This document summarizes the common fragmentation patterns observed in mass spectrometry for different functional groups. It describes the typical bond cleavages and fragment ions formed. For example, it notes that alkanes commonly form fragment ions of m/z 43 and 57 due to C3H5+ and C4H7+ ions. Alcohols typically undergo alpha cleavage of the C-C bond next to the hydroxyl group. Aromatic compounds often involve cleavage of the bond beta to the aromatic ring. The document provides examples of characteristic fragmentation for each functional group class.

1. Mass Spectrometry Fragmentation Pattern
Sr.
NO
TYPE OF
functional
Group
Group Sub Group Rule 1 Rule 2 example
1 Hydrocarbo
ns
Alkanes Straight-chain
alkanes
highly branched and arise via
molecular rearrangements
The most intense peaks are at
mle 43 and 57 due to C 3Hj and C 4H; fragment
ions, respectively
Branched-
chain alkanes
Bond cleavage favourably occur at
the branch point
because it gives more stable
carbocations
Generally, the largest substituent at a
branch point is eliminated most readily as a radical
because it is stabilized by
delocalization of the lone electron
Cycloalkanes. In cycloalkanes with side chains,
cleavage tends to occur at
the a bond, i.e. the fission of bond
between the ring and side chain
occurs. This
is just a special case of fragmentation
at brauch point.
Fragmentation of the ring
requires the fission of at least two bonds.
Alkenes
(Oiefins)
The most common fragmentation of
alkenes is the
allylic cleavage, i.e. cleavage of the
band ß to the double band resulting in
the
formation of a resonance stabilized
allylic cation:.
Alkenes having a yhydrogen
with respect to the double band also undergo the
McLafferty rearrangement.

2. Cycloalkenes. Cyclohexene and its derivatives
undergo characteristic
fragmentation through retro-Diels-
Alder reaction in which a diene and a
monoene
fragments are formed.
Alkynes In alkynes, the fragment ions (with
composition CnH2n_3) are generally
formed
by loss of alkyl radicals. Thus, M-15,
M-29, M-43 etc. peaks are commonly
present in the mass spectra of
all<ynes.
Alkynes having a y hydrogen with respect to the
triple bond also undergo the McLafferty
rearrangement
Aromatic
Hydrocarbo
ns
Molecular ion peaks in aromatic
compounds are fairly !arge because
an aromatic
ring stabilizes the molecular ion.
In alkylbenzenes, the dominant fragmentation
involves
the cleavage of the bond ß to the aromatic ring
(benzylic cleavage) because it
gives resonance stabilized carbocations
2 (ii) Halogen
Compounds
A compound containing two
chlorines, or two bromines, or one
chlorine and
one bromine will show M + 2 and M
+ 4 peaks.

3. (a) Alkyl
Halides
The intensities of molecular ion peaks
of alkyl halides follow the order:
RI > RBr > RCI > RF
The intensity of the molecular ion decreases with
increase in chain length and
increase in branching.
Cleavage of a C-C bond ß to the halogen atom is
the favourable mode of
fragmentation.
The
intensity of these ions is attributed to the stability
of the five-membered cyclic
structure.
(b) Aryl
Halides
The molecular ion peaks are strong in
aryl halides. M-X peak is intense for
all
compounds containing X directly
attached to the ring
Benzyl halides lose halogen to form benzyl eation
whieh ehanges to the more
stable tropylium ion. For example,
3 Hydroxy
Compounds
(a) Aliphatic
Alcohols
In all the three classes of aleohols, i.e.
primary, seeondary and tertiary
alcohols,
the a-eleavage of C-C bond is
eharaeteristie. The largest alkyl group
is expelled
most readily as a radieal because a
Iong-ehain radieal is stabilized by
delocalization
of the lone eleetron

4. Maclaferty Rearrangement
b) Aromatic
Alcohols
(Molecular ion peak is generally
strong in benzyl alcohols. Benzylic
cleavage
occurs and the charge is retained by
the aryl group
.
(c) Phenols The most common fragmentations in
phenols involve
the loss of CO (M-28) and CHO (M-
29). In addition, a small peak at M-1
is also
observed due to loss of hydrogen
radical.

5. 4 a) Aliphatic
Ethers
( Cleavage of the C-C bond next to the
oxygen atom. The loss of the !arger
fragment as a radical is preferred. A
weak M-1 peak is also formed by loss
of an
a-H
(b) Aromatic
Ethers
Primary fragmentation occurs at the
bond ß to the ring, and the ion thus
formed fragments further, e.g. anisole
gives
ions of m/e 93 and 65
In alkyl aryl ethers, when the alkyl group has two
or more carbon atoms,
cleavage ß to the ring is accompanied by hydrogen
rearrangement. Here, C-C
cleavage next to the oxygen atom is insignificant
(c) Acetalsand
Ket
als Their mass spectra show very weak
molecular
ion peaks. Following is the
characteristic fragmentation mode of

