrates, or some combination of all three (Fig. 35.1) [46].
Polyketides are complex and highly stereogenic compounds that are constructed
from acyl-coenzyme A building blocks, often by huge modular enzyme complexes
called polyketide synthases (PKSs) [7]. Nonribosomal peptides (NRPs), as the
name implies, are amino acid-derived molecules wherein the peptide bonds are
not produced by the traditional translational machinery of the ribosome, but in-
stead on large modular enzyme complexes called nonribosomal peptide synthases
(NRPSs) [8]. Carbohydrate moieties, very commonly deoxysugars in secondary
metabolites, are produced by more traditional nonmodular biosynthetic path-
ways [911]. Illustrations of the typical biosynthetic pathways are shown in Fig. 35.2.
The relaxed specicity demonstrated by some of the enzymes involved in pro-
ducing these compounds, as well as the modular nature of some of the systems,
have allowed researchers to produce new natural products by cleverly reengi-
neering the biosynthetic pathways. Such engineering is usually called combinatorial
biosynthesis, and is often achieved by substituting (in combinatorial fashion) dier-
ent non-natural building blocks and the enzymes that can utilize them into a poly-
ketide, nonribosomal peptide, or deoxysugar biosynthetic pathway [1218]. The
reprogramming of biosynthetic pathways has the potential to be enormously use-
ful for combinatorial chemistry, since it creates a method for the parallel synthesis
of a large number of complex molecules whose conventional organic syntheses are
generally too complex to be easily adapted for combinatorial production. Another
advantage is that these combinatorial biosynthetic libraries are often closely related
to natural products that have already shown some useful activity, so the chances of
harvesting pharmaceutical lead compounds from them may be higher than those
from a synthetic combinatorial library. Finally, combinatorial biosynthesis could
provide a convenient method for creating libraries that could be further manipu-
lated by synthesis, reducing some of the time and cost associated with synthetic
For all of these reasons, many corporate and academic research groups are work-
ing to manipulate biosynthetic pathways for use in combinatorial biosynthesis [19].
35.2 Combinatorial Biosynthesis: Creation of Novel Small-molecule Natural Products 1065
Fig. 35.1. Representative examples of polyketide-derived, non-

ribosomal peptide-derived, and deoxysugar-derived natural
products.
Fig. 35.2. Biosynthetic pathways. (A) The A. Seven amino acid incorporation modules
modular erythromycin polyketide synthase (17), coded by three genes srfA-A, srfA-B, and
produces 6-deoxyerythronolide B, which is then srfA-C, are shown with the growing chain. The
converted to erythromycin A by downstream b-hydroxy fatty acid side-chain is incorporated
nonmodular processing enzymes. The modular at the beginning of the biosynthesis by an
polyketide synthase has a loading module (L) unknown mechanism. P, incorporation of b-
and six chain elongation modules (16) hydroxy fatty acid (not part of module); A,
expressed from three genes DEBS13. AT, acyl amino acid adenylation domain; T, thiolation
transferase domain; CP, acyl carrier protein; domain; C, condensation; E, epimerization
KS, ketosynthase domain; KR, ketoreductase domain; TE, thioesterase (cyclization) domain.
domain; DH, dehydratase; ER, enoyl reductase; (C) Biosynthesis pathway for d-desosamine,
TE, thioesterase (cyclization) domain. (B) The the deoxysugar of the secondary metabolites
modular peptide synthase-producing surfactin methamycin/neomethamycin.
Salient examples of the combinatorial biosynthetic engineering of polyketides, non-

ribosomal peptides, and carbohydrates are illustrated below.
35.2.1
Polyketide Combinatorial Biosynthesis
Polyketide biosynthesis has been the focus of intense study for several years. Sev-
eral excellent reviews summarizing the current state of knowledge in this area
have been published elsewhere [2023]. The enzyme systems responsible for pol-
yketide biosynthesis can be roughly assigned to four categories: the type I modular,
type I iterative, type II, and higher plant PKSs, each with dierent characteristics.
Type I modular PKSs are bacterial in origin and produce mostly macrolide-type
natural products, such as erythromycin, and have a separate catalytic module for
each chain elongation step (including modications along the way, such as reduc-
tions). Type I iterative PKSs, generally found in fungi, have only one module
which iteratively processes the polyketide chain through numerous steps [24]. In
Fig. 35.2. (continued)
these PKSs, some activities can be turned on and o at dierent points in the bio-
synthesis [25], and this process probably occurs through the intercession of
helper proteins outside the module [26]. The complexity of the type I iterative
systems has to this point precluded attempts to reengineer them for combinatorial
biosynthesis. Type II PKSs are multisubunit enzymes that usually make aromatic
polyketides, such as actinorhodin (see Fig. 35.3). Each subunit is responsible for
catalyzing a specic type of reaction. Finally, the higher plant PKSs utilize para-
coumaroyl-CoA as a starter unit and produce complex hydroxylated aromatics. In-
terestingly, they utilize a single enzyme active site for the chain elongation, de-
carboxylation, cyclization, and aromatization steps along the biosynthetic pathway,
Fig. 35.3. Actinorhodin biosynthesis pathway. Reactions not

occurring via the act minimal PKS are indicated with a reaction
arrow. KR, ketoreductase; ARO, aromatization; CYC, cyclization.
an impressive feat of enzymatic control seemingly dictated by only a few highly

conserved residues acting in concert [27, 28].
The modularity of type I PKSs perhaps makes them the most attractive targets
for combinatorial biosynthesis eorts, and the majority of eort in combinatorial
reengineering has been spent in mixing and matching modules through genetic
engineering. However, a signicant eort has also been placed on manipulating the
type II PKSs to produce new natural products. A few examples are noted below.
35.2.1.1 Combinatorial Biosynthesis from Type II PKSs

The initial reports of the combinatorial biosynthesis of novel polyketides from type
II PKSs were from Hopwood, Khosla, and coworkers [2933], and were at least par-
tially driven by eorts to unravel the mechanistic enzymology of the type II sys-
tems. These eorts were rewarded by the identication of the minimal PKS,
which consists only of a ketosynthase, a chain length factor, and an acyl carrier pro-
tein, which is sucient to produce a polyketide chain of specic size poised for
cyclization at a specic position [29, 32, 34]. Every type II PKS system could be
considered to be composed of a minimal PKS, along with other enzymes respon-
sible for other functionalizations on the polyketide chain, such as additional cycli-
zations, aromatizations, or glycosylations (Fig. 35.3). Combinatorial biosynthetic
libraries can thus be created by producing hybrid type II PKSs containing a mini-
mal PKS with dierent modifying (or nonmodifying) subunits from various natu-
ral type II PKSs. The engineered actinorhodin PKS systems produced several novel
Fig. 35.4. Novel aromatic polyketides produced from

engineered variants of the actinorhodin PKS. Some of the
products are derived from an actinorhodin/tetracenomycin
(tem) or a frenolamycin/actinorhodin ( fre) hybrid.
aromatic polyketides, some of which are shown in Fig. 35.4. Subsequent reports of
combinatorial biosynthesis using type II PKSs, while generally successful, showed
that the hybrid enzyme systems did not always perform as expected [35, 36], which
has reduced the ability to design combinatorial biosynthesis libraries from type II
PKSs with predictable structures. Additionally, the assignments of the roles of dif-
ferent parts of the minimal PKS in specifying chain length and point of initial
cyclization have been shown to be incorrect, at least for some type II PKSs [3739].
Despite this limitation, or perhaps because of it, several previously unknown aro-
matic polyketides have been created, sometimes with quite intricate and unexpected
structures (Fig. 35.5). Work on combinatorial biosynthesis of aromatic polyketides
Fig. 35.5. Unpredicted products from the whiE minimal PKS.
from type II PKSs continues, but has perhaps been overshadowed by develop-
ments in engineering type I modular PKSs for production of combinatorial bio-
synthesis libraries [14, 18, 20, 40, 41].
35.2.1.2 Combinatorial Biosynthesis from Type I Modular PKSs

To date, the best studied and most successful type I modular PKS combinatorial
biosynthesis system is based around the erythromycin polyketide synthase com-
plex (DEBS) [15, 20, 42]. DEBS is a three-unit PKS (DEBS1, DEBS2, and DEBS3)
containing a loading module and six processing modules that ultimately produce
Fig. 35.6. Incorporation by feeding of alternative diketide

precursors into the erythromycin pathway results in novel
variants of erythromycin A.
6-deoxyerythronylide B (see Fig. 35.2A). This aglycon unit is processed by down-

stream enzymes that oxidize the backbone and append deoxysugars to give eryth-
romycin A.
To explore the potential of combinatorial biosynthesis with type I modular PKSs,
the DEBS system has been manipulated in several ways to produce combinatorial
biosynthetic libraries. At the entry of the pathway, new biosynthetic products can
be made either by utilizing alternate diketides (Fig. 35.6), which has also been
possible with type II PKSs [43], or by changing the loading module [44]. Propionyl
CoA is the natural starter unit, but replacing the DEBS loading module with the
avermectin PKS loading module, which demonstrates broader specicity, results in
the production of new polyketides (Fig. 35.7) [44]. In the pathway, combinatorial
libraries have been produced by (1) altering the extension of the chain by replacing
the native acyl transferase units in modules with non-native acyl transferase do-
mains [45], (2) altering the state of reduction of the ketone at each chain position
through changes in the reduction domains in each module [46], (3) altering the
stereochemistry at tertiary and quaternary carbons through alteration in the appro-
priate domains [47, 48], or (4) feeding substrates that can be utilized by downstream
modules [49, 50]. Additionally, diverse products can be made by lengthening or
shortening the total length of the chain through adding or removing modules [51
53].
Most DEBS-derived libraries to date, while presenting exciting advances in com-
binatorial biosynthesis, have been small by combinatorial library standards [54],
since genetic manipulation of the very large type I modular PKS systems can be
cumbersome. A clever approach that should allow for easier manipulation and
larger combinatorial libraries is to utilize multiple PKS gene-containing plasmids
Fig. 35.7. Replacing the wild-type ery loading module with the
avermectin loading module, which displays reduced specicity,
results in iso-propyl- and sec-butyl-containing erythromycin
variants.
(Fig. 35.8) [5558]. For two or more plasmids (circular segments of DNA) to coex-
ist in a single cell, they must be compatible (containing compatible origins of rep-
lication). In the multiplasmid PKS approach, compatible plasmids are introduced
into an appropriate expression host, i.e. one that produces no polyketides, or has
had the polyketide-producing pathways it normally contains completely eliminated.
These plasmids contain dierent sets of genes coding for dierent PKS modules,
and each plasmid may harbor PKS genes that have mutations providing further
permutations. By introducing dierent combinations of plasmids through cotrans-
formation, each host cell has the capability to produce a dierent polyketide. Such
an approach has led to the simplied production of a library of novel polyketides
based around the DEBS architecture (Fig. 35.9) [55]. As the collection of suitable
PKS module-containing plasmids multiplies, the ability to produce more novel
Fig. 35.8. The multiplasmid approach to possible combinations are transformed into a
combinatorial biosynthesis. For each module a suitable host organism. Growth on all three
separate plasmid is used. Each plasmid also antibiotics ensures that each host cell contains
contains a dierent antibiotic resistance gene. all three types of modules.
Modications are made to each module, then
polyketides increases exponentially. Additionally, because the rational or predictive

design of polyketides is possible due to the modular design of these type I PKSs, it
should eventually be possible to produce almost any polyketide backbone with in-
telligently placed functionalities by transforming the right combination of plasmids.
The production and manipulation should also be aided by expression of these sys-
tems in more easily handled organisms instead of the natural hosts [59]. Some
progress toward this goal has been recently reported, with the high-level production
of 6-deoxyerythronylide B in an engineered strain of Escherichia coli [60]. Finally,
further understanding of how PKS modules interact and communicate throughout
a polyketide construction will be very important to the proper mixing and match-
ing of modules in combinatorial biosynthesis eorts [6163].
Fig. 35.9. A selection of dierent 6-deoxyerythronolide B

variants that were produced using the multiplasmid
approach with the erythromycin modules.
35.2.2
Combinatorial Biosynthesis of Nonribosomal Peptide Products
Nonribosomal peptides are produced over a wide range of species and probably
function in their native organisms mainly as signaling, siderophoric, and defensive
molecules [4]. In contrast to the PKSs, all known nonribosomal peptide synthases
(NRPSs) appear to utilize a modular structure. Several excellent reviews summarize
the state of knowledge concerning NRP biosynthesis from genetic, enzymologic,
and structural viewpoints [22, 6467]. NRP-containing products have a number
of useful medical and biological functions, including biocidal, antibiotic, anti-
cholesterolic, and immunosuppressive [8]. As with polyketide natural products,
the ability to produce new NRPs would thus be a boon to drug discovery. While the
eld of nonribosomal peptide combinatorial biosynthesis is still emerging, some

signicant progress has been made.
The initial work on the reengineering of NRPSs for combinatorial biosynthesis
was with the synthase that naturally produces surfactin A, a heptapeptide product
from Bacillus subtilis [68, 69]. Three large gene products, srfA-A, srfA-B, and srfA-C,
encode the seven modules involved in the biosynthesis after the incorporation of a
fatty acid side-chain (Fig. 35.2B) [70]. Through genetic recombination, the second
leucine incorporation module in srfA-A was replaced with modules from Bacillus
brevis or from Penicillium chrysogenum that incorporate phenylalanine or ornithine,
resulting in new surfactin analogs (Fig. 35.10A) [71, 72]. Truncated peptides were
also created by moving the terminal thioesterase domain immediately downstream
of the srfA-A gene (Fig. 35.10B) [73].
While these experiments are promising, a considerable amount of work remains
to show whether true combinatorial libraries can be created by mixing and match-
ing NRP modules. It also remains to be seen whether NRPs will be amenable
to the multiplasmid approach (discussed above), which holds much promise for
the engineering of PKS combinatorial biosynthesis. This approach depends on
whether NRP modules that are expressed apart can properly reconstitute entire
NRPs. Alternatively, direct recombinant engineering of NRPSs may be more feasi-
ble than for PKSs, provided workable fusion sites can be identied for mixing and
matching NRP modules. Dimodular and trimodular hybrid NRPSs have been suc-
cessfully created thus far through this approach [74, 75]. Another important issue
in developing NRP combinatorial biosynthesis is the recognition of amino acids by
adenylation domains. The potential to incorporate dierent amino acids and other
starter units into NRPs exists, but we must rst determine (and then subvert for
our own uses) the strategy by which adenylation domains recognize the correct
amino acid. Progress toward this goal has been made [7678].
35.2.3
Combinatorial Biosynthesis from Hybrid PKS/NRPS Systems
A number of natural products are produced through hybrid PKS/NRPS biosyn-

