The document discusses various fragmentation patterns seen in mass spectrometry for different functional groups. For alcohols, cleavage of the carbon-carbon bond adjacent to the oxygen is common, as is loss of a water molecule. Aromatic ethers often fragment through cleavage of the carbon-oxygen bond or rearrangement within the aromatic ring. Carboxylic acids may lose a hydroxyl group or carboxyl group through cleavage of bonds adjacent to the carbonyl. The presence of halides is indicated by isotopic peaks from chlorine or bromine atoms.

1. BY
K RAKESH GUPTA

2. INTERPRETATION
* Mass of M+•- most abundant isotope masses of each element in
the molecule
* MS have unit mass resolution-atomic mass- nominal mass
* M+•-identified as the ion with highest m/z ratio
* But with caution- may be an impurity/ an isotope of M+•
* Many compounds- no M+• - Low energy EI or CI for confirmn.
* Base peak- Ion with greatest abundance-need not be M+•
* Mass Spectrum- finger print of molecular structure
* Computer data bases can be used to identify unknown compounds

3. Characteristics of Molecular Ions
* Most compounds have an even molecular mass-exception is ‘N’ rule
* Nitrogen rule: Compound with an odd number of ‘N’ –odd M +•
* Compounds with even or zero number –even molecular mass
* CH4 (16), NH3 (17), C9H7N (129), N2H4 (32), C27H46O (386)
* Nitrogen- odd valence and even mass
•M +•, the next highest mass fragment-loss of a neutral fragment
•Look for the ratio of M+. to M+2 peak- 3:1-Cl and 1:1 -Br

4. M- Ion
1 H
3-14 None
15 CH3
16 O, NH2
17 OH, NH3
18 H2O
21-25 None
26 C2H4
Reasonable Losses due to Fragmentation

5. OH NH2
C6 H12 O C6 H14 N
MW→100
100/13 = 7C+0→C7H16
1 O: C7 H16 -CH4 +O
MW →99 odd!
99/13 = 7C→ C7H16
1 N: C7 H16 -CH2
+N
Nitrogen Rule

6.  m/z 57 (100), m/z 43 (2), m/z 42 (2), m/z 41 (50),
m/z 29 (45)
 CH3CH=CH-NH2 (M+. m/z 57)
 m/z 42 (M-CH3); m/z 41 (M-NH2); m/z 43 (-14 units)
 Loss of CH2 is rare and unlikely- so m/z 57 is not M+.
 It may be fragment ion- CH3-C(CH3)3
+.

7. Natural Abundances of the Isotopes
C13, N15, S33- contribute to M+1; O18, S34 Cl35, Br81to M+2
CH4, M+1, 1.1%; C2H6- 2.2%

8. Mass and Relative Abundance of Organic
Elements
 Elements containing only one isotopic form :
 Element Mass
 H(A) 1
 F(A) 19

 Elements containing two isotopic forms :
 Element Mass % Abundance Mass % Abundance
 C (A + 1) 12 100 13 1.10
 O (A + 2) 16 100 18 0.20
 Elements containing three isotopic forms :
 Element Mass % Abundance Mass % Abundance Mass %
Abundance
 S (A + 2) 32 100 33 0.80 34
4.4
 Si (A + 2) 28 100 29 5.10 30
3.4

10. 
Molecular Formula from Mass
Spectra
Inferences from graph :
m/z Relative abundance
(x) (y)
64 100.0
65 0.9
66 5.0
With the error limits,
m/z Relative abundance
(x) (y)
64 100.0
65 0.9 ± 0.20
66 5.0 ± 0.50
m/z Relative abundance S O2
64 100.0 100.0 100.0
65 0.9 ± 0.20 0.8 0.08
66 5.0 ± 0.5 4.4 0.4
Conclusions :
Presence of an sulfur atom and O2 due to (A+2) pattern and from the peaks in
the corresponding spectra.

