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Mass Spectrometry IMP
Mass Spectrometry IMP
I. Introduction
A. General overview
1. Mass Spectrometry is the generation, separation and
characterization of gas phase ions according to their
relative mass as a function of charge
3. Common to all is the need for very high vacuum (~ 10-6 torr), while still
allowing the introduction of the sample
Mass Spectrometry
4. Ions (+) are accelerated using a (-) anode towards the focusing magnet
As the ions enter a magnetic field, their path is curved; the radius of the
curvature is given by: e = charge on ion
r = mv
eH
2. The most abundant ion formed in ionization gives rise to the tallest peak
on the mass spectrum – this is the base peak
fragment ions
Mass Spectrometry
2. Remember that carbon is a mixture of 98.9% 12C (mass 12), 1.1% 13C
(mass 13) and <0.1% 14C (mass 14)
4. The mass spectrometer, by its very nature would see a peak at mass 12
for atomic carbon and a M + 1 peak at 13 that would be 1.1% as high
M = n + r
13 13
1 = Bright, J. W., and Chen C. M., Journal of Chemical Education, 60 (1983): 557
Mass Spectrometry
Consider this, if the # of carbon atoms in the molecule is over 100 the
chance that there is one 13C is: 100 x 1.08% = 108%!
The M+2, 3, … peaks become even more prominent and molecules that
contain nothing but the most common isotopes become rare!
M+
M+1
Here is the molecular ion
peak(s) for a peptide
M+2 containing 96 carbon
atoms – note that the M+1
M+3 peak is almost as intense
as the M+ peak
Lung Cancer:
Interpretation of E.I.Biological SamplesData
Mass Spectrometric
c-X-1 Elements
6Li, 7Li; 10B, 11B; 50V, 51V
3-Polyisotopic element:
95 M+. + 1
96 M+. + 2
Mass Spectrometry
atoms
79Br is 50.52% and 81Br is 49.48% of naturally occurring
bromine atoms
M+
relative abundance
m/e
Mass Spectrometry
M+ M+2
relative abundance
The M+2 peak
would be about
the size of the M+
if one Br is present
m/e
1-Why M+4 and M+6 peaks are observed? 2-How we can calculate intensity pattern?
http://www.sisweb.com/mstools/isotope.htm
Mass Spectrometry
2.Using the M+1 peak (if visible) make some inference as to the number of
carbon atoms (for small molecules this works as H, N and O give very low
contributions to M+1)
3.If M+2 becomes apparent, analyze for the presence of one or more Cl or
Br atoms (sulfur and silicon can also give prominent M+2s)
Interpretation of E.I. Mass Spectrometric Data
C 4 12
H 1 1
O
Br
2
1
16
79/81 Nitrogen is the only common element
S 2 32
Cl
N
1
3
35/37
14
which has an ODD valency and
an EVEN atomic mass
C C C C
+
b. cleavage of C-heteroatom
C Z C Z
+
Mass Spectrometry
C C Z C + C Z
C C Z C C + Z
C C Z C + C Z
Mass Spectrometry
C C Z C C + H Z
H
b. Retro-Diels-Alder
Full mechanism +
Abbreviated:
+
Mass Spectrometry
H H
Full mechanism +
H H
Abbreviated:
+
3. Other types of fragmentation are less common, but in specific cases are
dominant processes
CH2 + H2C
CH3
Fragment Neutral fragment
obs. by MS inferred by its loss
– not observed
Is written as:
57
Mass Spectrometry
+ CH3
+ CH3
Mass Spectrometry
43
57
M+
Mass Spectrometry
• Peaks at 43 and 57 are the most common as these are the iso-
propyl and tert-butyl cations
Mass Spectrometry
57 M+ 114
Mass Spectrometry
H2C CH2
HC C R
+ H2C CH2
H H
C
H2
n
M - 28 = 56
M+ 84
Mass Spectrometry
M+ 140
Mass Spectrometry
55
M+ 70
Mass Spectrometry
56
41
M+ 84
Mass Spectrometry
M+ 70
Mass Spectrometry
• Retro-Diels-Alder is significant
observed loss of 28
81
68
M+ 96
Mass Spectrometry
H 67
39
M+ 68
Mass Spectrometry
53
M+ 68
Mass Spectrometry
CH3 CH2
Mass Spectrometry
m/z 91
CH3 CH3
H3C
M+ 106
Mass Spectrometry
H H
+
92
M+ 134
91
Mass Spectrometry
secondary OH +
O H 45
OH + O H 59
tertiary
Mass Spectrometry
H H
R H H R O
O
+
Mass Spectrometry
H OH H OH H OH H OH
H H +
m/z 57
• dehydration
H OH
, + H2O
M - 18
Mass Spectrometry
H H
OH OH
+
42
-H2O
OH
70
31
M+ 88
Mass Spectrometry
OH
45
M+ 88
Mass Spectrometry
OH
59
OH
87
M+ 102
Mass Spectrometry
H OH H OH
57
M+ 86
Mass Spectrometry
O
-CO -H
C
Mass Spectrometry
-CO 66
-HCO 65
M+ 94
Mass Spectrometry
M+ 108
H H
OH
“tropyliol” - CO
+
79 M – 1, 107
“tropyliol”
HO
+ H2
77
Mass Spectrometry
H
R C O R R CH + O R
R R
Mass Spectrometry
R
O O
R + C O + C5H5+
Mass Spectrometry
45
M+ 88
Mass Spectrometry
O
M+ 108
77
R H
R C O + H M-1 peak
O
R + H C O m/z 29
R H
O
O
m/z R+
R
H
R + M - 41
H can be R-subs.
