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Computational Chemistry

Shubin Liu, Ph.D.

Research Computing Center

University of North Carolina at Chapel Hill

Outline

Introduction

Methods in Computational Chemistry

Ab Initio

Semi-Empirical

Density Functional Theory

New Developments (QM/MM)

Hands-on Exercises

The PPT format of this presentation is available here:

http://its2.unc.edu/divisions/rc/training/scientific/

/afs/isis/depts/its/public_html/divisions/rc/training/scientific/short_courses/

its.unc.edu

About Us

ITS Information Technology Services

its.unc.edu

http://its.unc.edu

http://help.unc.edu

Physical locations:

401 West Franklin St.

211 Manning Drive

10 Divisions/Departments

Information Security

Research Computing Center

User Support and Engagement

Communication Technologies

Enterprise Applications

Teaching and Learning

Office of the CIO

Communications

Finance and Administration

3

Research Computing

Where and who are we and what do we do?

Website

http://its.unc.edu/research-computing.html

Groups

Infrastructure -- Hardware

User Support -- Software

Engagement -- Collaboration

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About Myself

Ph.D. from Chemistry, UNC-CH

Currently Senior Computational Scientist @ Research Computing Center, UNC-CH

Responsibilities:

Support Computational Chemistry/Physics/Material Science software

Support Programming (FORTRAN/C/C++) tools, code porting, parallel computing, etc.

Offer short courses on scientific computing and computational chemistry

Conduct research and engagement projects in Computational Chemistry

Development of DFT theory and concept tools

Applications in biological and material science systems

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About You

Name, department, research interest?

Any experience before with high

performance computing?

with computational chemistry

approaches?

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Think BIG!!!

What is not chemistry?

From microscopic world, to nanotechnology, to daily life, to

environmental problems

From life science, to human disease, to drug design

Only our mind limits its boundary

From small molecules, to DNA/proteins, 3D crystals and surfaces

From species in vacuum, to those in solvent at room temperature,

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From structure, to properties, to spectra (UV, IR/Raman, NMR,

VCD), to dynamics, to reactivity

All experiments done in labs can be done in silico

Limited only by (super)computers not big/fast enough!

Central Theme of

Computational Chemistry

STRUCTURE

DYNAMICS

REACTIVITY

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SEQUENCE

STRUCTURE

DYNAMICS

FUNCTION

EVALUTION

Multiscale Hierarchy of

Modeling

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What is Computational

Chemistry?

Application of computational methods and

algorithms in chemistry

Quantum Mechanical

i.e., via Schrdinger Equation

also called Quantum Chemistry

Molecular Mechanical

i.e., via Newtons law F=ma

also Molecular Dynamics

Empirical/Statistical

ii

H

H

tt

Focus

FocusToday

Today

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10

Deal with?

Assuming typical computing setup (number of CPUs,

memory, disk space, etc.)

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DFT method: ~1000 atoms

Semi-empirical method: ~10,000 atoms

MM/MD: ~100,000 atoms

11

Schrodinger Equation

ii

H

H

tt

H E

N

Z

h2

2

H i -

2m

i 1

1 ri

n

j i

i 1

1

rij

1

H h i

i 1

ji i 1 rij

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12

Equation to Solve in

ab initio Theory

H E

Known exactly:

3N spatial variables

(N # of electrons)

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To be approximated:

1. variationally

2. perturbationally

13

electrons

electrons 22

nuclei

electrons

nuclei 22

electronsnuclei

nuclei e 22Z

2

2

e ZAA

2

2

H

i

A

H

i

A

2

m

2

m

riA

e

A

2

m

2

m

riA

ii

AA

ii

AA

e

A

electrons

nuclei

electronse 22

nucleie 22Z Z

e ZAA ZBB

e

i i j j

rijr A B RRAB

ij

AB

A B

kinetic energy of the nuclei

electrostatic interaction between the electrons and

the nuclei

electrostatic interaction between the electrons

electrostatic interaction between the nuclei

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14

AbInitio Methods

Accurate treatment of the electronic distribution using the

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Can be systematically improved to obtain chemical accuracy

Does not need to be parameterized or calibrated with respect

to experiment

Can describe structure, properties, energetics and reactivity

What does ab intio mean?

