Identification of

Unknown Compounds

Steps in the Identification of

Unknown

Identify Molecular ion M.+

Determine Molecular Formula (odd / even mass)
Analyze heteroatom (M+1 and M+2 )
S, Si, Cl, Br, .
Use rule of 13 to determine # Carbons (M+1 and
M+2 )
Compare with 13C-NMR (# carbons)
carbons with APT
experiment (J-MOD) ( # protons)
protons
Compare with proton NMR ( # protons)
protons
Identify base peak (note if even / odd)
odd
One or two bond fragmentation
Test your conclusions: in lab make derivatives (TMS
or Na or K complexes mass shift)
2

Solving problems in MS
Try to identify the Molecular Ion or decide if it is
present (most critical step in solving a structure)
Check if [M+1]+ ion is too large to accommodate reasonable
number of carbons. (the [M+1]+ ion might be the very small M+
instead!)
Determine the first loss from proposed molecular ion. Some
loss are impossible (e.g 12, 14, 23 daltons)
Does the spectrum appear dirty? (lots of small peaks even at high
mass)
If GC of the comopund Is available, compare retention time

Is the molecular weight even or odd?

An odd mass can be associated with an odd number of Nitrogen
An even mass means no Nitrogen or an even number of Nitrogen
This Rule is applicable only to Molecular ion and to odd-electron ions

Examine ion cluster for isotopic natural abundance

(look for special heteroatom pattern). Try to calculate
number of carbons

Solving problems in MS
From the overall appearance: is it a fragile compound?
Is it likely to be aromatic or aliphatic?
Look in the low mass ions. Do you see any clues of the
family of compounds that you might be dealing with?
Make a list of suggested losses from the molecular ion
and try to make a pattellsrn from them.
Look for intense odd-electron ions in the spectrum: this is
almost impossible in compounds containing Nitrogen!
These provides clues for rearrangements (retro Diels
Alder, McLafferty)
Speculate on the structure using all that information
Index of Hydrogen deficiency/Degree of Unsaturation (DU)
CxHyNzOn

Index = x y + z +1
4

Nitrogen rule
M+ even even # of N
M+ odd odd # of N

0, 2, 4,
1, 3, 5,

Index of Hydrogen deficiency

Index = C H/2 X/2 + N/2 + 1
e.g. C7H7NO Index = 7 - 3.5 + 0.5 + 1 = 5
Hydrogen deficiency can be unsaturation (multiple bonds)
or cyclic structure

R-CN
I=2
I=2 (1 DB + cycle)

I=4 (3 DB + cycle)
5

Neutral losses and Ion series

M-1

M-15

CH3

M-16

O (rare) , NH2

M-17

OH , NH3 (rare)

M-18

H2O

M-19

M-20
M-26

HF (very rare)

M-30

NO (Nitro compounds),
H2 CO (anisoles)

M-31

CH3O

M-32

CH3OH

M-35

Cl

M-36

HCl

M-42

CH2=C=O, CH2=CH-CH3

M-43

CH3CO , C3H7

M-44

CO2

M-45

CH3CH2O , CO2H

HCCH , CN

M-27

HCN

M-28

H2C=CH2 , CO

M-29

CH3CH2 , HCO

Neutral losses and Ion series

Figuring out which peak is molecular ion can be supported by identifying
what fragment is lost.
There can be sometimes 2 consecutive loss:
In steroid, M-33 is often observed: comes from the loss of Me and H2O

The ions loss are only useful from molecular ion

There is no fragment in organic compounds between M-1 and M-15
Loss of M-14 is never observed!
Other gaps in mass loss are: between 21-25,
21-25 33-34,
33-34 37-41
Ions in these areas should be viewed suspiciously:
suspiciously either compound is not
pure or postulated molecular ion is wrong
7

Neutral losses and Ion series

Among the losses: most common are
Loss of H, CH3 , H2O (from some oxygenated compounds),
HCCH (from aromatic compounds),
HCN (from aromatic compounds containing Nitrogen),
CO and CH2=CH2 (both at 28! Difficult to tell which one is lost)
Ethyl radical (29)
Methoxy radical (31)
Cl and HCl (35, 36)
Acetyl (43) accompanied by m/z 43 prominent and propyl (43) radical

