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isotopes
You will know in theory that most elements naturally exist as mixtures of isotopes. If you didn’t
believe it, now you will. Chlorine is normally a 3:1 mixture of 35Cl and 37Cl (hence the obviously
false relative atomic mass of ‘35.5’ for chlorine) while bromine is an almost 1:1 mixture of 79Br and
81Br (hence the ‘average’ mass of 80 for bromine!). Mass spectrometry separates these isotopes so
that you get true not average molecular weights. The molecular ion in the E.I. mass spectrum of the
bromo-amide below has two peaks at 213 and 215 of roughly equal intensity. This might just repre-
sent the loss of molecular hydrogen from a molecular ion 215, but, when we notice that the first frag-
ment (and base peak) has the same pattern at 171/173, the presence of bromine is a more likely
explanation. All the smaller fragments at 155, 92, etc. lack the 1:1 pattern and also therefore lack
bromine.
52 3 . Determining organic structures
the two black bonds share two electrons
electron bombardment
H C
H
H
H
H
CH4 CH4
CH4
CH3 +
electron lost under
proposed structure of CH5
NH2 CH3
CH2
NH2
CH2
CH2
NH2
M+• very small
= 121 = C6H11N
91
uncharged radical – 
not seen
E.I. E.I.
++
91
(15%)
30
(100%)
the radical cation can fragment in two ways
30
uncharged radical – 
not seen
The mass spectrum of chlorobenzene (PhCl, C6H5Cl) is very simple. There are two peaks at 112
(100%) and 114 (33%), a peak at 77 (40%), and very little else. The peaks at 112/114 with their 3:1
ratio are the molecular ions, while the fragment at 77 is the phenyl cation (Ph+ or C6H5
+).
The mass spectrum of DDT
is very revealing. This very
effective insecticide became
notorious as it accumulated in
the fat of birds of prey (and
humans) and was phased out
of use. It can be detected easily
by mass spectrometry because the five chlorine atoms produce a complex molecular ion at
252/254/256/258/260 with ratios of 243:405:270:90:15:1 (the last is too small to see). The peak at 252
contains nothing but 35Cl, the peak at 254 has four atoms of 35Cl and one atom of 37Cl, while the
invisible peak at 260 has five 37Cl atoms. The ratios need some working out, but the first fragment at
235/237/239 in a ratio 9:6:1 is easier. It shows just two chlorine atoms as the CCl3 group has been lost
as a radical.
Mass spectrometry 53
148.0
143.0
74.0 81.0
80
92.1
171.0
98.0 105.5
100
117.0
120
124.0 132.0
140
0
20
40
60
80
100
0
20
40
60
80
100
160
155.0
180 200
186.0 198.9
213.0
224.0
220
236.0
240
H
N
Br
O
NH2
Br
NH2
fragmentation
M+ 213/215 171/173 92
P
It’s worth remembering that the
Ph+ weighs 77: you’ll see this
mass frequently.
Table 3.1 Summary table of main isotopes for mass spectra
Element Carbon Chlorine Bromine
isotopes 12C, 13C 35Cl, 37Cl 79Br, 81Br
rough ratio 1.1% 13C (90:1) 3:1 1:1
P
Remember: mass spectroscopy is
very good at detecting minute
quantities.
Carbon has a minor but important isotope 13C
Many elements have minor isotopes at below the 1% level and we can ignore these. One important
one we cannot ignore is the 1.1% of 13C present in ordinary carbon. The main isotope is 12C and you
may recall that 14C is radioactive and used in carbon dating, but its natural abundance is minute.
The stable isotope 13C is not radioactive, but it is NMR active as we shall soon see. If you look back at
the mass spectra illustrated so far in this chapter, you will see a small peak one mass unit higher than
each peak in most of the spectra. This is no instrumental aberration: these are genuine peaks con-
taining 13C instead of 12C. The exact height of these peaks is useful as an indication of the number of
carbon atoms in the molecule. If there are n carbon atoms in a molecular ion, then the ratio of M+ to
[M + 1]+ is 100: (1.1) × n.
54 3 . Determining organic structures
Isotopes in DDT
The ratio comes from the 3:1 isotopic ratio like this:
• chance of one 35Cl in the molecule:
• chance of one 37Cl in the molecule: 
If the molecule or fragment contains two chlorine atoms, as does our C13H9Cl2, then
• chance of two 35Cls in the molecule:
• chance of one 35Cl and one 37Cl in the molecule: 
• chance of two 37Cls in the molecule: 
The ratio of these three fractions is 9:6:1, the ratio of the peaks in the mass spectrum.
