PENENTUAN STRUKTUR MOLEKUL

3. Mass Spectrometry
Department of Chemistry
University Indonesia
 INSTRUMENTAL METHODS OF
STRUCTURE DETERMINATION
1. Nuclear Magnetic Resonance (NMR) – Excitation of the nucleus of
atoms through radiofrequency irradiation. Provides extensive
information about molecular structure and atom connectivity.
2. Infrared Spectroscopy (IR) – Triggering molecular vibrations
through irradiation with infrared light. Provides mostly information
about the presence or absence of certain functional groups.
3. Mass spectrometry – Bombardment of the sample with electrons
and detection of resulting molecular fragments. Provides information
about molecular mass and atom connectivity.
4. Ultraviolet spectroscopy (UV) – Promotion of electrons to higher
energy levels through irradiation of the molecule with ultraviolet light.
Provides mostly information about the presence of conjugated
systems and the presence of double and triple bonds.
OUTLINE

Introduction to Mass Spectrometry

Ionization Methods

Mass Analyzer

Fragmentation and MS Interpretation

 Mass Spectrometry
Introduction

• Mass spectrometry is a technique used for measuring

the molecular weight and determining the molecular
formula of an organic compound.
• In a mass spectrometer, a molecule is vaporized and
ionized by bombardment with a beam of high-energy
electrons.
• The energy of the electrons is ~ 1600 kcal (or 70 eV).
• Since it takes ~100 kcal of energy to cleave a typical 
bond, 1600 kcal is an enormous amount of energy to
come into contact with a molecule.
• The electron beam ionizes the molecule by causing it
to eject an electron. 4
 A. Mass Spectrometry of Small
Molecules:Magnetic-Sector Instruments
Bonds in cation radicals
begin to break (fragment)

Sample
vaporized and
subjected to
bombardment
by electrons
that remove an
electron
creating a Mass to charge (m/z)
cation radical ratio is measured
Molecular ion (M+)
shows molecular weight

5
Ionization Methods
 Electron bomb Ionization (EI)

 Chemical Ionization (CI)

 Field ionization (FI)

 Matrix Assisted Laser Desorption Ionization (MALDI)
 Fast atom bombardment (FAB)
 Electro Spray Ionization (ESI)

6
 Electron Bomb Ionization ( EI )
Sample is heated and energized by a beam of electrons, usually
gives a molecular ion (M+) and a lot of fragments 。
H H
H C C H
H H
H H H H
e- + H C C H H C C+ H
H H H H

H H
Mass Spectrum (M-R )+
2
(M-R1)+ H C+ C H
(M-R3)+ M+ H H
Types of Mass Analyzers
 Magnetic sector analyzer

 Time of Flight analyzer (TOF)

 Quadrupole analyzers
 Fourier Transform Ion-Cyclotron
Magnetic Sector Analyzer
Magnetic sector analyzer – Uses electric and/or
magnetic fields to separate ions
 Mass Spectrometry

• When the electron beam ionizes the molecule, the species that is
formed is called a radical cation, and symbolized as M+•.
• The radical cation M+• is called the molecular ion or parent ion.
• The mass of M+• represents the molecular weight of M.
• Because M is unstable, it decomposes to form fragments of radicals
and cations that have a lower molecular weight than M+•.
• The mass spectrometer analyzes the masses of cations.
• A mass spectrum is a plot of the amount of each cation (its relative
abundance) versus its mass to charge ratio (m/z, where m is mass, and
z is charge).
• Since z is almost always +1, m/z actually measures the mass (m) of the
individual ions.

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 Mass Spectrometry
Consider the mass spectrum of CH4 below:

• The tallest peak in the mass spectrum is called the base peak.
• The base peak is also the M peak, although this may not always
be the case.
• Though most C atoms have an atomic mass of 12, 1.1% have a
mass of 13. Thus, 13CH4 is responsible for the peak at m/z =11 17.
This is called the M + 1 peak.
 Mass Spectrometry

• The mass spectrum of CH4 consists of more peaks than

just the M peak.
• Since the molecular ion is unstable, it fragments into
other cations and radical cations containing one, two,
three, or four fewer hydrogen atoms than methane itself.
• Thus, the peaks at m/z 15, 14, 13 and 12 are due to these
lower molecular weight fragments.

