Department of Organic Chemistry, IMM, Radboud University Nijmegen

Mass Spectrometry

• Introduction
• Ionization
• Separation
• Fragmentation
• Isotope Effects
• High Resolution

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 Department of Organic Chemistry, IMM, Radboud University Nijmegen

Introduction Mass Spectrometry

Mass Spectrometry allows the weight of
individual molecules to be determined
accurately.

The molecules must be

brought into vapour phase (by working in
vacuo),
charged (by bombarding them with fast
electrons)
and separated (by making them follow different
paths in a magnet field).
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 Department of Organic Chemistry, IMM, Radboud University Nijmegen

Schematic Representation of a Mass Spectrometer

Ions with a
large mass

Recorder
Ions with a
small mass

Magnetic Field Ion beam

(perpendicular
to page) dc-Amplifier
Accelerating Exit slit
Vacuum
potential
Collector

Anode Filament for

electronbeam

Sample molecules
Ionisation area
Electrometer
Sample leak
tube
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Mass Spectrometry, special aspects

In the mass spectrum, differences in isotope
composition are detected (as satellite peaks).
The structures of the weighted molecules can
be determined by studying how the molecular
ion fragments (fragmentation).
By very accurate measurements, and from the
pattern of satellite peaks, the element
composition of a molecular ion can be
determined.

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 Department of Organic Chemistry, IMM, Radboud University Nijmegen

Example of Mass Spectrum

- Peak at 136, nominal molecular weight of ester
- Base (most intense) peak at 105, loss of methoxy group
- Further fragments (phenyl, cyclobutadienyl cation)
due to loss of CO, CH2=CH2

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Volatilization

Low pressure: 10-6 torr or lower is applied

Sample can be heated to 200 – 300 oC

This is enough to bring most small organic molecules
in the vapour phase:
Polar organic molecules till MW 300
Apolar organic molecules till MW 1000

In vapour phase, molecules can be ionized by

‘electron impact’ (EI) or ‘chemical ionization’ (CI)

For larger and more polar molecules, more advanced

techniques are required for desorption/ionization

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 Electron Impact (EI)
Department of Organic Chemistry, IMM, Radboud University Nijmegen

Ionization (1)

Sample is volatilized near

heated filament

Electrons are accelerated from

filament to anode by a
potential difference of 70 eV:
70 eV electrons

Interaction (not strictly collision)

of electrons with volatilized
molecules:
Ionization (7 – 10 eV required)
to give molecular radical
cation M+.

No electrons taken up to give

radical anions
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Electron Impact (EI) Ionization (2)

Impact of 70 eV electrons leads to ionization of 1 out of 104 molecules
Loss of electron from HOMO, typical: n > π > σ
.
M + e → M+ + 2e
Typical ionization energy 7 – 13 eV (1 eV ≈ 23 kcal/mole ≈ 96 kJ/mole)

Ionization potential (eV) of some monofunctionalized aliphatic

compounds CH2CH2CH2X

X = -H 11.07 X = -ONO2 11.07 X = -Cl 10.82

-CH3 10.63 -OAc 10.54 -Br 10.18
-C2H5 10.34 -OH 10.17 -I 9.26
-CHO 9.86 -NH2 8.78
-CH=CH2 9.5
-COCH3 9.34

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Electron Impact (EI) Ionization (3)

Ion picks up 2-7 eV which can give fragmentation (typical bond 4 eV)

Fragmentation possibilities:
.
a) Loss of radical M+ → A+ + B
.
i.e. an odd electron (OE) ion gives
an even electron ion (EE) + a radical
. .
b) Loss of neutral fragment, even-electron molecule M+ → C+ + D
i.e. OE ion gives other OE ion

Examples of energies of some common bonds in

organic molecules (kcal/mol per bond)
C-H 98.7 C-F 116.0 C=C 145.8 C=C 199.6
C-C 82.6 C-Cl 81.0 C=N 147.0 C=N 212.6
C-N 72.8 C-Br 68.0 C=O 179.0
C-O 85.5 C-I 51.0 C=S 128.0
C-S 65.0

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Massaspectrometrie
Depending O +.
on the energy OH
Benzoic acid
of the electron C7H6O2, Mr 122

beam, .OH (17)

O
fragmentation
+
can occur to C7H5O (105)
various extents
CO (28)
upon electron
impact ionization. +

