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Introduction to Mass Spectrometry (MS)
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1
A mass spectrometer produces a spectrum of masses
based on the structure of a molecule.
The x-axis of a mass spectrum represents the masses of
ions produced (m/z)
The y-axis represents the relative abundance of each ion
produced
The pattern of ions obtained and their abundance is
characteristic of the structure of a particular molecule
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Ionization (the formation of ions)
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A molecule is bombarded with a beam of high energy
electrons
An electron is dislodged from the molecule by the
impact, leaving a positively charged ion with an
unpaired electron (a radical cation)
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2
This initial ion is called the molecular ion (M+.) because it has
the same molecular weight as the analyte
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Fragmentation
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Excess vibrational energy is imparted to the molecular ion by
collision with the electron beam - this causes fragmentation
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3
The fragmentation pattern is highly characteristic of the structure
of the molecule
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Fragmentation by Cleavage at a Single
Bond
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Cleavage of a radical cation gives a radical and
a cation but only the cation is observable by MS
In general the fragmentation proceeds to give
mainly the most stable carbocation
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11
In the spectrum of propane the peak at 29 is the
base peak (most abundant) 100% and the peak at
15 is 5.6%
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Fragmentation Equations
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The M+. Ion is formed by loss of one of its most
loosely held electrons
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12
If nonbonding electron pairs or pi electrons are
present, an electron from one of these locations is
usually lost by electron impact to form M+.
In molecules with only C-C and C-H bonds, the
location of the lone electron cannot be
predicted and the formula is written to reflect
this using brackets
Example: The spectrum of hexane
13
Example: spectrum of neopentane
Fragmentation of neopentane shows the propensity of cleavage
to
occur at a branch point leading to a relatively stable
carbocation
o
The formation of the 3 carbocation is so favored that almost
no
molecular ion is detected
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14
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Carbocations stabilized by resonance are also formed
preferentially
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15
Alkenes fragment to give resonance-stabilized allylic
carbocations
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Carbocations stabilized by resonance are also formed
preferentially
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Carbon-carbon bonds next to an atom with an
unshared electron pair break readily to yield a
resonance stabilized carbocation
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15
Alkenes fragment to give resonance-stabilized allylic
carbocations
Z=N, O, or S R may be H
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Carbocations stabilized by resonance are also formed
preferentially
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Carbon-carbon bonds next to an atom with an
unshared electron pair break readily to yield a
resonance stabilized carbocation
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15
Alkenes fragment to give resonance-stabilized allylic
carbocations
Z=N, O, or S R may be H
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16
Carbon-carbon bonds next to carbonyl groups
fragment readily to yield resonance stabilized
acylium ions
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16
Carbon-carbon bonds next to carbonyl groups
fragment readily to yield resonance stabilized
acylium ions
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17
Alkyl substituted benzenes often lose a
hydrogen or alkyl group to yield the relatively
stable tropylium ion
Other substituted benzenes usually lose their
substitutents to yield a phenyl cation
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Fragmentation by Cleavage of 2 Bonds
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18
The products are a new radical cation and a
neutral molecule
Alcohols usually show an M+.-18 peak from loss
of water
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19
Cycloalkenes can undergo a retro-Diels Alder
reaction (section 13.11) to yield an alkadienyl
radical cation
http://www.cem.msu.edu/~reusch/VirtualText/
Spectrpy/MassSpec/masspec1.htm
The masses of molecular and fragment ions also
reflect the electron count, depending on the number
of nitrogen atoms in the species.
Ions with no nitrogen or an even # N atoms
Molecular Ion
odd-electron ions
even-number mass
Fragment Ions
even-electron ions
odd-number mass
Ions having an odd # N atoms
Molecular Ion
odd-electron ions
odd-number mass
Fragment Ions
even-electron ions
even-number mass
The masses of molecular and fragment ions also
reflect the electron count, depending on the number
of nitrogen atoms in the species.