12
 The Mass Spectrum
 Plot mass of ions (m/z) (x-axis) versus the intensity of the signal
(roughly corresponding to the number of ions) (y-axis)
 Tallest peak is base peak (100%)
 Other peaks listed as the % of that peak

 Peak that corresponds to the unfragmented radical cation is

parent peak or molecular ion (M+)

H H H
Propane H C C C H
MW = M+ = 44 H H H

13
 Mass Spectrometry

Figure.2
Mass spectrum of hexane
(CH3CH2CH2CH2CH2CH3)

14
 Interpreting Mass Spectra

M+ peak Example:
 Possible formulas can be determined from the mass. (M+)

Predict possible molecular formulas containing C, H, and

maybe O if :
M+ = 86 M+ = 156

15
 M+ peak Example:
 Possible formulas can be predicted from the mass. (M+)

Predict possible molecular formulas containing C, H, and

maybe O if :
M+ = 86 M+ = 156
C6H14 C11H24 C10H4O2
C5H10O C12H12 C9H16O2
C4H6O2 C11H8O C8H12O3
C3H2O3 C10H20O C7H8O4
C6H4O5

16
 Mass Spectrometry

The Nitrogen Rule

• Hydrocarbons like methane (CH4) and hexane (C6H14), as well as

compounds that contain only C, H, and O atoms, always have a
molecular ion with an even mass.
• An odd molecular ion indicates that a compound has an odd
number of nitrogen atoms.
• The effect of N atoms on the mass of the molecular ion in a
mass spectrum is called the nitrogen rule: A compound that
contains an odd number of N atoms gives an odd molecular
ion. A compound that contains an even number of N atoms
(including zero) gives an even molecular ion.

17
 Mass Spectrometry

The Nitrogen Rule

Nitrogen rule: A compound that contains an odd number

of N atoms gives an odd molecular ion.

•Two “street” drugs that mimic the effect of heroin

illustrate this principle.

18

18
Relative Abundance of Isotopes
Atomic weight of an element is a weighted average of the naturally
occurring isotopes.
Isotopic Ratio from the Spectra
Mass spec. can be used to measure the isotopic ratios
 Mass Spectrometry
Alkyl Halides and the M + 2 Peak
• Most elements have one major isotope.
• Chlorine has two common isotopes, 35
Cl and 37
Cl,
which occur naturally in a 3:1 ratio.
Thus, there are two peaks in a 3:1 ratio for the
molecular ion of an alkyl chloride.
The larger peak, the M peak, corresponds to the
compound containing the 35Cl. The smaller peak, the M
+ 2 peak, corresponds to the compound containing 37Cl.
Thus, when the molecular ion consists of two peaks (M
and M + 2) in a 3:1 ratio, a Cl atom is present.
• Br has two isotopes—79Br and 81
Br, in a ratio of ~1:1.
Thus, when the molecular ion consists of two peaks
(M and M + 2) in a 1:1 ratio, a Br atom is present. 21
 Mass Spectrometry

Alkyl Halides and the M + 2 Peak

Figure.4
Mass spectrum of
2-bromopropane [(CH3)2CHBr]
22
Mass Spectrum with Bromine

=>
Chapter 12 23
Mass Spectrum with Chlorine

=>
Chapter 12 24
Continuation of Isotopes

Chlorine (35Cl to 37Cl is 3:1, give M + 2)

 M+ peak :
 Peaks above the molecular weight appear as a result
of naturally occurring heavier isotopes in the sample
 (M+1) from 1.1% 13C in nature
 (M and M+2) in 75.8%/24.2% ratio = 35Cl and 37Cl
 (M and M+2) in 50.7%/49.3% ratio = 79Br and 81Br

H H H
Propane
H C C C H
MW = M+ = 44
H H H

M+1 = 45
From 1.1% 13C

26
 Click on image to enlarge

M+ peak: Halides
M+ and M+2 in
75.8%:24.2% CH3Cl
(~ 3:1) ratio
= 35Cl and 37Cl

M+ and M+2 in Br
50.7%:49.3%
(~ 1:1) ratio
= 79Br and 81Br

27
 Mass-Spec Fragmentation Patterns
 Molecular ions break into characteristic fragments that can be
identifed
 Serves as a “fingerprint” for comparison with known materials in
analysis (used in forensics)
 Positive charge goes to fragments that best can stabilize it

28
Mass-Spec Fragmentation Patterns

M -15 = 57

CH3=15

MW=72;
M+ peak not seen
29
 Mass Spec: Fragmentation of Hexane
Hexane (m/z = 86 for parent) has peaks at
m/z = 71, 57, 43, 29

71=Loss of CH3 (15)

57=Loss of CH3CH2 (29)

30
 CH3

Learning Check: MW=98 MW=98

Identify the following MS as that of methylcyclohexane or ethylcyclopentane.