Neutral losses and Ion series

Among the losses: most common are
Loss of H, CH3 , H2O (from some oxygenated compounds),
HCCH (from aromatic compounds),
HCN (from aromatic compounds containing Nitrogen),
CO and CH2=CH2 (both at 28! Difficult to tell which one is lost)
Ethyl radical (29)
Methoxy radical (31)
Cl and HCl (35, 36)
Acetyl (43) accompanied by m/z 43 prominent and propyl (43) radical

SPECTROSCOPY IS A POWERFUL TOOL

Generally, with only three pieces of data
1) empirical formula (or % composition)
2) infrared spectrum
3) NMR spectrum
a chemist can often figure out the complete
structure of an unknown molecule.

10

EACH TECHNIQUE YIELDS VALUABLE DATA

FORMULA

Gives the relative numbers of C and H

and other atoms
INFRARED SPECTRUM

Reveals the types of bonds that are present.

NMR SPECTRUM

Reveals the enviroment of each hydrogen

and the relative numbers of each type.
11

Typical Infrared Absorption

Regions
C-Cl

WAVELENGTH (m)
2.5

O-H

C-H

6.1

C=O

C N

N-H

5.5

C C
X=C=Y

Very
few
bands

(C,O,N,S)
4000

2500

2000

6.5

15.4

C-Cl
C-O
C=C
C-N
C-C
N=O N=O *
C=N

1800 1650

1550

650

FREQUENCY (cm-1)
12

How to Use an Infrared Spectrum

1)

2)

Molecular formula:
calculate index of hydrogen deficiency
Check for carbonyl:
note any shift from 1715 cm-1

3)

Check for O-H, N-H

4)

Check for triple bonds

5)

Check for C=C, benzene rings

13

How to Use an Infrared Spectrum

CONTINUED

6)

-1
Look below 1550 cmcheck
;
for C-O and
nitro

7)

Go back over spectrum for refinements;

check the C-H region for aldehydes
and for peaks above 3000 cm-1
(alkenes and terminal alkynes)
14

THE MINIMUM YOU NEED TO KNOW

BASE VALUES

OH
NH
CH

3600
3400

EXPANDED CH

3000
3300 3100 2900
C-H

=C-H

-C-H

2850
2750
-CHO

3000
CH2 and CH3 bend :

1465 and 1365

C N 2250
C C 2150

1800 1735 1725 1715 1710 1690

C=O 1715

acid
chloride

C=C 1650

anhydride :

C-O

benzene C=C : between

1100

aldehyde
acid
ester
ketone

amide

1810 and 1760

EXPANDED C=O

1400 and 1600

15
Know also the effects of H-bonding, conjugation and ring size.

YES

C=O present ?

YES

NO

YES

anhydride

2 C=O Peaks

OH present ?

alcohol

acid

OH present ?

NH present ?

amine

amide

NH present ?

C-O present ?

ether

ester

C-O present ?

= present ?
C=N

nitrile

aldehyde

CHO present ?

= present ?
C=C

alkyne

C=C present ?
(benzene ?)

alkene

NO2 present ?

nitro cpds

C-X present ?

halides

ketone

NO

aromatic

16

17

NMR Correlation Chart

-OH -NH
DOWNFIELD
DESHIELDED

UPFIELD
SHIELDED

CHCl3 , H

TMS

12

RCOOH

11

10

RCHO

H
C=C

CH2F
CH2Cl
CH2Br
CH2I
CH2O
CH2NO2

CH2Ar
CH2NR2
CH2S
C C-H
C=C-CH2
CH2-CO

(ppm)

C-CH-C
C
C-CH2-C
C-CH3

Ranges can be defined for different general types of protons.

This chart is general, the next slide is more definite.