thetic pathways. A typical example is epothilone, the biosynthetic gene organiza-
tion of which is shown in Fig. 35.11 [79]. These mixed systems are of course also
suitable targets for combinatorial biosynthesis [80]. While no examples of such an
approach yet exist, it is easy to imagine how novel epothilone analogs could be gen-
erated. For instance, the NRPS module could be replaced with another NRPS mod-
ule, which would in eect provide alternate starter units for the PKS (Fig. 35.11).
Alternatively, the PKS could be altered to create thiazole-containing combinatorial
biosynthesis libraries. Much work remains to be done in elucidating the organiza-
tion and structure of hybrid PKSs/NRPSs, however, before combinatorial biosyn-
thesis with these systems can be undertaken. Some initial progress has been made
in characterizing PKS/NRPS pathways [81].
Fig. 35.10. (A) Surfactin A, which is produced domain immediately downstream of the
by the seven modules. Two new analogs were srfA-A gene (which encodes the rst three
produced by replacing the d-Leu module with amino acid incorporation modules) results in
phenylalanine and ornithine incorporation the production of the expected truncated
modules. (B) Placing the thioesterase peptide.
Fig. 35.11. Biosynthesis of epothilone, a PKS/NRPS hybrid.
35.2.4
Combinatorial Biosynthesis of Carbohydrates
Deoxysugars are essential appendages for many secondary metabolites. Their bio-
synthesis has been reviewed extensively elsewhere [911, 82, 83]. In natural prod-
ucts they often act as guidance systems, determining the specicity and biological
activity toward a target [84, 85]. The ability to create diverse deoxysugars and incor-
porate them into larger structures provides an opportunity to devise natural prod-
uct analogs with altered targets, specicity, activity, and physical properties.
As indicated in Fig. 35.2C, three types of enzymes are necessary for the incor-
poration of deoxysugar moieties into larger natural products: (1) nucleotidyl-
transferases are responsible for adding nucleotide diphosphate appendages to car-
bohydrates; (2) modifying enzymes, which, for example, alter the oxidation state of
the molecule or replace hydroxyls with amines; and (3) glycosyltransferases, which
couple the fully derivatized sugar with its intended aglycon partners. To produce
novel deoxysugars, one can alter or relax the specicity of enzymes through the
introduction of mutations, replace a natural enzyme in one pathway with those
from other pathways, or take advantage of the relaxed specicity some of these
enzymes already demonstrated to incorporate non-natural substrates.
In one example, non-natural analogs of desosamine, the sugar moiety found
in methymycin and neomethymycin, were produced (Fig. 35.12). The desosamine
biosynthetic cluster was altered by deletion of the desV (reductive amination) and
desVI (dimethylation) genes [86, 87]. Several new macrolides were produced from
the deletion mutants, including some that were quite unexpected. In addition to
Fig. 35.12. Deletion of DesV or DesVI results in the production

of two new methamycin analogs.
producing potentially useful new macrolides, this work also demonstrates that the
glycosyltransferase involved has a relaxed substrate specicity, in that it could in-
corporate a variety of deoxysugars.
The ability to swap genes between pathways is another important demonstration
of the potential for deoxysugar combinatorial biosynthesis. In the methymycin
pathway, the desVI gene can be replaced without diculty by an analogous gene,
tylM1, that is involved in the biosynthesis of mycaminose in the tylosin pathway
(Fig. 35.13) [88]. Similarly, the tylB gene can replace desV [87]. The ease of such
replacements might suggest that very few proteinprotein interactions are essential
in the deoxysugar biosynthetic pathway, thus reducing the chances that communi-
cation problems may be stumbling blocks when mixing and matching deoxysugar
biosynthetic proteins in combinatorial biosynthesis.
The appending of alternative sugar moieties to aglycons for combinatorial bio-
synthesis also rests upon our ability to reengineer or utilize the existing reduced
specicity of the nucleotidyltransferases and glycosyltransferases involved. For
instance, the wild-type a-d-glucopyranosyl phosphate thymidylyltransferase (Ep )
shows very broad acceptance of sugar substrates for coupling to thymidylate (Fig.
35.14) [89, 90]. Structural analysis suggested that introducing specic point muta-
tions should further relax the specicity and better allow incorporation of deoxy-
sugars modied at C2, C3 or C6 [91]. The pooled Ep mutants were capable of
incorporating non-natural deoxysugars, including some that are unable to be in-
Fig. 35.13. DesV and DesVI can be replaced by analogous or

similar genes from the tylosin pathway.
corporated by the wild-type Ep . These results demonstrate the feasibility of a ratio-

nal redesign approach.
Another strategy for combinatorial biosynthesis using deoxysugars takes advan-
tage of the broad specicity of some glycosyltransferases [92]. In one striking ex-
ample, a cosmid (essentially, a very large piece of circular DNA) that contained 25
kb of the elloramycin biosynthetic pathway from Streptomyces olivaceus was trans-
formed into mutants of Streptomyces fradiae and Streptomyces argillaceus (Fig. 35.15)
[93]. The wild-type versions of these strains normally produce urdamycin A or mi-
thramycin, respectively, but the PKS genes for these natural products were deleted
in the mutant strains. The glycosyltransferase gene from the elloramycin path-
way was capable of accepting the alternate deoxysugars produced by the mutants,
resulting in the production of new glycosylated tetracenomycins. Further investi-
gation revealed that this glycosyltransferase was capable of glycosylating tetraceno-
mycins with several non-native deoxysugars, including a disaccharide. This glyco-
syltransferase element has been recently identied [94]. A related approach has
also been used with the erythromycin-producing strain Saccharopolyspora erythraea
[95]. The inverse approach instead of employing dierent deoxysugars, using
several dierent macrolides as substrates for a single glycosyltransferase has also
been successful with the glycosyltransferase from the picromycin biosynthetic path-
way in Streptomyces lividans [96].
The ability to reengineer enzymes or to introduce wild-type enzymes into new
deoxysugar biosynthetic pathways holds great promise for the combinatorial bio-
synthesis of a highly diverse array of deoxysugar-containing macrolides. While
a substantial amount of work has already been devoted to understanding the
genetics and enzymology of deoxysugar biosynthesis, further insight can only as-
sist eorts to produce combinatorial deoxysugar-containing biosynthetic libraries.
Recent identication of the elements in a glycosyltransferase responsible for sub-
strate specicity and catalytic activity is an important advance along these lines [97].
Fig. 35.14. (A) Reaction catalyzed by Ep , the pooled mutants (described in the text). WT
glycosylation of thymine by glucose phosphate. percentage, incorporation by the WT (wild
(B) Ep shows broad specicity for a variety of type) Ep ; Pool percentage, the eciency with
glucose phosphate analogs. Analogs with which the pool was able to incorporate the
numbers below them were evaluated by the sugar.
Fig. 35.15. (A) Mithramycin and urdamycin A, decient mutants of Streptomyces argillaceus
naturally produced by Streptomyces argillaceus and Streptomyces fradiae results in the
and Streptomyces fradiae respectively. (B) production of a variety of novel carbohydrate-
Expressing the elloramycin PKS genes in PKS- containing elloramycins.
35.3
Other Combinatorial Aspects of Biology
Pools of random oligonucleotides (DNA or RNA), peptides, or proteins might also

be considered combinatorial libraries, since they are also collections of diverse bio-
molecules (in this case, biopolymers) created in parallel. The fundamental dier-
ence between these libraries and those resulting from combinatorial biosynthesis
is the method of production. In contrast to small-molecule natural products, larger
biomolecules are synthesized in a template-directed fashion via the ribosome in
vivo or in vitro. This method can provide numerous advantages compared with the
production of small-molecule combinatorial libraries. First, it is quite easy to gen-
erate biopolymer libraries using recombinant DNA techniques, and the size, di-
versity, and quality can be readily analyzed (most commonly via DNA sequencing)
[98, 99]. This approach is in contrast to the wholly synthetic production of combi-
natorial biosynthesis libraries, in which complex product mixtures must be con-
tended with, or sophisticated spatial addressing methods must be employed, if one
is to productively screen compounds for activity. Second, several methods have
been developed for the in vivo or in vitro selection or screening from DNA-encoded
libraries, and so complex biopolymer mixtures can be screened or selected en masse
and readily separated into active and inactive components [100]. Those members
of biopolymer libraries with interesting properties can be easily identied by se-
quencing of the DNA template, and further optimization of a hit in a biopolymer
library can be readily undertaken via simple mutagenesis and directed evolution
methods.
While combinatorial biosynthesis certainly contains potential for the drug dis-
covery process through the generation of novel natural products, it has also been
very useful as a tool for studying the enzymology and organization of the biosyn-
thetic systems involved. Combinatorial libraries of DNA, RNA, small peptides, and
proteins may also one day be very useful for pharmaceutical or medicinal purposes,
but they are currently used mostly for the study of catalysis, folding, and molecular
recognition. What follows are brief discussions of how these combinatorial libraries
are currently being created and applied.
35.3.1
Combinatorial Libraries of Random DNA and RNA
Oligonucleotide molecules with a wide variety of functions have been selected from
RNA or DNA combinatorial libraries. Such libraries are routinely generated with as
many as 10 15 unique members. Because the structure, function, and genetic infor-
mation is self-contained for each molecule, the in vitro recovery and amplication
of rare genes with a desired phenotype is straightforward and very ecient. Con-
sequently, combinatorial libraries of oligonucleotides can be easily subjected to
multiple cycles of selection and enrichment.
The selection of RNA aptamers with a broad range of receptor-like activities
from large combinatorial RNA libraries has been particularly successful [101104].
Using such an approach, and a number of clever in vitro selection methods, RNA
aptamers have been identied with binding ability for small molecules [105109],
sometimes with very high specicity [110, 111]. Aptamers have also been selected
from large oligonucleotide combinatorial libraries with anity to a number of
medically and biologically important protein targets, including the CD4 antigen
[112], surface proteins specic to African trypanosomes [113], the cellular prion
protein PrP c (but not the infectious scrapie prion form PrP Sc ) [114], the hepatitis
C virus protein 3 protease [115], the human immunodeciency virus (HIV) TAT-I
protein [116], and human angiogenin [117].
RNA and DNA catalysts, termed ribozymes or DNAzymes, have also been se-
lected from combinatorial ensembles for a wide array of reactions [118122], in-
cluding oligonucleotide modications [123, 124], alkylation and acylation reactions
Fig. 35.16. Selection experiment for a self-ligating ribozyme.
[125, 126], peptide bond formation [127], and DielsAlder cycloadditions [128].
While these ribozymes are often poorly active, in some cases very high levels of
catalysis have been achieved through the further optimization of an initial lead
[129].
The direct selection of highly ecient self-ligating ribozymes (i.e. phosphoryl
transferases) from large RNA combinatorial libraries is one of the most impressive
accomplishments thus far in the eld of nucleotide-based catalysis (Fig. 35.16)
[130]. A library of @10 15 dierent RNAs with 220 random nucleotides was con-
structed, and from this ensemble roughly 1 in 10 13 members had the desired ligase
activity. Further cycles of diversication and selection were then used to evolve the
initially selected group of ligase ribozymes, and one of these was subsequently
reengineered with the ability to catalyze an intermolecular ligation with multiple

turnovers [131]. This enzyme exhibited a rate constant of >1 s1 , which corre-
sponds to a rate acceleration approaching 10 9 over background.
Nucleic acid-based receptors and catalysts from combinatorial libraries are or-
thogonal analogs of their protein counterparts, and have potential value as drugs
or diagnostic agents. The strategies used in their creation and selection, observa-
tions of how the initially identied hits further evolve to optimize function, and
insight into the comparative advantages and disadvantages with respect to proteins
should prove useful in our eorts to create and optimize novel protein catalysts
(see Section 35.3.3).
35.3.2
Peptide Combinatorial Libraries
Short peptides are good inhibitors for a number of enzymes, and are thus suitable
lead structures for developing potent nonpeptide inhibitors, which may have in-
creased bioavailability and half-lives in vivo. Peptide ligands and inhibitors are also
valuable for collecting a wealth of information about the structure, specicity, and
size of receptor binding pockets and enzyme active sites. Since it is often dicult
to predict which peptide sequence will have optimal inhibitory activity, selection
from combinatorial peptide libraries is attractive. Additionally, the selection results
may reveal new, previously unidentied components of the targeted pathway, which
may, in turn, represent formidable targets for inhibition by small organic mole-
cules.
Because short peptides are often quickly degraded in the cell, peptide libraries
for in vivo selection are usually displayed inside a larger protein scaold. For ex-
ample, combinatorial hexadecameric peptide libraries were displayed (by insertion
at the genetic level) into a surface loop of a biologically inert carrier protein (an
inactive mutant of staphylococcal nuclease) [132]. From a @10 6 -member yeast-
transformed library, three peptides that inhibited the spindle checkpoint and 29
peptides that inhibited a mating pheromone signaling pathway (29 peptides) were
identied by in vivo genetic selection in cleverly engineered yeast strains. The pu-
tative in vivo targets were subsequently identied using yeast two-hybrid analysis
[133] and genetic dissection of the target pathways. A similar in vivo genetic selec-
tion approach was recently used to identify members from a combinatorial non-
apeptide library that block intracellular dimerization of HIV-1 protease, albeit in E.
coli [134].
Peptide combinatorial libraries can also be evaluated in vitro for binding or
inhibitory activity. As opposed to in vivo peptide selections, in vitro selection has
three particular advantages. First, no carrier protein is required to protect the short
peptides from in vivo degradation. Of course, this freedom also increases the con-
formations available to the peptide, which may reduce the anity of the peptide to
a potential target [135, 136]. Secondly, much larger (@ 10 13 ) peptide libraries can
be assayed in vitro than in vivo (maximally 10 9 , which is the practical upper limit
because of plasmid transformation eciencies [137, 138]). Finally, unnatural amino
Fig. 35.17. The mRNA display method.
acids can be utilized in the peptide combinatorial libraries through the use of sup-
pressor codons or other strategies [139142].
Perhaps the most powerful method for in vitro selection of peptide combinato-
rial libraries is mRNA display, which works by utilizing direct covalent attachment
of each member of the peptide combinatorial library to its encoding mRNA (Fig.
35.17) [143, 144]. Such covalent constructs are formed by in vitro translation of 3 0 -
puromycin mRNA templates. After mRNA translation, puromycin enters the pep-
tidyl transferase site of the ribosome and is covalently attached to the C-terminus
of the nascent peptide. The peptide moiety of the resulting mRNApeptide conju-
gate can then be selected as described for the other formats.
In a recent example, 20 dierent peptide aptamers to streptavidin were identi-
ed from a combinatorial library of 10 13 dierent 88 amino acid sequences [145].
These aptamers had binding anities (KD 510 nM) that were three orders of
magnitude better than a commercially available streptavidin-binding decapeptide
(KD 1372 mM). Truncation analysis showed that one of these peptides could
be reduced to only 38 amino acids, and also indicated that the sequence motif of
histidineprolineglutamine (HPQ) was essential for binding activity (as in other
peptides with anity for streptavidin [146]). Interestingly, all 20 aptamers that
were identied were not from the intended reading frame but from the third read-
ing frame that results from a two-base insertion. This outcome is probably because
the HPQ motif occurs more frequently in the third reading frame.
35.3.3
Protein Combinatorial Libraries
Protein design and engineering is an attempt to understand the factors involved in