Start from beginning, with first principle

Who invented the word of the ab initio method?

Bob Parr of UNC-CH in 1950s; See Int. J. Quantum Chem.

37(4), 327(1990) for details.

15

Three Approximations

Born-Oppenheimer approximation

simplifying the Schrdinger equation

Independent particle approximation

Electrons experience the field of all other electrons as

a group, not individually

Give birth to the concept of orbital, e.g., AO, MO, etc.

LCAO-MO approximation

Molecular orbitals (MO) can be constructed as linear

combinations of atom orbitals, to form Slater

determinants

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16

Born-Oppenheimer

Approximation

the nuclei are much heavier than the electrons and move more slowly than the electrons

freeze the nuclear positions (nuclear kinetic energy is zero in the electronic

Hamiltonian)

electrons

22 22 electrons

i

22mme i

ii

electrons

electrons

H

Helel

ii

2

2

electronse 2 nuclei

nucleie 2Z Z

ee22ZZA electrons

e

e ZAA ZBB

A

ij A

rriA

rrAB

AA

i i j j rr

ABB

iA

ij

AB

nuclei

nuclei

**

el

elelH

eleldd

el

E , E

H

Helel elel Eelel , E

**

el el dd

el the

el nuclear-electron attraction and nuclear E depends on the nuclear positions through

E = 0 corresponds to all particles at infinite separation

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17

Approximate Wavefunctions

Construction of one-electron functions (molecular orbitals,

MOs) as linear combinations of one-electron atomic basis

functions (AOs) MO-LCAO approach.

NN

l qqi

uukl k rri ii ;;

l

i

kl k

i

1

k

k 1

--up)

(spin

(spin

up)

ii

(spin

(spin--down)

down)

anti-symmetrized products are denoted as Slaterdeterminants).

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18

a 1 b 2 c 3 z n

a 1 b 2 c 3 z n

1n1!

b 2 2c 3 3

z n n a 2 2b 11c 3 3

z n n

a 1

a

b

c

z

a

b

c

z

n!

a 11

a

b 11

b

1n1! c 11

c

n!

z 11

z

a 2 2

a

b 2 2

b

c 2 2

c

z 2 2

z

a 3 3

a

b 3 3

b

c 3 3

c

z 3 3

z

a n n

a

b n n

b

c n n

c

z n n

z

a 11b 2 2c 3 3

z n n abc

z

a

b

c

z

a b c

z

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19

One determinant: The HartreeFock method.

1 2 3 N

HF

HF 11 122 2 33 3 NN N

There are N MOs and each MO is a linear combination of N AOs.

Thus, there are nN coefficients ukl, which are determined by

making stationary the functional:

N

HF H HF

EE

ij

HF

HF HF H HF

ij

i , j 1

i , j 1

uu SS uu ij

ij

k ,l 1

k ,l 1

N

N

*

*

ki kl lj

ki kl lj

All possible determinants: The full CI method.

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20

2N

2 N

n n

CICI

cc; ;

1

1

There are

EE

CICI CICI HH CICI

2N

2 N

n n

cc SS cc

, 1

, 1

2N

from a set of 2N AO basis functions.

The number of determinants gets easily much too large. For

example:

40

9

Davidsons method can be used to find one

9

40 10

10

10

or a few eigenvalues of a matrix of rank 109.