18

19

200

150

100

50

8 - 30

R-CH3
Saturated carbon - sp3
no electronegativity effects

R-CH2-R

15 - 55

R3CH / R4C

20 - 60
40 - 80

C-O

Saturated carbon - sp3

electronegativity effects

35 - 80

C-Cl
C-Br
C

Unsaturated
carbon - sp2

C=C

25 - 65

Alkyne
carbons - sp

65 - 90
100 - 150

Aromatic ring
carbons
C=O
C=O
200

110 - 175

Acids Amides
Esters Anhydrides
Aldehydes
Ketones
150

100

RANGE

155 - 185
185 - 220
50

Correlation chart for 13C Chemical Shifts (ppm)

0
20

Problem 1: C3H5BrO2, MW = 152

CxHyNzOn
Index (DU) = x y + z
= 3 (5+1)/2 + 1
=1

21

Typical Infrared Absorption

Regions
C-Cl

WAVELENGTH (m)
2.5

O-H

C-H

6.1

C=O

C N

N-H

5.5

C C
X=C=Y

Very
few
bands

(C,O,N,S)
4000

2500

2000

6.5

15.4

C-Cl
C-O
C=C
C-N
C-C
N=O N=O *
C=N

1800 1650

1550

650

FREQUENCY (cm-1)
22

Problem 1: C3H5BrO2, MW = 152

23

NMR Correlation Chart

-OH -NH
DOWNFIELD
DESHIELDED

UPFIELD
SHIELDED

CHCl3 , H

TMS

12

RCOOH

11

10

RCHO

H
C=C

CH2F
CH2Cl
CH2Br
CH2I
CH2O
CH2NO2

CH2Ar
CH2NR2
CH2S
C C-H
C=C-CH2
CH2-CO

(ppm)

C-CH-C
C
C-CH2-C
C-CH3

Ranges can be defined for different general types of protons.

This chart is general, the next slide is more definite.

24

200

150

100

50

8 - 30

R-CH3
Saturated carbon - sp3
no electronegativity effects

R-CH2-R

15 - 55

R3CH / R4C

20 - 60
40 - 80

C-O

Saturated carbon - sp3

electronegativity effects

35 - 80

C-Cl
C-Br
C

Unsaturated
carbon - sp2

C=C

25 - 65

Alkyne
carbons - sp

65 - 90
100 - 150

Aromatic ring
carbons
C=O
C=O
200

110 - 175

Acids Amides
Esters Anhydrides
Aldehydes
Ketones
150

100

RANGE

155 - 185
185 - 220
50

Correlation chart for 13C Chemical Shifts (ppm)

0
25

26

27

28

Problem 2: C8H14O4, MW = 174

CxHyNzOn
Index (DU) = x y + z
= 8 14/2 + 1
=2

29

THE MINIMUM YOU NEED TO KNOW

BASE VALUES

OH
NH
CH

3600
3400

EXPANDED CH

3000
3300 3100 2900
C-H

=C-H

-C-H

2850
2750
-CHO

3000
CH2 and CH3 bend :

1465 and 1365

C N 2250
C C 2150

1800 1735 1725 1715 1710 1690

C=O 1715

acid
chloride

C=C 1650

anhydride :

C-O

benzene C=C : between

1100

aldehyde
acid
ester
ketone

amide

1810 and 1760

EXPANDED C=O

1400 and 1600

30
Know also the effects of H-bonding, conjugation and ring size.

Problem 2: C8H14O4, MW = 174

31

32

Problem 3: C9H12, MW = 120

CxHyNzOn
Index (DU) = x y + z
= 9 12/2 + 1
=4

33

THE MINIMUM YOU NEED TO KNOW

BASE VALUES

OH
NH
CH

3600
3400

EXPANDED CH

3000
3300 3100 2900
C-H

=C-H

-C-H

2850
2750
-CHO

3000
CH2 and CH3 bend :

1465 and 1365

C N 2250
C C 2150

1800 1735 1725 1715 1710 1690

C=O 1715

acid
chloride

C=C 1650

anhydride :

