The document discusses mass spectrometry and provides information on various topics related to it including: - Types of ions produced including molecular ions, fragment ions, and metastable ions. - Common fragmentation patterns for different functional groups such as alkanes losing alkyl groups, alkenes forming allylic ions, and aromatics fragmenting at benzylic carbons. - General rules for fragmentation including favored cleavage at branched points and loss of the largest substituent from a branch. - Examples of mass spectra and prominent peaks are shown for compounds like ethanol, 2-pentanone, and hydrocinnamaldehyde to illustrate fragmentation patterns.

1. Mass Spectrometry
Presented By :- Ms. ARTI R RAJPUT
M.Pharm, (SUCOP,Pune)
1

2. Contents
 Introduction of Mass spectrum.
 Types of Ions
Molecular ion,
Metastable ions,
Fragment ions.




Fragmentation procedure
Fragmentation patterns
Fragment characteristics
Relative abundances of isotopes.
2

3. Introduction of MS

The impact of a stream of high energy electrons causes the
molecule to lose an electron forming a radical cation.

A species with a positive charge and one unpaired electron
H
H C H
H
+
-
e
H
H C H
-
+ 2e
H
Molecular ion (M+)
m/z = 16
3

4. Introduction of MS
Only cations are detected.
- Radicals are “invisible” in MS

The amount of deflection observed depends on the mass to
charge ratio (m/z).
-Most cations formed have a charge of +1 so the amount of
deflection observed is usually dependent on the mass of
the ion.

.
4

5. Molecular ion
Base peak
M+
Radical cation
Fragment ions
The ion obtained by the loss of an electron from the
molecule also called parent ion
The most intense peak in the MS, assigned 100%
intensity
Symbol often given to the molecular ion.
Mol. With an unpaired e+ve charged species with an odd number of electrons
Lighter cations formed by the decomposition of the
molecular ion. also called daughter ion

6. Mass Spectrum
 The resulting mass spectrum is a graph of the mass of each
cation vs. its relative abundance.
 Relative abundance of an ion means the % of total ion
current.
 Mass spectrum is an analytical techniques which can provide
information concerning the molecular structure of organic
comp.
 Base peak is the highest peak or the most intense peak in the
spectrum.
6

7. Types of Ion

Types of ion produced in MS
1.Molecular ions (parent ion)
2.Metastable ions
3.Fragment ions (Dissociation process)
4.Rearrangement ions
5.Multiple charged ions
6.Isotopes ions
7.Negative ions
8.Base peak
7

8. Molecular ion

Molecular ion (parent ion):
-The radical cation corresponding to the mass of the
original molecule
H
H C H
H

H C C H
H H
H H
The molecular ion is usually the highest mass in
the spectrum
8

9. Molecular ion

When a sample sub.is bombarded with electrons
of energies of 9 to 15eV, the molecular ion
is produced by loss of a single electron.

This will give rise to a very simple mass spectrum
with essentially all of the ion appearing in one
peak called parent peak.

M + e = M+ + 2e-

Most important ion.
9

10. Molecular ion

In organic compound there is generally a small peak
appearing one mass unit higher than the parent peak
(M+1) due to small but observable ,natural abundance
of C13 and H2 in these compound.

The relative height of parent peak decreases in the
following order,
aromatic>conjugated olefins>sulphides>
unbranched>hydrocarbon>ketones>amine>ester>
ethers >carboxylic acid>branched hydrocarbons.
10

11. Molecular ion

If a molecule yields the parent peak due to molecular
ion ,the exact molecular weight can be calculated.

Molecular ion are formed in the ground state and in
the electronically excited state.
11

12. Mass Spectrum

Mass spectrum of ethanol (MW = 46)
• Mass spectrum of ethanol (MW = 46)
M+ +
M
12

13. Introduction of MS
The mass spectrum of ethanol
base peak
M+
.
13

14. Fragment ion

The molecular ion produced in MS is generally left
with considerable excess energy.

This energy is rapidly lost by the molecular ion
resulting in one or more cleavages in it with or without
some rearrangement.

One of the fragment retains the charge where as the
remaining fragment may be stable molecule or
radicals.
14

15. Fragment ion

If the electron beam energy is further increased to
apparent potential of a molecule ,then the excited
molecule ions undergoes decomposition to give rise to
variety of fragment ions which leaves smaller masses
than the molecular ion.

