-

UNIT 12 MASS SPECTROMETRY

Structure
12.1 Introduction
Objectives
12.2 Principle
'

12.3 The Mass Spectrometer

12.4 The Mass Spectrum: Various Important Features
12.5 Fragmentation Patterns
Simple Cleavage
Effect of a Hetero Atom
Formation of Resonance Stabilised Cations
Loss of Small Molecules
Rearrangement
12.6 Summary
12.7 Terminal Questions
12.8 Answers

12.1 INTRODUCTION
In the last two units (Units 10 and 11of this block), you studied about the spin
magnetic resonance spectroscopy. You learnt there that the spin magnetic resonance
spectroscopy helps in structure elucidation. You may also remember that rotation,
vibration, Raman and electronic spectroscopy are the other techniques which help in
the determination of molecular structure. You have already studied about these
techniques in detail in the various units of earlier blocks of this course. In this unit,
we will introduce to you one more technique which is useful in the determination of
structure of atoms and molecules as well as atomic and molecular masses. This
technique is known as mass spectrometry.

In this unit, we will first explain the principle of mass spectrometry. Then we will tell
you about the salient features of a mass spectrometer. This will be followed by a
discussion on how a mass spectrum is presented and how to deduce information
available from the mass spectrum. You will also be told about the fragmentation
types of various species and factors affecting fragmentation. We will also discuss
McLafferty rearrangement.
I
Finally we will illustrate the applications of mass spectrometry by taking some simple
examples.

0 bjectives
After studying this unit, you should be able to:

explain the principle involved in the mass spectrometry,

highlight the important features of a mass spectrometer,
I
draw a typical mass spectrum and explain the information derived from it,
1
discuss various fragmentation types and factors affecting fragmentation,
I
explain the McLafferty rearrangement, and
correlate the mass spectra of simple systems to their structure.
t
Spectroscopy
12.2 PRINCIPLE
Mass spectrometry is based upon a principle which is different from that underlying
thevarious forms of spectroscopy which you studied earlier. Most of the spectral
techniques which we discussed in the earlier units involved absorption of energy
from various regions of electromagnetic spectrum. But, in mass spectrometry the
sample is bombarded with high energy electrons which knock off a n electron from
the sample leading to a positively charged radical ion, [MI*.

This radical ion being highly energetic, may fragment further yielding smaller
fragments as shown below:

The radical ion and other fragments are separated according to their m/z ratio where
m is the mass and z is the charge of the ion. The record of m/z values of these species
verses their relative abundance is known as mass spectrum of the sample. You will
study in the later sections of this unit that mass spectrum of a sample gives important
information about the structure of its atoms or molecules. Although the mass
spectrometry differs in principle from other spectroscopic techniques, it is
considered alongwith them because it complements the information regarding the
structure of the atoms and molecules obtained by other spectroscopic techniques.

12.3 THE MASS SPECTROMETER

Fig. 12.1 (a) shows .the basic features of a simple mass spectrometer while
Fig. 12.1 (b) shows t h e components of a modern high resolution mass
spectrometer.

Fig. 12.1 (a) shows a vapour inlet from where sample vapours are introduced to the
ionisation chamber.

Various methods of ionisation are available as given below:

(i) Electron Ionisation o r Electron Impact (abbreviated as EI)

(ii) Chemical Ionisation (CI)
(iii) Fast Atom Bombardment (FAB)
Note that the radical cation is In electron ionisation method, the sample vapour is bombarded with
both i) radical as well as a cation.
(i)
high energy electrons having energy about 1.12 x 10-l7 J. The electron
on strikin'g the sample M, takes away one electron from it and the sample
gets ionised as shown below:
e+M- [MI*+&- ... (12.1)
radical
cation
A very low pressure (lo4 N m-3 is maintained in the ionisation chamber so that
collisions between ions and unionised atoms o r molecules are at a minimum level.
In EI method, we study the molecular ion and Ragment ions.

(ii) In chemical ionisation method, a reagent gas (such as CH4 o r NH3) is passed
into the ionising chamber where it ionises, fragments and collides with neutral 1
molecules to yield CH; or N H reagent
~ ions. This process is shown below for I
I
II
methane.
 Mass Spectrometry

---
t
Aderatine
Plth d positive i a u
poetntid applied

reservoir

Iv) Collector-DeWw

Flg. 12.1 :Mass Spectrometer: (a) Basic features.