3
4
1
4
3
4
3
4
9
16
× =
3
4
1
4
1
4
3
4
6
16
×



+ ×



=
1
4
1
4
1
16
× =
0 100 200 300 400
100
80
60
40
20
0
re
l. 
ab
un
da
nc
e
mass spectrum of DDT
m/z
CCl3
ClCl
CCl3
Cl Cl
CCl3
Cl Cl
fragmentation
+
stable cation
stable
radical
L
•
⊕ denotes the cation radical produced
by E.I.
The electron impact mass spectrum of BHT gives a good example. The molecular ion at 220 has
an abundance of 34% and [M + 1]+ at 221 has 5–6% abundance but is difficult to measure as it is so
weak. BHT is C15H26O so this should give an [M + 1]
+ peak due to 13C of 15 × 1.1% of M+, that is,
16.5% of M+ or 34 × 16.5 = 5.6% actual abundance. An easier peak to interpret is the base peak at
205 formed by the loss of one of the six identical methyl groups from the t-butyl side chains (don’t
forget what we told you in Chapter 2—all the ‘sticks’ in these structures are methyl groups and not
hydrogen atoms). The base peak (100%) 205 is [M—Me]+ and the 13C peak 206 is 15%, which fits
well with 14 × 1.1% = 15.4%.
Other examples you have seen include the DDT spectrum, where the peaks between the main
peaks are 13C peaks: thus 236, 238, and 240 are each 14% of the peak one mass unit less, as this frag-
ment has 13 carbon atoms. If the number of carbons gets very large, so does the 13C peak; eventually
it is more likely that the molecule contains one 13C than that it
doesn’t. We can ignore the possibility of two 13C atoms as 1.1% of
1.1% is very small (probability of 1.32 × 10–5).
Table 3.2 summarizes the abundance of the isotopes in these
three elements. Notice that the ratio for chlorine is not exactly 3:1
nor that for bromine exactly 1:1; nevertheless you should use the
simpler ratios when examining a mass spectrum. Always look at the
heaviest peak first: see whether there is chlorine or bromine in it,
Mass spectrometry 55
BHT
BHT is used to prevent the
oxidation of vitamins A and E in
foods. It carries the E-number
E321. There has been some
controversy over its use because it
is a cancer suspect agent, but it is
used in some ‘foods’ like chewing
gum. BHT stands for ‘Butylated
HydroxyToluene’, but you can call it
2,6-di-t-butyl-4-methylphenol if you
want to, but you may prefer to look
at the structure and just call it BHT.
You met BHT briefly in Chapter 2
when you were introduced to the
tertiary butyl group.
0 50 200 250
100
80
60
40
20
0
re
l. 
ab
un
da
nc
e
mass spectrum of BHT
m/z
OH
150100
‘BHT’
OH OH
fragmentation
C15H26O C14H23O
Table 3.2 Abundance of isotopes for carbon, chlorine, and bromine
Element Major isotope: abundance Minor isotope: abundance
carbon 12C: 98.9% 13C: 1.1%
chlorine 35Cl: 75.8% 37Cl: 24.2%
bromine 79Br: 50.5% 81Br: 49.5%
and whether the ratio of M+ to [M + 1]+ is about right. If, for example, you have what seems to be M+
at 120 and the peak at 121 is 20% of the supposed M+ at 120, then this cannot be a 13C peak as it would
mean that the molecule would have to contain 18 carbon atoms and you cannot fit 18 carbon atoms
into a molecular ion of 120. Maybe 121 is the molecular ion.
Atomic composition can be determined by high resolution mass spectrometry
Ordinary mass spectra tell us the molecular weight (MW) of the molecule: we could say that the bee
alarm pheromone was MW 114. When we said it was C7H14O we could not really speak with
confidence because 114 could also be many other things such as C8H18 or C6H10O2 or C6H14N2.
These different atomic compositions for the same molecular weight can nonetheless be distinguished
if we know the exact molecular weight, since individual isotopes have non-integral masses (except 12C
by definition). Table 3.3 gives these to five decimal places,