Organic Spectroscopy

Mass Spectrometry
 General
The mass spectrum is a plot of ion abundance versus m/e ratio (mass/charge ratio).
The most abundant ion formed in the ionization chamber gives to rise the tallest
peak in the mass spectrum, called the base peak.

By using one of the many ionization methods, the simple removal of an electron
from a molecule yields a positively charged radical cation, known as the
molecular ion and symbolized as [M]+.

After formation of molecular Ion in the ionization chamber, excess energy causes
further fragmentation of the molecular ion. Various positively charged masses
(and/or positively charged radical cations) show up in the spectrum.

The mass of the molecular ion can be determined to an accuracy of ± 0.0001 of a

mass unit, which yields a high resolution (hi-res) mass spectrum.

Ionization Methods
The most common method of ionization involves Electron impact (EI) in which
molecule is bombarded with high-energy electrons. This is the strongest ionization
method which usually causes further fragmentation. Since the molecular ion gets
fragmented, the molecular ion usually produces a small peak with this method.
Mass Spectrum of Isobutyrophenone

O 105
(base peak)
C6H5CO+

molecular
weight = 148

77
C6H5+

molecular ion, M M+1

(148)
 Facts Concerning the Molecular Ion Peak

1. The peak must correspond to the ion of highest mass excluding the
usually much smaller isotopic peaks that occur at M+1, M+2, etc.

2. To be a molecular ion, the ion must contain an odd number of electrons.

One electron is lost, forming a radical-cation.

To determine this, calculate the IHD. It must be a whole number.

Consider an ion at m/z = 112. A possible molecular formula is C6H8O2.
The IHD = 3 (a whole number), so this could be the molecular ion.
However, an ion at 105 could correspond to a molecular formula of
C7H5O. The IHD is 5.5 (not a whole number), so this can’t be the
molecular ion.

3. The ion must be capable of producing smaller, fragment ions by loss

of neutral fragments of predictable structure.
 The Lifetimes of Various Molecular Ions
Aromatics > conjugated alkenes > alicyclic compounds> organic sulfides >
unbranched hydrocarbons > mercaptans > ketones > amines > esters >
ethers > carboxylic acids > branched hydrocarbons > alcohols

Therefore, alcohols produce small or non-existent molecular ions because

their lifetimes are too short. They fragment before they can be detected.

CH3CH2CH2CH2OH
MW = 74

No M
visible
 The Nitrogen Rule
The nitrogen rule states that an odd number of nitrogen atoms will form
a molecular ion with an odd mass number. An even number of nitrogen
atoms (or none at all) will produce a molecular ion with an even mass
number. This occurs because nitrogen has an odd-numbered valence.

Examples: C6H5CH2NH2 MW = 107

H2NCH2CH2NH2 MW = 60
 Determining Possible Molecular Formulas
from the Molecular Ion: Rule of 13

• Rule of Thirteen: Based upon the assumption that CnHn

and its mass of 13 is present in most organic compounds.
• Divide the molecular ion by 13. This gives a value for n
and any remainder (R) = additional H’s.
• For a M+ = 106, n = 8(106/13) with a R of 2. A possible
molecular formula for this ion is C8H8+2 = C8H10
• For each CH there are heteroatom equivalents.
Rule of 13 Heteroatom Equivalents
Element CH Element CH
Equivalent Equivalent
1H C 31P C2H7
12
16O CH4 32S C2H8
14N CH2 16O32S C4
16O14N C2H6 35Cl C2H11
19F CH7 79Br C6H7
28Si C2H4 127I C10H7
 Candidate molecular formulas for M+. = 108

108/13 = 8, R = 4  C8H12

O = CH4; therefore, C8H12 – CH4 + O = C7H8O

or C8H12 – 2(CH4) + 2O = C6H4O2

or C8H12 – C6H7 + Br = C2H5Br

Calculate three candidate molecular formulas for C10H18.

When an odd amu M+. is seen, suspect one nitrogen or an odd
multiple. Candidate molecular formulas for a M+. = 121 are:

121/13 = 9, R = 4  C9H13; IHD = 3.5 so it can’t be M+.

