Organic Spectra
Mass Spectrometry
H. D. Roth
THEORY and INTERPRETATION of ORGANIC SPECTRA
H. D. Roth
Mass Spectrometry
Mass spectrometry is an analytical technique (not a spectroscopic
technique; no photon is absorbed) based on the determination of the mass-tocharge ratios, m/z, of ions in the gas phase. The experiment has three stages:
1)
evaporation
2)
ionization
3)
mass analysis
1. Introduction of the sample
The experiment works only if the sample can be introduced into the
apparatus. In many cases (direct probe) evaporation occurs instantly in the
heated inlet given the high vacuum of the ionization chamber. Alternatively a
leak valve can be used. The output of a GC (GC/MS, vide infra) can be
introduced via a membrane or by a jet separator as inlet. High molecularweight or ionic samples can be introduced by “electro-spray”.
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Organic Spectra
Mass Spectrometry
H. D. Roth
2. Ionization
We will consider three different ways to ionize target molecules:
a)
ionization by electron impact using 70 MeV electrons
neutral molecule
diamagnetic
even electron (EE)
M + e– → M+ + 2e–
molecular ion
odd electron ion (OE)
The molecular ion has a positive charge and one unpaired
electron; it is a radical cation, written as M•+ (“M dot plus”).
b)
ionization by electron attachment
neutral molecule
M + e– → M –
negative ion
The ions resulting from electron attachment have a negative
charge and one unpaired electron; they are radical anions, written as
M•– (“M dot minus”).
c1)
chemical ionization (conversion to an ion by proton transfer)
CH4
+ e– → CH4+ + 2e–
CH4+ + M → MH+ + •CH3
Chemical ionization is an excellent method to determine the
mass of the parent molecule.
c2)
chemical ionization (conversion to an ion by electron transfer)
M1 + e– → M1+ + 2e–
M 1+ + M 2 → M 2+ + M 1
In this version of chemical ionization a relatively high-energy
molecular ion is generated; electron transfer from a molecule to this
species generates the molecular ion of that molecule.
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Organic Spectra
Mass Spectrometry
H. D. Roth
3. Mass Analysis
For the purpose of mass analysis the positive ions generated by
electron impact (2a) or chemical ionization (2c) are accelerated by a
series of electric field gradients and forced into a circular path
(trajectory) by a magnetic field (remember the effect of magnetic fields
on charges); the curvature of the trajectory is determined by the
magnetic field strength (variable) and by m/z. Neutral molecules (or
neutral fragments formed coincidentally) are not affected by electric or
magnetic fields and, therefore, cannot be detected.
The analysis of negative ions (method 2b) requires a separate,
dedicated spectrometer (Negative Ion MS). Molecules bearing electron
withdrawing groups (–CN or –NO2) are good targets for negative ion
MS.
NC
CN
NO2
NO2
The resolution (M/ΔM) of a mass spectrometer is the ability to
recognize ions of different values of m/z at 10% overlap.
High resolution, M/ΔM = 50,000 (e.g., Δm = 0.002, M = 100), allows
determination of the exact mass to the 2nd or 3rd decimal and may reveal the
exact composition of a sample compound.
Exact masses of some nuclei:
1
H = 1.00783
12
C = 12.000 (Standard)
14
16
O = 15.9949
N = 14.0031
Peak of Mass 30
NO
14.0031
H2C=0
2.01566
12.0000
15.9949
15.9949
29.9980
30.01056
The ΔM of 0.0113 requires a resolution of ~8000 to differentiate
between these ions, readily accomplished in a high-resolution MS.
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Organic Spectra
Mass Spectrometry
Peak of Mass 60
C 2H 8N 2
CH2
NH2
CH2
H. D. Roth
NH2
24.0000
8.0635 CH3
28.0062
60.0697
C 3H 8O
CH2
CH2
OH
36.0000
8.0635
15.9949
60.0584
The ΔM of 0.01256 requires a resolution of ~9000 to differentiate
between these ions, readily accomplished in a high-resolution MS.
Other suitable examples include series such as a) C7H14, C6H10O,
C5H6O2, C5H10N2; b) NO, H2C=0, H2N2; or c) C2H8N2, C3H8O, C2O2.
For this course we will limit our discussion essentially to:
a) electron impact MS b) positive ion MS and c) low resolution MS.
Fragmentation of molecular ions
Many molecular ions, M+ (or M•+), are not stable under the
conditions of their formation in a mass spectrometer – they break into smaller
fragments by breaking weak bonds; each fragmentation forms one neutral
and one positively charged fragment (vide infra).
Depending on the nature of the initially ionized species chemical
ionization can lead to different fragmentation patterns. Species like CH4+ or
CH3OH+ proceed by soft collision, resulting in few fragment ions. In contrast
N2+ as the initially ionized species results in hard collisions, producing many
fragment ions.
