Mass Spectroscopy

How to predict the

the chemical
structure from
fragment ions ?
2
 Signals of Isotopic Elements
Isotope Natural Isotope Relative Isotope Natural
abundance abundance abundance
(%) (%) (%)
12
C 100 13
C 1.11

H
1
100 H
2
0.016
16
O 100 17
O 0.04 O
18
0.20
14
N 100 15
N 0.38
35
Cl 100 37
Cl 32.7
79
Br 100 81
Br 98

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 Unit-Molecular Ion and Isotopic Peaks
% (M+1)  1.1 x no. of C atoms + 0.36 x no. of N atoms

% (M+2)  (1.1 x no. of C atoms)2/200 + 0.20 x no. of O atoms

e.g., C7H7NO
Molecular weight = 7x12C + 7x1H + 1x14N = 1x16O = 121
% (M + 1) ≈ 8
% (M + 2) ≈ 0.5

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 Molecular Ion (m/z) = 121

e.g., C7H7NO
Molecular weight = 7x12C + 7x1H + 1x14N = 1x16O = 121
% (M + 1) ≈ 8
% (M + 2) ≈ 0.5 5
Nature of Carbon Signals (M+1)

Isotopic Carbon Signals (M+1)

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Nature of Chlorine Signals

Isotopic Chlorine Signals (M+2)

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Nature of Bromine Signals

Isotopic Bromine Signals (M+2)

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How would you know the number of carbon
atoms?

Relative intensity of M + 1 peak

Number of C atoms =
0.011 x (Relative intensity of M peak)

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High Resolution Mass Spectrometry

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 Mass Fragmentation by EI

• Relative height of molecular ion peak (↑) for a straight chain

compound
• Relative height of molecular ion peak (↓) for the degree of
branching increases.
• Relative height of molecular ion peak (↓) Vs. Molecular weight
(↑) (Exception of fatty ester).
• Cleavage is favoured as the alkyl-substituted C atoms; the more
substituted, the more likely is cleavage.

Stability order: CH3+ < R’CH2+ < R’2CH+ < R’3C+

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• Double bonds, cyclic structures and aromatic
(heteroaromatic) rings stabilizes the molecular ion
and thus increase the probability of its appearance.
• Double bonds favour allylic cleavage and give the
resonance-stabilized allylic carbocations (does not
hold for simple alkenes, does hold for cycloalkenes)

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Very stable ions

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 Mass Fragmentation Process

Most abundant ion (100 %) or Base peak

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Fragmentation of Hydrocarbon Compounds
e.g., (1) n-pentane

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e.g., Fragmentation of n-pentane

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 + -H + -H
CH3CH2CH2 [CH3CHCH2] CH2CH=CH2
m/z = 43 m/z = 42 m/z = 41

Peaks are commonly observed at m/z values one

and two units less than the m/z values of the
carbocation.

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Fragmentation of Hydrocarbon Compounds
e.g., (2) 2-methylbutane

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2-methylbutane is more likely than n-pentane to
form more stable the sec-carbocation.
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 Fragmentation of Functional Groups
e.g., n-propylbromide

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Fragmentation of n-propylbromide

79 81
CH3CH2CH2 Br + CH3CH2CH2 81Br
79
CH3CH2CH2 Br + CH3CH2CH2 Br

1-bromopropane m/z = 122 m/z = 124

79 81
CH3CH2CH2 + Br + Br
m/z= 43

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e.g., iso-propylchloride

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e.g., Fragmentation of iso-propylchloride

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Fragmentation of Ester Compounds
e.g., Ethylbenzoate

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e.g., Ethylbenzoate

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Fragmentation of Ether Compounds

1. Electron bombardment → one of the lone-pair electrons from oxygen.

R– Ọ+ – R’

2. Two principal ways from molecular ion:

a. C - O bond is cleaved heterolytically

b. C - C bond is cleaved homolytically at α C

- Stable cation with shared by C and O atom

- Most stable radical (at alkyl group)

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Fragmentation of Ether Compounds
e.g., sec-butyl isopropyl ether

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Fragmentation of stable ion peak (Base peak)

1. Electron bombardment → one of the lone-pair electrons from oxygen.

C - O bond is cleaved heterolytically

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Homolytical Cleavage at α position
C - C bond is cleaved homolytically at α C
- Stable cation with shared by C and O atom
- Most stable radical (at alkyl group)

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 Please Quiz!
1-methoxybutane, CH3-CH2-CH2-CH2-OCH3 (OR) 2-methoxybutane, CH3-
CH(OCH3)CH2-CH3 (OR) 12-methoxy-2-methylpropane, (CH3)3C-OCH3
QUIZ!
1-methoxybutane, CH3-CH2-CH2-CH2-OCH3 (OR) 22-methoxybutane, CH3-
CH(OCH3)CH2-CH3 (OR) 2-methoxy-2-methylpropane, (CH3)3C-OCH3
QUIZ!
1-methoxybutane, 3CH3-CH2-CH2-CH2-OCH3 (OR) 2-methoxybutane, CH3-
CH(OCH3)CH2-CH3 (OR) 2-methoxy-2-methylpropane, (CH3)3C-OCH3
QUIZ!
1-methoxybutane, CH3-CH2-CH2-CH2-OCH3