70 eV is C6H5 (77)

standard ! HC CH
(26)
+
C4H3 (51)
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Drawbacks of EI (1)
a) No molecular ion observed for molecules that are prone
to fragmentation. See the example of a branched alkane

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Drawbacks of EI (2)

b) It is often difficult to distinguish between isomers.

c) Thermal lability:
decomposition prior to
ionization, or
fragmentation after
ionization, because of the
temperatures required
for vaporization.

d) Many compounds not

volatile enough, e.g.
polymers.
Example of thermal lability:
Boc-Leu-Ala-OMe
e) Peaks at mass > M (e.g.
MH+) due to ion-molecule
reactions.
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Chemical Ionization (1)

Chemical Ionization:
ionization of a reactant gas
(1 torr) by EI (300 eV),
followed by protonation
of the analyte M to give MH+
with peak at m/z M+1.

Less energy impacted,

a softer ionization technique.

The possibility of
fragmentation depends
on the energy
transferred with the
protonation, i.e.
on the strength of the acid
produced from the
reaction gas.
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Chemical Ionization (2)

Example of reactant gas: CH4, 1 torr, 300 eV, low analyte vapour pressure
CH + e +. CH4 + 2e
4

. .
CH4+ CH3+ + H

. .
CH4+ CH5+ + CH3

CH3+ + CH4 C2H5+ + H2

48 % CH5+, 41 % C2H5+, produced, strong Brønsted acids

If analyte can accept protons: If not:
CH5+ + M CH4 + MH+ CH5+ + M CH4 + (M-H)+ + H2

C2H5+ + M C2H4 + MH+ C2H5+ + M C2H4 + (M-H)+ + H2

So either a (M + 1)+ or a (M – 1)+ peak appears in the mass spectrum

An even-electron (EE) Quasi-molecular ion
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Chemical Ionization (2)

Fragmentation with CI dependent on energy of ion and exothermicity
of H+-transfer, strength of Brønsted acid, i.e. choice of reactant gas:

CH4 > isobutane > NH3 CH4 most commonly used !

Little exothermic H+ transfer with NH4+, little fragmentation.

Even electrophilic addition possible if analyte does not accept H+,
Quasi-molecular ion at [M+NH4]+

Negative ion chemical ionisation, reactant gas CH4/N2O 1/1

.
N O+e 2 N +O- 2

. .
O - + CH4 OH- + CH3

M + OH- [M-H]- + H2O

An EE [M-1]- peak appears in negative mode MS.

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EI and CI (CH4 reagent) of ephedrine

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 Ion Ionization and Separation
Department of Organic Chemistry, IMM, Radboud University Nijmegen

source
Acceleration in electric field:
To ½.m.v2 = z.e.V
vacum m = mass of ion
pump v = velocity
z = charge
e = unit charge (electron)
V = potential of electrostatic field
Magnet
Bending by Lorentz force
in magnet (centripetal force)
FL = B.z.e.v

In circular path also centrifugal force:

FC = m.v2/r
Ion
collector FC = FL, so
m/z = B2.r2.e/V

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Path of ion in Magnetic Analyser

With the detector slit at a distance 2r from the source slit, V can be
varied with a fixed B so that ions with a certain m/z reach the detector.

More common: Fix V and

scan m/z by variation of B.

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Accurate Isotope Weights

Element/ isotope Natural Abundance Isotope Weight

Hydrogen 1H 99.985 % 1.007 825

2H (D) 0.015 % 2.014 102
Carbon 12C 98.9 % 12.000 000
13C 1.1 % 13.003 354
Nitrogen 14N 99.64 % 14.003 074
15N 0.36 % 15.000 108
Oxygen 16O 99.8 % 15.994 915
17O 0.04 % 16.999 133
18O 0.2 % 17.999 160

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Element/ isotope Natural abundance Isotope weight

Hydrogen 1H 99.985 % 1.007 825

2H (D) 0.015 % 2.014 102
Carbon 12C 98.9 % 12.000 000
13C 1.1 % 13.003 354
Nitrogen 14N 99.64 % 14.003 074
15N 0.36 % 15.000 108
Oxygen 16O 99.8 % 15.994 915
17O 0.04 % 16.999 133
18O 0.2 % 17.999 160
Fluorine 19F 100 % 18.998 40
Silicon 28Si 92.21 % 27.976 93
29Si 4.70 % 28.976 49
30Si 3.09 % 29.97 376
Phosphorus 31P 100 % 30.973 76
Sulfur 32S 95.0 % 31.972 07
33S 0.76 % 32.971 46
34S 4.22 % 33.967 86
36S 0.014% 35.967 09
Chlorine 35Cl 75.8 % 34.968 855
37Cl 24.2 % 36.965 896
Bromine 79Br 50.5 % 78.918 348
81Br 49.5 % 80.916 344
Iodine 127I 100 % 126.900 4
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Resolution