Formed by both heterolytic and homolytic cleavage of
bond.

They are formed by simple cleavage and
rearrangement process.
15

16. Fragment ion

Bond dissociation energy stability of neutral fragment
are steric factors are some of the major factor which
determine formation of fragment ions.

E.g. : Ethyl chloride.

CH3-CH2-Cl + e- = CH3-CH2-Cl + + 2e-

CH3-CH2-Cl + = CH3-CH2+ + Cl. Or
CH2-CH2+ + HCl. (Fragment ion)
16

17. M + e-
M+* + 2e-
OR
+*
1
M
+
M2
M4+
Fragmentation Process
+
M3*

18. Metastable ion

The ions in a mass spectrometer that have sufficient
energy to fragment sometime after leaving the ion
source but before arriving at the detector.

M+
(m1/z)

M+ with large amount of internal energy will fragment
in the ionization source, producing “normal” A+ ions.
These A+ ions will be seen as narrow peaks at m/z
values correct for the mass and charge on the ion A+.

M+ having only a small excess of internal energy,
reach detector before decomposition can occur.
Narrow peaks for “normal” M+ appear
A+ + N
(m2/z) (m1-m2)
18

19. Metastable ion

M+ which posses excesses of internal energy that are
in between the those in above two cases, may
fragment after leaving the ion source and before
reaching the detector. The product ions, A+, are seen
in the mass spectrum as broad peaks, centered at m/z
values that are nor correct for the mass and charge on
the ion A+.


These broad peaks are called “metastable ion peaks”
These ““metastable ion peaks” do not represent
metastable M+ ions, but represent products of
decomposition of metastable ions.
The cause of A+ ions from metastable ion
decomposition being detected differently form “normal”
A+ ions is due to their different momentum.

19

20. FRAGMENTATION MODES
The RA of fragment ion formed depends upon’
1)The stability of the ion
2)Also the stability of radical lost.
The radical site is reactive and can form a new bond.
The formation of new bond is a powerful driving force for
ion decompositions.
The energy released during bond formation is available for
the cleavage of some bonds in the ion.
Some imp. Fragmentation modes are described below
1)Simple cleavage :
Involves i) Homolytic or
ii) Heterolytic cleavage
of a single covalent bond.
20

21. Fragmentation modes
 1) Homolytic cleavage :
odd electron ions have unpaired electron which is
capable of new bond formation.
Bond is formed , energy is released , help offset the
energy required for the cleavage of some other bond in
the ion.
Homolytic cleavage reactions are very common.
2) Heterolytic cleavage :
It may be noted the cleavage of C-X (X=
0,N,S,Cl) bond is more difficult than that of C-C bond.
In such cleavage , the positive charge is carried by the
carbon atom and not by the heteroatom.
R-CH2-Cl.+ = Cl. + RC+H2
21

22. Fragmentation modes
2) Retro –Diels –Alder reaction
The reaction is an example of multicentre
fragmentation which is characteristic of cyclic olefins.
It involves the cleavage of two bonds of a cyclic system ,
result the formation of 2 stable unsaturated fragment in
which 2 new bonds are formed.
This process is not accompanied by any hydrogen
transfer rearrangement.
The charge can be carried by any one of the fragment.
22

23. •
•
3)Mc Lafferty Rearrangement:
This involves migration of hydrogen atom from one part of the ion to
another.
To undergo a Mc Lafferty Rearrangement a molecule must possess
a) An appropriately located heteroatom e.g. O, N
b) A pi electron system ( usually a double bond) &
c) An abstractable hydrogen atom gamma to the C = X system
Gamma hydrogen atom is transferred through a six membered transition
state to an electron deficient centre followed by cleavage at beta
bond.
The reaction results in the elimination of a neutral molecule.
23

24. 24

25. 25

26. Rules
 A number of general rules for predicting prominent peak
in electron impact spectra are recorded and can be
summarized below
 1) most compound give molecule ion peak but some do
not . Existence of molecular ion peak in the spectrum is
dependent on the stability of molecule
 2)In case of alkenes , the relative intensity of the
molecule ion peak is greatest for the straight chain
compound but,
a) The intensity decreases with increases degree of
branching.
b) The intensity decreases with increasing molecular
weight in a homologous series.
26