10

its.unc.edu

21

1 2 3 N

HF

HF 11 122 2 33 3 NN N

*

*S u

EE

u

HFHF HFHF H HFHF i

ijij

ukiki Sklkl uljlj ijij

, j 1

k ,l 1

i , j 1 k ,l 1

N

N

NN

NN

N

N

NN

E P h 11 P mk nl ; P u **u

HFHF HH

HFHF Enucnuc Pmnmn hmnmn 22 Pklkl mk nl ; Pklkl ukikiulili

mm, n, n11

k k,l,l 11

i i 11

E HF 0

uuki E HF 0

ki

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HartreeFock equations

22

c F c S

Overlap integral

F H P

S |

| 1 |

2

occ

Density Matrix

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P 2 ci ci

i

23

Self-Consistent-Field (SCF)

c F c S

2. Construct Fock Matrix with coefficients

3. Solve Hartree-Fock-Roothaan equations

4. Repeat 2 and 3 until ingoing and outgoing

coefficients are the same

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24

Ab Initio Methods

Semi-empirical

Semi-empiricalmethods

methods

(MNDO,

(MNDO,AM1,

AM1,PM3,

PM3,etc.)

etc.)

excitation

excitationhierarchy

hierarchy

(CIS,CISD,CISDT,...)

(CIS,CISD,CISDT,...)

(CCS,

(CCS,CCSD,

CCSD,CCSDT,...)

CCSDT,...)

Hartree-Fock

Hartree-Fock

(HF-SCF)

(HF-SCF)

perturbational

perturbationalhierarchy

hierarchy

(MP2,

MP3,

MP4,

(MP2, MP3, MP4,)

)

excitation

excitationhierarchy

hierarchy

(MR-CISD)

(MR-CISD)

perturbational

perturbationalhierarchy

hierarchy

(CASPT2,

CASPT3)

(CASPT2, CASPT3)

Multiconfigurational

MulticonfigurationalHF

HF

(MCSCF,

(MCSCF,CASSCF)

CASSCF)

Full

FullCI

CI

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25

Whos Who

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26

Size vs Accuracy

Full CI

Accuracy (kcal/mol)

0.1

Coupled-cluster,

Multireference

Nonlocal density functional,

Perturbation theory

Hartree-Fock

Semiempirical Methods

10

1

its.unc.edu

10

100

Number of atoms

1000

27

AN EXAMPLE

Equilibrium structure of (H2O)2

W.K., J.G.C.M. van Duijneveldt-van de Rijdt, and

F.B. van Duijneveldt, Phys. Chem. Chem. Phys. 2, 2227 (2000).

95.7 pm

symmetry:

RCOO,e

= 291.2

s

96.4 pm

95.8 pm

pm

ROO2 = 297.6 0.4 pm

SAPT-5s potential [E.M. Mas et al., J. Chem. Phys. 113,6687(2000)]:

ROO2 ROO,e= 6.3 pm ROO,e(exptl.) = 291.3 pm

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28

Enthalpy Changes He in kJ/mol

Exptl.

Exptl. CCSD(T)

CCSD(T)

SCF

SCF

G2

G2

DFT

DFT

CH

CH44

CH22++H

H22

CH

544(2)

544(2)

542

542

492

492

534

534

543

543

CC22H

H44

H22++H

H22

CC22H

203(2)

203(2)

204

204

214

214

202

202

208

208

H

H22CO

CO

CO++H

H22

CO

21(1)

21(1)

22

22

3

3

17

17

34

34

22NH

NH33

N22++33H

H22

N

164(1)

164(1)

162

162

149

149

147

147

166

166

22H

H22O

O

H22O

O22++H

H22

H

365(2)

365(2)

365

365

391

391

360

360

346

346

22HF

HF

FF22++H

H22

563(1)

563(1)

562

562

619

619

564

564

540

540

Gaussian2(G2)methodofPopleandcoworkersisacombinationofMP2andQCISD(T)

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29

cc

functions

more accurate approximations to the molecular orbitals

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orbital functions

30

Basis Functions

Slaters (STO)

Gaussians (GTO)

exp(r)r)