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Organic Spectra
Mass Spectrometry
H. D. Roth
The peak with the highest m/z is the molecular ion; using electron
impact ionization (EI) no ion can have a mass larger than M•+. Due to the
very low concentration of ions and molecules in a high vacuum reactions
between two ions (ion–ion reactions) or with a neutral molecule (ion–
molecule reactions) are highly improbable. The largest peak in the spectrum
is called the base peak; it is assigned the intensity 100 (%); the intensity of
the other peaks is given as a percentage relative to the base peak.
100
M•+
The abundance of the M•+ peak is determined by the depth of its
potential well: molecular ions with a deep well are stable, giving rise to
prominent M•+ peak. In contrast, molecular ions with a shallow potential
well are unstable, causing the M•+ peak to be small or negligible.
Fairly stable
less stable
prominent M•+
weaker M•+
highly unstable
little or no M•+
only F1+ + F2• or F1•+ + F2
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Organic Spectra
Mass Spectrometry
H. D. Roth
In fact, some compounds have dissociative molecular ions, which
fragment rapidly; in such cases the ion with highest mass is not the molecular
ion. Substrates whose molecular ions readily dissociate include:
a) haloalkanes, especially 3° ones
Br
•+
+
Br
+ Br•
b) acetals
O
R
O
R'
e–
–2e–
O
R
.+
O
O + O
R
R'
O
F•+
O
+
R
M•+ – mass of R'•
c) alcohols, R–OH typically give very poor M•+ peaks; ions of M–18
(loss of H2O) are prominent fragment ions.
Criteria for a parent peak (molecular ion)
1.
Even mass, unless the ion has an odd number (1, 3 …) of N atoms
NH2
NO2
NH2
N
NH2
60
123
94
2.
The molecular ion peak is accompanied by (M+1) and (M+2) peaks
because of isotopes; (M + 1) and (M + 2) peaks can be significant and
they are useful for recognizing structural elements).
3.
the molecular ion peak is accompanied by fragment ion peaks due to
loss of typical small fragments (M–18, loss of H2O indicates R–OH).
The role of isotopes in MS (recognizing the presence of isotopes)
All mass spectra of carbon-containing compounds have small peaks
one mass number [(M+1)•+] higher than the molecular ion peak. These
peaks are due to the small fraction of molecules containing one 13C atom.
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Organic Spectra
Mass Spectrometry
H. D. Roth
Compounds with 1, 2, 3 . . . n carbon atoms have 1.1, 2.2, 3.3 . . . nx1.1% of
the (M+1)+ peak. Nitrogen containing compounds have an insignificant
contribution from
15N;
the probabilities are additive. Only 1
13C
is present;
(M + 2) peaks due to the presence of 2 13C or 2 15N are negligible (2nd 13C:
0.011 x 0.011). The intensity of the (M + 1) peak (in %) is
I(M + 1) = I(M) x (1.1 x #13C)/100 + (0.36 x #15N)/100
The natural abundance of 2H, 15N, 17O, and 18O are too low to be
recognized in a mass spectrum; 19F, 31P, and 127I are isotopically pure.
However, bromine (50.54 % 79Br, 49.46 % 81Br), chlorine (75.53 % 35Cl,
24.47 % 37Cl) and sulfur (95 % 32S, 5 % 34S) have significant fractions of
a second isotope, giving rise to significant and important (M + 2) peaks.
Natural Abundances of Key Isotopes
35Cl
76;
37Cl
24;
I(M + 2) = 32% M
79Br
51;
81Br
49;
I(M + 2) = 96% M
32S
95;
34S
18O
19F
5;
0.2;
I(M + 2) =
5% M
I(M + 2) =
0.2% M
127I
100;
100.
Presence of more than 1 Halogens or S
M : (M + 2) : (M + 4)
Cl
100 :
63
: 10
Br
52 :
100
: 48
S
100 :
5
:
0.2
(M+2) and (M+4) peaks can be significant and important.
Using chlorine as an example:
The first halogen forms
M•+
:
(M+2)•+
76
:
24
in the ratio of
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Organic Spectra
Mass Spectrometry
H. D. Roth
Given the 76% of ion M•+, the second halogen will generate M•+ or
(M+2) •+ in the ratio of 76x0.76 : 76x0.24
Given the 24% of ion (M+2) •+, the second halogen will generate
(M+2)•+ or (M+4)•+ in the ratio of 24x0.76 : 24x0.24,
giving total abundances of
M•+ : (M+2)•+ : (M+4)•+ = (abuna)2 : 2(abuna)(abunb) : (abunb)2
Notable fragment ion peaks due to loss of small fragments:
M•+ –1
M•+ –2
M•+ –15
loss of •H
loss of •CH3
leaves EE
M•+ –18
loss of H2O
leaves OE
leaves EE
loss of H2 (rarely) leaves OE
Mass Spectral Reactions - Fragmentations
MS fragmentations can take two pathways:
a)
radical ion
→
OE
free radical
not observed
+
cation
even # of electrons (EE)
fragmentation of a radical cation (odd electron, OE) into a radical (OE)
plus a cation (EE), where spin and charge are apportioned to separate
fragments:
M•+ →
F1 • + F2 +
OE
OE
EE
Examples include the loss of CH3• (or R• in general). For most
molecular ions this is the major pathway.
