CH437 ORGANIC STRUCTURE ANALYSIS
CLASS 6: MASS SPECTROMETRY 6
Synopsis. Fragmentation behavior of ions containing certain functional groups:
alkanes, cycloalkanes, alkenes, aromatic hydrocarbons, alcohols, aldehydes and
ketones. Bond fission processes. Rearrangements.
Fragmentations Associated with Organic Functional Groups
Alkanes
Linear Alkane fragmentation patterns are characterized by the progressive loss of
larger and larger alkyl radicals, the ion abundances (intensities) tending to increase
with the size of the radical lost, as illustrated by the EI mass spectrum of n-octane,
below.
It is known that fragmentation of n-alkyl ions occurs by loss of ethene (C2H4), so
that the ion of m/z 57 in the mass spectrum of n-octane, above, is probably derived
from two pathways, as shown below.
It should be noted that interpretation of the mass spectra of alkanes is complicated
by the rearrangements of primary cations to secondary cations (etc), prior to
fragmentation, hence it is difficult to obtain a definitive structure for an alkane with
more than, say 8 carbon atoms.
Branched alkanes show similar patterns, except that molecular ions are of low
intensity and the base peaks usually correspond to the most stable cation.
Compare the EI mass spectra of 2-methylheptane and 2,2,3-trimethylpentane
(below) with that of n-octane (above).
The base peak (m/z = 43) in the top spectrum corresponds to (CH 3)2CH+ and for
the bottom spectrum, (CH3)3C+ (m/z = 57). Note the presence of M+. – CH3. (M –
15) peaks in the above two spectra: these are generally not observed in the mass
spectra of n-alkanes.
Cycloalkanes and Alkenes
The mass spectra of cycloalkanes and alkenes show some distinct similarities. For
example, the base peak in the spectra of both types of compound is due to the
most stable cation, often allyl (CH2=CH-CH2+, m/z = 41) or methylallyl CH3CH=CH-CH2+, m/z = 55). This suggests that ring opening occurs during the
fragmentation of cycloalkane ions. Also, it is thought that the molecular ion of
alkenes rearranges to cyclic structures prior to fragmentation. Hence fragmentation
of alkenes and cycloalkanes appears to share some common pathways and
intermediates.
See
below
for
the
mass
spectra
ethylmethylcyclopentane and 1,2-dimethylcyclohexane.
of
4-octene,
1-
Aromatic Hydrocarbons
Unlike other hydrocarbons, the mass spectra of aromatic hydrocarbons are
characterized by the presence of comparatively intense molecular ions and by low
m/z peaks of low intensity, as illustrated by the EI spectra of benzene, toluene and
n-propylbenzene below.
Nonetheless, the fragmentation pathways associated with aromatic hydrocarbons
are well documented, as illustrated below.
Primary Single Bond Cleavage Processes Associated with some Common
Functional Groups
Primary single bond cleavages (mostly -cleavages) of molecular ions, with some
summary of subsequent fragmentation routes are given for a selection of common
functional groups in the table below.
Functional Group
Fragmentation
Bromide
R
Iodide
Br
R
Alcohol/
Thiol(X = O,
S)
I
R
R'
+.
R+ +
Br.
+.
R+ +
I.
+.
XH
CH
R
_
R(CH2)nN
Amine
CH2
Ether/
Thioether
(X = O, S)
+.
R(CH2)nX
+
R(CH2)nN
CH
_ R'.
R'
+
R(CH2)nX
Ketone
+.
O
C
+.
O
OR'
R
+
R(CH2) CH=CH2
n-2
R''
CH R''
+
R'. (comment as
above)
+
R'. (comment as
above)
O
R
+
O
C
R'
Ester
CH2
+
HX
alkene
CHR'' + R(CH2) CH=CH2
n-2
alkene
+
O
O
R
+
HN
(comment as
above)
R'
R'
CH2
R''
(comment as
above)
R''
R
Ketal
R'.
R'
R''
+
.
o
o
XH + R' (R' bigger than R, or if 2 or 3 )
CH
at
C
O
at
R
+
O
C
C
+
O
especially if R' = CH3 (methyl esters)
OR'
There follows some additional discussion on fragmentations of selected functional
groups, in order to expand upon some of the features in the above table, but also
to introduce fragmentations that occur by rearrangement – that is, fragmentations
involving several synchronous bond fissions.
Alcohols
The two most common fragmentation pathways for alcohol molecular ions are cleavage (one-bond fission) and dehydration (two-bond fission).
The EI mass spectrum of 3-pentanol (below) illustrates the -cleavage route.
Carbonyl Compounds: Aldehydes and Ketones
Both aldehydes and ketones undergo mass spectral fragmentation via -cleavage:
of a bond between the carbonyl group and the neighboring () carbon atom. For
ketones, cleavage usually occurs on both sides of the carbonyl function, the more
abundant cleavage reflects the relative stabilities of both the acylium cation and the
radical. Also, carbonyl compounds that have a hydrogen atom on a carbon three
atoms away from the carbonyl carbon (i.e. a -hydrogen) undergo a highly
characteristic multi-bond fission rearrangement known as the McLafferty
rearrangement. Both of these are illustrated below.