27. Rules
 3) cleavage is favored at alkyl substituted carbons ,the
more substituted ,the more likely is the cleavage .Hence
the tertiary carbocation is more suitable than secondary,
which is more turn stable then primary. The cation
stability order is CH3 < R-CH2 <R2 CH+ <
R3C+.Generally the largest substituent at a branch is
eliminated most readily as a radical, presumably
because a long chain radical can achieve some stability
by delocalization of the lone electrons.
4)In alkyl substituted ring compounds, cleavage is
favoured at the bound at the bond beta to the ring giving
the resonance stabilized benzyl ion.
5)Saturated rings containing side chain, lose the side
chains at the alpha bond. the ve+ charge tend to stay
with ring fragment.
27

28. Rules
6)The cleavage of a C-X bond is more difficult than that
of a C-C bond (X=O, N, S, F, CI, etc). If occurred ,the
positive charge is carried by the carbon atoms, and not
to the heteroatom.the halogens having great electron
affinity do not have tendency to carry the positive
charge.
7)Double bonds favour allylic cleavage and give the
resonance stabilized allylic carbonium ion.
8)Compounds containing a carbonyl group tend to break at
this group with positive charge remaining with the
carbonyl portions.
28

29. Rules
9)During fragmentation, small, suitable neutral molecules
e.g. water, carbon monoxide, alcohol, ammonia,
hydrogen cyanide, carbon dioxide, ethylene etc,
are eliminated from appropriate ions.
29

30. Fragmentation Pattern for org. comp.
Organic molecules will fragments in very specific ways
depending upon what functional groups are present in the
molecule.
These fragments (if positively charged are detected in
mass spectroscopy)
The presence or absence of various mass peaks in the
spectrum can be used to deduce the structure of the
compound in question.
30

31. Fragmentation rules in MS
1. Intensity of M.+ is Larger for linear chain than
for branched compound
2. Intensity of M.+ decrease with Increasing MW.
(fatty acid is an exception)
3. Cleavage is favored at branching
 reflecting the Increased stability of the ionR
Stability order: CH3+ < R-CH2+ <
R CH
R
R
CH+ < R C+
R
R’
R”
Loss of Largest Subst. is most favored
31

32. Fragmentation Patterns

The impact of the stream of high energy electrons
often breaks the molecule into fragments, commonly a
cation and a radical.
- Bonds break to give the most stable cation.

Alkanes
- Fragmentation often splits off simple alkyl groups:
Loss of methyl
•Loss of ethyl
•Loss of propyl
•Loss of butyl
M+ - 15
M+ - 29
M+ - 43
M+ - 57
-Branched alkanes tend to fragment forming the most stable
carbocation's.
32

33. Fragmentation Patterns

Mass spectrum of 2-methylpentane
33

34. Fragmentation Patterns

Alkenes:
-Fragmentation typically forms resonance stabilized allylic
carbocation.
34

35. Fragmentation Patterns

Aromatics:
-Fragment at the benzylic carbon, forming a resonance
stabilized benzylic carbocation .
(which rearranges to the tropylium ion)
H
H C Br
H
H
H C
H C
or
M+
35

36. Fragmentation Patterns

Aromatics may also have a peak at m/z = 77 for the
benzene ring.
NO2
77
M+ = 123
77
36

37. Fragmentation Patterns

Alcohols :
-Fragment easily resulting in very small or missing parent ion
peak
-May lose hydroxyl radical or water
-M+ - 17 or M+ - 18
- Commonly lose an alkyl group attached to the carbinol
carbon forming an oxonium ion.
-1o alcohol usually has prominent peak at m/z = 31
corresponding to H2C=OH+
37

38. Fragmentation Patterns

MS for 1-propanol
CH3CH2CH2OH
H2C OH
M+-18
M+
38

39. Fragmentation Patterns

Amines:
-Odd M+ (assuming an odd number of nitrogen are present)
−α-cleavage dominates forming an iminium ion
CH3CH2 CH2 N CH2 CH2CH2CH3
H
CH3CH2CH2N CH2
H
m/z =72
iminium ion
39