Better behaved than Gaussians

2-electron integrals hard

22

xxllyymmzznn **exp

r

exp r

Wrong behavior at nucleus

Decrease too fast with r

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31

Minimal

STO-nG

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Each

Eachatom

atomoptimized

optimizedSTO

STOisisfit

fitwith

withnn

GTOs

GTOs

Minimum

Minimumnumber

numberof

ofAOs

AOsneeded

needed

Contracted

ContractedGTOs

GTOsoptimized

optimizedper

peratom

atom

Doubling

Doublingof

ofthe

thenumber

numberof

ofvalence

valenceAOs

AOs

32

Polarization /

Diffuse Functions

Polarization: Add AO with higher angular

momentum (L) to give more flexibility

as anions or excited states

Example: 6-31+G*, 6-311++G**

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33

Correlation-Consistent

Basis Functions

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cc-pVDZ DZ with ds on heavy atoms, ps on H

cc-pVTZ triple split valence, with 2 sets of ds and

one set of fs on heavy atoms, 2 sets of ps and 1 set

of ds on hydrogen

can also be augmented with diffuse functions (augcc-pVXZ)

34

Pseudopotentials,

Effective Core Potentials

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interactions

nuclei and of the core electrons

electrostatic potential of the nuclei and of the core

electrons

atom (but introduces additional approximations)

relativistic effects that otherwise would be costly to treat

35

Correlation Energy

HF does not include correlations anti-parallel electrons

Eexact EHF = Ecorrelation

Post HF Methods:

Mller-Plesset Perturbation series (MP2, MP4)

Density Functional Theory (DFT)

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36

Configuration-Interaction (CI)

In Hartree-Fock theory, the n-electron wavefunction is approximated by one single

Slater-determinant, denoted as:

HF

follow from the Hartree-Fock calculation in a given one-electron basis set of

atomic orbitals (AOs) are known as virtual orbitals. For simplicity, we assume that

all spin-orbitals are real.

Sometimes, we only use a few determinants, and sometimes, we use millions of

them:

In this notation,

is a Slater

determinant that is obtained by

CI HF c

occupied orbitals by virtual ones.

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37

CIS, CISD, CISDT, etc.

We start with a reference wavefunction, for example the HartreeFock determinant.

HF i 11j 2 2k 3 3

NN NN

HF

i

j

k

are not occupied in the reference state (virtual orbitals).

2 replacements, triples (T) indicate 3 replacements, etc., leading

to CIS, CISD, CISDT, etc.

ia aa 11j 2 2k 3 3

NN NN , ,

i

a

j

k

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ijababa 11b 2 2k 3 3

NN NN , ,

ij

a

b

k

etc.

etc.

38

Truncated

Configuration Interaction

Number of linear variational parameters

in truncated CI for n = 10 and 2N = 40.

Levelof

excitation

Numberof

parameters

Example

CIS

n(2Nn)

300

CISD

+[n(2Nn)]2

78,600

CISDT

+[n(2Nn)]3

18106

FullCI

2N

n

109

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39

Multi-Configuration

Self-Consistent Field (MCSCF)

The MCSCF wavefunctions consists of a few selected determinants or CSFs. In the

MCSCF method, not only the linear weights of the determinants are variationally

optimized, but also the orbital coefficients.

prescribed active orbitals (complete active space, CAS). This is the CASSCF method.

The CASSCF wavefunction contains all determinants that can be constructed from a

given set of orbitals with the constraint that some specified pairs of - and -spinorbitals must occur in all determinants (these are the inactive doubly occupied

spatial orbitals).

the individual CSFs or determinants of the MCSCF (or CASSCF) reference wave

function.

Internally-contracted MRCI:

MR - CISD (ck C1k C 2 k ) k

k

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k

40

Coupled-Cluster Theory

System of equations is solved iteratively (the convergence is

the iterative subspace, DIIS).

CCSD(T), CCSD[T], CCSD-T.

orbitals that are optimized such that singles dont contribute.

(e.g., QCISD) is obtained.