@) High resolution doubk focusslog lnstrumtnl
Spectroscopy

CH,+F- CH;+X (ionisation) ...(12.2)

CH;+- CH~+H. (fragmentation) ... (12.3)
CH; + CH4- C H+
~C H ~ (collision with neutral

and C H+
~ CH4- C,H; + H2 molecule, CH4) ... (12.4)
These reagent ions protonate the sample to yield MH+ ions which are one unit higher
in mass than the sample.

In CI method, we study MH'

M+c%++----, MH++CH,
ions. Chemical ionisation is a milder method of ionisation as compared to electron
ionisation. This is also useful in the determination of relative molar mass (mol. wt.)
because fragmentation of MH+ is very little in this case. However, in EI method M+
undergoes extensive fragmentation and hence is not observed most of the time in mass
spectra. But the fragmentation is otherwise helpful in structure determination of the
sample.
(iii) Fast atom bombardment involves the bombardment of the sample with high
energy xenon atoms. This method is used for large or involatile molecuIes. The

-
ionisation is carried out in solution phase and hence thermally unstable
compounds can be studied by using this technique.
xe
A+B- A++B- ... (12.5)
ionic
compound

Now you have learnt a lot about what can happen in the ionisation chamber. Let us
look at Fig. 12.l(a) again. The ions are generated in the ionisation chamber. The ions
are then passed through accelerating plates. The accelerating plates accelerate only
the positively charged ions. The negative ions and neutral particles are not
accelerated but are continuously removed. From the accelerating plates, the positive
ions pass through the analyser tube where a magnet is used which reflects them along
a curved path. By varying the magnetic field, ions of different masses can be recorded.

Fig. 12.1 (b) shows a high resolution double focusing mass spectrometer. You can see
that the basic features of the instrument are same as in Fig. 12.1 (a). But in addition it
has an electrostatic analyser which carries out a preliminary focusing and then the
ions are passed through the magnetic analyser. This is known as double focusing. The
The term high resolution will be ions are then allowed to enter the collector detector system where they impinge upon
explained in the next section. an electron multiplier detector and produce a current. The current is amplified by an
amplifier and is proportional to the intensity of the ions. The current so produced is
fed to a computer which processes the data and then usually records it in the form of a
bar graph using a recorder.
Let us now study how does a typical mass spectrum look and what are its salient
features.

SAQ 1
+ +
Calculate the m/r values for ZH3, OCH3 and OCCH,.
 Mass Spectrometry
12.4 THE MASS SPECTRUM: VARIOUS
IMPORTANT FEATURES

m/z
Fig. 122: Mass spectrum of ethanol

Fig. 12.2 shows the mass spectrum of ethanol. You can see that the mass spectrum is Re,ative is
a plbt of relative abundance (on y-axis) of positively charged ions verses their mass also Lnm as intensig.
to charge (m/z) ratio ( onx-axis). Since most of the particles are singly charged
(z = I), the m/z of these ions is equal t o their masses. You have learnt in the
previous sections that loss of an electron from a molecule yields a radical cation, i.e.

M + e-- M* + 2-
radical
cation

This iadical cation is also known as molecular ion. The mass of M+ can be taken as
equal to that of M because the mass of the electron lost is negligible. Thus, if we get
the value of m/z of M' from the mass spectrum, we get the molecular weight of M.
The mass spectrum of ethanol shows a peak at m/z 46. Let us see if it corresponds to
its molecular ion o r not? Let us add the relative atomic masses of atoms present in
ethanol (C+H50H) as given below.
2 x atomic mass of carbon + 6 x atomic mass of H +'1 x atomic mass of 0
= (2 x 12) + (6 x 1) + (1 x 16)

Thus, the peak at m/z = 46 corresponds to the molecular ion of ethanol which is
(c~H~oH)+.But this is not the peak of highest intensity.
The peak of highest intehsity is called the base peak. The base peak in the mass
spectrum of ethanol is at m/z 31. The intensity of the base peak is assigned a value of
100 and the intensities of other peaks are expressed relative to that of the base peak.
You can see in the figure that there is a small peak at m/z 47 also. This can be called
as M + 1peak. But where from it has come? The origin of this peak can be
understood if we take into account the natural abundance of the constituent atoms.
Most of the elements exist in nature as predominantly one isotope. But some
elements exist as more than one isotope (Table 12.1) and carbon is one such element.
Carbon exists in nature a :c
' as well as 'ZC.
The natural abundance of ':cis 1.1%
as compared to 'ZC. If 'ZC is present in ethanol molecule, it will show an M+1
'70 isotope and H also occurs as @ isotope. The
peak. Similarly, 0 also occurs as 8
presence of an isotope of these elements would also lead to M+ 1peak. Similarly, if
the molecule contains two :'c atoms or a ':c and $3 or 'i0
atoms, the mass
spectrum would show an M+2 peak also. The other peaks in the spectrum appear
due to the fragmentation of the molecular ion.
Table 12.1 shows the natural abundance of isotopes of some common elements.
 Table 12.1 :Natural abundance of isotopes of some elements.
Isotope Abundance % Isotope Abundance, % Isotope Abundance, %