O = CH4; N = CH2

or C9H13 – CH2 + N = C8H11N; IHD = 3, so it may be M+.

or C9H13 – 2(CH2) + 2N = C7H9N2; IHD = 4.5 so it can’t be M+.

or C9H13 – 3(CH2) + 3N = C6H7N3; IHD = 5, so it may be M+.

or C9H13 – (CH2) – (CH4) + N + O = C7H7NO IHD = 5,

so it may be M+.
 Determining the Molecular Formula from the
Molecular Ion: Isotope Ratio Data
In this method, the relative intensities of the peaks due to the molecular ion
and related isotopic peaks are examined.
Advantage:
• Does not require an expensive high-res MS instrument.
Disadvantages:
• Isotopic peaks may be difficult to locate.
• Useless when the molecular ion peak is very weak or does not appear.

3-pentanone
 Relative Abundances of Common Elements and Their isotopes

Relative Relative Relative

Element Isotope Abun- Isotope Abun- Isotope Abun-
dance dance dance

Carbon 12C 100 13C 1.08

Hydrogen 1H 100 2H 0.016

Nitrogen 14N 100 15N 0.38

Oxygen 16O 100 17O 0.04 18O 0.20

Sulfur 32S 100 33S 0.78 34S 4.40

Chlorine 35Cl 100 37Cl 32.5

Bromine 79Br 100 81Br 98.0

 Example: 3-pentanone, C5H10O
%(M + 1) = 100 (M + 1)/M = 1.08 x # C atoms + 0.016 x # H atoms + 0.04 x # O atoms
= 1.08 x 5 + 0.016 x 10 + 0.04 x 1= 5.60
Actual spectrum: [1% (M +1)/17.4% (M)] x 100 = 5.75
Relative Intensities of Isotope Peaks for Bromine and Chlorine

Halogen M M+2 M+4 M+6

Br 100 97.7
Br2 100 195.0 95.4
Br3 100 293.0 286.0 93.4
Cl 100 32.6
Cl2 100 65.3 10.6
Cl3 100 97.8 31.9 3.47
BrCl 100 130.0 31.9
Br2Cl 100 228.0 159.0 31.2
Cl2Br 100 163.0 74.4 10.4
 Br

156 158

MW = 156
 236

Br

Br
MW = 234
234 238
 112
Cl

MW = 112

114
 Cl
192
Br
MW = 190
190

194
 Determining the Molecular Formula from
the Molecular Ion: High Resolution MS (HRMS)
Using low resolution (LR) MS, you could not distinguish between the following
molecular formulas, each of which has a mass of 60:

C3H8O = (3 x 12) + (8 x 1) + 16 = 60

C2H8N2 = (2 x 12) + (8 x 1) + (2 x 14) = 60

C2H4O2 = (2 x 12) + (4 x 1) + (2 x 16) = 60

CH4N2O = 12 + (4 x 1) + (2 x 14) + 16 = 60

However, they can be distinguished using HRMS.

Precise Masses of Some Common Elements
Element Atomic Weight Isotope Mass
Hydrogen 1.0097 1H 1.00783
2H 2.01410
Carbon 12.01115 12C 12.0000
13C 13.00336
Nitrogen 14.0067 14N 14.0031
15N
Using precise masses:
15.0001
Oxygen 15.9994 16O 15.9949
C3H8O = 60.05754
17O 16.9991
18O 17.9992
C2H8N2 = 60.06884
Fluorine 18.9984 19F 18.9984
Silicon 28.086 28Si 27.9769
C2H4O2 = 60.02112
29Si 28.9765
30Si 29.9738
CH4N2O = 60.03242
Phosphorus 30.974 31P 30.9738
Sulfur 32.064 32S 31.9721
33S 32.9715
34S 33.9679
Chlorine 35.453 35Cl 34.9689
37Cl 36.9659
Bromine 79.909 79Br 78.9183
81Br 80.9163
Iodine 126.904 127I 126.9045
 Fragmentation Patterns
Most common: one-bond cleavage to produce an odd-electron neutral fragment,
(radical, which is not detected) and an even-electron carbocation. Ease of frag-
mentation to form cations follows the scheme below:

CH3+ < RCH2+ < R2CH+ < R3C+ < CH2=CH-CH2+ < C6H5-CH2+
Difficult Easy

Radical (not detected)

 Fragmentation Patterns (cont.)
Two-bond cleavage: The odd-electron molecular ion produces an odd-electron
fragment ion and an even-electron neutral fragment (not detected).