creating folded protein structures with specic behaviors, such as thermal stability
or specic catalytic activity, and then utilize that understanding to create novel pro-
teins with useful functions. Owing to our currently incomplete knowledge of the
relationship between structure and function, however, the full de novo design of a
Fig. 35.18. Experimental outline for the selection of ATP-

binding proteins from a 10 12 -member combinatorial protein
library.
functional protein from rst principles is not yet an achievable goal. As an alter-
native, researchers have begun producing combinatorial libraries of proteins with
varying levels of randomization, and then screening or selecting from these libraries
for valued function.
Given the size of typical protein domains, fully randomized protein combinatorial
libraries are, for practical purposes, innitely large. For a 100-amino-acid protein,
for example, there are 20 100 (10 130 ) possible sequences, and it is thus impossible
to examine a substantial portion of this diversity. To evaluate as large a fraction as
possible, researchers have turned to in vitro selection methods (discussed in Sec-
tion 35.3.2) such as mRNAprotein fusions. Using the same mRNA display system
outlined in Section 35.3.2, but selecting for protein behavior instead of peptide
behavior, Keefe and Szostak recently identied four ATP binders starting from a
library of 6 10 12 proteins in which 80 contiguous amino acids were randomized
(Fig. 35.18) [147]. One of these variants showed very high anity (KD 5 nm) and
specicity for ATP, and was capable of being further truncated to a protein of only
45 residues. Like most in vitro selection strategies, the ATP-binding proteins were
identied based on their ability to elicit binding responses, but it is possible to
select proteins on the basis of their catalytic activity [148150], which may also
allow the directed evolution of novel enzymatic activities.
Fully randomized combinatorial protein libraries are of limited practical utility,
since the frequency of foldable, much less functional, sequences in them is ex-
pected to be very low. As an alternative, partially randomized protein combinatorial
libraries can provide the same benets of randomization but in a sequence that is
predicted to fold into a stable structure. For example, the utilization of basic struc-
tural information, such as the sequence preferences of helices and sheets, termed
Fig. 35.19. (A) Structure of the AroQ-scaold (X phenylalanine, isoleucine, leucine, or

chorismate mutase. (B) Using a two-stage methionine; Z aspartate, glutamate,
selection procedure, active chorismate asparagine, or lysine) in the helical regions of
mutase variants were selected that had a the protein.
dramatically reduced amino acid palette
binary patterning [151153], has been used to design scaolded combinatorial

libraries from which soluble proteins were selected [154156]. To further probe
the utility of such libraries, not only for folding structures but also for functional
catalysts, we have randomized up to 80% of the total sequence of a six-helix bundle
chorismate mutase, using a binary pattern and only eight dierent amino acids
in the randomized regions (Fig. 35.19) [157]. Using in vivo genetic selection for
chorismate mutase catalytic activity [158], we identied proteins that upon further
analysis had physical properties characteristic of natural enzymes. Our results sug-
gest that such patterned combinatorial protein libraries could be useful for protein
design projects.
Analogous to the way that some small-molecule chemotypes make attractive start-
ing scaolds for combinatorial chemistry libraries, some protein structures have
been suggested as being very suitable scaolds into which any number of possible
activities could be built by randomizing or rationally mutagenizing specic regions
of the scaold. In particular, the (a/b)8 barrel, which is perhaps the most com-
monly occurring protein fold [159], has been suggested as the best starting point
from which to produce combinatorial libraries to screen for new functions [160,
161]. One impressive example of the combinatorial redesign of the (a=b)8 barrel is
the conversion of one enzyme on the tryptophan biosynthesis pathway, indole-3-
glycerol-phosphate synthase (IGPS), into another (phosphoribosylanthranilate iso-
merase, PRAI) with very high catalytic activity (Fig. 35.20) [162]. Rational redesign
was used to remodel the IGPS structure by elimination of an a-helix and the re-
Fig. 35.20. (A) Biosynthesis of tryptophan synthase; IGP, indole-3-glycerol phosphate; TS,
from chorismate. AS, anthranilate synthase; tryptophan synthase; GAP, glyceraldehyde-3-
PRPP, phosphoribosylpyrophosphate; APRT, phosphate. (B) Directed evolution was used to
anthranilate phosphoribosyl transferase; PRA, create a novel PRAI, which catalyzes the
N-(5 0 -phosphoribosyl)anthranilate; PRAI, conversion of PRA to CdRP, from IGPS, which
phosphoribosylanthranilate isomerase; CdRP, catalyzes the cyclization of CdRP to IGP. (C)
10 -(2 0 -carboxyphenylamino)-10 -deoxyribulose 5 0 - Both PRAI and IGPS are TIM barrel proteins
phosphate; IGPS, indole-3-glycerol phosphate but have somewhat dierent loop structures.
Fig. 35.21. Structure of triosephosphate isomerase. In separate

experiments, randomized libraries of the a/b-loops, b/a-loops,
a-helices, and b-sheets were produced and variants selected in
vivo for triosephosphate isomerase activity.
placement of two loop sequences, and then combinatorial protein libraries were
created from the remodeled protein by randomizing positions in the loops. In vivo
genetic selection was used to identify members from the combinatorial library
capable of behaving as PRAIs.
To further probe the mutability of the (a/b)8 scaold, Harbury and coworkers
created combinatorial protein libraries by randomizing portions of an (a/b)8 barrel
triose phosphate isomerase (TIM) (Fig. 35.21) [163]. They then selected for mem-
bers of the libraries that were capable of complementing a TIM-decient strain.
Their results suggest that the (a/b)8 barrel is quite mutable in some of the loop
regions, which would be the probable site for introducing combinatorial random-
ization for the creation of new catalytic activities. This study has set the platform
for the rational design and creation of further combinatorial libraries from the
(a/b)8 barrel from which new function can be selected.
A third type of protein combinatorial library can be created through minor
changes designed to optimize or alter activity or to improve physical properties,
and then using selection or screening techniques to identify members of the library
with the desired characteristic. Such a procedure is usually called directed evolution,
and has been reviewed extensively elsewhere [164170]. These directed evolution
protein libraries could be considered analogous to lead optimization combinatorial
libraries that are created to nd an initial hit and optimize the scaold for use as a
drug.
In directed evolution experiments, mutations are introduced by error-prone PCR
[171] or DNA shuing [172, 173] and related techniques [174, 175]. After a suit-
able selection step, selected library members can be recombined to blend additively
positive mutations with the selection procedure carried out on the further evolved
library (Fig. 35.22). Using such a strategy, a number of proteins have been further
evolved to improve the activity [176], alter the selectivity [177190], or increase the
thermal stability [191, 192]. In some cases, even multistep processes utilizing sev-
Fig. 35.22. DNA shuing.
eral dierent proteins have been optimized by producing combinatorial libraries of

entire genetic operons [193].
35.4
Perspectives
Perhaps the chief driving force in the development of combinatorial chemistry is

the opportunity to streamline the discovery process of compounds for human
benet. Conversely, the combinatorial aspects of biology have been used mostly by
Nature for evolutionary processes. As our understanding of biosynthetic systems,
protein structure and function, and catalysis continues to improve, however, we
are increasingly able to harness the combinatorial aspects of biology for our own
35.4 Perspectives 1091
use. For instance, combinatorial biosynthesis holds great potential for the produc-
tion of potential lead compounds for drug discovery. These leads could then be
further optimized by more traditional synthetic and combinatorial chemistry.
Additionally, combinatorial biosynthesis could be used to produce starting material
intermediates (perhaps for further combinatorial chemistry) and nal products
that are not easily made using current synthetic methods. One example of this
potential utility is the use of a thioesterase domain from the tyrocidine NRPS for
catalyzing the cyclization of a variety of short, synthetic peptides [194, 195].
Combinatorial chemistry could play similar roles for combinatorial biology. For
instance, an attractive scaold that is identied through combinatorial chemistry
could also act as the lead for which a more complexly functionalized (and syn-
thetically challenging) combinatorial biosynthesis library could be prepared. Deoxy-
sugar libraries prepared by combinatorial chemistry could be used as feeding pre-
cursors for more complex polyketide- or NRP-based combinatorial biosynthesis
libraries utilizing low-specicity glycosyltransferases.
Peptide combinatorial libraries, as mentioned above, are very attractive for pro-
ducing initial leads for drug development, as well as for providing insight into the
structure, activity, and specicity of biological receptors and enzymes. But their
poor behavior in vivo often precludes their use as eective drugs. Combinatorial
chemistry is thus essential for producing nonpeptide drugs based around the ini-
tial peptide leads. Clearly, combinatorial biology will never supplant combinatorial
chemistry; rather, both elds will continually augment each other.
Large-molecule combinatorial libraries of proteins and DNA or RNA may also
nd eventual use as drugs, but currently they are of interest to researchers mainly
for their ability to probe issues of structure and catalysis. In addition to this, how-
ever, the production of such libraries has dramatically increased our knowledge
and ability to engineer and develop suitable selection and screening systems, some
of which have found their way to the combinatorial chemistry bench. Additionally,
our ability to engineer and create proteins or oligonucleotides with desired func-
tion may one day provide combinatorial chemists with another catalytic repertoire,
one that is based around environmentally friendly enzymatic reactions. Current
work on structural redesign of nucleotidyltransferases [91], and on the utilization
of glycosyltransferases with relaxed specicity [93], is a step in this direction.
What does the future hold for our utilization of combinatorial biology for human
benet? Given the promise of the multiplasmid approach in polyketide combina-
torial biosynthesis, and the predictive nature of modular biosynthetic systems, it is
conceivable that we will someday have the ability to produce virtually any polyketide-
or NRP-derived product, appended with appropriate deoxysugars, in high yield,
merely by transforming the right combination of plasmids into a suitable produc-
tion strain. It is also likely, given our ever-increasing understanding of protein
structure and function, that we will someday be able to design and engineer novel
enzymes with catalytic activities that are useful for applications in chemistry (in-
cluding combinatorial chemistry) or medicine. Additionally, our ability to rapidly
select useful or interesting variants from combinatorial libraries steadily improves.
Coupling binding or catalytic activity with genotypic information is currently pos-
sible with DNA-encoded libraries, and the same linkage may someday also be pos-
sible with natural product combinatorial biosynthesis libraries.
With the advent of the genomic, or postgenomic era, there will be a ood of
potential new medical targets. The ability to utilize biological tools can only help
our combinatorial eorts in designing drugs to control them.
Acknowledgments
The helpful suggestions and support of Professor Don Hilvert during the prepara-
tion of this chapter are gratefully acknowledged, as well as Kinya Hotta and Gavin
Macbeath for the preparation of graphics.
References
1 H. Muller, O. Brackhagen, R. 14 C. R. Hutchinson, Curr. Opin.

Brunne, T. Henkel, F. Reichel in: Microbiol. 1998, 1, 319329.
The Role of Natural Products in Drug 15 J. Staunton, Curr. Opin. Chem. Biol.
Discovery, vol. 32. Mulzer, J., 1998, 2, 339345.
Bohlmann, R. (eds), Springer-Verlag, 16 C. J. Tsoi, C. Khosla, Chem. Biol.
New York 2000, pp. 205216. 1995, 2, 355362.
2 D. J. Newman, G. M. Cragg, K. M. 17 A. Koltermann, U. Kettling,
Snader, Nat. Prod. Rep. 2000, 17, Biophys. Chem. 1997, 66, 159177.
215234. 18 C. Khosla, Chem. Rev. 1997, 97,
3 G. M. Cragg, D. J. Newman, K. M. 25772590.
Snader, J. Nat. Prod. 1997, 60, 5260. 19 L. Rohlin, M. K. Oh, J. C. Liao,
4 A. L. Demain, in D. Chadwick, J. Curr. Opin. Microbiol. 2001, 4, 330
Whelan (eds), Secondary Metabolites: 335.
Their Function and Evolution, vol. 171. 20 J. Staunton, K. J. Weissman, Nat.
John Wiley & Sons, New York 1992, Prod. Rep. 2001, 18, 380416.
pp. 316. 21 L. Katz, Chem. Rev. 1997, 97, 2557
5 R. Verpoorte, Drug Discov. Today 2575.
1998, 3, 232238. 22 T. A. Keating, C. T. Walsh, Curr.
6 A. L. Demain, Appl. Microbiol. Opin. Chem. Biol. 1999, 3, 598606.
Biotechnol. 1999, 52, 455463. 23 C. Khosla, R. S. Gokhale, J. R.
7 R. Bentley, J. W. Bennett, Annu. Jacobsen, D. E. Cane, Annu. Rev.
Rev. Microbiol. 1999, 53, 411446. Biochem. 1999, 68, 219253.
8 M. C. Moffitt, B. A. Neilan, FEMS 24 L. Hendrickson, C. R. Davis, C.
Microbiol. Lett. 2000, 191, 159167. Roach, D. K. Nguyen, T. Aldrich, P.
9 A. Kirschning, A. F. W. Bechthold, McAda, C. D. Reeves, Chem. Biol.
J. Rohr, Topics Curr. Chem. 1997, 188, 1999, 6, 429439.
184. 25 C. R. Hutchinson, J. Kennedy, C.
10 T. M. Hallis, H. W. Liu, Acc. Chem. Park, S. Kendrew, K. Auclair, J.
Res. 1999, 32, 579588. Vederas, Antonie van Leeuwenhoek
11 H. W. Liu, J. S. Thorson, Annu. Rev. 2000, 78, 287295.
Microbiol. 1994, 48, 223256. 26 J. Kennedy, K. Auclair, S. G.
12 D. E. Cane, C. T. Walsh, C. Khosla, Kendrew, C. Park, J. C. Vederas,
Science 1998, 282, 6368. C. R. Hutchinson, Science 1999, 284,
13 J. Staunton, B. Wilkinson, Curr. 13681372.
Opin. Chem. Biol. 2001, 5, 159164. 27 J. M. Jez, J.-L. Ferrer, M. E. Bowman,
References 1093
R. A. Dixon, J. P. Noel, Biochemistry 44 A. F. A. Marsden, B. Wilkinson, J.