Fragmentation patterns

C - O Cleavage
CH3-CH2-CH2-CH2 + O-CH3
m/z= 57
CH3-CH2-CH2-CH2-O-CH3
m/z = 88
CH3-CH2-CH2-CH2-O + CH3
m/z=15

C - C Cleavage

CH3-CH2-CH2-CH2-O-CH3 CH3-CH2-CH2 + CH2=O-CH3

m/z = 45
m/z = 88
QUIZ!
2-methoxybutane, CH3-CH(OCH3)CH2-CH3

C - O Cleavage
CH3-CH2-CH-CH3 + O - CH3
CH3 m/z= 57
CH3-CH2-CH- O - CH3 CH3
CH3 - CH2 - CH- O + CH3
m/z = 88 m/z=15

C - C Cleavage
CH3 - CH = O - CH3 + CH2- CH3
CH3
m/z = 59
CH3-CH2-CH- O - CH3
CH3 - CH2 - CH = O - CH3 + CH3
m/z = 88 m/z = 73
QUIZ!
2-methoxy-2-methylpropane, (CH3)3C-OCH3
C - O Cleavage CH3

CH3 - C + O - CH3
CH3
CH3
CH3 - C - O - CH3 m/z= 57
CH3
CH3

m/z = 88 CH3 + O - C - CH3

m/z=15
CH3

C - C Cleavage
CH3

CH3 - C - O - CH3 CH3 - C = O - CH3 + CH3

CH3 CH3
m/z = 88 m/z = 73
2-methoxy-2-methylpropane, (CH3)3C-OCH3

C - O Cleavage CH3

CH3 - C + O - CH3
CH3
CH3
CH3 - C - O - CH3 m/z= 57
CH3
CH3

m/z = 88 CH3 + O - C - CH3

m/z=15
CH3

C - C Cleavage
CH3

CH3 - C - O - CH3 CH3 - C = O - CH3 + CH3

CH3 CH3
m/z = 88 m/z = 73
 QUIZ!
2-methoxybutane, CH3-CH(OCH3)CH2-CH3

C - O Cleavage
CH3-CH2-CH-CH3 + O - CH3
CH3 m/z= 57
CH3-CH2-CH- O - CH3 CH3
CH3 - CH2 - CH- O + CH3
m/z = 88 m/z=15

C - C Cleavage
CH3 - CH = O - CH3 + CH2- CH3
CH3
m/z = 59
CH3-CH2-CH- O - CH3
CH3 - CH2 - CH = O - CH3 + CH3
m/z = 88 m/z = 73
QUIZ!
1-methoxybutane, CH3-CH2-CH2-CH2-OCH3

C - O Cleavage
CH3-CH2-CH2-CH2 + O-CH3
m/z= 57
CH3-CH2-CH2-CH2-O-CH3
m/z = 88
CH3-CH2-CH2-CH2-O + CH3
m/z=15

C - C Cleavage

CH3-CH2-CH2-CH2-O-CH3 CH3-CH2-CH2 + CH2=O-CH3

m/z = 45
m/z = 88
Fragmentation of Alcohol Compounds
e.g., 2-hexanol

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α- cleavage of –OH group

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 Important fragmentation occurs in alcohols.

H OH

CH3CH2CH CH2CHCH3 CH3CH2CHCH2CHCH3 + H2O

  
m/z = (102 - 18) = 84

Formation of H2O molecule from –OH group of

alcohol and γ-hydrogen

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The fragmentations of alkyl halides, ethers, and
alcohols

1. C – X or C - O bond (Heterolytic cleavage)

2. C – C or C - H bond (Heterolytic cleavage)

3. To break the weakest bonds and the formation of the most

stable cation.
*Primary alcohols have a strong peak at m/z 31.
Fragmentation of Ketone Compounds
e.g., 2-pentanone

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Homolytically cleavage at the C - C bond
adjacent to the C = O bond

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 McLafferty rearrangement

Homolytically cleavage between α-C and β-C atom; and H

atom from γ- C migrates to O atom.
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Fragmentation of Ketone Compounds
e.g., 1,3-diphenylpropanone

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e.g., 1,3-diphenylpropanone

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Fragmentation of Ether or Alcohol Compounds

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e.g., t-butyl ethyl ether

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How could their mass spectra distinguish the following compounds?

(1) CH3 - CH2 - C - CH2 - CH3

O
(2) CH3 - C - CH2 - CH2 - CH3

(3) CH3 - C - CH - CH3

CH3
Identify the ketones that are responsible for the mass
spectra shown in Figure 13.9.
 REFERENCES
Bruice P. Y. (1987). “Mass Specrometry”. Organic Chemistry. 4 th
Edition. John Wiley and Sons, Inc., New York
Hoffman R. V. (2004). “Structure Determination of Organic
Compounds”. Organic Chemistry. An Intermediate Text. 2nd
Edition. A John Wiley and Sons. New Jercy
Silverstein R.M. and Webster F.X. (1998). “Spectroscopic
Identification of Organic Compound”, 6th Edition, John Wiley
and Sons, Inc., New York
US.EPA Method 8270 performed withTrace 1310 GC ISQ LT
GC-MS and Two Carrier Gases: He and H2
www.thermoscientific.com/ISQ

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