31
 CH3

Solution: MW=98 MW=98

Identify the following MS as that of methylcyclohexane or ethylcyclopentane.

98-69=29 loss of (CH3CH2)

98-83=15 (loss of CH3)

M+ =98

32
 CH3

Learning Check:
MW=98 MW=98
Identify the following MS as that of methylcyclohexane or ethylcyclopentane.

33
 CH3

Solution:
MW=98 MW=98
Identify the following MS as that of methylcyclohexane or ethylcyclopentane.

98-83=15 (loss of CH3)

M+ =98

34
 Mass Spectrometry
High Resolution Mass Spectrometers
• Low resolution mass spectrometers report m/z values to the nearest
whole number. Thus, the mass of a given molecular ion can
correspond to many different molecular formulas.
• High resolution mass spectrometers measure m/z ratios to four (or
more) decimal places.
This is valuable because except
for 12C whose mass is defined as
12.0000, the masses of all other
nuclei are very close—but not
exactly—whole numbers.
Table 13.1 lists the exact mass
values for a few common nuclei.
Using these values it is possible
to determine the single molecular
formula that gives rise to a 35

molecular ion.
 Mass Spectrometry

High-Resolution Mass Spectrometers

• Consider a compound having a molecular ion at m/z = 60
using a low-resolution mass spectrometer. The molecule
could have any one of the following molecular formulas.

36
Gas Chromatography—Mass Spectrometry (GC-MS)

• Mass spectrometry can be combined with gas chromatography

into a single instrument used to analyze mixtures of compounds.
• A gas chromatograph (GC) consists of a thin capillary column
containing a viscous high-boiling liquid, all housed in an oven.
When the sample is injected into the GC, it is vaporized and
swept by an inert gas through the column.
• The components travel through the column at different rates,
often separated by boiling point, with lower boiling compounds
exiting the column before higher boiling compounds.
• Each component then enters the mass spectrometer where it is
ionized to form a molecular ion and lower molecular weight
fragments
• The GC-MS records a gas chromatogram of the mixture, and
yields a plot of the amount of each component versus its
retention time (the time required to travel through the column),
37

and its molecular ion in the mass spectrum.

 Mass Spectrometry
Gas Chromatography-Mass Spectrometry (GC-MS)

Figure 5
Compound analysis
using GC–MS

38
 Mass Spectrometry
Gas Chromatography-Mass Spectrometry (GC-MS)

• To analyze a urine sample for tetrahydrocannabinol, (THC) the

principal psychoactive component of marijuana, the organic
compounds are extracted from urine, purified, concentrated and
injected into the GC-MS.
• THC appears as a GC peak, and gives a molecular ion at 314, its
molecular weight.

Figure 13.6
Mass spectrum of
tetrahydrocannabinol (THC)

39
 Esters, Acids, Amides:
 Major Fragmentation pattern is alhpa
cleavage resulting in loss of side-chain and
formation of acylium ion Also McLafferty
Rearrangement where possible!

40
Alkanes

 Fragmentation tends to occur in the middle of

unbranched chains rather than at the ends
 The difference in energy among allylic,
benzylic, 3°, 2°, 1°, and methyl cations is
much greater than the difference among
comparable radicals
 where alternative modes of fragmentation are
possible, the more stable carbocation tends to
form in preference to the more stable radical
Alkanes

MS of octane

-14 -14 -14 -14 -29

Alkanes

MS of 2,2,4 trimethylpentane
 Fragmentation Patterns
 Mass spectrum of 2-methylpentane
Alkanes

MS of methylcyclopentane
 Alkenes
 Alkenes characteristically
* show a strong molecular ion peak
* cleave readily to form resonance-stabilized allylic
cations
+
[CH2=CHCH2 CH2 CH3 ] • CH2 =CHCH2 + + •CH2 CH3
Alkenes:
Cyclohexenes

cyclohexenes give a 1,3-diene and an alkene, a

process that is the reverse of a Diels-Alder reaction.
+
CH3 •
+
CH3 •

C +
H3 C CH2
C
H3C CH2
Limonene A neutral diene A radical cation
(m/z 136) (m/z 68) (m/z 68)
Alkynes
 Alkynes typically
 show a strong molecular ion peak
 cleave readily to form the resonance-stabilized
propargyl cation or a substituted propargyl cation

3-Propynyl cation HC C-CH + +

(Propargyl cation) 2 HC C=CH2
 Mass Spec: Amines
 Nitrogen Rule: Amines with odd # of N’s have Odd M+
 Amines undergo -cleavage, generating radicals