C
+.
+.
H
H
O
C
O
+
C
C
C
C
R
M+.
C
C
R
[M - alkene (olefin)]+.
The EI mass spectrum of 3-heptanone, below, indicates that the base peak (m/z
57) is formed by –cleavage on the butyl side of the ketone function, but a
significant peak at m/z 85 suggests that some –cleavage also occurs on the ethyl
side. The peak at m/z 72 is due to McLafferty rearrangement of the molecular ion
(on the butyl side of the ketone function).
Rearrangement Fragmentations
Several multibond-fission fragmentations, involving the migration of hydrogen and
the ejection of a small molecule, have already been discussed (see McLafferty
rearrangement and dehydration of an alcohol molecular ion, above). Some further
examples are described next.
Fragmentation by loss of an alkene molecule is frequently seen in the EI mass
spectra of ethers and amines:
H
CH3
CH
+.
O
CH3
fission
CH3
_ CH .
3
CH
CH3
CH3
CH
+
O
CH2
CH
CH3
m/z = 102 (~1%)
m/z = 87 (20%)
CH3
CH
+
O
+
H
CH2
CH
CH3
m/z = 45 (100%)
(CH3)2CH
CH
+.
NHC2H5
CH3
H
fission
CH3
+
NH
CH
CH2
CH2
_ (CH ) CH.
32
m/z = 129 (~2%)
m/z = 72 (100%)
CH3
CH
+
NH2
+
CH2
CH2
m/z = 44 (30%)
These rearrangements often of the four center type (compare solution chemistry,
where 5- and 6-center rearrangements are the most common), and although they
are commonly written as synchronous processes, they may well be stepwise.
Other rearrangement type fragmentations can involve the loss of small molecules
such as H2 and NH3:
H
H
+
+
+
m/z = 77
m/z = 79
H
Ph
CH3
CH
+
NHCH3
Ph
m/z = 136
Other
H2
Kinds
CH
+
NHCH3
+
CH4
m/z = 120
of
Fragmentations:
Cyclizations
and
Charge
Remote
Fragmentations
Cyclizations, with charge migration, can occur in the fragmentation of bifunctional
molecules, especially if the functionalities are stereoelectronically well placed for
anchimeric assistance (a kind of internal SN2 process):
H
CH3
H
O
N
+
N
CR2
H
+
HN
+
NH3
CR2
N
H
H
O
+
O
CH3
+
NH3
O+
(This only occurs in the mass spectra of 4- and 5-aminoalcohols)
Fragmentations of this kind are most frequently observed in the CI mass spectra.
Charge remote fragmentations involve bond fissions that occur at locations several
atoms removed from the ionization site: they occur only if the electron density in
the intervening bonds can be rearranged to stabilize the charge. Such
fragmentations are more or less limited to highly conjugated and aromatic
molecules. An example is shown below.
CH3
CH3
OH
OH
H
CH3

C2H5
+
O

CH3
C2H5
CH3

+.
O
.
CH3
m/z = 314
_
CH2
CHC2H5
CH3
CH3
OH
OH
H
. H
CH3
CH3
+
O
CH3
CH3
+
O
CH3
H
.
CH2
m/z = 258
The above example occurs in the EI mass spectrum of 9–tetrahydrocannabinol
and such a fragmentation is not observed in other tetrahydrocannabinols that do
not possess a -hydrogen atom at the position shown above.