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41

Mller-Plesset Perturbation

Theory

The Hartree-Fock function is an eigenfunction of the

n-electron operator

F.

Hamiltonian into two parts:

HHHH 0 0 HH11

HH 0 0 FF

HH11 HHFF

number denotes order to which

energy is computed (2n+1 rule)

(e.g., MR-PT, CASPT2, CASPT3, )

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42

Semi-Empirical Methods

These methods are derived from the HarteeFock model, that is, they

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They only consider the valence electrons.

A minimal basis set is used for the valence shell.

Integrals are restricted to one- and two-center integrals and

subsequently parametrized by adjusting the computed results to

experimental data.

Very efficient computational tools, which can yield fast quantitative

estimates for a number of properties. Can be used for establishing

trends in classes of related molecules, and for scanning a

computational poblem before proceeding with high-level treatments.

A not of elements, especially transition metals, have not be

parametrized

43

Semi-Empirical Methods

Number 2-electron integrals () is n4/8, n = number of basis functions

Treat only valence electrons explicit

Neglect large number of 2-electron integrals

Replace others by empirical parameters

Models:

Complete Neglect of Differential Overlap (CNDO)

Intermediate Neglect of Differential Overlap (INDO/MINDO)

Neglect of Diatomic Differential Overlap (NDDO/MNDO, AM1, PM3)

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44

Approximations of 1-e

integrals

H

U

H

VVABAB

U

Vvalue per atom pair

BBAA

H

H 00

H

ABSS

H

AB

11 A B

AB

AB

B

22 A

One parameter per element

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45

Popular DFT

Noble prize in Chemistry, 1998

In 1999, 3 of top 5 most cited journal

articles in chemistry (1st, 2nd, & 4th)

articles in chemistry

journal articles in chemistry:

functional (1993)

3rd, Beckes exchange functional

(1988)

Citations of DFT on JCP, JACS and PRL

http://www.cas.org/spotlight/bchem.html

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46

First speculated 1920

Thomas-Fermi (kinetic energy) and Dirac

(exchange energy) formulas

Becoming popular later 1990

Pinnacled in 1998 with a chemistry Nobel

prize

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47

GGA, ~3-5 kcal/mol error in energy

G2/G3 level, some systems, ~1kcal/mol

Good at structure, spectra, & other

properties predictions

excited states, etc.

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48

Two Hohenberg-Kohn theorems:

Given the external potential, we know the

know the electron density .

Energy

Energy E

The energy density functional is variational.

E E 0 if 0

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49

E[] = TS[] + Vne[] + J[] + Vnn[] +

Exc[]

The Coulombic interactions are easy to compute:

E nn [ ]

nuclei

A B

Z AZ B

, E ne [ ] r Vext r dr, J [ ]

rAB

1

2

r r

r r drdr ,

But what about the kinetic energy TS[] and exchange-correlation energy

Exc[]?

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50

Kohn-Sham Scheme

H nk nk nk ,

exact density.

generates

this

exact

density

(=

Slater

determinant of system of

N

non-interacting

electrons

with

same

density ).

exactly from a Slater

determinant.

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unknown is to calculate

where

H K Vne (r ) Vee ( r ) Vxc (r )

and

K

1 2

,

2

The Only

, Unknown

Za

a | r Ra |

(r ) 3

Vee (r )

d r,

| r r |

E xc

Vxc ( r )

,

Vne (r )

( r ) f nk | nk (r ) |2 ,

nk

51

Energy Density Functional

Q f r, r , r , dr

2

XC

only

and |(r)|

function of ts(r), kinetic

energy density

Hartree-Fock exchange energy

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according to the vision of John Perdew with indication of

some of the most common DFT functionals within each rung.