40. Fragmentation Patterns
86
CH3CH2
CH2
N CH2
CH2CH2CH3
H
72
40

41. Fragmentation Patterns

Ethers
- α-cleavage forming oxonium ion
- Loss of alkyl group forming oxonium ion
- Loss of alkyl group forming a carbocation
41

42. Fragmentation Patterns

MS of diethyl ether (CH3CH2OCH2CH3)
CH3CH2O CH2
H O CH2
H O CHCH3
42

43. Fragmentation Patterns

Aldehydes (RCHO)
- Fragmentation may form acylium ion
RC O
- Common fragments
RC O
M+ - 1 for
R
(i.e. RCHO - CHO)
M+ - 29 for
43

44. Fragmentation Patterns
 MS for hydrocinnamaldehyde
105
91
H H O
M+ = 134
C C C H
H H
133
91
105
44

45. Fragmentation Patterns

Ketones :
O
RCR'
-Fragmentation leads to formation of acylium ion:
-Loss of R forming
-Loss of R’ forming
R'C O
RC O
45

46. Fragmentation Patterns

MS for 2-pentanone
O
CH3CCH2CH2CH3
CH3C O
CH3CH2CH2C O
M+
46

47. Fragmentation Patterns

Esters (RCO2R’)
-Common fragmentation patterns include:
Loss of OR’
-peak at M+ - OR’
Loss of R’
-peak at M+ - R’
47

48. Fragmentation Patterns
105
77
O
C O CH3
105
77
M+ = 136
48

49. • Summary of
Fragmentation pattern:
49

50. Alkanes
good M+
14-amu fragments
distinct M+
CH2=CH+
m/e = 41
CH2=CHCH2+
M-15, M-29, M-43, etc...
Alkenes
m/e = 27
loss of alkyl
strong M+
Cycloalkanes M-28
M-15, M-29, M-43, etc...
loss of CH2=CH2
loss of alkyl
strong M+
m/e = 105
C7H7+
C6H5+
m/e = 65 (weak)
C5H5+
M+ and M+2
Cl and Br
m/e = 49 or 51
Halides
m/e = 91
m/e = 77
Aromatics
C8H9+
CH2=Cl+
m/e = 93 or 95
CH2=Br+
M-36, M-38
loss of HCl
M-79, M-81
loss of Br·

51. M+ weak or absent
M-15, M-29, M-43, etc...
m/e = 31
CH2=OH+
m/e = 45, 59, 73, ...
RCH=OH+
m/e = 59, 73, 87, ...
R2C=OH+
M-18
loss of H2O
M-46
Alcohols
loss of alkyl
loss of H2O and CH2=CH2
strong M+
Phenols
strong M-1
loss of H·
M-28
loss of CO
M+ stronger than alcohols
M-31, M-45, M-59, etc...
loss of OR
CH2=OR+
M+ weak or absent
Amines
loss of alkyl
m/e = 45, 59, 73, ...
Ethers
M-15, M-29, M-43, etc...
Nitrogen rule
m/e = 30
CH2=NH2+ (base peak)
M-15, M-29, M-43, etc...
loss of alkyl
51

52. weak M+
m/e = 29
M-29
loss of HCO
M-43
loss of CH2=CHO
m/e = 44, 58, 72, 86, ...
McLafferty rearrangement
strong M+
aromatic aldehyde
M-1
Aldehydes
HCO+
aromatic aldehyde loss of H·
M+ intense
M-15, M-29, M-43, etc...
m/e = 43
CH3CO+
m/e = 55
+CH2CH=C=O
m/e = 42, 83
in cyclohexanone
m/e = 105, 120
Ketones
loss of alkyl
in aryl ketones
M+ weak but observable
M-17
M-45
Carboxylic Acids
loss of OH
loss of CO2H
m/e = 45
CO2H+
m/e = 60
·CH2C(OH)2+
M+ large
aromatic acids
52

53. M+ weak but observable
M-31
methyl esters loss of OCH3
m/e = 59
methyl esters CO2CH3+
m/e = 74
methyl esters
CH2C(OH)OCH3+
M+ weaker
Esters
methyl esters
higher esters
M-45, M-59, M-73, etc...
loss of OR
m/e = 73, 87, 101
CO2R+
m/e = 88, 102, 116
·CH2C(OH)OR+
m/e = 61, 75, 89
RC(OH)2+ (long alkyl ester)
m/e = 108
loss of CH2=C=O (benzyl,
acetate)
m/e = 105
C6H5CO+ (benzoate)
M-32, M-46, M-60
loss of ROH (ortho effect)
53

54. RA of Isotopes

RELATIVE ABUNDANCES OF ISOTOPES
 Isotope peak : The isotope peak are obtained when a molecule
contains heavier isotope of certain atoms than the
common isotopes.