11. (a+b)n ; a=3, b=1 for Cl; for Br a=2 and b=2

12. M+. Cl35, Br79; =3x2=6
M+2 Cl37, Br79 & Cl35, Br81= 8
M+4 Cl37, Br81=2

13. Mass spectral reactions:
Unimolecular, competitive and consecutive
Ions with wide range of internal energy
ABCD + e-  ABCD +• + 2e
ABCD + e-  A +• + BCD•
 AB+ + CD•  A+ + B
 AB• + CD+ C+ + D (I)
 AD+ + BC• (II)
ABCD +• + ABCD  [ ABCD ABCD ]+  ABCDA+(III)
“Cool ions” appear as M +•
(I) Simple cleavages
(II) Rearrangements
(III) ion-molecule reactions
MS FRAGMENTATION OF HYPOTHETICAL MOLECULE

14. Abundance of ions depends on:
 Stability of the +ve charge in the cation or +.
 ion stabilization- e- sharing –hetero atoms nonbonding
orbital CH3-C + =O  CH3-CO +
 Resonance stabilization:CH2=CH-CH2
+  +CH2-CH=CH2
 Stability of radical or neutral species
 Steric arrangements of atoms or groups of atoms-
favoring Rearrangements
 Stevenson Rule: ABCD+.  A + + BCD• or A . + BCD+
Radical of high IE, Ion of low IE
 Loss of largest alkyl group-most abundance ion-exception
C2H5CH(CH3)-C4H9
+  [C2H5CH(CH3)+] >[CH(CH3)-C4H9
+ ]
> [C2H5CH-C4H9
+] > [C2H5C(CH3)-C4H9
+ ]

15. 
---- C – C ---- ---- C
+ . C ----+
---- C – Z ---- ---- C
+ . Z ----+
At heteroatom
+ .
+ .
a to heteroatom
---- C - C – Z ---- C=Z
+ ---- C
.
+
+ .
---- C - C – Z ---- Z
+ . ---- C = C
+
+ .
Fragmentation process
Cleavage of s
bond

16. 
+
.
---- HC – C – Z ---- ---- C=C
+ HZ
+
Retro Diels-alder
+ .
CH2
CH2
CH2
CH2
+
+ . + .
McLafferty
Z
H
Z R
CH2
CH2
Z
H
Z R
+
.
Fragmentation process
Cleavage of 2 s bond (rearrangements)

17. 
R
R
CH+ < C+
R
R
R
R
R”
CH
R’
Loss of Largest Subst. Is most favored
Alkanes
Intensity of M.+ is Larger for linear chain than for
branched compound
Intensity of M.+ decrease with Increasing M.W.
(fatty acid is an exception)
Cleavage is favored at branching
 reflecting the Increased stability of the ion
Stability order: CH3
+ < R-CH2
+ <

18. Molecular ion peaks are present, possibly with low intensity. The
fragmentation pattern contains clusters of peaks 14 mass units apart
(which represent loss of (CH2)nCH3).
Alkane

19. 
Illustration of first 3 rules (large MW)

20. CH3
CH3
CH3
CH3
CH3
CH3
CH3
MW=170
M.+ is absent with heavy branching
Fragmentation occur at branching: largest fragment los
Branched alkanes

21. Molecular ion is stronger than
in previous sample

22. Molecular ion smaller than linear
alkane
Cleavage at branching is favored
43
(Branched alkane with Smaller MW)

23. 
Alkanes
Cleavage Favored at branching
Loss of Largest substituent
Favored
intensity of M
.+
is smaller with branching

24. 
CH2
+
CH CH2 R
- R
.
CH2
+
CH CH2
CH2 CH CH2
+
Aromatic Rings, Double bond, Cyclic
structures stabilize M.+
Double bond favors Allylic Cleavage
 Resonance – Stabilized Cation

25. 
Aromatic ring has stable M.+

26. 
Cycloalkane
ring has stable
M.+

27. R
+ .
+
-R
.
CH2
CH2
CH2
CH2
+
+ . + .
Saturated Rings lose a Alkyl Chain
(case of branching)
Unsaturated Rings  Retro-Diels-Alder

28. 
+ . + .
Retro Diels-Alder

29. a-and -ionones-different spectra-position of db
a--ionone-RDA frgment m/z 136-abundant
-ionone-RDA not favorable-unsubstituted olefin

30. 
C
CH
+
R
-R
.
CH
+
CH2 CH2
+
+
m/z 91
O CH2
+
O
+
Aromatic Compounds Cleave in

 Resonance Stabilized
Tropylium
Tropylium ion

31. +
+
Tropylium ion

32. 
R CH2 CH2 Y R
x
CH2 Y R
+
CH2
+
Y R
x
R2
C
R1
O
C
R1
O
+
C
+
R1
O
- [RCH2]
- [R2]
larger
C-C Next to Heteroatom cleave leaving
the charge on the Heteroatom

33. Esters lose a molecule of acid- similar to loss of H2O from alcs.
Deuterium expts- ‘H’ comes from -position
When -H not available- a ketene is eliminated
Rearrangement reactions in OMS involve ‘H’ atom transfer