50
 Amines
 Odd M+ (assuming an odd number of
nitrogens are present)
 -cleavage dominates forming an iminium ion

CH3CH2 CH2 N CH2 CH2CH2CH3 CH3CH2CH2N CH2

H H
m/z =72
iminium ion
Amines
86

CH3CH2 CH2 N CH2 CH2CH2CH3

H

72
Ethers
 -cleavage forming oxonium ion

 Loss of alkyl group forming oxonium ion

 Loss of alkyl group forming a carbocation

Ethers
MS of diethylether (CH3CH2OCH2CH3)

H O CH2 CH3CH2O CH2

H O CHCH3
Alcohols

 One of the most common fragmentation patterns of

alcohols is loss of H2O to give a peak which
corresponds to M-18
 Another common pattern is loss of an alkyl group
from the carbon bearing the OH to give a resonance-
stabilized oxonium ion and an alkyl radical
Mass Spec: Alcohols
CH3
CH
H3C

56
Alcohols

 MS for 1-propanol

CH3CH2CH2OH

H2C OH

M+-18 M+

SDBSWeb : http://riodb01.ibase.aist.go.jp/sdbs/ (National Institute of

Advanced Industrial Science and Technology, 11/28/09)
Alcohols

MS of 1-butanol
Aldehydes and Ketones
 Characteristic fragmentation patterns are
 cleavage of a bond to the carbonyl group
(α-cleavage)
 McLafferty rearrangement
H +
• McLafferty H +
•
O rearrangement + O

Molecular ion m/z 58

m/z 114
O
+ + •
+
O • m/z 43
-cleavage
O
m/z 128
+ +
CH3•
m/z 113
 Aldehyde
 MS for hydrocinnamaldehyde
105 91

H H O
C C C H
M+ = 134
H H
133 105
91

SDBSWeb : http://riodb01.ibase.aist.go.jp/sdbs/ (National Institute of

Advanced Industrial Science and Technology, 11/28/09)
 Ketones O
CH3CCH2CH2CH3
 MS for 2-pentanone

CH3C O

CH3CH2CH2C O

M+

SDBSWeb : http://riodb01.ibase.aist.go.jp/sdbs/ (National Institute of

Advanced Industrial Science and Technology, 11/28/09)
MS of 2-octanone
Carboxylic Acids

 Characteristic fragmentation patterns are

 α-cleavage to give the ion [CO2H]+ of m/z 45
 McLafferty rearrangement
O
-cleavage +
• + O=C-O-H
OH
Molecular ion m/z 45
m/z 88
H +
•
McLafferty +
O rearrangement H •
+ O
OH OH
Molecular ion m/z 60
m/z 88
Carboxylic Acids

MS of butanoic acid
 Esters

 α-cleavage and McLafferty rearrangement

O
+ + •OCH3
O +
•
m/z 71
-cleavage
OCH3
O
Molecular ion + +
OCH3
m/z 102
m/z 59

+ +
H • McLafferty H •
O O
rearrangement
+
OCH3 OCH3
Molecular ion m/z 74
m/z 102
Esters

MS of methyl butanoate
 Esters
77 105

O
C O CH3
77
M+ = 136
105

SDBSWeb : http://riodb01.ibase.aist.go.jp/sdbs/ (National Institute of

Advanced Industrial Science and Technology, 11/28/09)
Aromatic Hydrocarbons
most show an intense molecular ion peak
most alkylbenzenes show a fragment ion of m/z 91
H H
+
•
-H• H
CH 3 + H Tropylium cation
H (m/z 91)
H
T
oluene radical H
cation
 Aromatic Hydrocarbons
 Fragment at the benzylic carbon, forming a
resonance stabilized benzylic carbocation (which
rearranges to the tropylium ion)

H
H H H C
H C Br H C
or

M+
 Aromatic Hydrocarbons
Aromatics may also have a peak at m/z = 77 for the
benzene ring.