Element composition with a mass of approximately 29,

possibilities:
C2H5 29.03915 ΔM 0.02512 (M/ΔM)10% 1154
HCO 29.01403 ΔM 0.01130 (M/ΔM)10% 2566
N2H 29.00273

Resolution
defined
as (M/ΔM)10%

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Double Sector Instrument

Electrostatic analyser with voltage E

Centripetal force FE = z.e.E, centrifugal FC = m.v2/r
Radius of path r = m.v2/z.e.E = ½.m.v2/z.e.E
i.e. selection by kinetic energy
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Resolution, Peak Match

a) Accurate measurement of mass

VG 7070: m/Δm ± 3000 over whole spectrum
accurate to 2 decimals

b) Exact mass of a peak determined by peak match:

relate to an exactly known mass in region of unknown mass
PFK (perfluorokerosene) reference compound CF3(CF2)nCF3

Resolution 5,000 – 15,000, accurate to 3-4 decimals

A peak match gives an element composition and is accepted as

evidence for the proposed formula of a compound, but
support it with a careful discussion of significance of
difference with other possible formulas (σ etc.)

It is not a substitute for Elemental Analysis as it is not a measure of

the purity of the compound !
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 Department of Organic Chemistry, IMM, Radboud University Nijmegen

Isotope Effects
Spectrum of HCl

Atom weights:
H: 1; Cl: 35,5

Expected (naively):
M+. at 36,5
Cl+ fragment at 35,5

Observed:
Strong peaks at 36 and 38
Weak at 35 and 37

Reason: Cl occurs as
a mixture of isotopes
35Cl and 37Cl in

approx. 3 : 1 ratio
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Natural Abundance and Distribution of Isotopes

Nominal (non-accurate) weights
A A+1 A+2 Type of
Element Weight % Weight % Weight % element
H 1 100 2 0.015 - - A
C 12 100 13 1.1 - - A+1
N 14 100 15 0.37 - - A+1
O 16 100 17 0.04 18 0.2 A+2
F 19 100 - - - - A
Si 28 100 29 5.1 30 3.4 A+2
P 31 100 - - - - A
S 32 100 33 0.79 34 4.4 A+2
Cl 35 100 - - 37 32.0 A+2
Br 79 100 - - 81 97.3 A+2
I 127 100 - - - - A
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Isotopes, Satellite Peaks

The occurrence of
various isotopes with
different weights leads
to the observation of
so-called satellite peaks
in the mass spectrum.

35Cland 37Cl occur in

approx. 3 : 1 ratio → an
ion with 1 Cl has peaks
at M and M+2, in 3:1 ratio.

Cf. 79Br and 81Br in approx.

equal quantities → an ion
with 1 Br has 1:1 peaks at
M and M+2.

See graph for mixed Cl-Br

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Calculation of Intensity of Satellite Peaks

The multiplicity and intensities of the satellite peaks can be calculated

with n of Newton’s binomium:
k

(a + b)n = an + n.an-1.b + n(n-1)an-2.b2 + ....

1! 2!

For 3 Br atoms, a = b = 1 : 1
(a + b)3 = a3 + 3a2b + 3ab2 + b3 = 1 + 3 + 3 + 1
i.e. 4 peaks with intensity ratio 1 : 3 : 3 : 1

In general, for a combination of element x, in ratio a : b, combined

with m atoms of element y, with ratio c : d, use the coefficients of

(a + b)n (c + d)m

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Summary
In conventional MS techniques, small (apolar, < MW 1000;
polar, < MW 300) molecules are volatilized, ionized, and the ions
separated by a magnet.

Ionization is by Electron Impact (EI) and can lead to fragmentation

which is dependent on the energy.

With Chemical Ionization (CI) the sample is indirectly ionized by

way of a ‘superacid’ from a reaction gas, and the energy transfer
can be tuned by choice of reaction gas.

Fragmentation can help to elucidate the structure.

A double (electrostatic + magnetic) sector instrument is used if high

resolution is required.

The natural abundance of several isotopes for an element leads to

satellite peaks.
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