52

LDA Functionals

Thomas-Fermi formula (Kinetic) 1

parameter

TTF C F

5/3

3

r dr, CF 3 2

10

2/3

E CX

S

X

4/3

3 1/ 3 2 / 3 1/ 3

r dr , C X 3 4

8

r

W

EC a

dr

1 / 3

1 b r

its.unc.edu

53

Two most well-known functionals are the Becke exchange functional

Ex[] with 2 extra parameters &

2

2

B

LDA

4/3

EX EX

,

1 2

4/3

EcLYP a

1

1 2

1

2 / 3

5/3

2

t

W

W

F

1 d 1/ 3

9

18

c

e

1 / 3

dr

The B3LYP functional is augmented with 20% of Hartree-Fock

exchange:

E

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B3LYP

xc

aE E

B

x

LYP

c

m , n 1

k ,l 1

b Pmn Pkl km nl

54

VWN5

BLYP

HCTH

BP86

TPSS

M06-L

B3LYP

B97/2

MPW1K

MPWB1K

M06

its.unc.edu

Density Functionals

LDA

local density

GGA

gradient corrected

Meta-GGA

kinetic energy density

included

Hybrid

exact HF exchange

component

Hybrid-meta-GGA

system size

Allow density fitting for

even

better scaling

Meta-GGA is bleeding

edge and therefore

largely untested (but

better in theory)

Hybrid makes bigger

difference in cost and

accuracy

Look at literature if

somebody

has compared

functionals for

systems similar to

yours!

55

Density Functionals

journal titles and abstracts, analyzed from the ISI Web of Science (2007).

its.unc.edu

S.F. Sousa, P.A. Fernandes and M.J. Ramos, J. Phys. Chem. A 10.1021/jp0734474 S1089-5639(07)03447-0 56

ground-state theory only

universal functional still unknown

even hydrogen atom a problem: self-interaction

correction

GGA, etc.

proven exact in theory, is not trivial in implementation

and still far from being generally accessible thus far

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57

DFT Developments

Theoretical

Extensions to excited states, etc.

Better functionals (mega-GGA), etc

Understanding functional properties, etc.

Conceptual

More concepts proposed, like electrophilicity, philicity, spin

Dynamic behaviors, profiles, etc.

Computational

Linear scaling methods

QM/MM related issues

Applications

its.unc.edu

58

its.unc.edu

59

Chemical reactivity theory quantifies the reactive propensity of

isolated species through the introduction of a set of reactivity indices

or descriptors. Its roots go deep into the history of chemistry, as far

back as the introduction of such fundamental concepts as acid, base,

Lewis acid, Lewis base, etc. It pervades almost all of chemistry.

-- Morrel H. Cohen, and Adam Wasserman, J. Phys. Chem. A 2007, 111,2229

Woodward-Hoffman rules

Well developed: Nobel prize in Chemistry, 1981

Problem: conceptual simplicity disappears as computational

accuracy increases because its based on the molecular orbital

description

Density Functional Theory (DFT)

Conceptual DFT, also called Chemical DFT, DF Reactivity Theory

Proposed by Robert G. Parr of UNC-CH, 1980s

Still in development

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60

General Consideration

E E [N, (r)] E []

Taylor Expansion: Perturbation resulted from an

(r), N and (r),

E E N N , r r E N , r

E

N

N

2!

r dr

N

N 2

N 2

N

2E

N r dr

2E

2 r

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61

Conceptual DFT

Basic assumptions

E E [N, (r)] E []

Chemical processes, responses, and changes

expressible via Taylor expansion

of the partial derivatives

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62

Electronegativity (chemical potential)

Hardness / Softness

HOMO LUMO

1 2E

LUMO HOMO

, S 1 /

Maximum Hardness

(MHP)

2Principle

2 N

2

HSAB (hard and Soft Acid and Base) Principle

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63

Fukui

function

f r

Nucleophilic attack

f r N 1 r N r

Electrophilic attack

r N r N 1 r

f r f r

f r

2

its.unc.edu

64

Electrophilicity Index

2

2

Physical meaning: suppose an electrophile is immersed in an

electron sea

1

E N N 2

2

The maximal electron flow and accompanying energy decrease

are

N max

E min

its.unc.edu

65

Prez, P. J. Org. Chem. 2003, 68, 5886. Prez, P.; Aizman, A.; Contreras, R. J. Phys. Chem. A 2002, 106, 3964.

its.unc.edu

66

Analogous to the maximum hardness principle (MHP)

Separately proposed by Noorizadeh and Chattaraj

Concluded that the natural direction of a chemical reaction is

toward a state of minimum electrophilicity.