2000, 39, 890902. Cortes, N. J. Dunster, J. Staunton,
28 J.-L. Ferrer, J. M. Jez, M. E. Bowman, P. F. Leadlay, Science 1998, 279, 199
R. A. Dixon, J. P. Noel, Nat. Struct. 202.
Biol. 1999, 6, 775784. 45 X. Ruan, A. Pereda, D. L. Stassi,
29 R. McDaniel, S. Ebert-Khosla, D. A. D. Zeidner, R. G. Summers, M.
Hopwood, C. Khosla, Science 1993, Jackson, A. Shivakumar, S. Kakavas,
262, 15461550. M. J. Staver, S. Donadio, L. Katz, J.
30 C. Khosla, R. McDaniel, S. Ebert- Bacteriol. 1997, 179, 64166425.
Khosla, R. Torres, D. H. Sherman, 46 C. M. Kao, M. McPherson, R. N.
M. J. Bibb, D. A. Hopwood, J. McDaniel, H. Fu, D. E. Cane, C.
Bacteriol. 1993, 175, 21972204. Khosla, J. Am. Chem. Soc. 1997, 119,
31 H. Fu, R. McDaniel, D. A. 1133911340.
Hopwood, C. Khosla, Biochemistry 47 I. E. Holzbaur, R. C. Harris, M.
1994, 33, 93219326. Bycroft, J. Cortes, C. Bisang, J.
32 H. Fu, S. Ebert-Khosla, D. A. Staunton, B. A. M. Rudd, P. F.
Hopwood, C. Khosla, J. Am. Chem. Leadlay, Chem. Biol. 1999, 6, 189
Soc. 1994, 116, 41664170. 195.
33 R. McDaniel, S. Ebert-Khosla, D. A. 48 I. E. Holzbaur, A. Ranganathan,
Hopwood, C. Khosla, Nature 1995, I. P. Thomas, D. J. A. Kearney, J. A.
375, 549554. Reather, B. A. M. Rudd, J.
34 R. McDaniel, S. Ebert-Khosla, D. A. Staunton, P. F. Leadlay, Chem. Biol.
Hopwood, C. Khosla, J. Am. Chem. 2001, 8, 329340.
Soc. 1993, 115, 1167111675. 49 J. R. Jacobsen, D. E. Cane, C.
35 P. J. Kramer, R. J. X. Zawada, R. Khosla, Biochemistry 1998, 37, 4928
McDaniel, C. R. Hutchinson, D. A. 4934.
Hopwood, C. Khosla, J. Am. Chem. 50 J. R. Jacobsen, A. T. Keatinge-Clay,
Soc. 1997, 119, 635639. D. E. Cane, C. Khosla, Bioorg. Med.
36 E. Kunzel, S. E. Wohlert, C. Chem. 1998, 6, 11711177.
Beninga, S. Haag, H. Decker, C. R. 51 C. M. Kao, G. L. Luo, L. Katz, D. E.
Hutchinson, G. Blanco, C. Mendez, Cane, C. Khosla, J. Am. Chem. Soc.
J. A. Salas, J. Rohr, Chem.-Eur. J. 1995, 117, 91059106.
1997, 3, 16751678. 52 J. Cortes, K. E. H. Wiesmann, G. A.
37 B. Shen, R. G. Summers, E. Wendt- Roberts, M. J. B. Brown, J.
Pienkowski, C. R. Hutchinson, Staunton, P. F. Leadlay, Science
J. Am. Chem. Soc. 1995, 117, 6811 1995, 268, 14871489.
6821. 53 I. Bohm, I. E. Holzbaur, U.
38 B. Shen, C. R. Hutchinson, Proc. Hanefeld, J. Cortes, J. Staunton,
Natl. Acad. Sci. USA 1996, 93, 6600 P. F. Leadlay, Chem. Biol. 1998, 5,
6604. 407412.
39 H. Petkovic, A. Thamchaipenet, 54 R. McDaniel, A. Thamchaipenet, C.
L. H. Zhou, D. Hranueli, P. Raspor, Gustafsson, H. Fu, M. Betlach, M.
P. G. Waterman, I. S. Hunter, J. Betlach, G. Ashley, Proc. Natl. Acad.
Biol. Chem. 1999, 274, 3282932834. Sci. USA 1999, 96, 18461851.
40 D. A. Hopwood, Chem. Rev. 1997, 97, 55 Q. Xue, G. Ashley, C. R. Hutchinson,
24652497. D. V. Santi, Proc. Natl. Acad. Sci.
41 C. W. Carreras, D. V. Santi, Curr. USA 1999, 96, 1174011745.
Opin. Biotechnol. 1998, 9, 403411. 56 R. B. Ziermann, M. C. Betlach,
42 R. Pieper, C. Kao, C. Khosla, G. L. Biotechniques 1999, 26, 106110.
Luo, D. E. Cane, Chem. Soc. Rev. 57 L. Tang, S. Shah, L. Chung, J.
1996, 25, 297302. Carney, L. Katz, C. Khosla, B.
43 H. Fu, S. Ebert-Khosla, D. A. Julien, Science 2000, 287, 640642.
Hopwood, C. Khosla, J. Am. Chem. 58 C. Hertweck, Chembiochem 2000, 1,
Soc. 1994, 116, 64436444. 103106.
59 B. A. Pfeifer, C. Khosla, Microbiol. 78 G. L. Challis, J. Ravel, FEMS

Mol. Biol. Rev. 2001, 65, 106118. Microbiol. Lett. 2000, 187, 111114.
60 B. A. Pfeifer, S. J. Admiraal, H. 79 B. Julien, S. Shah, R. Ziermann, R.
Gramajo, D. E. Cane, C. Khosla, Goldman, L. Katz, C. Khosla, Gene
Science 2001, 291, 17901792. 2000, 249, 153160.
61 N. Wu, S. Y. Tsuji, D. E. Cane, C. 80 L. Du, B. Shen, Curr. Opin. Drug Disc.
Khosla, J. Am. Chem. Soc. 2001, 123, Dev. 2001, 4, 215228.
64656474. 81 B. Silakowski, G. Nordsiek, B.
62 R. S. Gokhale, S. Y. Tsuji, D. E. Kunze, H. Blocker, R. Muller,
Cane, C. Khosla, Science 1999, 284, Chem. Biol. 2001, 8, 5969.
482485. 82 D. A. Johnson, H. W. Liu, Curr.
63 R. S. Gokhale, C. Khosla, Curr. Opin. Chem. Biol. 1998, 2, 642649.
Opin. Chem. Biol. 2000, 4, 2227. 83 A. Trefzer, J. A. Salas, A.
64 D. Konz, M. A. Marahiel, Chem. Bechthold, Nat. Prod. Rep. 1999, 16,
Biol. 1999, 6, R39R48. 283299.
65 M. A. Marahiel, T. Stachelhaus, 84 A. C. Weymouth-Wilson, Nat. Prod.
H. D. Mootz, Chem. Rev. 1997, 97, Rep. 1997, 14, 99110.
26512673. 85 H. J. Allen, E. C. Kisailus, Glyco-
66 C. T. Walsh, A. M. Gehring, P. H. conjugates: Composition, Structure, and
Weinreb, L. E. N. Quadri, R. S. Function. Marcel Dekker, New York
Flugel, Curr. Opin. Chem. Biol. 1997, 1992.
1, 309315. 86 L. S. Zhao, D. H. Sherman, H. W.
67 T. A. Keating, D. E. Ehmann, R. M. Liu, J. Am. Chem. Soc. 1998, 120,
Kohli, C. G. Marshall, J. W. 1025610257.
Trauger, C. T. Walsh, Chembiochem 87 L. S. Zhao, N. L. S. Que, Y. Q. Xue,
2001, 2, 99107. D. H. Sherman, H. W. Liu, J. Am.
68 A. W. Bernheimer, L. S. Avigad, J. Chem. Soc. 1998, 120, 1215912160.
Gen. Microbiol. 1970, 61, 361369. 88 H. W. Chen, Z. H. Guo, H. W. Liu,
69 A. Kakinuma, A. Ouchida, T. Shima, J. Am. Chem. Soc. 1998, 120, 9951
H. Sugino, H. Isono, G. Tamura, K. 9952.
Arima, Agricult. Biol. Chem. 1969, 33, 89 J. Q. Jiang, J. B. Biggins, J. S.
16691671. Thorson, J. Am. Chem. Soc. 2000,
70 M. M. Nakano, M. A. Marahiel, P. 122, 68036804.
Zuber, J. Bacteriol. 1988, 170, 5662 90 J. Q. Jiang, J. B. Biggins, J. S.
5668. Thorson, Angew. Chem. Intl. Ed. 2001,
71 T. Stachelhaus, A. Schneider, 40, 15021505.
M. A. Marahiel, Science 1995, 269, 91 W. A. Barton, J. Lesniak, J. B.
6972. Biggins, P. D. Jeffrey, J. Q. Jiang,
72 A. Schneider, T. Stachelhaus, K. R. Rajashankar, J. S. Thorson,
M. A. Marahiel, Mol. Gen. Genet. D. B. Nikolov, Nature Struct. Biol.
1998, 257, 308318. 2001, 8, 545551.
73 F. deFerra, F. Rodriguez, O. 92 J. S. Thorson, T. J. Hosted, J. Q.
Tortora, C. Tosi, G. Grandi, J. Biol. Jiang, J. B. Biggins, J. Ahlert, Curr.
Chem. 1997, 272, 2530425309. Org. Chem. 2001, 5, 139167.
74 S. Doekel, M. A. Marahiel, Chem. 93 S. E. Wohlert, G. Blanco, F. Lombo,
Biol. 2000, 7, 373384. E. Fernandez, A. F. Brana, S. Reich,
75 H. D. Mootz, D. Schwarzer, M. A. G. Udvarnoki, C. Mendez, H.
Marahiel, Proc. Natl. Acad. Sci. USA Decker, J. Frevert, J. A. Salas, J.
2000, 97, 58485853. Rohr, J. Am. Chem. Soc. 1998, 120,
76 T. Stachelhaus, H. D. Mootz, M. A. 1059610601.
Marahiel, Chem. Biol. 1999, 6, 493 94 G. Blanco, E. P. Patallo, A. F.
505. Brana, A. Trefzer, A. Bechthold, J.
77 G. L. Challis, J. Ravel, C. A. Town- Rohr, C. Mendez, J. A. Salas, Chem.
send, Chem. Biol. 2000, 7, 211224. Biol. 2001, 8, 253263.
References 1095
95 S. Gaisser, J. Reather, G. Wirtz, L. 115 K. Fukuda, D. Vishnuvardhan, S.

Kellenberger, J. U. Staunton, P. F. Sekiya, J. Hwang, N. Kakiuchi, T.
Leadlay, Mol Microbiol. 2000, 36, 391 Kazunari, K. Shimotohno, P. K. R.
401. Kumar, S. Nishikawa, Eur. J.
96 L. Tang, R. McDaniel, Chem. Biol. Biochem. 2000, 267, 36853694.
2001, 8, 547555. 116 J. Kawakami, H. Imanaka, Y. Yokota,
97 D. Hoffmeister, K. Ichinose, A. N. Sugimoto, J. Inorg. Biochem. 2000,
Bechthold, Chem. Biol. 2001, 8, 557 82, 197206.
567. 117 V. Nobile, N. Russo, G. F. Hu, J. F.
98 C. R. Geyer, R. Brent, Methods Riordan, Biochemistry 1998, 37, 6857
Enzymol. 2000, 328, 171208. 6863.
99 N. F. Viti F, Demartis S, Huber A, 118 Y. Takagi, M. Warashina, W. J.
Neri D, Methods Enzymol. 2000, 326. Stec, K. Yoshinari, K. Taira, Nucleic
100 S. V. Taylor, P. Kast, D. Hilvert, Acids Res. 2001, 29, 18151834.
Angew. Chem. Intl. Ed. 2001, 40, 3310 119 E. A. Doherty, J. A. Doudna, Annu.
3335. Angew. Chem. 2001, 40, 3408 Rev. Biochem. 2000, 69, 597615.
3436. 120 D. S. Wilson, J. W. Szostak, Annu.
101 M. Famulok, A. Jenne, Curr. Opin. Rev. Biochem. 1999, 68, 611647.
Chem. Biol. 1998, 2, 320327. 121 M. Famulok, A. Jenne, Topics Curr.
102 D. J. Patel, A. K. Suri, F. Jiang, L. C. Chem. 1999, 202, 101131.
Jiang, P. Fan, R. A. Kumar, S. Nonin, 122 R. R. Breaker, Chem. Rev. 1997, 97,
J. Mol. Biol. 1997, 272, 645664. 371390.
103 M. Famulok, G. Mayer, M. Blind, 123 N. Carmi, S. R. Balkhi, R. R.
Acc. Chem. Res. 2000, 33, 591599. Breaker, Proc. Natl. Acad. Sci. USA
104 T. Hermann, D. J. Patel, Science 1998, 95, 22332237.
2000, 287, 820825. 124 R. R. Breaker, G. F. Joyce, Chem.
105 M. Koizumi, R. R. Breaker, Biol. 1995, 2, 655660.
Biochemistry 2000, 39, 89838992. 125 C. Wilson, J. W. Szostak, Nature
106 M. N. Stojanovic, P. de Prada, D. W. 1995, 374, 777782.
Landry, J. Am. Chem. Soc. 2001, 123, 126 P. A. Lohse, J. W. Szostak, Nature
49284931. 1996, 381, 442444.
107 S. Jeong, T. Y. Eom, S. J. Kim, S. W. 127 B. L. Zhang, T. R. Cech, Nature
Lee, J. Yu, Biochem. Biophys. Res. 1997, 390, 96100.
Commun. 2001, 281, 237243. 128 T. M. Tarasow, S. L. Tarasow, B. E.
108 K. Gebhardt, A. Shokraei, E. Eaton, Nature 1997, 389, 5457.
Babaie, B. H. Lindqvist, Biochemistry 129 A. A. Beaudry, G. F. Joyce, Science
2000, 39, 72557265. 1992, 257, 635641.
109 D. H. Burke, D. C. Hoffman, A. 130 D. P. Bartel, J. W. Szostak, Science
Brown, M. Hansen, A. Pardi, L. 1993, 261, 14111418.
Gold, Chem. Biol. 1997, 4, 833843. 131 E. H. Ekland, J. W. Szostak,
110 D. Kiga, Y. Futamura, K. Sakamoto, D. P. Bartel, Science 1995, 269, 364
S. Yokoyama, Nucleic Acids Res. 1998, 370.
26, 17551760. 132 T. C. Norman, D. L. Smith, P. K.
111 A. A. Haller, P. Sarnow, Proc. Natl. Sorger, B. L. Drees, S. M. ORourke,
Acad. Sci. USA 1997, 94, 85218526. T. R. Hughes, C. J. Roberts, S. H.
112 E. Kraus, W. James, A. N. Barclay, J. Friend, S. Fields, A. W. Murray,
Immunol. 1998, 160, 52095212. Science 1999, 285, 591595.
113 M. Homann, H. U. Goringer, 133 S. Fields, O.-K. Song, Nature 1989,
Nucleic Acids Res. 1999, 27, 20062014. 340, 245246.
114 S. Weiss, D. Proske, M. Neumann, 134 S.-H. Park, R. T. Raines, Nature
M. H. Groschup, H. A. Biotechnol. 2000, 18, 847851.
Kretzschmar, M. Famulok, E. L. 135 M. A. McLafferty, R. B. Kent, R. C.
Winnacker, J. Virol. 1997, 71, 8790 Ladner, W. Markland, Gene 1993,
8797. 128, 2936.
136 P. A. Nygren, M. Uhlen, Curr. Opin. Xiong, J. M. Babik, M. H. Hecht,