77
NO2

M+ = 123
77
Fragmentasi Retro-Diels Alder
Fragmentasi Retro-Diels Alder
Fragmentasi Benzilik
Hexane 
C6H14 
MW = 86.18

74
3-Pentanol 
C5H12O 
MW = 88.15

75
3-Phenyl-2-propenal 
C9H8O 
MW = 132.16

76
3-Methylbutyramide 
C5H11NO 
MW = 101.15

77
n-Butylamine 
C4H11N 
MW = 73.13

78
n-Methylbenzylamine 
C8H11N 
MW = 121.18

79
Naphthalene 
C10H8 
MW = 128.17

80
2-Butenoic acid 
C 4H 6O2 
MW = 86.09

81
Ethyl acetate 
C 4H 8O2 
MW = 88.11

82
Ethyl methyl ether 
C3H8O 
MW = 60.10

83
1-Bromopropane 
C3H7Br 
MW = 123.00

84
4-Heptanone 
C7H14O 
MW = 114.19

85
86
87
88
 Mass Spectrum  Formula

Procedure
•Chem 14C atoms: H C N O F S Cl Br I

•M = molecular weight (lowest mass isotopes)

•M+1: gives carbon count

•M+2: presence of S, Cl, or Br

•No mass spec indicator for F, I Assume absent unless otherwise specified
•Accounts for all atoms except O, N, and H

•MW - mass due to C, S, Cl, Br, F, and I = mass due to O, N, and H

•Systematically vary O and N to get formula candidates

•Trim candidate list with nitrogen rule and hydrogen rule

89
 Mass Spectrum Formula
Example #1

m/z Molecular ion Relative abundance Conclusions

102 M 100% Mass (lowest isotopes) = 102
Given information

Even number of nitrogens

103 M+1 6.9% 6.9 / 1.1 = 6.3 Six carbons*

104 M+2 0.38% < 4% so no S, Cl, or Br

Oxygen?

*Rounding: 6.00 to 6.33 = 6; 6.34 to 6.66 = 6 or 7; 6.67 to 7.00 = 7

90
 Mass Spectrum Formula
Example #1

Mass (M) - mass (C, S, Cl, Br, F, and I) = mass (N, O, and H)
102 - C6 = 102 - (6 x 12)= 30 amu for N, O, and H

Oxygens Nitrogens 30 - O - N = H Formula Notes

0 0 30 - 0 - 0 = 30 C6H30 Violates hydrogen rule

1 0 30 - 16 - 0 = 14 C6H14O Reasonable

2 0 30 - 32 - 0 = -2 C6H-2O2 Not possible

0 2* 30 - 0 - 28 = 2 C 6 H2 N 2 Reasonable
*Nitrogen rule!
•Other data (functional groups from IR, NMR integration, etc.) further trims the list
91
 Mass Spectrum Formula
Example #2

m/z Molecular ion Relative abundance Conclusions

157 M 100% Mass (lowest isotopes) = 157
Odd number of nitrogens

158 M+1 9.39% 9.39 / 1.1 = 8.5

Eight or nine carbons

159 M+2 34% One Cl; no S or Br

92
 Mass Spectrum Formula
Example #2

Try eight carbons: M - C8 - Cl = 157 - (8 x 12) - 35 = 26 amu for O, N, and H

Oxygens Nitrogens 26 - O - N = H Formula Notes

0 1* 26 - 0 - 14 = 12 C8H12ClN Reasonable
*Nitrogen rule!

Not enough amu available for one oxygen/one nitrogen or no oxygen/three nitrogens

93
 Mass Spectrum Formula
Example #2

Try nine carbons: M - C9 - Cl = 157 - (9 x 12) - 35 = 14 amu for O, N, and H

Oxygens Nitrogens 14 - O - N = H Formula Notes

0 1* 14 - 0 - 14 = 0 C9ClN Reasonable
*Nitrogen rule!

Not enough amu available for any other combination.

94
 Formula Structure

What does the formula reveal about molecular structure?

Functional groups
•Absent atoms may eliminate some functional groups
•Example: C7H9N has no oxygen-containing functional groups

Pi bonds and rings

•Recall from previous: one pi bond or one ring reduces max H count by two
•Each two H less than max H count = double bond equivalent (DBE)
•If formula has less than full H count, molecule must contain one pi bond or rin

95
 Formula Structure
Calculating DBE

DBE may be calculated from molecular formula:

hydrogens and halogens nitrogens

DBE = C - H + N + 1
2 2
carbons
•One DBE = one ring or one pi bond
•Two DBE = two pi bonds, two rings, or one of each
•Four DBE = possible benzene ring

Example DBE = C - (H/2) + (N/2) + 1 Four pi bonds and/or ring

C8H10ClN = 8 - [(10+1)/2] + (1/2) + 1 Possible benzene ring
=4

96
 Formula Structure
Common Math Errors

Small math errors can have devastating effects!

•No calculators on exams

Avoid these common spectroscopy problem math errors:

•Divide by 1.1  divide by 1.0
•DBE cannot be a fraction
•DBE cannot be negative

Next lecture: Infrared spectroscopy part 1

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