Noorizadeh, S. J. Phys. Org. Chem. 2007, 20, 514.

Chattaraj, P.K. Ind. J. Phys. Proc. Ind. Natl. Sci. Acad. Part A 2007, 81, 871.

non-

-0.093

-0.093

LA

Aa

-0.091

0.085

Bb

-0.089

-0.172

-0.088

-0.089

-0.171

0.246

-0.083

-0.090

-0.087

-0.0842

0.087

-0.230

-0.220

0.247

Bb

-0.087

0.088

0.084

Aa

0.0892

-0.226

-0.2518

0.218

-0.247

-0.233

0.221

0.2161

-0.226

-0.2506

0.2157

its.unc.edu

67

Yue

Xia, Dulin Yin, Chunying Rong, Qiong Xu, Donghong Yin , and Shubin Liu, J. Phys. Chem. A, 2008, 112, 9970.

Nucleophilicity

Much harder to quantify, because it related to local

hardness, which is ambiguous in definition.

universal scale of nucleophilicity for an nucleophile.

1 B

A

2 A B

= -N - S()2

Minimizing in Eq. (14) with respect to ,

one has

=-N and = - N2.

Making use of the following relation

A B

A B

Jaramillo, P.; Perez, P.; Contreras, R.; Tiznado, W.; Fuentealba, P. J. Phys. Chem. A 2006, 110, 8181.

its.unc.edu

68

Philicity: defined as f(r)

Still a very controversial concept, see JPCA 108, 4934(2004);

Chattaraj, et al. JPCA, in press.

5353(2002)

( )2

E n A

2

( )2

Ee I

2

Ayers, P.W.; Anderson, J.S.M.; Rodriguez, J.I.; Jawed, Z. Phys. Chem. Chem. Phys. 2005, 7,

1918.

Ayers, P.W.; Anderson, J S.M.; Bartolotti, L.J. Int. J. Quantum Chem. 2005, 101, 520.

its.unc.edu

69

Dual Descriptors

3rd-order cross-term derivatives

2

f r

2 N r

f 2 r dr 0

f 2 r f

2 E

r 2 N

r f r

f r

f 2 r LUMO r HOMO r

its.unc.edu

Ayers, P.W.; Morell, C., De Proft, D.; Geerlings, P. Chem. Eur. J., 2007, 13, 8240

70

Geerling, P. De Proft F. Phys. Chem. Chem. Phys., 2008, 10, 3028

Steric Effect

one of the most widely used concepts

in chemistry

atom in a molecule

electron exchange correlation

energy pressure

its.unc.edu

71

Assume

since

Ee[] = Vne[] + J[] + Vnn[]

Eq[] = Exc[] + EPauli[] = Exc[] + Ts[] - Tw[]

Es[] E[] - Ee[] - Eq[] = Tw[]

we have

1

TW

8

dr

S.B. Liu and N. Govind, J. Phys. Chem. A 2008, 112, 6690.

S.B. Liu, N. Govind, and L.G. Pedersen, J. Chem. Phys. 2008, 129, 094104.