'H 99.985 0.015

12C 98.89 13C 1.1 1

'"N 99.63 "N 0.37

160 99.76 '0 0.04 180 0.20

3 2 ~ 95.0 3 3 ~ 0.76 3 4 ~ 4.2

"F 100

3 5 ~ ~ 75.5 3 7 ~ ~ 24.5

79~r 50.5 81~r 49.5

127* 100
L

You can see in Table 12.1 that Br exists as two isotopes: 7 9 ~and
r "Br in the ratio
50.5 and 49.5. Thus, in the mass spectrum of bromomethane (CH3Br) shown in
Fig. 12.3 you can see an M+2 peak of almost equal intensity as M+ peak.

rn 12
Fig. 12.3: Mass spectrum of bromomethane.

Similarly when chlorine is present in the molecule, the pattern in the spectrum near
M+ region will be as shown below:

Fig. 12.4: PaUern of mass spectrum near M+ region for a molecule containing a chlorine atom.
 Mass Spectrometry
Note that the intensity of M+2 peak is about one third of M+ peak In case a
compound contains a nitrogen atom, it shows an odd numbered molecular ion peak.
This is called the nitrogen rule. In case, the number of nitrogen atoms is even, a molecular ion
peak having an even mass will be observed.
So far we have discussed the m/z values which differed from each other by one unit.
This is termed as unlt resolution. Thus, by unit resolution, we shoul&be able to
differentiate a peak of say m/z 400 from that of m / z 399 or 401. To determine the
resolution of an instrument, two adjacent peaks in the mass spectrum having
approximately the same intensity are chosen and are designated as Mn and M, where
M, represents the higher mass number peak out of the two. The resolution R is then
given by the following equation:

There are two kinds of instruments available:

i) Low Resolution and (ii) High Resolution
These molecular masses are
Arbitrarily, low resolution instruments are categorised as those which can resolve ,Icula,d the following
masses upto 2000. The high resolution instruments, on the other hand can atomic masses:
differentiate the mass 500 from 499.95. Thus, by using a high resolution mass
spectrometer it is possible t o differentiate between the following species: 1
H - 1.00782

Using low resolution instrument all these species yield the peak at m/z 28 and could
not be differentiated.
Thus, using high resolution mass spectrometer one can chose the correct structure
out of the various possibilities.

12.5 FRAGMENTATION PATTERNS

You are aware that the molecular ion formed undergoes fragmentation.
Fragmentation involves the lose of free radicals or small neutral molecules from the
molecular ion. It is important to note that the fragmentation does not take place in a
random way but it takes place in such a fashion that the most stable fragments
possible are formed. We will now discuss the common fragmentation patterns by
taking the example of some organic compounds.

12.5.1 Simple Cleavage

Let us start with the simple case of alkanes. The mass spectrum of n-hexane is shown
in Fig. 12.5.
Molecular ion of n-hexane can be written as follows:

You can see a peak at m/z 86 corresponding to the molecular ion.

Let us find out the base peak. It appears at m/z 57. Its origin can be explained if we
consider the loss of 86-57 = 29 units as QHS radical from M+ ion giving the n-butyl
cation as follows: .

n-butyl cation ethyl radical

m/z = 57 (not detectable)
Note that the positive charge is carried by one fragment and the odd electron is on the
other fragment. The reverse could have also happened, i.e. the ethyl cation and butyl
radical could have formed as given below:
+
[ C H ~ C H ~ C H ~ C H ~ C--+
H ~ C HCH~CH~CH,CH,
~]~ + CH2CH3
m/z 29
(not detectable)

+
Thus, we can expect a peak at m/z 29 due to CH2CH3.Remember that it is the
positively charged ion which is detected by mass spectromety. If you look at Fig. 12.5,
you can find a peak at m/z 29 also.

