CHAPTER 4

MASS SPECTROSCOPY

Learning outcome

Understand MS concept
Capable to read the mass spectrum

Mass Spectrometry (MS)

Mass spectrometry (MS) is an analytical technique

that ionizes chemical species and sorts the ions
based on their mass to charge ratio. In simpler
terms, a mass spectrum measures the masses within
a sample.

Mass Spectrometry (MS)

m/e= H2r2/2v

Mass Spectrometry (MS)

Electron Ionization MS
In

the ionization chamber, the sample is bombarded with a

beam of high-energy electrons.
Collisions between these electrons and the sample result in
loss of electrons from sample molecules and formation of
positive ions.
H
H C H + e
H

+
H
+2 e
H C H
H
Molecular ion
(a radical cation)

Gas Chromatography-Mass
Spectroscopy (GC-MS)

Gas chromatographymass spectrometry. Gas

chromatographymass spectrometry (GC-MS) is
an analytical method that combines the features of
gas-chromatography and mass spectrometry to
identify different substances within a test sample
Drawback- need a rapid scanning by MS (the
scanning must be done before all compound exist
from the GC column)

Mass Spectrum

Mass spectrum: A plot

of
the
relative
abundance
of
ions
versus their mass-tocharge ratio.
Base peak: The most
abundant
peak.
Assigned an arbitrary
intensity of 100.
The relative abundance
of all other ions is
reported as a % of
abundance of the base
peak.

MS of dopamine
A partial mass spectrum of dopamine showing all peaks
with intensity equal to or greater than 0.5% of the base
peak.

Determination of molecular weight

Molecular ions-accelerated-sent to magnetic fielddetect

Life time at least 10-5/s can react with the detector
without breaking- can detect direct m/e=mw
Consideration-isotopes / bombardment

Molecular peaks

Mass higher in spectrum (M+ intensity)

Ion has odd no of electron
Forming important fragment ions in spectrum (highly
branched substances undergoes fragmentation
easily)
Nitrogen rule
Halogens
Molecular ions life times

Determination of molecular formula

Precise mass determination

Eg: mw=60 will have many possibility
C3H8O, C2H8N2, CH4N2O (compared with chemical
method in chapter 1)

Resolution

Resolution: A measure of how well a mass spectrometer

separates ions of different masses.
Low

Resolution MS (LR-MS): Refers to instruments capable

of separating only ions that differ in nominal mass; that
is ions that differ by at least 1 or more atomic mass units
(amu).

High

resolution MS (HR-MS): Refers to instruments

capable of separating ions that differ in mass by as little
as 0.0001 amu.

Resolution
C3H6O

and C3H8O have nominal masses of 58 and 60, and

can be distinguished by low-resolution MS.
C3H8O and C2H4O2 both have nominal masses of 60 which
occurs due to isotopes of the same elements.
distinguish between them by high-resolution MS.

Molecular N ominal Precise

Formula
Mass
Mas s
C3 H8 O
60
60.05754
C2 H4 O2
60.02112
60

Determination of molecular formula of

Isotopes
Virtually all
elements
common to
organic
compounds are
mixtures of
isotopes with
different
relative
abundances.

Atomic
Mas s Relative
Element w eigh t Isotope (amu ) A bun dance
hydrogen 1.0079 1H
1.00783 100
2
H
2.01410
0.016
12
carbon
12.011 13 C
12.0000 100
C
13.0034
1.11
14.0031 100
nitrogen 14.007 14 N
15
N
15.0001
0.38
16
oxygen
15.999
O
15.9949 100
18
O
17.9992
0.20
su lfu r
32.066 32 S
31.9721 100
34
S
33.9679
4.40
ch lorine 35.453 3 5Cl
34.9689 100
37
Cl
36.9659
32.5
bromine 79.904 79Br
78.9183 100
81
Br
80.9163
98.0

Determination of molecular formula of

Isotopes
for example, in nature is 98.90% 12C and
1.10% 113C.
There are 1.11 atoms of carbon-13 in nature for
every 100 atoms of carbon-12. So low intensity
M+1 peak is very likely to appear along with M+
peak.
Carbon,

Determination of molecular formula

Isotope ratio data
Formula for calculating the intensity of M+1 peak is as
follows:
%(M+1)= 100[(M+1)/M]= 1.1x no. of C atoms+ 0.0016
no. of H atoms+ 0.38 no of N atoms...