M. Torrent-Sucarrat, S.B. Liu and F. De Proft, J. Phys. Chem. A 2009, 113, 3698.

its.unc.edu

72

In 1956, Taft constructed a scale for the steric effect of different substituents, based

on rate constants for the acid-catalyzed hydrolysis of esters in aqueous acetone. It

was shown that log(k / k0) was insensitive to polar effects and thus, in the absence

of resonance interactions, this value can be considered as being proportional to

steric effects. Hydrogen is taken to have a reference value of EsTaft= 0

its.unc.edu

73

QM/MM Example:

Triosephosphate Isomerase (TIM)

DHAP

H2O

GAP

494 Residues, 4033 Atoms, PDB ID: 7TIM

Function: DHAP (dihydroxyacetone phosphate) GAP (glyceraldehyde 3-phosphate)

its.unc.edu

74

DHAP

GAP

its.unc.edu

75

Mechanism

QM Size: 37 atoms

QM: Gaussian98

Method: HF/3-21G

MM: Tinker

Force field: AMBER all-atom

Number of Water: 591 Model for Water: TIP3P

MD details: 20x20x20 3 box, optimize until the RMS energy

gradient less than 1.0 kcal/mol/. 20 psec MD. Time step 2fs.

SHAKE, 300 K, short range cutoff 8 , long range cutoff 15 .

its.unc.edu

76

=====================

Energy Barrier (kcal/mol)

-----------------------------------QM/MM

21.9

Experiment

14.0

=====================

its.unc.edu

77

O(N) Method

Numerical Bottlenecks:

diagonalization ~N3

orthonormalization ~N3

matrix element evaluation ~N2-N4

100

90

80

Theoretical Basis: near-sightedness of density

70

matrix or orbitals

Strategy:

CPUsecondsper CGstep

60

Diagonalization

50

40

30

matrix

gradient

OLMO

NOLMO

20

10

0

methods

100

200

300

400

500

600

700

800

900

Atoms

its.unc.edu

78

What Else ?

Solvent effect

its.unc.edu

Relativity effect

Transition state

Excited states

Temperature and pressure

Solid states (periodic boundary condition)

Dynamics (time-dependent)

79

of ab initio quantum

chemistry

its.unc.edu

80

Popular QM codes

Gaussian (Ab Initio, Semi-empirical, DFT)

Gamess-US/UK

Spartan

MOPAC/2000

(Semi-Empirical)

DMol3/CASTEP

(DFT)

Molpro

(Ab initio)

ADF (DFT)

ORCA

its.unc.edu

(DFT)

81

Reference Books

Grant and W. G. Richards (Oxford University Press)

(Addison Wesley Longman)

Essentials of Computational Chemistry Theories and Models,

C. J. Cramer (Wiley)

Foresman and A. Frisch (Gaussian Inc.)

its.unc.edu

82

Please

Pleasedirect

directcomments/questions

comments/questionsabout

aboutresearch

researchcomputing

computingtoto

E-mail:

E-mail:research@unc.edu

research@unc.edu

Please

Pleasedirect

directcomments/questions

comments/questionspertaining

pertainingtotothis

thispresentation

presentationtoto

E-Mail:

E-Mail:shubin@email.unc.edu

shubin@email.unc.edu

http://its2.unc.edu/divisions/rc/training/scientific/

/afs/isis/depts/its/public_html/divisions/rc/training/scientific/short_courses/

its.unc.edu

83

Hands-on: Part I

Purpose: to get to know the available ab

initio and semi-empirical methods in the

Gaussian 03 / GaussView package

ab initio methods

Hartree-Fock

MP2

CCSD

Semiempirical methods

AM1

The WORD .doc format of this hands-on exercises is available here:

http://its2.unc.edu/divisions/rc/training/scientific/

/afs/isis/depts/its/public_html/divisions/rc/training/scientific/short_courses/labDirections_compchem_2009.doc

its.unc.edu

84

Hands-on: Part II

Purpose: To use LDA and GGA DFT methods to

calculate IR/Raman spectra in vacuum and in

solvent. To build QM/MM models and then use

DFT methods to calculate IR/Raman spectra

DFT

LDA (SVWN)

GGA (B3LYP)

QM/MM

its.unc.edu

85

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