The cleavage could have taken place in the middle of the molecule also as shown
below:

You can see a weak peak at m/z 71 which corresponds to M-15 fragment. This
indicates the loss of .CH3 radical as 15 units. The peak is weak because the .CH3
radical produced is not very stable. The other possibility of charge being carried by
+
methyl as CH3 is not observed. . .

not observed
Out of the above two pathways possible, first one takes place indicating that the
stability of the cation is more important than the stability of the radical.Thus,
+ +'
fragmentation yields the more stable CH3CH2CH2CH2CH2
cation and not CH3 cation.
Stability of cation is also observed in case of branched alkanes. In branched alkanes,
fragmentation primarily occurs at the branch. For example in 2-methylpropane,

[ YH3
C)SCHCH3
]' W
(ii)
3 C
I
+H +
"
-CH3

CH3
\ CH3 CH + 6H3
fragmentation occurs predominantly via the first pathway because the cation obtained
is more stable as compared to the methyl cation obtained in the second pathway.
Similarly, for Zmethylpentane fragmentation at branches can lead to peaks at m/z 71
and m/z 43 as shown below:
Note that both the carbocations ( m / z 71 and 43) are secondary carbocations and are
stable. You can locate these peaks in the mass spectrum of Zmethylpentane shown in
Fig. 12.6.

CH3
CH3- CH-
I CHI- CHI-CH3

m/z
Fig. 126: Mnss spectrum of 2-metb;lpentant

You can also observe from the above examples that alkanes show homologous series of
M-14 fragments due to the lose of CH2 groups.

SAQ 2

Explain the origin of peaks at m / z 114,85,71,57 in the mass spectrum of n-octane.

..........................................................................................................................................................
12.5.2 Effect of a Heteroatom
Mass spectra of compounds containing heteroatoms (N, 0,
halogens etc.) show
 a-cleavage, i.e. cleavage of bond to the carbon that is a to the heteroatom. For
example, two such a cleavages are shown above in case of alcohol.

The resulting cations (a) and (b) can resonance stabilise t o structures (I) and (II),.
respectively. It is here in this resonance stabilisation that the role of heteroatom
comes into play. The unshared pair of electrons on the heteroatom helps in
delocalisation of the positive charge which helps to stabilise the carbocations
(a and b) formed initially.

The a-cleavage rule applies to compounds containing -NRR1, S R , -OR, -C1 and
carbonyl functional groups. Two such examples follow.

a-cleavage
(arnine)

a-cleavage
(ether)

It is also worth considering here the fact that where more than one site of a-cleavage
is possible, the ejection of largest alkyl radical gives the largest peak. We can
understand this by taking the following example. In the case of 2-butanol, the most
abundant peak is at m/z 45 resulting from the ejection of ethyl radical.
OH
I ++ H
I
C H ~ C H+ ~ +C-H
largest
radical
OH

I
CH3
- (iii)
(iii)
FH3cHA:>]+(ii)
1 (i) y,,I
dH3cH2-c

CH3
m/z 73

OH
I
dn 45 (base peak) CHICH~--&-H
. +
+ CH,
mlz 59
In case of carbony1 compounds, R1> C = 0 , cleavage can occur on either side of
R2
the C = 0 group. This leads to the following possibilities:

..
: and R; are stable, they are also formed via (i) (b)
In case the alkyl carboutions R
and (ii) (b) pathways.
 12.5.3 Formation of Resonance ~tabilisedCations Mass Spectrometry

Molecular ions of alkenes and alkylbenzenes fragment to yield resonance stabilised

cations. In alkenes, the b o n d p to the double bond is cleaved to yield a resonance
stabilised ally1 cation. Similarly, the following fragmentation of the alkylbenzenes
takes place because the resulting benzylic cation, which is stabilised by resonance, is
also in equilibrium with the tropylium ion.

The mass spectrum of butylbenzene shown in Fig. 12.7 exibits a peak at m/z 91
, and it is in fact the base peak.
\

80
P~I-CH~CH~CH~CH~
I n-butylbenzene

mlz
Flg. 12.7 : Mass spectrum of butylbenzene

SAQ 3
The mass spectrum of trans 2-hexene shows peaks at m h 84 and 55.Account for
them.

12.5.4 Loss of Small Molecules

Small stable molecules such as H20, C02, 'CO, q H 4 etc. can be lost from a
molecular ion. For example, alcohols easily lose H20 molecule and show prominent
M-18 peak.

The loss of H 2 0 from alcohols is s o facile t h y no molecular ion peak is observed in

their mass spectrum. Mass spectrum of 2-methyl -2-butanol as shown in Fig. 12.8
illustrates this point.
57
Spectroscopy

Fig. 12.8: Mass spectrum of2-methyl-2-butanol.