Struct. Biol. 1997, 7, 463469. Science 1993, 262, 16801685.
137 D. Hanahan, J. Jessee, F. R. Bloom, 155 S. Roy, M. H. Hecht, Biochemistry
Methods Enzymol. 1991, 204, 63113. 2000, 39, 46034607.
138 J. R. Thompson, E. Register, J. 156 S. Roy, G. Ratnaswamy, J. A. Boice,
Curotto, M. Kurtz, R. Kelly, Yeast R. Fairman, G. McLendon, M. H.
1998, 14, 565571. Hecht, J. Am. Chem. Soc. 1997, 119,
139 L. Wang, A. Brock, B. Herberich, 53025306.
P. G. Schultz, Science 2001, 292, 157 S. V. Taylor, K. U. Walter, P. Kast,
498500. D. Hilvert, Proc. Natl. Acad. Sci. USA
140 T. J. Magliery, J. C. Anderson, P. G. 2001, 98, 1059610601.
Schultz, J. Mol. Biol. 2001, 307, 755 158 P. Kast, M. Asif-Ullah, N. Jiang, D.
769. Hilvert, Proc. Natl. Acad. Sci. USA
141 A. K. Kowal, C. Kohrer, U. L. 1996, 93, 50435048.
RajBhandary, Proc. Natl. Acad. Sci. 159 D. Reardon, G. K. Farber, FASEB J.
USA 2001, 98, 22682273. 1995, 9, 497503.
142 V. Doring, H. D. Mootz, L. A. 160 G. Winter, C. Milstein, Nature 1991,
Nangle, T. L. Hendrickson, V. de 349, 293299.
Crecy-Lagard, P. Schimmel, P. 161 R. K. Wierenga, FEBS Lett. 2001, 492,
Marliere, Science 2001, 292, 501504. 193198.
143 R. W. Roberts, J. W. Szostak, Proc. 162 M. M. Altamirano, J. M. Blackburn,
Natl. Acad. Sci. USA 1997, 94, 12297 C. Aguayo, A. R. Fersht, Nature
12302. 2000, 403, 617622.
144 R. W. Roberts, Curr. Opin. Chem. 163 J. A. Silverman, R. Balakrishnan,
Biol. 1999, 3, 268273. P. B. Harbury, Proc. Natl. Acad. Sci.
145 D. S. Wilson, A. D. Keefe, J. W. USA 2001, 98, 30923097.
Szostak, Proc. Natl. Acad. Sci. USA 164 U. T. Bornscheuer, M. Pohl, Curr.
2001, 98, 37503755. Opin. Chem. Biol. 2001, 5, 137143.
146 L. B. Giebel, R. T. Cass, D. L. 165 F. H. Arnold, Acc. Chem. Res. 1998,
Milligan, D. C. Young, R. Arze, 31, 125131.
C. R. Johnson, Biochemistry 1995, 34, 166 F. H. Arnold, A. A. Volkov, Curr.
1543015435. Opin. Chem. Biol. 1999, 3, 5459.
147 A. D. Keefe, J. W. Szostak, Nature 167 M. Chartrain, P. M. Salmon, D. K.
2001, 410, 715718. Robinson, B. C. Buckland, Curr.
148 C. Gao, C.-H. Lin, C.-H. L. Lo, S. Opin. Biotechnol. 2000, 11, 209214.
Mao, P. Wirsching, R. A. Lerner, 168 M. T. Reetz, K. E. Jaeger, Topics Curr.
K. D. Janda, Proc. Natl. Acad. Sci. Chem. 1999, 200, 3157.
USA 1997, 94, 1177711782. 169 P. A. Patten, R. J. Howard, W. P. C.
149 P. Soumillion, L. Jespers, M. Stemmer, Curr. Opin. Biotechnol. 1997,
Bouchet, J. Marchand-Brynaert, G. 8, 724733.
Winter, J. Fastrez, J. Mol. Biol. 1994, 170 J. Minshull, W. P. C. Stemmer, Curr.
237, 415422. Opin. Chem. Biol. 1999, 3, 284290.
150 K. D. Janda, L.-C. Lo, C.-H. L. Lo, 171 R. C. Cadwell, G. F. Joyce, PCR
M.-M. Sim, R. Wang, C.-H. Wong, Meth. Appl. 1992, 2, 2833.
R. A. Lerner, Science 1997, 275, 945 172 W. P. C. Stemmer, Proc. Natl. Acad.
948. Sci. USA 1994, 91, 1074710751.
151 J. U. Bowie, R. T. Sauer, Proc. Natl. 173 W. P. C. Stemmer, Nature 1994, 370,
Acad. Sci. USA 1989, 86, 21522156. 389391.
152 J. U. Bowie, N. D. Clarke, C. O. 174 H. Zhao, L. Giver, Z. Shao, J. A.
Pabo, R. T. Sauer, Proteins 1990, 7, Affholter, F. H. Arnold, Nature
257264. Biotechnol. 1998, 16, 258261.
153 M. W. West, M. H. Hecht, Prot. Sci. 175 Z. Shao, H. Zhao, L. Giver, F. H.
1995, 4, 20322039. Arnold, Nucleic Acids Res. 1998, 26,
154 S. Kamtekar, J. M. Schiffer, H. 681683.
References 1097
176 K. U. Walter, S. V. Taylor, G. 187 C. Jurgens, A. Strom, D. Wegener,

Mader, P. Kast, D. Hilvert, S. Hettwer, M. Wilmanns, R.
unpublished. Sterner, Proc. Natl. Acad. Sci. USA
177 T. Yano, S. Oue, H. Kagamiyama, 2000, 97, 99259930.
Proc. Natl. Acad. Sci. USA 1998, 95, 188 E. A. Hart, L. Hua, L. B. Darr, W. K.
55115515. Wilson, J. H. Pang, S. P. T.
178 S. Oue, A. Okamoto, T. Yano, H. Matsuda, J. Am. Chem. Soc. 1999,
Kagamiyama, J. Biol. Chem. 1999, 274, 121, 98879888.
23442349. 189 D. R. Liu, T. J. Magliery, M.
179 A. Crameri, S. A. Raillard, E. Pastrnak, P. G. Schultz, Proc. Natl.
Bermudez, W. P. C. Stemmer, Nature Acad. Sci. USA 1997, 94, 10092
1998, 391, 288291. 10097.
180 H. Viadiu, J. Osuna, A. L. Fink, X. 190 D. R. Liu, P. G. Schultz, Proc. Natl.
Soberon, J. Biol. Chem. 1995, 270, Acad. Sci. USA 1999, 96, 47804785.
781787. 191 J. Hoseki, T. Yano, Y. Koyama, S.
181 J. F. Petrosino, T. Palzkill, J. Kuramitsu, H. Kagamiyama, J.
Bacteriol. 1996, 178, 18211828. Biochem. 1999, 126, 951956.
182 M. Zaccolo, E. Gherardi, J. Mol. 192 L. Giver, A. Gershenson, P.-O.
Biol. 1999, 285, 775783. Freskgard, F. H. Arnold, Proc. Natl.
183 C. Cantu, W. Huang, T. Palzkill, J. Acad. Sci. USA 1998, 95, 12809
Biol. Chem. 1996, 271, 2253822545. 12813.
184 W. Huang, J. Petrosino, M. Hirsch, 193 A. Crameri, G. Dawes, E. Rodriguez
P. S. Shenkin, T. Palzkill, J. Mol. Jr., S. Silver, W. P. C. Stemmer,
Biol. 1996, 258, 688703. Nature Biotechnol. 1997, 15, 436438.
185 S.-I. Ohnuma, K. Hirooka, H. 194 J. W. Trauger, R. M. Kohli, H. D.
Hemmi, C. Ishida, C. Ohto, T. Mootz, M. A. Marahiel, C. T.
Nishino, J. Biol. Chem. 1996, 271, Walsh, Nature 2000, 407, 215218.
1883118837. 195 R. M. Kohli, J. W. Trauger, D.
186 K. M. Munir, D. C. French, D. K. Schwarzer, M. A. Marahiel, C. T.
Dube, L. A. Loeb, Protein Eng. 1994, 7, Walsh, Biochemistry 2001, 40, 7099
8389. 7108.
1099
Index
absorption 725, 744 addition to carbon-hetero multiple bonds 322

Accelab Arcosyn98 200 addition to CbC double bonds 306
acetylation 906 addition to CN double bonds 322, 334
N-acetyl-b-amino acid 520 addition to CN triple bonds 339
acetylcholinesterase inhibitor 640 addition to NbCbN 335
acid chlorides 347, 789 adenosine diphosphate 714
reductions 418 adenylation domains 1075
acid uorides 348 ADME properties 744f, 774
acrylate ester 280 Advanced ChemTech 203
acrylates of 1,3-oxazolin-2-ones 456 agricultural chemistry 3
acrylic acids 232, 448 AHB linker 65
actinorhodin 1067 AIBN 228, 231, 234
activated magnesium 488 Ala-scan 592
active esters 348 albumins 751, 758, 891
acyl transferases 905 alcoholysis 71, 134
acylation 788, 790, 1082 aldehyde reductions 387, 417
acylcarbene tagging strategy 174 aldol condensation 629, 673, 873
addition reaction 482, 915 aldol diastereoselective reductive reaction
addition electrophilic 313 921
addition (electrophilic) to isolated double aldol reaction 148, 492, 580, 522
bonds 306 Evans type 497
1,2-addition 478 using imines 324f
1,4-addition 503 alkanes 149
1,4-addition to a,b-unsaturated carbonyl alkenes 149
systems 317 alkene epoxidation 916
addition of carbon nucleophiles 324 alkenylaziridines 483
addition of dialkyl zincs 1004 alkenylstannanes 81
addition of N-nucleophiles to CN double alkylation 508, 513, 1006, 1082
bonds 331 enolates 506
addition of N-nucleophiles to nitriles glycines 513
340 phenolate 250
addition of phosphorus nucleophiles to CN alkynes 150, 299, 481
double bonds 332 alkynone 297
addition of sulfur nucleophiles 333, 342 N-allylation 571
addition of O-nucleophiles to CN double allyl boronic acid pinacolates 476
bonds 333 allyl ester 568
addition to CcC triple bonds 318 allyl glycosides 599
addition to CbS double bonds 338 allyl indium 476
Handbook of Combinatorial Chemistry. Drugs, Catalysts, Materials.

ISBN: 3-527-30509-2
1100 Index
allyl transfer 625 arylbromides 150

allyl-based linkers 68 arylhydrazides 73
allylic amides 443 arylmagnesium bromides 295
allylic phosphates 1006 arylspiropiperidines 736
allylic substitutions 94, 915 aryltosylimines 461
p-allylpalladium complex 568 arylzinc reagents 553
allylstannane 232 aspartic acid 233
aluminium hydride reagents 127, 390 asymmetric cyclopropanation reactions 907,
amidines 142 928
amination of aromatic halides 561 asymmetric Diels-Alder reactions 906
amine tag 616 asymmetric dihydroxylation 311
amines 234 asymmetric epoxidation 917
a-amino acids 233, 234, 513, 785 asymmetric induction 1010
b-amino acids 520, 649 asymmetric reductions 389
b-amino alcohols 521 atactic polypropylene 935
aminoimidazoles 701 atom transfer radical processes (ATRP) 1054
b-aminoketone 520 atom-transfer 242
aminolysis 489, 674 ATP-binding proteins 1086
aminomethylanthracenes 960 Auto-MATE 879
aminomethylphosphines 895 automated sample processing 219
aminoquinolinone 671 automated synthesizer 802
ammonation 978 Available Chemicals Directory (ACD) 729,
ammonia process 833 765, 926
amorphous microporous mixed oxide (AMM) aza-Diels-Alder reaction 325, 450, 655, 908f,
supports 955 922
amphiphilic lipid molecules 1046 aza-Wittig reaction 335
analysis of combinatorial libraries 217 azepanes 662
anatase compositions 1034 azepinone 662
anchoring of molecules 60 2-azetidinones 649
anemia 784 azide reductions 319, 406
angiotensin converting enzyme (ACE) azides 129
inhibitor enalapril 923 aziridines 643
angiotensin I 769 azo dyes 894
anion exchange resins 211 azomethine ylides 651
anomeric conguration 707
anomeric stereochemistry 709 baccatin III 620
antibiotic resistance gene 1073 Bacillus brevis 1075
antibodies 892 Bacillus subtilis 1075
antibody-catalyzed dehydration 902 backbone amide linkers (BAL) 137
anticancer agent clavularin B 1012 Bamford-Stevens reaction 110
antitumor antibiotics 230 Barton-McCombie deoxygenation 240
arene bromination 273 Barton esters 232
ArgoGel2 36 Baylis-Hillman reaction 317, 489, 524, 690
Argonaut Trident 208 bead sizes 25
Arnstein tripeptide (ACV) 891 BEMP resin 505, 513
Array microchannel reactors 945 benzazepines 561, 662f
Arrhenius equation 809 benzimidazoles 104, 131, 260, 379
articial lattices 1024 benzimidazolones 260
articial receptors 1046 benzisoxazoles 131
aryl halide 228 benzodiazepines 4f, 75, 104, 259, 379, 735
aryl iodides 150 benzodiazepinones 104
aryl radical cyclizations 229 benzofurans 106, 109, 295, 676
aryl sulfonates 79, 115 benzofurans 66 551
arylacetic acid 507 benzofuroxanes 129
Index 1101
benzohydroquinones 479 carbamate reductions 400