Formula for calculating the intensity of M+2 peak is as

follows:
%(M+2)= 100[(M+2)/M]= (1.1x no. of C atoms)2/200+
(0.0016 no. of H atoms)2/200+ 0.20 no of O atoms...

isotope peak
patterns for Cland Br- containing
ions

Fragmentation Patterns

Molecules ion which has life time greater than 105/sec =peaks refer to molecular ion appear in mass
spectrum
Molecules ion which has life time less than 10-5/sec,
break apart into fragment before they are
accelerated within the ionization chamber

Fragmentation of M+

Fragmentation of a molecular ion, M, produces a

radical and a cation.
Only

A-B

the cation is detected by MS.

Molecular ion
(a radical cation)

A +
B+
Radical
Cation
A+ + B
Cation
Radical

Fragmentation Patterns
Fragmentation involves the loss of an electrically
neutral fragment
Mode of fragmentation:
#One bond
CH3+<RCH2+<R3C+<CH2=CH-CH2+<C6H5-CH2+
#Two bond

General modes of fragmentation:

Fragmentation of the molecular ion takes place in following
modes:
* Simple cleavage
1. Homolytic cleavage
2. Heterolytic cleavage
3. Retro Diels-Alder reaction
* Rearrangement reactions accompanied by transfer of atoms.
1. Scrambling
2. Mc Lafferty rearrangement
3. Elimination

Simple cleavage

1.Homolytic cleavage

Here fragmentation is due to electron redistribution between

bonds.
R CH2 CH2 R'

R CH2 : CH2 R
e-

R CH2+ + CH2 R'

.

2.Heterolytic cleavage
Fragmentation by movement of two electrons:
In this type of cleavage both the electrons of the bond are taken
over by one of the atoms; the fragments are an even electron
cation and a radical with the positive charge residing on the
alkyl group. It is designated by a conventional arrow ( or )
to signify the transfer of a pair of electrons in the direction of
the charged site.

3. Retro Diels-Aldel reaction

Elimination by multiple bond rupture:
cyclohexene is broken down to Diene and Dienophile.

Rearrangement

1. Scrambling
Fragmentation giving rise to stable carbocation:
In certain cases fragmentation takes place at bond, which gives
stable carbocation.
Ex- Molecular ion from the alkyl benzene undergoes
fragmentation at the benzylic bond and final product is seven
membered cyclic ion known as Tropylium ion.

2. Mc Lafferty rearrangement:

Fragmentation due to rearrangement of Molecular or Parent ion:

Compounds containing hydrogen atom at position gamma to carbonyl

group have been found to a relative intense peak. This is probably due to
rearrangement and fragmentation is accompanied by the loss of neutral
molecule. This rearrangement is known as McLafferty rearrangement.
The rearrangement results in the formation of charged enols and a neutral
olefins

To undergo McLafferty rearrangement, a molecule

must posses:

a. An appropriately located heteroatom (ex.oxygen)

b. A double bond
c. An abstractable Hydrogen atom which is (gamma)
to C=O system.

Table for the

common McLafferty
peak in the spectra
of carbonyl group.

Compound type

Substituent (R)

McL peak

Aldehyde

-H

44

Methyl
ketone

-CH3

58

Amide

-NH2

59

Acid

-OH

60

Ethyl ketone

-CH2CH3

72

Methyl ester

-OCH3

74

3. elimination
Fragmentation due to loss of small molecule:
Loss of small stable molecules such as H2O, CO2, CO,C2H4
from molecular ion during fragmentation.
Ex- An alcohol readily looses H2O molecule and shows a peak
18 mass units less than the peak of molecular ion.

Fragmentation Patterns

Alkane (octane)

Fragmentation adjacent to the

branching point
In case of branched alkanes, bond fission takes
place adjacent to the branching point. Hence
this leads to the formation of more stable
carbocation
Ex: 3-methyl pentane

Fragmentation Patterns

Alkane (isooctane)

Fragmentation Patterns

cycloalkane

Fragmentation Patterns

Alkenes characteristically
show

a strong molecular ion peak.

cleave to form resonance-stabilized allylic cations.
+
[CH2 =CHCH2 CH2 CH3 ]

CH2 =CHCH2 + +

CH2 CH3

Fragmentation Patterns
Cyclohexenes

give a 1,3-diene and an alkene, a process

that is the reverse of a Diels-Alder reaction.
CH3

CH3

H3 C

H3 C

CH2

CH2

Limon ene
(m/z 136)

A neu tral d iene

(m/z 68)

A radical cation
(m/z 68)

Fragmentation Patterns

Alkynes typically
show

a strong molecular ion peak.

cleave readily to form the resonance-stabilized propargyl
cation or substituted propargyl cations.
+
+
3-Propynyl cation
(Propargyl cation)

HC C-CH2

HC C=CH2

Fragmentation Patterns
Aromatic compounds:
It shows prominent mol ion peak, as compared to the alkanes and
alkenes containing same number of C atoms. This is as a result of the
stabilizing effect of the ring.
If aromatic ring is substituted by an alkyl groups a prominent peak is
formed at m/z 91.
+
Here benzyl cation (C6H5C H2) formed rearranges
to tropylium cation (C7H7+); m/z 91.
This may eliminate a neutral acetylene molecule to give a peak at m/e
65.