Not detected

McLafferty Rearrangement

+ +
H R
O R O H
+
H3C O H3C O
 71
CH3
H3C C CH2CH3 MW = 86
Cleavage at branch points
CH3

57

57

71
-cleavage to hetero atoms 87 43 MW = 102
H3C O CH3

CH3 CH3
cleavage  to hetero atoms

CH3-CH=OH+

43 87
 91

-cleavage to aromatic ring MW = 134

91

92 (from McLafferty
Rearrangement)

CH2
 43

Cleavage  to carbonyl groups O

MW = 86
H3C CH3

43
 60
O
McLafferty rearrangement
OH
carboxylic acids

OH
60
CH2 C OH
 74
McLafferty rearrangement O
esters MW = 102
CH3
O

OH
CH2 C OCH3

74
 Hexane
C6H14
MW = 86.18
Molecular ion peaks are present, possibly with low intensity.
The fragmentation pattern contains clusters of peaks 14 mass
units apart (which represent loss of (CH2)nCH3).
 3-Pentanol
C5H12O
MW = 88.15

An alcohol's molecular ion is small or non-existent.

Cleavage of the C-C bond next to the oxygen usually
occurs. A loss of H2O may occur as in the spectrum below.
 3-Phenyl-2-propenal
C9H8O
MW = 132.16

Cleavage of bonds next to the carboxyl group

results in the loss of hydrogen (molecular ion less 1)
or the loss of CHO (molecular ion less 29).
 3-Methylbutyramide
C5H11NO
MW = 101.15

Primary amides show a base peak

due to the McLafferty rearrangement.
 n-Butylamine
C4H11N
MW = 73.13
Molecular ion peak is an odd number.
Alpha-cleavage dominates aliphatic amines.
n-Methylbenzylamine
C8H11N
MW = 121.18
Another example is a secondary amine shown below.
Again, the molecular ion peak is an odd number.
The base peak is from the C-C cleavage adjacent to the C-N bond.
 Naphthalene
C10H8
MW = 128.17
Molecular ion peaks are strong due to the stable structure.
 2-Butenoic acid
C4H6O2
MW = 86.09
In short chain acids, peaks due to the loss of OH
(molecular ion less 17) and COOH (molecular ion less 45)
are prominent due to cleavage of bonds next to C=O.
Fragments appear due to bond cleavage next to C=O
(alkoxy group loss, -OR) and hydrogen rearrangements.

Ethyl acetate
C4H8O2
MW = 88.11
 Ethyl methyl ether
C3H8O
MW = 60.10

Fragmentation tends to occur alpha to the

oxygen atom (C-C bond next to the oxygen).
 1-Bromopropane
C3H7Br
MW = 123.00

The presence of chlorine or bromine atoms is

usually recognizable from isotopic peaks.
 4-Heptanone
C7H14O
MW = 114.19

Major fragmentation peaks result from cleavage

of the C-C bonds adjacent to the carbonyl.
 Which structure supports the following mass spectrum?

MW = 100 MW = 100 MW = 114

MW = 100 MW = 86
 Which structure supports the following mass spectrum?
NH2 NH2
NH
MW = 101 MW = 87 MW = 87

NH2

NH2

MW = 87 MW = 73
Which structure supports the following mass spectrum?

O O O

O O O
MW = 116 MW = 130 MW = 116
O
O
O
O
MW = 116 MW = 102
An unknown compound has the mass spectrum shown below. The IR spectrum
shows peaks in the 3100-3030 and the 2979-2879 cm-1 ranges and a strong
absorption at 1688 cm-1. Suggest a structure consistent with this data.
An unknown compound has the mass spectrum shown below. The IR
spectrum shows peaks in the 2963-2861 cm-1 range and a strong
absorption at 1718 cm-1. Suggest a structure consistent with this data.