benzophenones 295 carbene complexes 586
benzopyrans 82, 287, 364, 636 carbene complex-mediated cleavage reactions
benzopyrones 297 597
benzotriazole linker 483 carbenoid 300
benzotriazoles 86 carbodiimides 335
benzoxazines 353 carbohydrates 706
benzyl carbamates 71 carbohydrate orthosters 287
benzyl-type linkers 63 carbohydrate-binding proteins 595
biased libraries 739 carbohydrate-functionalized oligomers 596
Biginelli reaction 692 carbon electrophiles 272
BINAP ligands 32 carbon nucleophiles 470
BINAP-Ru catalyst 422 carbonyl insertion 352
binding anity 772 carbonyl reactivity 401
binding proteins 595 carbopalladation 142
bioavailability 745 carbozincation 526
biocatalyzed transformations 294 carpanone 634
bioinformatics 886 cascade radical annulation 374
bioisosteric pharmacophores 740 Castro sulfonamide betain 250
biological barriers 746 catalysts 3, 6, 885, 935
biological combinatorial libraries 1063 catalyst discovery 991
biological targets 4 catalyst multifunctional 993
biotage 214 catalyst oxazaborolidine 428
biphenyl 237 catalyst pellets 974
biphenyltetrazole 736 catalyst research 831
Bischler-Napieralski cyclization 413 catalytic acetylation 906
Bischler-Napieralski reaction 674, 277 catalytic combustion 971
bitstring 731 catalytic oxygenation 904
blood pressure 784 catch-and-release purication 430
blood-brain barrier 747 cathepsin D 488, 773
Boba resin 65, 139 cathode ray tubes (CRTs) 1038
bond-scission 293 cathodoluminesent 1041
borane-amine adducts 430 cation exchanger resin 211
borane-based reductions 399, 426 CBS catalyst 427
borohydride reagents 387, 392 CaC bond-forming reactions 1012
boron enolates 495 CCK-A receptor 769
boronates 76 CD4 antigen 1082
boronic acids 96, 152 cell phones 1037
boronic acid ester 76 cellular prion protein 1082
boronic acid Mannich reaction 326 cellulose supports 4, 50, 183
brain-blood distribution 752 cerium ammonium nitrate (CAN) 380
bromination 271, 471 charge-coupled device (CCD) camera 1039
bromoacetals 230 Charybdis Technologies Illiad PS 207
a-bromo esters 231 chelation-controlled reduction 389
g-butyrolactones 230, 379, 676 chemical biology 3
chemical encoding methods 170, 171
()-carvone 621 chemical optimization 787
calcium channels 659 chemical space 795
calorimetry 860 chemical stability of resins 33
capacitance 1021 chemical vapor deposition 1022
capacity factor 754 chemoinformatics 886, 1018
capillary array electrophoresis (CAE) 978 Chemspeed ASW2000 system 202
capillary electrophoresis (CE) 977 chips 5
capital investments 19 chip format 709
1102 Index
chiral auxiliary 234, 232, 120, 446, 928 critical temperatures 1025
chiral catalyst 991 Crixivan2 912
chiral Lewis acids 450 cross metathesis 94, 587
chiral pentamines 912 cross-coupling reactions 86, 531
chiral separation methods 7 crosslinked (insoluble) polymers 24
chiral stationary phases (CSPs) 921, 1046 crosslinked acrylamides 41
chiral synthon chiron 910 crosslinked PEGs 44
chirality multiplication 906 crosslinked polymer beads 27
2-chlorotrityl resin 67 crosslinked-ethoxylate acrylate resins
chorismate mutase 1087 (CLEAR) 43
Christ vacuum centrifuge 222 crosslinkers 25, 32
chromaticity 1030 cross-metathesis 664, 929
chromatography 284 crystallization 212
chromenones 75 C2 -symmetric chiral ligands 993
chromium arene complexes 108 C3 -symmetric triarylphosphines 920
cinnolines 86 cuprates 482
Ciprooxacin2 262 Curtis rearrangement 336
circular dichroism (CD) 1049 Curtius degradation 356
detection 966 2-cyanoethylphosphate protecting group 291
Claisen 515 4-cyanotrityl protection group 68
condensations 515, 792 cyanuric chloride 255
reaction 791 cyclative cleavage 103, 526, 629, 631, 633,
rearrangements 465 654, 789
Claisen-Schmidt reaction 661 to hydantoins 791
clearance 744, 752 cyclic alkenes 588
clinical candidates 10 cyclic amide 143
clinical research 12 cyclic peptides 592, 594
C log P 726 cyclization reaction 314
clustering 732 5-exo cyclizations 228, 232
cobalt enolates 521 2+2 cycloaddition 463, 586
b-C,O bond scission 292 3+2 cycloadditions 453
cocatalysts 992 4+2 cycloadditions 441
colorimetric spot test 921 6+3 cycloaddition 464
colossal magnetoresistance 1034 cyclo cleavage 789
CombiFlash TM from Isco 212 cycloaddition 649, 651, 698, 701
combinatorial antibody library 892 cycloaddition imine 459
combinatorial biosynthesis 1064, 1075 cycloading 636
combinatorial catalysis 886f, 927, 1019 cyclobutanones 464
combinatorial libraries 764 cyclofragmentation 295
combinatorial semisynthesis 614 cyclopentenones 1010
combinatorial total synthesis 626 cyclorelease 631, 633
composition conditions 1020 cycloreversions 299, 676
composition spread technique (CCS) 1035 cyclotriphosphazene 49
computer-controlled multiplexer 969 cysteine 289
condensation reactions 685 cytochrome P450 753
contamination 94 cytochrome P450 oxygenase 904
continuous composition spread (CCS) 1022 cytomegalovirus 628
controlled pore glass (CPG) support 46
copper alkynes 329 Danishefskys diene 298, 325, 441, 480, 909,
Coreys chiral oxazaborolidine catalyst 928 922
coumarin 519 DART (development automated reaction
para-coumaroyl-CoA 1067 toolkit) 833, 870
coupling reagents 347f data-handling system 854
C-radicals 231 daughter libraries 925
Index 1103
dealkylation 238 dihydropyridones 482

deconvolution methods 1048 2,3-dihydro-4-pyridones 298
degradation chemistry 614 dihydropyrimidine-2,4-diones 104
dehydroalanine 280, 289, 446 dihydroquinolinones 463, 818
Delrin cylinder 969 dihydroquinone 399
dendritic polyester 53 dihydroxylation 309
dendritic polyether 53 diisoamylborane 388
dendritic polymeric supports 51 diketomorpholine 104
dendritic TADDOL 32 b-diketones 516
6-deoxyerythronylide B 1071 diketopiperazines 64, 104
deoxygenation 674 2,2-dimethylbenzopyran 737
deoxysugar 1064 dimethyldioxirane 80, 308, 309, 443
descriptors 731 2,5-dioxopyrrolidines 653
design of libraries 11, 13 diphenyl methane 736
design of the experiments 1020 1,3-cycloaddition 299
design process 11 dipolarophiles 108, 453
desosamine 1077 dipoles 453
Dess-Martin oxidation 307, 309, 372, 394 direct methanol fuel cell (DMFC) 948
development phase 12 directed evolution 1089
device optimization 1042 discovery phase 12
dialkylated amino acids 515 distribution coecient 745, 747f, 749, 751,
dialysis 47f 754
diaminopyrimidine 772 dithianes 71
diaryl ether synthesis 263 dithiocarbamate alkylation 251
diaryl methane 79 diversity 730, 734, 776, 795, 802
diastereoselective ketone reductions 389 diversity assessment 762
diastereoselective reductive aldol reaction 921 diversity-based reaction development 992
1,2-diazines 301 divinyl ketone 657
a-diazocarbonyl 300 DNA shuing 1089
diazo compounds 271 DOCK 772
diazomethane 71 DOE 866, 872
diazonium salts 83 Doebner-quinoline 674
diazotization of aromatic compounds 274 dopants 1020
1,3-dicarbonyls compounds 508, 510, 513 drug discovery 6, 802
g-alkylation 510 drug optimization 727
1,5-dicarbonyls 506 drug-like character 744, 746, 763f, 770, 776
2,3-dichloro-5,6-dicyanobenzoquinone (DDQ) drug-like index 730
332 drug-like libraries 739
dicobaltoctacarbonyl 150 drug-like molecules 6, 778
Dieckmann condensations 516 drug-like properties 728
Diels-Alder reactions 13, 301, 441, 448, 450, duocarmycin 230
601, 634, 678, 1083 dynamic random access memory (DRAM)
dienamines 441 chips 1037
1,3-dienes 97
diethylzinc 234 Edman degradation 173
dierential IR thermography 940 eight-channel microreactor 970
dierential scanning calorimetry 882 electrochemical cleaving step 79
dierential thermal analysis 1030 electrochemical reduction 951
diusion coecients 747 electrohydrodimerization 947
dihydrofolate reductase 772 electroluminescent at panel displays 1038
dihydropyrans 678 electron capture detection (ECGC) 174
dihydropyridazinones 785 electron transport layer (ETL) 1043
dihydropyridine (DHP) 659, 689 electron-beam evaporation 1022
linker 653 electronic tracking 14
1104 Index
electro-optic coecients 1031 Evans oxazolidinone 446, 496f, 510

electrophiles 88 evaporation 221
electrophilic addition 313 everninomicin 287
electrophilic addition to isolated double evolutionary combinatorial libraries 1063
bonds 306 evolutionary selection 636
electrophilic substitution 270 exo-glycosidase 714
electrospray ionization mass spectroscopy 178 extraction 284
electrospray ionization tandem mass
spectrometry (ESI-MS/MS) 935 faujasite 1027
eliminations feature trees 771
reactions 73, 279, 293, 745 feedback loop 1020
b-elimination reaction 149, 228, 279, 285f, ferroelectric materials 7, 1035
288f ferromagnetic semiconductors 1033
b-H elimination 1005 ltration 285
1,4-elimination 295 ne chemicals 838
1,6-elimination 293 ngerprints 755
elloramycin biosynthetic pathway 1079 2D nger prints 77
enamines 442 rst-phase screening 1008
enaminones 655 Fischer indole synthesis 666
enantiopurity 1001 tness function 775
enantioselective Michael additions 505 FlashMaster TM 213
enantioselective reducing agent 415 avilylium salts 147
enantioselective reductions 906 exible descriptors 731
enantioselective synthesis 991 FlexX 772
encoding strategies 5 uorene-based linkers 291
encoding technologies 17 uorescence detection 178
Endeavor TM 873 uorescence dyes 933
enolates 492, 503, 793 uorescent optical microscopy 890
alkylation 506, 510 uorescent resonance energy transfer (FRET)
enones 494 959
environmental chemistry 894 uorescent sensors 888f
environmental impact 1018 uorinated linkers 62
enzymatic synthesis of oligosaccharides 711 uorous chemistry 5, 293, 241, 430
enzyme 98, 294 focal plane array (FPA) detector 953
enzyme mimics 903 Focus-2D 770
enzyme-sensitive linkers 710 focused libraries 730, 743, 761, 765, 796
epibatidine 452 formation of amides 347
(G)-epimaritidine 21, 417 formation of carbamates 354
epitaxial overlayer 1024 formation of carbon-carbon bonds 492
epothilones 97, 370, 494, 600, 628, 1075 formation of esters 353
epoxidation 287, 306, 707 formation of guanidines 338
epoxidation with dimethyldioxirane 443 formation of ketones 355
epoxide 109, 296 formation of thioamides 357
epoxide opening 306 Fourier transform infrared (FTIR)
epoxide opening by amines 253 spectrometers 956
epoxide reductions 418 fraction dose absorbed 747
erythromycin 1066 fragmentation reaction 107
erythromycin polyketide synthase complex free concentration 750
1070 freeze-drying 221
erythropoietin 784 Freidinger lactam 599
ester reductions 390 frequency agile lters 1036
esterases 294 Friedel-Crafts acylation 272, 877
ether synthesis 263, 925, 249 FT-IR methods 217
ethylene polymerization 931 FTIR spectrum 387
Index 1105
fumitremorgin 276 Hantzsch synthesis 338

functionalized polypropylene pins 5 Hantzsch thiazole synthesis 251
furans 300, 444, 460, 676 Hantzsch three-component condensation
reaction 897
Gabriel-Cromwell reaction 253, 643 HATU 616
Gabriel synthesis 553 Heck reaction 86, 95, 229, 555, 663, 666, 558
galactose 714 Heck reaction catalyst 958
galanthamine 639 a-helical peptide/phosphine-Rh(I) catalysts
G-coupled protein receptor 282 913
gel 26 hematocrit 784, 796
genes 1077 Henry reaction 522
genetic algorithm 771, 775, 945, 1051 hepatitis C virus protein 3 protease 1082
genetic operons 1090 heterogenous catalysis 17, 586, 939, 1018
Genevac vacuum centrifuge 222 hexapeptide library 893
germanium linker 75, 111 high internal phase emulsion polymers 40
giant magnetoresistance 1033 high pressure reactions 846
Gilson ThermoQuest 216 high-energy electron diraction (RHEED)
Gilson-HPLC 215 1025
glycals 708f high-loading immobilized catalysts 39
glycobiology 720 high-performance liquid chromatography
glycolipids 706 (HPLC) 4, 15, 19, 198, 203, 215f, 788, 810,
glycopeptide 406 1046f
glycoproteins 706 high-throughput catalyst screening 918, 993
a1 -glycoprotein 758 high-throughput parallel synthesis 4
glycosidases 712 high-throughput screening 4, 190, 726, 761,
glycosidations 139, 238, 708 785, 806
glycosides 83 history of Combinatorial Chemistry 4
glycosyl uorides 708, 714 HiTOPS system 182
glycosyl halides 707f HIV-1 protease 1084
glycosyl phosphates 708, 710 (HIV) TAT-1 protein 1082
glycosyl phosphites 708 Hiyama coupling 960
glycosyl sulfoxides 707f Hofmann elimination 280
glycosyltransferases 711, 716, 1077 hole transport layer (HTL) 1042f
glycosynthase 712, 714 Holmes photolinker 893
gmelinite 1027 homochiral organometallic catalysts 996
gold complexes 937 homogeneous catalysis 887
gold electrodes 951 homolytic processes 227
G-protein-coupled receptors 735, 766 Horner-Emmons olenations 357
graft copolymers 26 Horner-Wadsworth-Emmons reaction 451,
graphical encoding 170 632
Grieco three-component reaction 691 Horner-Wittig condensation 633
Grignard reagents 146, 283, 295, 328, 441, host structure 1020
473, 478 HPQ motif 1085
group-transfer 242 human angiogenin 1082
Grubbs metathesis catalyst 929 human genome project 634
guanidines 140 Hunsdicker reaction 243
hybrid PKS/NRPS systems 1075
HAL linker 63, 65 HYCRAM 69
halide reductions 418 HYCRON 69
a-haloacrylate 643 hydantoins 5, 104, 789
haloaromatic binary coding 173 hydrazines 128, 794
Hantzsch condensation 661 hydrazones 128
Hantzsch dihydropyridine synthesis 125 hydrobenzofuran 228
Hantzsch reaction 689 hydroboration 316
1106 Index
hydroboration/oxidation 316 iodoetherication 313

hydrocarbons 148 iodolactonization 313
hydrogen peroxide 310 iodo-lactonization 510
hydrogenations 315, 422, 874 ion exchange resins 30
hydrolysis of esters 354 ion-beam implantation 1022
hydrometallation 316 ionophores 889
hydrophobic collapse 736 ionophore library 890
hydrosilation catalysts 958 Ireland-Claisen rearrangement 465, 525
hydrostannylate 81 Irori TM 209, 619, 637, 795
hydrostannylation 318 irradiation 237, 292, 233
hydroxamic acids 142 isocyanides 693, 698f, 702
b-hydroxy carbonyls 493 isopenicillin N synthase (IPNS) 890f
b-hydroxy ketones 494 isoquinolines 131, 379
hydroxylamine linkers 283 isoxazoles 453, 794
hyperbranched polymers 52 isoxazolidines 453
isoxazolines 131, 379, 453
IBX oxidation 317 isra system 197
imidates 710 iterative optimization 915
imidazoles 131, 300, 461, 695, 699, 857, 860 iterative optimization approach 913
imidazolidinones 875 iTOPS 882
imidazoline 695
imines 479 Jarvis-Patrick method 732
imine cycloaddition 459
imine formation 401f Kaisers oxime resin 341
imine reductions 411 Kenner linker 100
imino aldol reaction 324f ketal/acetal-based linkers 70
imino-Sakurai reaction 327 ketene silyl acetals 498, 502, 520
immobilized articial membranes 754 a-ketoamides 297
immobilized dipeptides 1048 b-ketoamides 689
in silicio screening 761 a-ketoesters 297
indazoles 379 b-ketoester 689
indigo 963 ketone reductions 388, 417
indinavir 912 ketones 485
indolactam 145 ketoreductase 1068
indoles 131, 565, 665, 812 kinases 766
indole-3-glycerol-phosphate synthase (IGPS) kinetic resolution 968
1087 kinetic studies 1002
indolines 637 kinetics reaction 36, 61, 103
indolizines 379, 462 Knoevenagel condensations 450, 518, 661,
infrared (IR) thermography 906 690, 897
infrared radiation 953 Koenigs-Knorr method 707
inkjet deposition 940 Krohnke pyridine synthesis 661
inorganic supports 46
insertion catalysts 927 laboratory automation 14
insertion reaction 919 b-lactams 377, 463, 522, 671
instrumentation 190 b-lactam antibiotics 649
integrated circuit (IC) chips 1022 d-lactones 483
integrated data management 1017 lactonization 314
interfaces 1020 laminar supports 183
intramolecular Diels-Alder reaction 448 Langmuir monolayers 1046
intramolecular ether-forming reactions 925 lanthanide complexes 903
intramolecular Heck reaction 558 Larock annulation 565
iodination 274 laser encoding 186
iodine-magnesium exchange 475 laser optical synthesis chip 186
Index 1107
laser-induced uorescence (LIF) 978 manual synthesis 802