Commonly seen isotope peak are (M+1)+ peaks or
(M+2)+ peaks
 Intensity of an isotope peak is much lesser than that of
the (M)+ peak except when Cl or Br is present in the
molecule.
54

55. ISOTOPES

Most elements occur naturally as a mixture of isotopes.
-The presence of significant amounts of heavier isotopes leads
to small peaks that have masses that are higher than the
parent ion peak.

M+1 = a peak that is one mass unit
higher than M+

M+2 = a peak that is two mass units
higher than M+
55

56. RA of Isotopes

RELATIVE ABUNDANCES OF ISOTOPES
 intensity of an isotope peak depends on the relative
abundance of that isotope in nature.
 The relative abundance of an isotope is calculate on
the basis of 100molecules.
 From RA, the intensity of (M+1)+, (M+2)+ peaks can
be determined.
 For a compound containing one carbon atom , out of
every 100 molecules, 98.892 molecule contain C12
isotope and 1.108 molecule contain C13 isotope
56

57. RA of Isotopes

RELATIVE ABUNDANCES OF ISOTOPES
 Hence , the intensity of (M+1)+ peak is about 1.1% of
the intensity of the (M) +peak and the ratio of the
intensities of M+ and (M+1)+ peak is 98.892:1.108.
 For compound containing silicon , the intensities of
(M) + peak corresponding to Si28 isotope , (M+1) + peak
corresponding to Si29 isotope and (M+2) + peak
corresponding to Si30 isotope are in proportion of their
relative abundance in the nature , i.e. 92.18:4.71:3.12.
57

58. RA of Isotopes





RELATIVE ABUNDANCES OF ISOTOPES
For compound containing sulphur , the ratio of
intensities of (M) +: (M+2) + peaks , corresponding to
S32 and S34 isotopes is 95.018:4.215.
The height of the peak is the measure of intensity of
that peak.
Fluorine and iodine have only one naturally occurring
isotope corresponding to atomic mass of 19 and 127,
resp.
Hence they produced only one peak corresponding to
(M) + ion.
58

59. RA of Isotopes

RELATIVE ABUNDANCES OF ISOTOPES
S.
Isotope
Relative abundance
peak
1
1H:2H
99.985:0.015
(M+1)
2
12C:13C
98.892:1.108
(M+1)
3
14N:15N
99.635:0.365
(M+1)
4
16O:17O:18O
99.759:0.037:0.204
(M+1) ,
(M+2)
5
28Si:29Si:30Si
92.18:4.71:3:12
(M+1),
(M+2)
6
32S:33S:34S
95.018:0.75:4.215
(M+1),
(M+2)
7
35Cl:36Cl
75.529:24.471
(M+2)
8
79Br:81Br
50.52:49.48
(M+2)
59

60. References:
1. Silverstein R.M., & Webster F.X, Spectrometric Identification of
Organic Compounds, Sixth edition 2006, Page no. 2 – 28.
2. Sharma Y. R. Elementary Organic Spectroscpoy Principles and
Chemical Application, Fourth edition 2007, S. Chand &
Company, Page no. 280 – 339.
3. Chatwal G.R., Aanand S.K., Instrumental Methods ofAnalysis,
Himalaya Publishing House, 5th Edition, Page no. 2.272-2.302
4. http://www.chemistry.ccsu.edu/glagovich/teaching/316/index.ht
ml access date - 19 sept 2013
5. http://en.wikipedia.org/wiki/Mass_spectrometry
access date – 19 sept 2013
6. Dr. supriya s. mahajan,Instuumental methods of analysis , page no.
125 -154
60

61. 61

62. 62