91
M (92)

Mass spectrum of toluene

Fragmentation Patterns
Alcohols:

The molecular ion peak of 1 and 2alcohol is usually of low abundance

or may not detected in 3 alcohols.

The fragmentation of C-C bond (alkyl group) adjacent to oxygen atom is

the preferred fragmentation mode i.e. cleavage.
1 alcohols shows M-18 peaks, corresponding to the loss of water.

The CH2=OH+ ion is the most significant peak in the spectra of 1 alcohols.

Secondary alcohols cleave to give prominent peaks due R-CH=OH at

m/z=45,59,73

Fragmentation Patterns
Phenols:
The molecular ion peak is intense.
The peak due to the loss of hydrogen radical, M+ - H is small.
The fragment ion due to the loss of carbon monoxide is significant.
Cresols form very intense peak due to the formation of hydroxyl tropylium
ion.
OH

OH

+
m/z=107
+H.

+
m/z=79
+CO

Fragmentation Patterns
Ethers:

Aliphatic ethers undergo facile fragmentation and exhibit

a weak molecular ion peak because the resultant ion is
highly stabilized by resonance

The major fragmentation modes occur through

cleavage

cleavage : Cleavage of a bond to oxygen occurs, the

positive charge being retained on the carbon rather than on
oxygen (loss of an alkoxy group).

Fragmentation Patterns
Aldehydes

The Molecular ion peak of aliphatic Aldehydes is observable.

Aromatic Aldehydes shows moderate intense peak at:

H-C=O+ + R. (m/e=29)
R-CO+ + H. (M-1)
By -cleavage.
Second common feature of Aliphatic Aldehyde is cleavage.
For ex: Aldehyde with R+ + CH2=CHO. end group gives
rise to characteristic M-43 peaks.
McLafferty rearrangement-occurred when the carbon chain
attached to carbonyl group contains at least three carbon

-cleavage (M-43)

R + CH2=CHO.

Fragmentation Patterns
Ketones:
Molecular ion peaks are intense than Aldehyde.
Most of the abundant ions in the mass spectra of Ketones can
be accounted by cleavage and Mc Lafferty rearrangement.

Fragmentation Patterns
Ester:

Most of the abundant ions in the mass spectra of ester can be

accounted by cleavage and Mc Lafferty rearrangement.
-cleavage : loss of alkoxy group to form corresponding acylium
ion, RCO+
McLafferty rearrangment:

Mass spectrum of methyl butyrate:

Fragmentation Patterns
Carboxylic acid:

Principal modes of fragmentation resemble those of methyl ester.

-cleavage : loss of OH, COOH through -cleavage on either side
of the C=O group
McLafferty rearrangment:

Mass spectrum of butanoic acid

Fragmentation Patterns
amines:
Compound with odd no. of Nitrogen must have odd no. of MW.

-cleavage :
-cleavage:
McLafferty rearrangement:
Amides:
-cleavage :
McLafferty rearrangement:
Nitrile:
M-H
McLafferty rearrangement

Fragmentation Patterns
Nitro Compounds:
Aliphatic Nitro compounds fragment by loss of NO2
m/z= 30 (NO+ ion), m/z=46 (NO2+ ion)
aromatic nitro compound (nitrobenzene)

Fragmentation Patterns
Halogen Compounds:

A compound with 1 chlorine atom gives a M+2 peak, which is one third
the intensity of the molecular ion peak due to the presence of Molecular ion
containing 37Cl isotope.
In a mono bromo derivative the M+2 peak is almost of equal intensity to
the molecular ion and is due to the presence of molecular ion containing
81Br isotope.
Fluorine and Iodine being mono isotopic do not give these patterns.
Aliphatic chlorine compounds fragment mainly by the loss of HCl to give
peaks at M-36 and M-38. HCl peaks can also be seen at m/z 36, 38.
The relative abundance of the Molecular ion decreases with increase in
chain length and increase in branching.

Compound X contains a single oxygen atom but it does

not show any significant IR absorption peak above
3000 cm-1. The MS spectrum of compound X is shown:
1. determine the m/z values for the molecular ion
peaks
2. determine the m/z values for the base peaks
3. Generate the molecular formula for the compound X
using rule of thirteen
4. propose the structure. And show how the
fragmentation ions at m/=59 and m/z=31 are formed.