C-O

benzene C=C : between

1100

aldehyde
acid
ester
ketone

amide

1810 and 1760

EXPANDED C=O

1400 and 1600

34
Know also the effects of H-bonding, conjugation and ring size.

Problem 3: C9H12, MW = 120

35

NMR Correlation Chart

-OH -NH
DOWNFIELD
DESHIELDED

UPFIELD
SHIELDED

CHCl3 , H

TMS

12

RCOOH

11

10

RCHO

H
C=C

CH2F
CH2Cl
CH2Br
CH2I
CH2O
CH2NO2

CH2Ar
CH2NR2
CH2S
C C-H
C=C-CH2
CH2-CO

(ppm)

C-CH-C
C
C-CH2-C
C-CH3

Ranges can be defined for different general types of protons.

This chart is general, the next slide is more definite.

36

200

150

100

50

8 - 30

R-CH3
Saturated carbon - sp3
no electronegativity effects

R-CH2-R

15 - 55

R3CH / R4C

20 - 60
40 - 80

C-O

Saturated carbon - sp3

electronegativity effects

35 - 80

C-Cl
C-Br
C

Unsaturated
carbon - sp2

C=C

25 - 65

Alkyne
carbons - sp

65 - 90
100 - 150

Aromatic ring
carbons
C=O
C=O
200

110 - 175

Acids Amides
Esters Anhydrides
Aldehydes
Ketones
150

100

RANGE

155 - 185
185 - 220
50

Correlation chart for 13C Chemical Shifts (ppm)

0
37

38

Problem 4: C7H13Br, MW = 176

CxHyNzOn

Index (DU) = x y + z
= 7 (13+1)/2 + 1
=1

39

THE MINIMUM YOU NEED TO KNOW

BASE VALUES

OH
NH
CH

3600
3400

EXPANDED CH

3000
3300 3100 2900
C-H

=C-H

-C-H

2850
2750
-CHO

3000
CH2 and CH3 bend :

1465 and 1365

C N 2250
C C 2150

1800 1735 1725 1715 1710 1690

C=O 1715

acid
chloride

C=C 1650

anhydride :

C-O

benzene C=C : between

1100

aldehyde
acid
ester
ketone

amide

1810 and 1760

EXPANDED C=O

1400 and 1600

40
Know also the effects of H-bonding, conjugation and ring size.

Problem 4: C7H13Br, MW = 176

41

42

Problem 5: C5H8O, MW = 84
CxHyNzOn
Index (DU) = x y + z
= 5 8/2 + 1
=2

43

THE MINIMUM YOU NEED TO KNOW

BASE VALUES

OH
NH
CH

3600
3400

EXPANDED CH

3000
3300 3100 2900
C-H

=C-H

-C-H

2850
2750
-CHO

3000
CH2 and CH3 bend :

1465 and 1365

C N 2250
C C 2150

1800 1735 1725 1715 1710 1690

C=O 1715

acid
chloride

C=C 1650

anhydride :

C-O

benzene C=C : between

1100

aldehyde
acid
ester
ketone

amide

1810 and 1760

EXPANDED C=O

1400 and 1600

44
Know also the effects of H-bonding, conjugation and ring size.

Problem 5: C5H8O, MW = 84

45

46

Problem 6: C9H13NO, MW = 151

CxHyNzOn

Index (DU) = x y +
= 9 13/2 + 1/2
=4

47

THE MINIMUM YOU NEED TO KNOW

BASE VALUES

OH
NH
CH

3600
3400

EXPANDED CH

3000
3300 3100 2900
C-H

=C-H

-C-H

2850
2750
-CHO

3000
CH2 and CH3 bend :

1465 and 1365

C N 2250
C C 2150

1800 1735 1725 1715 1710 1690

C=O 1715

acid
chloride

C=C 1650

anhydride :

C-O

benzene C=C : between

1100

aldehyde
acid
ester
ketone

amide

1810 and 1760

EXPANDED C=O

1400 and 1600

48
Know also the effects of H-bonding, conjugation and ring size.

Problem 6: C9H13NO, MW = 151

49

50