Ions with no nitrogen or an even # N atoms
Molecular Ion
odd-electron ions
even-number mass
Fragment Ions
even-electron ions
odd-number mass
Ions having an odd # N atoms
Molecular Ion
odd-electron ions
odd-number mass
Fragment Ions
even-electron ions
even-number mass
http://en.wikipedia.org/wiki/Cocaine
Common Isotope Abundances
5
3 Classes of Isotopes
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M - only a single isotope
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M+1 - two isotopes with significant relative
abundance differing by 1 mass unit
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EX: F, P, I
EX: H, C, N
M+2 - two isotopes with significant relative
abundance differing by 2 mass units
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EX: O, S, Cl, Br
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Determination of Molecular Formulas & Weights
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The Molecular Ion and Isotopic Peaks
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6
The presence of heavier isotopes one or two mass units above
the common isotope yields small peaks at M+.+1 and M+.+2
Example: In the spectrum of methane one expects an M+.+1
peak of 1.17% based on a 1.11% natural abundance of 13C and a
0.016% natural abundance of 2H
Four Basic Rules
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7
If M+ is even, then the unknown contains an even number of
Nitrogen atoms (zero is an even number)
The abundance of M++1 indicates the number of Carbon atoms:
# of C = relative abundance/1.1
The abundance of the M++2 peak indicates the presence of O
(0.2%), S (4.4%), Cl (33%) or Br (98%)
The remaining unknown mass can be attributed to Hydrogen
1.
•m/z
•intensity
•% abundance
•78 (M+)
•10.00
•100%
•79
•.3
•3%
•80
•3.3
•33%
Is the molecular ion even?
Yes, there must be either an even number of N, or no Nitrogen atoms.
2.
How many Carbon atoms are there?
# Carbons = 3 / 1.1 ≈ 3 carbon atoms
3.
Is a O, S, Cl or Br present?
A M++2 peak of 33% indicates the presence of chlorine
4.
How many Hydrogen atoms are there?
H
78 = (1 * 35) + (3 * 12) + (H * 1)
78 = 71 + H
# of Hydrogen atoms = 7
8
H
H
H
C – C – C - Cl
C
H 3H
H7ClH
(M-1)
%
Intensity
86 (M+)
m/z
intensity
% abundance
86 (M+)
10.00
100%
87
.56
5.6%
88
.02
.2%
87 (M+1)
88 (M+2)
1.
Is the molecular ion even?
2.
How many Carbon atoms are there?
3.
Is an O, S, Cl or Br present?
4.
How many Hydrogen atoms are there?
Yes, there must be either 0, 2, 4 … Nitrogen atoms
# Carbons = 5.6 / 1.1 ≈ 5 carbon atoms
if there are 2 N atoms then the FW would be (5*12) + (2*14) = 88
Therefore, there are no nitrogen atoms
A M++2 peak of .2% indicates O
86 = (5 * 12) + (O*1)+ (H * 1)
86 = 76 + H
# of Hydrogen atoms = 10
# of Hydrogen atoms = 10
H
H
8
H
H
H
H
C–C–C –C–C=O
C5H10O
H
H
H
H
H
Determination of
Molecular Formula
distinguish between compounds of
same MW
C5H10O4 or C10H14
Determination of
Molecular Formula
distinguish between compounds of
same MW
C5H10O4
13C 5 * 1.11%
= 5.55%
2H
10 * 0.016% = 0.16%
17O 4 * 0.02%
= 0.08%
------135peak/134peak
5.79%
Determination of
Molecular Formula
distinguish between compounds of
same MW
C10H14
13C 10 * 1.11%
= 11.1%
2H
14 * 0.016% = 0.22%
------135peak/134peak
11.32%
The Numbers Approach
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If compound with formula CwHxNyOz ,
relative intensities of M, M+1, and M+2
ions will be given by:
M 1
 (1.11w  0.016x  0.38y  0.04z )%
M
2
M 2
 [(1.11w) / 200 0.2 z ]%
M
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High-Resolution Mass Spectrometry
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Low-resolution mass spectrometers measure
m/z values to the nearest whole number
High-resolution mass spectrometers measure
m/z values to three or four decimal places
The high accuracy of the molecular weight
calculation allows accurate determination of the
molecular formula of a fragment
Example
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9
One can accurately pick the molecular formula of a
fragment with a nominal molecular weight of 32
using high-resolution MS
The exact mass of certain nuclides is shown below
10
Elemental Composition
Search Report:
Target Mass:
Target m/z = 227.04987 ± .003
Charge = +2
Possible Elements:
Element: Exact Mass:
Min:
C
12.000000
H
1.007825 0
Cl
34.968853
N
14.003074
Max:
0
100
2
2
100
2
2
Additional Search Restrictions:
None
Search Results:
Number of Hits = 1
m/z
227.04963
Delta m/z DBE
0.00024 19.0
Formula
C28H20Cl2N2+2