Lawesson reagent 105 mass encoding 178
l-dopa (Monsanto) 912 mass spectrometry 818
lead compounds libraries 727 Matassas sulfonamide betain 250
lead nding 778 material costs 837
lead optimization 778 materials discovery 1041
lead structures 727, 786, 802 materials industries 1018
lead-nding libraries 762 materials science 1017
lead-like 6, 764, 778 matrix-assisted laser desorption 178
Lemieux-Johnson reagent 311 mean tissue concentration 749
Lewis acid catalysis 452 mechanical stability of resins 33
Lewis acids for catalysis 451 medical implant materials 1051
Li enolates 495 medicinal chemistry 6, 10, 190, 786, 802
LiBH4 388 medium-throughput screening 869
libraries from libraries concept 400 Meissner fraction 1031
libraries of mixtures 15 Meldrumss acid 654
libraries of saccharides 707 melting temperature 756f
library design 745 melting zone technique 1030
library optimization 774 membrane anity 754
ligands 888 membrane ltration 47
light-directed synthesis 180 mercaptoacyl prolines 653
lipase-catalyzed acetylation 955 Merrield resin 65, 633
lipases 294 metabolism 745, 752
Lipinskis rule of ve 726, 764, 776, 778 meta-chloroperbenzoic acid 306
lipophilicity 754 metalated aromatics 471
liquid chromatography/mass spectrometry 15 metalation 471
liquid-liquid extraction 203, 208, 212, 200, metal-ligation 1006
211 metallocenes 930
liquid-liquid phase separation 48 metalloproteins 891
lithiation 237, 471 metaloproteases 769
lithium aluminium hydride 127 metastable phases 1026
lithium iodide 283 metathesis reaction 97, 290, 588, 443
lithium organyles 328 ring-closing 587, 600, 629, 659, 662, 956
lithographic pattering 1029 ring-opening 603, 587, 595
living free radical polymerization 37, 1054f met-enkephalin 770
loop scan 592 methanol oxidation 975
Losartan 868, 938 4-methoxytrityl resin 68
luciferase reporter gene 785 2-methyl butyryl-CoA 1072
LUDI 773 N-methylmorpholine N-oxide (NMO) co-
luminescence 1021 oxident 310
luminescent materials 1038 4-methyltrityl resin 68
methymycin 1077
M log P 726 Mettler Toledo Myriad Core System 208
MACCS-II Drug Data Report 765 Michael addition 280, 317, 503f, 523
macrocyclic ligands 888 nitroalkanes 523
macrocyclization 254, 265 Michael enantioselective additions 505
macrolactones 105 microarray reactor 974
macrolides 406 microchannel reactors 976
macroporous resins 28 microliter plate-based positional encoding
MADLRE 65 181
magnetoresistant materials 1034 microphotoluminescence 1025
MAMP linker 66 microporous resins 31
Mannich reactions 325, 481, 521, 685, 687f, microreactor 185
895 microreactor eight-channel 970
1108 Index
microwave 447 nonlinear optical (NLO) materials 1045

miniaturization 1035 non-positional encoding 183
Mitsunobu reaction 238, 248, 618, 253 nonribosomal peptides (NRPs) 1064
mix-and-split type library 709 normal phase chromatography 212
mixed anhydride reductions 392 Norrish type I reaction 292
modular peptide-based ligand 995 NPE linkers 291
molecular diversity 5 nuclear hormone receptors 766
molecular ngerprints 731 nucleic acids 706
molecular frameworks 738 nucleotidyltransferases 1077
molecular imprinting 1050 nylon 947
molecular volume 744, 747
molecular-beam epitaxy 1022 octahydrobenzisoxazoles 636
molecular-layer epitaxy 1024 olen cross-metathesis 710
molecularly imprinted polymers (MIPs) 1050 olen metathesis 585
monitoring 61 oligomerization 447
monolithic reactor 975 oligonucleotide modications 1082
morphine 770 oligonucleotide-encoded libraries 171
morphology 27 oligosaccharides 97, 138, 706, 718, 721
mRNA display 1085 oligosaccharides, enzymatic synthesis 711
Mukaiyama aldol reaction 545, 498, 503 on-bead analytics 36
Mukaiyamas reagent 335 one bead-one concept compound 5
multidimensional screening approach 920, one-pot synthesis 717
923 online analysis 850
multifunctional catalysts 993 Oppolzers camphorsultam 234
multipins 5, 182 optical band-gap 1031
multiplasmid approach 1073 optical microscopy 1030
Multiple Core Structure Libraries 473 optical screening 1030
multisubstrate/one-catalyst screening 927 oral absorption 752
MultiSyn Tech Syro II 204, 794 orally bioavailable 725
multitube packed bed reactors 945 organic light-emitting device (LED) 1020
(dl)-muscone 632 organic polymeric materials 1019
organoboron reagents 532
NaBH4 392 organolithium reagents 124, 475
NaCNBH3 392 organolithium species 475
nanocrystals 1028 organomagnesium compounds 149
NanoKan TM 637 organomercurial compounds as radical
natural product-like libraries 634, 637 precursors 233
natural products 444, 613, 697 organometallic reagents 75
neighborhood behavior 730 organometallics 93
neighboring group participation 709 organotin reagents 543
neomethymycin 1077 organozinc bromides 473
neural networks 729 orthogonality-concept 88, 710, 721
neuromedins C and K 891 osmium tetroxide 309f
nitrile reduction 413 osmotic shock 33
nitro group reductions 409, 419 overalkylation 488
nitro-aldol reaction 522 oxabutadienes 678
NMR spectroscopy 61f, 217 oxazaborolidine catalyst 428
NaN bond reductions 413 oxazole 695
NaO bond reductions 413 oxazolidines 104
nonbiological induced t 902 oxazolidinone synthesis 253
nonchelation-controlled diastereoselective oxazolidinones 104
ketone reductions 389 oxazolines 695
non-chemical encoding methods 180 oxazolones 296
noncrosslinked (soluble) polymers 24 oxidation 369, 377, 457, 857
Index 1109
of alcohols 369 functionalized oligomers 596

of aldehydes 375 phosphines 1009
of CO 947 schi bases 994
of methanol 948 peptidyl transferase site 1085
of oximes 454 peptoid libraries 5, 180, 252
of phenoles 380 pericyclic reactions 465
of polymer-bound suldes to sulfoxides and Perkin-Elmer Solaris 530
sulfones 376 permeability 725, 744, 746
of selenium- and phosphorus-containing Petasis reaction 326, 481
compounds 378 pH sensors 960
oxidation-cyclization strategy 371 pharmacokinetic modeling 752
oxidative pharmacokinetic prole 796
aromatization 379 pharmacophores 453, 732, 743, 770, 764
cleavage 311, 379, 456 pharmacophoric ngerprints 770
coupling and cleavage 380 phase I transformations 753
coupling reactions 369 phase II transformations 753
cyclization or condensation 379 phase shifters 1036
dehydrogenation 944 phenanthridines 379
dehydrogenation 965 phenolic oxidation 380
oxidative formation of heterocycles 379 Phloxine B 963
thioester 937 Phoc linker 102
oxygenation 904 phosphine oxazoline ligand 911, 920
oxime ethers 234 phosphites 707, 709
oxindoles 560 phosphonium salts 115
(G)-oxomaritidine 21 phosphorescent materials 7
Oxone2 308 phosphoribosylanthranilate isomerase (PRAI)
oxyethylene chains 43 1087
ozonolysis 144, 312 photocatalysts 969
photochemistry 91, 180, 243
paclitaxel 619 photolabile linkers 80, 91
PAL linker 63, 65 photolabile protection group 5
Palladium catalysts 69, 115, 131, 273, 1012 photolithography 5, 180, 1024
parallel ash chromatography 212 photoluminescence 1055
parallel optimization equipment 847 photolysis 91
parallel processing 14 photometric eciency 1043
parallelization in process development 838 photo-sensitive linkers 710
Parallex TM System 214 photovoltaic materials 1028, 1031
partition coecients 754, 761 pH-sensitive uorophors 960
Passerini reaction 696 phytochelatins 1029
patterned lms 1024 Pictet-Spengler reaction 275, 294, 329, 489
Pbs linker 75 pin technique 5, 617, 912
Pd-mediated regioselective oxidation 1012 piperazine 281
PEI-based polymer 901 piperazinones 105
Penicillium chrysogenum 1075 piperidine 655
pentamine ligands 911 pipiridine alkaloids 298
pentenyl glycosides 707f piperidone 289
Pepsin-K resins 41 plasma mass spectroscopy 892
peptide 4, 18 plasma protein binding 758
aldehydes 371 plasma-enhanced chemical vapor deposition
bond formation 1083 1025
libraries 1084 plasmepsin II 773
nucleic acids 69 plasmids 1071
synthesis 190 platinum catalysts 953
tags 173 plug-ow reactor 973
1110 Index
poly(ethylen glycol)-copoly(N,N 0 - polymer-supported reducing agents 323

dimethylacrylamide) (PEGA) 42 polymer-supported ruthenium carbene
poly(N-acrylylpyrrolidine) (PAP) 42 complexes 589
poly(styrene-b-1-vinyl-alcohol) 50 polymer-supported scandium catalyst 325
poly(vinyl alcohol-b-1-vinyl-2-pyrrolidone) 50 polymer-supported Schi base catalysts 914
poly(vinyl) pyridinium dichromate 371 polymer-supported sulde ozonide reductions
polyacrylamide 50 421
polyacrylic acid 50 polymer-supported tinhydrides 239, 419
polycyclic structures 602 polymer-supported triphenylphosphine 359
polyethylene 16 polymer-supported triphenylphosphines for
polyethylene glycol (PEG) 50 the reduction of azides 421
polyethylene glycol (PEG) grafts 35 polymer-supported ylide 629
polyethylene glycol (PEG) resins 35 polymer-swelling/shrinking characteristics
polyfunctional linear polymeric supports 49 16
PolyHIPE 40 polymerization 934
polyketide synthases (PKSs) 1064 polynorbornene ROMF gel 50
polyketides 389, 495, 1065 polyolens 930
polymer carrier (bead) 16 polyoxometalate libraries 869, 935
polymer properties 27 polyoxyethylene-polyoxethane (SPOCC) 45
polymer-capture concept 488 polyoxyethylene-polyoxypropylene (POEPOP)
polymeric tin iodide 429 44
polymerization 576 polyoxyethylene-polystyrene (POEPS-3) 45
polymer-supported acrylates 445 polypropylene 16
polymer-supported aldehyde 283 polypropylene mesh containers 5
polymer-supported allyl stannane 242 polypropylene oxide (PPO) 50
polymer-supported amide coupling reagents polystyrene 16, 35, 38, 39, 50
350 polystyrene-trimethyl ammonium (TMA)
polymer-supported ammonium latex 902
cyanoborohydride 323, 415, 901 polyvinylalcohol 50
polymer-supported ammonium perchromate positional encoding 170, 180
371 positional scanning approach 913
polymer-supported aryl diazonium salts 274 position-sensitive photodiode 965
polymer-supported arylboron reagents 540 potassium ferricyanide 310
polymer-supported arylstannane 45 544 precipitation 47f
polymer-supported base 263 preformed linker concept 61
polymer-supported BINAP 580 primary screening libraries 730
polymer-supported carbodiimides 335 privileged structures 636, 735, 774, 762
polymer-supported catalysts 574, 422 process characterization 834, 849
polymer-supported catalysts 901 process development 831, 864f
polymer-supported dienes 441 process discovery 867
polymer-supported dienophiles 445 process hazards analysis 882
polymer-supported dihydropyridine-mediated process optimization 834, 847, 867
reductions 420 process screening 834, 841
polymer-supported isocyanates 351 process validation 834, 849, 869
polymer-supported palladium catalysts 579, processing conditions 1020
574 product-based design 734
polymer-supported perruthenata (PPS) 370, product-based selection 774
371, 373, 457 propionyl-CoA 1072
polymer-supported phenylselenyl bromide prostaglandins 71, 482, 626, 543, 481
314 protection groups 5, 62, 290, 88, 710, 721,
polymer-supported phenylselenyl phthalimide 20, 71, 68, 291, 706
314 protein catalysts 7, 1084
polymer-supported reagents 20, 238, 1018 protein families 766
polymer-supported reagents 6 protein kinase inhibitors 618
Index 1111
Prussian blue 963 reagent-based selection 774