b) fragmentation of a radical cation forming a neutral molecule (EE)
plus a radical cation (OE):
M•+ →
OE
F3 +
F 4 •+
EE
OE
Examples include loss of H2 (rarely), H2O, CO, CO2, SO2.
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Organic Spectra
Mass Spectrometry
H. D. Roth
Fragmentation may identify functional groups; for example the
molecular ion of butanol yields four major fragment ions (loss of H2O or α
cleavage); please note also which fragment ions are NOT formed or are
formed in very low yields.
+
•+
m/z = 43
[–31 - loss of •CH2OH]
•+
m/z = 56
[–18 - loss of H2O]
base peak
OH
+CH OH
2
+
m/z = 74
m/z = 41
[–33 - loss of •CH3OH2]
loss of •CH2OH + H2
m/z = 31
[–43 - loss of •CH2CH2CH3]
Factors Determining the Course of MS Fragmentations
Which bond(s) will break? Which fragments will be formed?
Generally fragmentation at the more highly substituted carbon and/or leading
to the most stable fragments will be preferred.
1. Energetic factors
a)
relative bond strengths (BDE)
b)
stability of the resulting ions or radical ions
c)
stability of the resulting radicals or neutrals
2. Kinetic factors
a)
1 a)
availability of a favorable cyclic transition state
Bond Strength
C–Cl
C–Br
C–I
81
68
51
CH3
CH3
CH–Br
CH2-CH2-Br
CH3
BDE 78
kcal mol-1
CH3—C–Br
CH3
68
9
67
Organic Spectra
Mass Spectrometry
H. D. Roth
b) Stability of the resulting ions or radical ions
+
>
+
+
>
increasing ease of fragmentation
[The stability of the product ion follows the same trend as the BDE of
the neutral molecule – the fragmentation of 3° bromides is very facile.]
Thermochemical cycle
BDEM
A–B
A•
+
ΔI
ΔI
BDEM•+
A–B• +
•B
ΔI
A+ + • B or A• + B+
Although BDEM may be a good guide, it does not identify BDEM•+
unambiguously
Generally, BDEM•+ < BDEM
Fast mesolytic cleavages (the term “heterolytic” is not appropriate,
because the cleavage yields a cation and a radical, not positive and negative
ions)
a)
benzylic halides
+
CH2–X
.
+
CH2
+
X•
EE
b)
allylic halides
+
X
.
+
EE
+
X
OE
+
X•
OE
.
+
+
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Organic Spectra
c)
Mass Spectrometry
H. D. Roth
alcohols
+•
OH
R• +
C
R
H
+O
C
H
R'
R'
H
OE
EE
In solution this EE species is accessible by protonation of an aldehyde.
d)
thiols – quite analogous to alcohols
HS
R• +
C
R
e)
OE
H
EE
ethers
R
+
O
R
R
O
R
.
OE
6 el
8 el
O
R
+
CH2
6 el
CH2
8 el
EE
f)
C
R'
R'
H
H
+S
•+
ketones
+O
O
O
R•
C
R
+C
R'
C
R'
R'
acylium ion – very stable
g)
Amines
H
H
N •+
C
R
R'
H
H
.
R
+N
OE
C
R'
H
H
EE
iminium ion is very stable
Summary: M•+ derived from halogen (X–) compounds cleave the C–X
bond; M•+ containing O–, S–, N– cleave a bond next to the C–X bond; these
reactions form EE ions and OE radicals (not detected).
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Organic Spectra
Mass Spectrometry
H. D. Roth
Secondary fragmentations of EE species
major
CH3-CH2-CH2+
CH3+ + CH2=CH2
EE
EE
minor
CH3• + CH2=CH2•+
OE
OE
solution
by 1,2-H shift followed
by nucleophilic capture
CH3-CH+-CH3
Secondary fragmentations occur mostly via the EE + EE pathway, as
shown for ethyl isobutyl ether; they rarely form OE + OE fragments.