Mass Spectrometry
O m/z R+
O
H +
Remember:
H aromatic ring can
be subs.
Mass Spectrometry
m/z 44
H H
O O
O +
C H
H
29
M-1
85
M+ 86
Mass Spectrometry
O M-1
119 M+ 120
H
91
Mass Spectrometry
R1 is larger than R
R C O + R
m/z 105
Remember:
aromatic ring can
be subs.
+ C O
m/z 77
Mass Spectrometry
H H +
m/z 55
O O O
m/z 70
- CO
m/z 42
Mass Spectrometry
43
H H
O O +
58
M+ 86
M-15
Mass Spectrometry
C O
m/z 105
m/z 77
M+ 134
Mass Spectrometry
c) The other -cleavage (most common with methyl esters, m/z 59)
involves the loss of the alkyl group
O O
R1 R + C O R1
R O
Mass Spectrometry
H H
O O
+
R1 R1
O O
e) Ethyl and longer (alkoxy chain) esters can undergo the McLafferty
rearrangement
H H
O O
+
R O R O
Mass Spectrometry
O O
R C
O + R
Can lose CO to
give m/z 77
Mass Spectrometry
O
O OH O
benzyloxy ester + C
H CH2
ketene
fragmentation
O
O
R C
ortho-alkylbenzoate ester O R
+ HO
H
C CH2
H2
Mass Spectrometry
O
O
O
O
71
29
both McLafferty
O (take home exercise)
O
m/z 88
43
M+ 116
Mass Spectrometry
O
O
O
O
71
29
both McLafferty
O (take home exercise)
O
m/z 88
43
M+ 116
Mass Spectrometry
119
O O
91 C
O O
CH2
O
m/z 118 M+ 150
Mass Spectrometry
c) The other -cleavage (less common) involves the loss of the alkyl
radical. Although less common, the m/z 45 peak is somewhat
diagnostic for acids.
O O
H R + C O H
R O
Mass Spectrometry
H H
O O
+ H
H
O O
m/z 60
O O
H C
O + H
+ further loss of
CO to m/z 77
Mass Spectrometry
O
O
H C
O H
ortho-alkylbenzoic acid + HO
H
C CH2
H2
Mass Spectrometry
H
O OH
OH OH
m/z 60
M+ 102
Mass Spectrometry
O OH
M+ 136
OH
119
91
Mass Spectrometry
R G O C G2 + R
O
R C O + G
R G
B -- -cleavage
O O
R R +
G G
C – McLafferty Rearrangement
R H R H
O O
+
G G
Mass Spectrometry
C C
R N R + N
NH2 NH H H H
+ H + HCN + H
NH2
30
M+ 87
Mass Spectrometry
H N
H
N
72
H
M+ 101
Mass Spectrometry
114
M+ 143
Mass Spectrometry
H H
O O
+
NH2 NH2
Mass Spectrometry
O
C
NH2
44 H
O
NH2
59
M+ 87
Mass Spectrometry
O NH2
C
77
M+ 121
O NH2
C
105
Mass Spectrometry
m/z 41
M-1 54
- HCN
M+ 55
Mass Spectrometry
N
C
H
N 43
C
H2C
m/z 41 N
54 C
M+ 83
Mass Spectrometry
b) Principle degradation is loss of NO+ (m/z 30) and NO2+ (m/z 46)
O O
R N R + N
O O
m/z 46
O O
R N R N R O N O R O + N O
O O m/z 30
Mass Spectrometry
NO2 O
+ NO + CO
m/z 93 m/z 65
NO2
+ NO2 C4H3 + HC CH
m/z 77 m/z 51
Mass Spectrometry
NO2
43
NO+ 30 NO2+ 46 M+ 89
Mass Spectrometry
NO2
91 M+ 137
C5H5+
O
m/z 107
Mass Spectrometry
k) For longer chain halides, the expulsion of a > carbon chain as the
radical is observed
R
X X
+ R
l) Aromatic halides give stronger M+, and typically lose the halogen
atom to form C6H5+
Mass Spectrometry
Cl
43
M+2
H2C Cl
m/z 49, 51 M+ 78
Mass Spectrometry
Cl
91
M+ 126
M+2
Mass Spectrometry
Br
57
M+2
M+ 136
H2C Br
Mass Spectrometry
Br
91
M+2
M+ 170
Mass Spectrometry
Br
M+2
Br Br
Br 169,
90 171 M+4
M+ 248
Mass Spectrometry
M+ 204
77
Mass Spectrometry
2. Squeeze everything you can out of the M+ peak that you can (once you
have confirmed it is the M+)
– Strong or Weak?
– Isotopes? M+1? M+2, 4, …
– Apply the Nitrogen rule
– Apply the Rule of Thirteen to generate possible formulas (you can
quickly dispose of possibilities based on the absence of isotopic
peaks or the inference of the nitrogen rule)
– Use the HDI from the Rule of Thirteen to further reduce the
possibilities
– Is there an M-1 peak?
Mass Spectrometry
5. Now consider the possible diagnostic peaks on the spectrum (e.g.: 29,
30, 31, 45, 59, 77, 91, 105 etc.)
6. Lastly, once you have a hypothetical molecule that explains the data,
see if you can verify it by use of other less intense peaks on the
spectrum – not 100% necessary (or accurate) but if this step works it
can add to the confidence level