pseudo dilution 16 rearrangement ngerprints 822
pulsed laser ablation 1022 receptor-assisted combinatorial synthesis 590
purine 617 reduction 387, 789
purine-based library 256 reduction electrochemical 951
purity of combinatorial libraries 217, 806, reduction of alkenes 316
210, 15 reduction of alkynes 316
puromycin 1085 reduction of amides 399, 430
pyran linker 627 reduction of disulde 396, 419
pyrazoles 108, 462, 789, 791 reduction of imines/enamines 361
pyrazolones 104, 521 reduction of sulfones 396
pyridazines 379 reduction of sulfurs 396
pyridines 131, 379, 661 reduction of thioesters 393
pyridones 657 reduction-chelation-controlled 389
pyrimidines 379, 258 reduction-enantioselective 415
pyrrole synthesis 299 reductions diastereoselective ketone 389
pyrroles 462, 655, 695, 699 reductions of epoxides 418
pyrrolidines 235, 458, 651 reductions of esters 390
reductions of ketones 388, 417
QSAR models 771 reductions of nitriles 413
Quad3 TM from Biotage 213 reductions of nitro groups 409, 429
quantitative structure-activity relationship reductions of NaN bonds 413
(QSAR) 745, 1029 reductions of NaO bonds 413
quartz wafer 945 reductions of quinones 399
quaternary masking 1023 reductive alkylation 280, 323, 448f, 792
quaternization 281, 283 reductive amination 401, 403, 416, 430
quinazolinediones 104 reductive cleavage 393
quinazolinones 379 reductive cyclizations 419
quinoline N-oxide 674 reductive dehalogenations 428
quinolines 672 reductive hydrocoupling 952
quinolinones 104, 671 reductive hydrodeselenation 314
quinolones 261 regenerative fuel cells 963
quinone reductions 399 Reissert intermediates 328, 108
quinones 147 Reissert-type reaction 277
quinoxalinones 131 REM resins 126, 281
REMPI 940, 944, 964
radical cyclization 678 repository 808
radiofrequency (RF) encoding 618, 18, 802, resin capture strategy 297
633 resin ylide 621
radiofrequency tags 183 resin-supported MOP ligand 580
radioimmunodetection (RIAD) 893 resolution of racemates 929
ramage linker 66 resonance-enhanced multiphoton ionization
random libraries 743, 765, 1081 (REMPI) 940
random selection 734 retro-aldol reaction 493
rasta silanes 37 retro-Diels-Alder reaction 444
rational design 4, 1089 retro-Michael reaction 80
of a catalyst 1012 retro-Michael addition reaction 131
Rauwolfa alkaloids 615 return on investment 1018
reactant-based design 734 reverse solid-phase peptide synthesis 64
reactant-biased algorithm 734 reversed-phase high-performance liquid
REACTarray TM 871 chromatography (HPLC) 176
reaction of CS in sp systems 339 rhodium(II) catalysts 300, 927
reaction kinetics 36, 61, 103 Richter reaction 86
reactive intermediates 151 rifgid descriptors 732
1112 Index
ring-closing metathesis 587, 600, 629, 659, self metathesis 587, 589
662 self-ligating ribozymes 1083
ring-closing reactions 254 self-similarity 763
ring-opening cross-metathesis 603 SEM linker 75, 83, 73, 144
ring-opening metathesis polymerization semiconductor gas sensors 972
(ROMP) 587, 595 sensing chemistry 894
Rink resin 136, 123, 67 serial processing 14
RNA aptamers 1082 serine proteases 769
RNA combinatorial libraries 1083 Sharpless asymmetric dihydroxylation 311
robot-arm-based systems 190 shelf life characterization 806
ROMP spheres 36 shikimic acid 455, 635
ROMP-based polymers 51 SiaH insertion reaction 926
route scouting 834, 840, 869, 869 sialyl trimetric Lewis X 713
RP-HPLC 214 sigmatropic rearrangements 465
Rutherford backscattering spectroscopy 1035 silyl amide linkers (SAL) 289
silyl enol ethers 441, 498, 505f, 520f
SAC linker 66, 75 silyl ketene acetals 505, 525
Saccharopolyspora erythraea 1079 silyl linkers 73
safety-catch linkers 73, 77, 80, 90, 99, 624 silylated resins 73
safety-catch procedure 444 similarity 770
safety-catch resin 282 similarity radius 734
Sakurai reaction 653, 327 similarity searching 763
SAL linker 66, 75 single compounds 3
salicylaldiminato ligands 934 size exclusion chromatography 47
samarium iodide 229, 284 sol-gel processing 1026, 940
sample logistics 219 solid-phase Bischler-Napieralski reaction 277
Sandmeyer reaction 129 solid-phase extraction (SPE) 203, 208, 211,
sarcodictyns 375, 620 908
SASRIN resin 63, 650, 65 solid-phase Friedel-Crafts acylation 272
Savant vacuum centrifuge 222 solid-phase iodination 274
Sc(OTf )3 502, 505, 521 solid-phase Mitsunobu reaction 253
SCAL (safety-catch) 67 solid-phase phenolate alkylation 250
scanning lectron microscope (SEM) 33 solid-phase Williamson ether synthesis 249
scanning electrochemical microscope 952 solid-state materials 1019
scanning evanescent microwave microscope solubility 727, 744, 748f, 755
(SEMM) 1031 soluble polymeric supports 46
scanning-tip microwave near-eld microscope soluble polystyrene polymer 626
1036 solution deposition methods 1022
scavenger resins 20, 63, 212, 452 Sonogashira reaction 329, 544, 688, 297
Schi base ligands 908 spacer group 61
screening intensity 839 spatial encoding 170
screening multisubstrate/one catalyst 927 spatially addressable electrolysis platform
screening strategies 851 (SAEP) 952
screening technologies 1017 spin eld eect transistors 1033
secondary amine binary coding 175 split-and-combine concept 4, 5, 17, 176, 886
selection algorithms 732 sporochnol 1009
selenenyl bromide 623 sputtering 1022
selenides 237, 286 srfA-A 1075
selenium 77 stannane-based linkers 81, 77
selenium bromide 636 Staphylococcus auerus 623
selenium reductions 397 statistical design 852
selenium-based linkers 81, 398 Staudinger reaction 407, 463, 650
selenol 293 stereoselective alkylations 510
selenoxides 286 enolates 510
Index 1113
steric hindrance 798 target family 765

Stille reactions 81, 95, 104, 273, 543, 630 targeted libraries 730
Strecker reaction 914, 1001 Taxol TM 629
Streptomyces argillaceus 1079 Tayol TM 619
Streptomyces fradiae 1079 tea-bag strategy 5, 183
Streptomyces lividans 1079 Tebbe olenation reaction 356, 443
Streptomyces olivaceus 1079 tentagel resin 61, 16, 35
structural fragment keys 731 ternary composition diagram 1021
Structure-Activity-Relationship (SAR) 795, tert-butyl hydroperoxide 310
802, 374, 743, 785, 801 tetracenomycins 1079
Structure-Activity-Relationship (SAR) by tetrahydrocarbolines 104
NMR 773 tetrahydrofurans 675
structure-property relationships 752 tetrahydroisoquinolines 330, 674
structure-stability relationships 806 tetrahydropyranol linker 907
Stuttgart Neural Network Simulator (SNNS) tetrahydropyridines 131
766 tetrahydroquinolines 668
substrate-controlled reduction 389 tetramic acids 517, 653
substructure analysis 738 tetrazoles 130, 694
sugar-based auxiliary 232 thermal decomposition 808
suicide inhibitor 307 thermal evaporation 1022
sulfone elimination reaction 288 thermally sensitive resistor 970
sulfur reductions 396 thiazoles 104, 338, 695
sulfur-based linkers 77 thiazole-containing combinatorial biosynthesis
b-sultams 464 libraries 1075
super high-throughput screening 966 thiazoline 695
superacylation catalysts PPY 962 thin-lm deposition 1022, 1025, 939, 1020
superconducting 1025 thin-layer organic light-emitting devices
superconducting materials 7 (OLEDs) 1042
surface proteins 1082 thioester reductions 393
surface-enhanced Raman scattering (SERS) thioether oxidation 937
1028 thioglycosides 707, 718
surfactin A 1075 thiohydantoins 104
surrogate analytes 616 thiohydroxamates 243
Surveyor TM 875 thioketene silyl acetals 502
Suzuki 316 thio-oligosaccharides 396
Suzuki reaction 95, 273, 868, 909, 960, 316, thiophenes 678
76, 898, 79 thiosilyl ketene acetal 521
Suzuki-Miyaura reaction 532 THP linker 70, 130
Swern oxidation 372, 370 THP-type linkers 144
syndiotactic polypropylene 934 three-component condensation 701
syn-elimination 286 three-dimensional ngerprint keys 763
synthesis of b-lactams 143 thrombin 773
synthesis of cyclopeptides 137 Ti-catalyzed cyanide additions 1000
synthesis of six-member heterocycles 450 tin-mediated nitro reductions 409
synthetic enzyme catalysts (synzyme) 899 Ti-peptide complexes 1000
synthon 289 Toray carbon 962
Toray paper 949
T1 linker 84 tosyl radicals 233
T1 triazene linker 95, 522 traceless cleavage 656
T2 linker 84 traceless linkers 19, 75, 90, 110, 237, 280,
Tamura tandem reaction 455 659, 662, 676, 737, 81
tandem Mannich-Michael mechanism 325 Tramadol2 126
tandem Mannich-Michael reaction 325, 480 transesterication 71, 134, 282
Tanimoto coecient 732, 763 transfer hydrogenations 424
1114 Index
transketalization 623 very-large-scale immobilized polymer

transmembrane ionophores 888 synthesis 180
transmetalation reaction 483 vicinal diols 309
transporters 726 vinyl cuprates 482
b-trialkylsilyl 289 vinyl sulfone 282
triangular libraries 947 vinyl triates 666
triazene-based linkers 83, 115 vinylogous systems 296
triazine template 256 vinylsulfones 456
trichloroacetimidate 708f vitamin D3 633
tridentate scaold 889
triethylborane 234f Wacker oxidation 1012
6-endo-trig cyclization 286 Wang linker 65
5-exo-trig cyclization 295 Wang resin 63
trimethylorthoformate 401, 788 Waters Micromass 216
(trimethylsilyl)acetylene 551 wavelength-divisible multiplexing (WDM)
2-(trimethylsilyl)ethylester 290 1025
triose phosphate isomerase (TIM) 1089 Weinreb amide linker 487
trityl resins 64, 67 Weinreb amide reductions 394
tropene 566 Weinreb amides 144, 485
tryptophan biosynthesis pathway 1087 well reactors 938
turnable resonators 1036 wolf-lamb strategy 515
b-turn mimetic library 396, 599 workstations 842
b-turn structural motif 911 work-up 838
two-component reactions 685 World Drug Index (WDI) 729, 777
two-dimensional adressable arrays 1022
two-dimensional ngerprint keys 762 xanthates 708
two-resin system 284 2-xanthates 709
tylosin pathway 1078 X-ray microdiraction 1027
Yb resin 298
UDP-galactose 714
Yb(OTf )3 503, 657, 670
Ugi reactions 409, 599, 601, 697, 699, 299,
yield determination 200
461, 487
yohimbinic acid 615
Ullmann aryl ether-forming reactions 925
ytterbium triate 451f, 456
ultraltration 48
ultrasound 85
zearalenone 474
g,d-unsaturated acids 231
(S)-zearalenone 630
a,b-unsaturated ketones 441, 494, 503
Zenyx Magellan synthesizer 205
urazines 451
zeolite synthesis 1026
urdamycin A 1079
zinc borohydride polymers 416
UV lasers 964
zinc organyles 328
UV-excited photoluminescence 1030
Zinsser Sophas 206
zirconium borohydride polymers 416
vacuum centrifuges 221 Zn enolates 494, 526
vancomycin 69, 110, 590, 623f zoom screens 949
vapor deposition techniques 1022 Zr-catalyzed 1004, 1006
Varian-HPLC 215 zymark 199

K. C. Nicolaou, Rudolf Hanko, Wolfgang Hartwig Handbook of Combinatorial Chemistry Drugs, Catalysts, Materials 2-Vol. Set PDF

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K. C. Nicolaou, Rudolf Hanko, Wolfgang Hartwig Handbook of Combinatorial Chemistry Drugs, Catalysts, Materials 2-Vol. Set PDF

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Handbook of

Handbook of Combinatorial Chemistry. Drugs, Catalysts, Materials.

W. Bannwarth, E. Felder (Eds.)

1999, ISBN 3-527-29869-X

Organic Synthesis on Solid Phase

2000, ISBN 3-527-29950-5

Combinatorial Strategies in Biology and

Drugs, Catalysts, Materials

Edited by K. C. Nicolaou, R. Hanko, and W. Hartwig

Printed in the Federal Republic of

Typesetting Asco Typesetters, Hong Kong

Part I General Aspects 1

1 Combinatorial Chemistry in Perspective 3

2 Introduction to Combinatorial Chemistry 10

3 Solid Phase and Soluble Polymers for Combinatorial Synthesis 24

3.2 Solid-phase Supports 25

4 Linkers for Solid-phase Synthesis 59

4.4.4.1 Cleavage with Ensuing Allylic Substitution or Cross-coupling

4.6.6.4 Linkers for Alkynes 150

5 Encoding Technologies 170

6 Instrumentation for Combinatorial Chemistry 190

6.2.3.2 Quad3TM from Biotage 212

Part II Synthetic Chemistry 225

7 Radical Reactions in Combinatorial Chemistry 227

8 Nucleophilic Substitution in Combinatorial and Solid-phase Synthesis 247

8.2.4 Sulfur Nucleophiles 251

9 Electrophilic Substitution in Combinatorial and Solid-phase Synthesis 270

10 Elimination Chemistry in the Solution- and Solid-phase Synthesis of

10.3.2 1,4-Conjugate Eliminations 295

11 Addition to CC Multiple Bonds (Except for CC Bond Formation) 305

12 Addition to CarbonHetero Multiple Bonds 322

12.2.6 Addition of Sulfur Nucleophiles 333

13 Chemistry of the Carbonyl Group 346

14 Oxidation Except CC Double Bonds 369

14.2.3 Examples of the Oxidation of Alcohols by Polymer-bound

15 Reductions in Combinatorial Synthesis 387

15.2.15 Imine Reductions (not Reductive Amination) 411

16 Cycloadditions in Combinatorial and Solid-phase Synthesis 440

17 Main Group Organometallics 470

17.3.4 Reaction with Enolates 481

18 Enolates and Related Species in Combinatorial and Solid-phase

19 Solid-phase Palladium Catalysis for High-throughput Organic

19.2.1 Cross-coupling Reactions 531

20 Olefin Metathesis and Related Processes for CC Multiple Bond

Part III Special Synthetic Topics 611

21 Solid-phase Synthesis of Natural Products and Natural Product-like

22 Solid-phase Synthesis of Heterocyclic Systems (Heterocycles Containing One

22.1 Introduction 643

23 Multicomponent Reactions 685

24 Strategies for Creating the Diversity of Oligosaccharides 706

Part IV Molecular Design and Combinatorial Compound Libraries 723

25 Design Criteria 725

26 Estimation of Physicochemical and ADME Parameters 743

27 Virtual Compound Libraries and Molecular Modeling 761

27.1 Introduction 761

28 Erythropoietin Sensitizer A Case Study 784

29 Estimation of Stability and Shelf Life for Compounds, Libraries, and

29.2.2 Modeling: from Compounds to Libraries 809

Part V Novel Applications of Combinatorial Chemistry 829

30 Concepts of Combinatorial Chemistry in Process Development 831

30.3.3 Requirements for Analytical Instruments 850

31 High-throughput Screening Applied to Process Development 864

32 Combinatorial Methods in Catalysis 885