The following fragmentation pathways explain the origin of various peaks in the
mass spectrum.

I
/
~7
\ 8 e' C H ~+ C&CH2-C-CH3
+
c9;"
mlr 73
f ~ ~ C&
H~ k
-d~~

I
CH3
C H ~ C H+~ + C -CH3 mlr 55
I
CH3 I I
i
: 6 ~
mlz59
CH3CH2-c
+OH
II-CH3
CH2 =C
I
CH3
- 6 ~ ~

12.5.5 Rearrangement
You might have observed in the earlier examples that a molecular ion with an even
mass value cleaves to give fragment ions with odd mass values and vice-versa. But if
the even mass molecular ion yields fragments of even mass and odd mass molecular
ion yields fragments of odd mass, it indicates that a rearrangement has taken place.
. ,

In case the mass difference between expected and the observed fragment ion is of one
unit, rearrangement involving migration of hydrogen atom can be expected.

A rearrangement known as McLafferty rearrangement is commonly observed in

the compounds having the following structure where X and Y can be C, 0,
S, N
and P.
Let us take the example of an aldehyde or a ketone having y-hydrogen. It can undergo Mass Spectrometry
the McLafferty rearrangement as shown below:

/\
alkene
Here X = C and Y = 0
When R = H, aldehyde
R = Alkyl, ketone

when R = H, aldehyde

R = alkyl, ketone

The mass spectrum of butanal (CH3CH2C~2CHO)

is shown in Fig. 12.9. It shows

Fig. 12.9: Mass spectrum of butanal.

prominent peaks at m / z 72,57,44 and 29. These peaks can be explained as follows:

m/z fragments

57 loss of d ~ (M-~ c&)+

, fragment

29 loss of ~ H ~ C H ~ C(MH-~c3H7)+
, fragment

The peak at m/z 44 (M-28) is an even mass peak from the even mass number .
molecular ion and hence indicates a rearrangement. The McLafferty rearrangement
explains this peak as follows:

H
c7
+
H
H H
ethene
(a1 kenel
Spectroscopy Similarly carboxylic acids and esters can also undergo McLafferty rearrangement
provided they have y-hydrogen.

SAQ 4

The mass spectrum of pentanoic acid shows a peak of m / z 60 involving McLafferty

rearrangement. Write the structures for the fragments formed.

12.6 SUMMARY
Let us now summarise the important points which you studied in this unit.

Mass spectrometry is different in principle from the other spectroscopic techniques.

It involves the bombardment of atoms and molecules with high energy electrons
which yields a molecular ion by the lose of an electron. This forms the basis of
electron ionisation.The molecular ion itself being energetic can undergo fragmentation..

Chemical ionisation and fast atom bombardment provide alternative means of

ionisation.
Mass spectrum is a plot of relative abundance of various positively charged
fragments vs their m / z values.
The peak corresponding to molecular ion gives the molecular mass.
The base peak is the ~jeakof highest intensity.
The pattern of peaks near the molecular ion region i.e., M + 1, M + 2 etc.
gives important information about the nature of heteroatoms present.
Various fragmentation patterns involve simple cleavage, a-cleavage, loss
of small molecules, formation of resonance stabilised cations and
rearrangements.
McLafferty rearrangement involves a y -hydrogen and a double bond between C,
0, N, S, P atoms.

12.7 TERMINAL QUESTIONS

1. The mass spectrum of chloroethane shows two peaks at m / z 64 and
66. The peak at m / z 66 is of one third intensity as the peak at m / z 64.
Which one is the molecular ion peak? Account for the origin of the other ~ e a k .

2. The mass spectrum of phenyl ethanone (C6H5COCH3) shows the peaks at m h

120, 105 and 77. Show how these peaks arise in the mass spectrum.

3. A compound shows the molecular ion peak at m / z 107. What is the nature of
the compound? '
12.8 ANSWERS
Self Assessment Questions

s C3 +C4 Cleavage +
CH3CH2CH2CH2CH2 + ~ H ~ C H ~ C H
"u

3. trans-2-hexane : peak at m/z 84 is due to [MI' and that at

m/z 55 is due to [M - CH~CHJ+

which is resonance stabilised aflylic cation as shown below:
Terminal Questions

The peak at rn/z 64 is the molecular ion peak having 3 5 isotope.

~ ~ The other
peak is M+2 peak having 3 7 ~ isotope.
1

2.

3. It contains one nitrogen atom.