34. 
x
CH2
CH2
H
CH2
O
C
Y
x
CH2
CH2
H
CH2
O
C
Y
McLafferty
Y  H, R, OH, NR2
Ion Stabilized
by resonance
- CH2=CH2
x
CH2
O
C
Y
H
Cleavage of small neutral
molecules
(CO2, CO, olefins, H2O ….)
Result often from rearrangement

35. McLafferty Rearrangement: Involves -H migration to a d.b-6TS
Requires- multiple bond. C=O, C=C, C=S, C=N, CC, CN and a -H
Interatomic distance of 1.8 A between -H and acceptor
Enol form is retained before
fragmentation

36. Neutral species like H2O, NH3, ROH etc.-eliminated from ortho
Disubstituted aromatic compounds- Ortho effect
Differentiation of Ortho- from meta- and para- isomers

38. 
-Et
-29
Most intense peaks are often:
m/z 41, 55, 69
Double Bond Stabilize M+
Double Bond favor
Allylic cleavage
CH2 CH CH+ Et
EtMe
+CH2 CH CH
EtMe
CH2 CH CH +
EtMe
M+ = 112 m/z = 83

39. 

40. Alcohol
An alcohol's molecular ion is small or non-existent. Cleavage of the
C-C bond next to the oxygen usually occurs. A loss of H2O may
occur as in the spectra below.

41. 16
Mass Spectral Cleavage Reactions
of Alcohols
 Alcohols undergo a-cleavage (at the bond next to the
C-OH) as well as loss of H-OH to give C=C

42. 
Alcohols

43. 
Phenol

45. H3C CH
NH2
CH2
NH2
m/z30m/z44
3:1
H3C C
OH
CH2
NH2
CH3
m/z59 m/z30
2:1
H3C C
OH
CH2
NH2
CH3
m/z58 m/z31
17:1
C6H5 CH2 CH2 OH
91 31
15:1
C6H5 CH2 CH2 NH2
91 30
1:10
CH3 C CH2
CH3
CH3
OH
57 31
3:1
R CH2
OH
CH2
+
OH
+.
R CH2
NH2
CH2
NH2
+
+.
m/z 31 m/z 30
R CH R
OH
CH
+
R'
OH
m/z 30+R'
' "'R C R'
OH
R"
-R"' C R'
OH
R"
+
m/z 29+R'+R"
+.
C
R
X
+ C
R
X
+R C
X
R R
.
:
+
X= N,S,O,cl

46. Molecular ion is prominent
1)
Cleavage in  of aromatic ring
Rearrangement
2)
x
O
R
O
+
C5H5
-CO
m/z 93 m/z 65
O
H
- CH2=CH2 x
O
H
H
x
O
H
H
m/z 94
- R
Aromatic Ether

47. 
• +
B
CH3 —CH2 —O—CH2 —CH2 —CH2 —CH3 CH3 —CH2 —O+ =CH2
CH3 —CH2 —O —CH2
+
Cleavage of C-C next to Oxygen
Loss of biggest fragment
m/z 59
Aliphatic Ether

48. m/z 73
m/z 45
B
CH3 —CH2—CH —O —CH2 —CH3
CH3
CH =O+ —CH2
CH3
H— CH2
Box rearr.
CH =O+ H
CH3
1- Cleavage of C-C next to Oxygen
m/z 73
m/z 45
M·+
2- Cleavage of C-O bond: charge on alkyl
Ether
Rearrangemen
t

49. Ether
Fragmentation tends to occur alpha to the oxygen atom

50. Aldehyde
Cleavage of bonds next to the aldehyde group results in the loss of
hydrogen (molecular ion less 1) or the loss of CHO.
Major fragmentation peaks result from cleavage of the C-C bonds adjacent
to the carbonyl
Ketone

51. Carboxylic Acid
In short chain acids, peaks due to the loss of OH (molecular ion less 17)
and COOH (molecular ion less 45) are prominent due to cleavage of bonds
next to C=O.
Ester
Fragments appear due to bond cleavage next to C=O (alkoxy group
loss, -OR) and hydrogen rearrangements

52. Amide
Primary amides show a base peak due to the McLafferty rearrangement
Amine
Molecular ion peak is an
odd number. Alpha-
cleavage dominates
aliphatic amines.
The base peak is
from the C-C
cleavage adjacent
to the C-N bond.

53. Halide
The presence of chlorine or bromine atoms is usually recognizable from
isotopic peaks