6. acetals which
is mediated by an oxygen atom and
this facile.
5 Aldehydes and
Ketones
a-Cleavage. This involves the
cleavage of the C-C bond next to the
oxygen atom to give resonance-
stabilized acylium ions as
Cleavage ( McLafferty rearrangement).
Aldehydes and ketones containing
a y-hydrogen atom undergo ~cleavage via
McLafferty rearrangement as
Aromatic aldehydes and ketones
undergo a-cleavage to give
characteristic
+
ArC===O ion which usually accounts
for the base peak.
Cyclic Ketones Theseshow prominent molecular ion
peak. Primary cleavage of
the C-C bond next to the oxygen
atom produces an ion which
undergoes
hydrogen rearrangement from a
primary radical to a more stable
conjugated
secondary radical
6 Carboxylic
Acids,
Estersand
Amides
Carboxyli
c Acids,
Estersand
Amides
(a) Aliphatic Aliphatic acids, esters and
amidesundergo a-cleavage, i.e.
cleavage ofbonds next to C =0, and
the positive
charge may remain with R or Y. R+
and y+ may also appear. In short-
chain acids,
peaks at M-
OH and M-COOH are prominent.
Long-ehain aeids exhibit two series of peaks
resulting from cleavage at eaeh
C-C bond with retention of eharge either on the
oxygen-eontaining fragment
(m/e 45, 59, 73, 87, ... )

7. Carboxylie aeids, esters and amides
undergo MeLafferty rearrangement if
they eontain y hydrogen.
Acetates eliminate CH3COOH and unsaturated
esters eliminate C02 as
In addition to a-cleavage and
McLafferty rearrangement (ß-
cleavage), suitable
amides also undergo y8 C-C bond
cleavage, e.g.
b) Aromatic Ortho effect. When a substituent and a hydrogen
are in close proximity to
form a six-membered transition state, the loss of
neutral molecules of H20,
ROH or NH3 occurs. This is called ortho effect
Benzyl and phenyl acetates eliminate ketenes to
form the base peak. In case
+
ofbenzyl acetate, peaks due to CH 3 C=O (m/e 43)
and tropylium ion (mle 91)
are also prominent.

8. 7 Amines (a) Aliphatic The cleavage of the C-C bond next to
the nitrogen atom is the most
favourable
fragmentation pattern of amines.
The primary fragment (I) from a secondary or
tertiary amine undergoes
fragmentation via hydrogen rearrangement similar
tothat described for aliphatic
ethers to 'give a peak
(b) Cyclic Their primary cleavage occurs at the bond next to
the nitrogen atom leading to loss
of an a-hydrogen atom to gi ve a strong M-1 peak,
(c) Aromatic Loss of one of the amino hydrogens of
aniline gives an intense M-1 peak. Loss of HCN
followed by loss of a H atom
also gives prominent peaks.
8 Aliphatic
Nitriles
The molecular ion peaks of aliphatic nitriles are
weak and sometimes undetectable.
M-1 peak formed by loss of a-hydrogen is weak but
very useful for their detection

9. 9 Nitro
Compounds
(a) Aliphatic
Their molecular ion peaks are weak
or absent. Presence of a nitro group is
+ +
indicated by peaks at m/e 30 (NO)
and 46 ( N0 2). The main peaks are
due to
the hydrocarbon fragments up to M-
46.
(b) Aromatic
Their molecular ion peak are strong. Elimination of
an N02 radical gives
M-46 peak (the base peak in nitrobenzene) and
neutral NO molecule is lost to
give strong M-30 peak due to the phenoxy cation
(mle 93).
When a substituent is present in the m- or p-
positions, e.g. in m- and pnitroanilines,
the fragmentation pattern similar tothat of
nitrobenzene is observed.
However, when a hydrogen-containing substituent
is present ortho to the nitro
group
10 Sulphur
Compounds
The molecular
ion peaks of sulphur compounds is
generally much more intense than the
corresponding oxygen-containing
compounds. This is because the
ionization
energy of the non-bonding sulphur
electron is lower than that of oxygen
(a)
Thioalcohols
(Thiols or
Mercaptans)
These show fragmentation modes very similar to
that of alcohols, i.e. a-cleavage,
the cleavage with loss of hydrogen sulphide (M-34)
and the cleavage with loss
of H 2S together with elimination of an olefin are
characteristic
(b) Thioethers
(Sulphides)
These show fragmentation modes very similar to
that of ethers. Cleavage of
a, ß C-C bonds occur with favourable loss of the
largest group.
11 Heterocyclic
Compounds
( Aromatic heterocyclic compounds show intense
molecular ion peak. They undergo
fragmentation similar to benzene, e.g. benzene
eliminates C2H2 from its molecular
ion, whereas pyrrole and pyridine loose HCN.
Similarly, thiophene eliminates

10. CHS and furan CHO from their parent ion. Pyrrole,
thiophene and furan also
• + + +
eliminate C 3H 3 from their molecular ions to give
HC:;:::N, HC==S and HC==O
ions, respectively