+
O CH2
H3C–H2C
– • C3 H7
m/z 59
– C2H4
.+
O CH2
H3C–H2C
i-C3H7
+
HO CH2
m/z 102
+
– • CH3
O CH2
– C4H8
i-C3H7
H2C
m/z 59
m/z 87
Elimination reactions
MS eliminations of an EE neutral species forming (OE) radical cations
are the minor pathway. They occur as α,β-elimination with loss of H2, HCl,
HBr, HI, H2O, H2S, CO, CO2, SO2, CH3OH, CH3-COOH.
H2C–CH2
loss of
+
H Cl
H-Cl
CH3-HC–CH2
+
H SH
loss of
H 2S
12
H2C=CH2
CH3-HC=CH2
Organic Spectra
Mass Spectrometry
H. D. Roth
Some α,ε-eliminations are known
CH2 —X
loss of
(CH)2 n
H–X
CH2
(CH2 )n
CH2
CH2 —H
The favored transition state has 5 (heavy) atoms (not counting the H
atom)
•+
H HO• +
CH2=CH2
and/or
•+
CH=CH2
H3C
H3C
Rearrangement of molecular ions
Some fragment ions cannot be explained by the simple cleavage of
bonds; they result from intramolecular rearrangements, such as migration of
H• to (or abstraction of H• by) a heteroatom.
McLafferty Rearrangement
•+
O
H
C6H5
•
OH
+
+
•+
OH
OH2
H
•
C6H5
C6H5
The McLafferty rearrangements occurs in molecular ions of various
substrates, including:
a) esters
OCH3
OCH3
C
C +
O
.
C H
C
H
.
O+
H
C6 H5
H
HO +
.
H2 C
H2 C
C6 H5
13
C
OCH3
CH
C6 H5
Organic Spectra
Mass Spectrometry
H. D. Roth
b) acetates
CH 3
C .+
O
O
H
116 C
H5 C2 H
CH 3
C +
O
O
.H
116 C
H5 C2 H
CH 2
+.
HO
C2 H5
(42)
CH 3
(60)
C
O
. + OH
H2 C
CH 48
C2 H5
.
C
74 O
O
CH 3–C≡O+ 43
C2 H5
(73)
c) alkylbenzenes
.+
C
H
.
H2 C
+
H H
H
C
CH 3
H
.
CH 2
CH 3
+
H H
C
H
CH 3
d) phenyl ethers
.
+O
.+
O
CH 2
H
H H
CH 2
The McLafferty rearrangement/cleavage is always accompanied by
the direct C–C cleavage forming an acylium ion,
CH3–C≡O+
.
O
H
H
C6H5
C6H5
Both reactions are directly analogous to photochemical reactions.
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Organic Spectra
Mass Spectrometry
H. D. Roth
Photochemistry
n,π*
•
.
CH3-C =O
.
.
O
H
H
C6H5
C6H5
α-cleavage
Norrish
Ciamician
OH
C6H5
1,4-biradical
leading to β-cleavage
Mass Spectrometry
.
.+
CH3-C+=O
OH+
O
H
H
C6H5
C6H5
.
C6H5
McLafferty rearrangement
leading to β-cleavage
α-cleavage
The main difference between the (n,π*) excited state and the
molecular ion is an (unpaired) electron in an antibonding (π*) orbital. A
photoreaction forms intermediates with two singly occupied orbitals; the MS
reaction generates intermediates with one singly-occupied and one empty
orbital.
LUMO
π∗
n SOMO
HOMO
n,π* state
molecule
15
molecular ion
Organic Spectra
Mass Spectrometry
H. D. Roth
Expulsion of Stable Neutral Molecules
Loss of Alkene – Retro Diels-Alder Cleavage
.+
+
.+
(extended, conjugated radical cations are more stable);
The retro Diels-Alder cleavage occurs in structures containing a
cyclohexene unit, including terpenes (e.g., limonene),
.+
+
.
m/z 136
m/z 68
or in norbornene,
.
+
.+
m/z 66
m/z 94
Ionone loses an isobutylene fragment, C4H8 (M•+ – 56)
O
O
CH3
CH3
.+
8
Cholesterol has 8 chiral centers and 2 stereoisomers.
.+
HO
obsd: C9H14O
HO
neutral C17H30
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Organic Spectra
Mass Spectrometry
H. D. Roth
Some bicyclic cyclohexene systems can undergo a retro Diels-Alder
reaction without a reduction of m/z,
+
.+
.
Cyclohexanol molecular ion shows an interesting cleavage-migrationcleavage sequence
•+
HO H
HO H
+
.
H
+O
HO H
+
. CH3
H
H
.
(–43)
Cyclopentanone molecular ion shows a related cleavage-migrationcleavage sequence.
Expulsion of Ketene
a)
from acetates
.+
O
CH2
C
O
R
b)
H
from enol esters
.+
O
C
O
H
O=C=CH2
(–42)
.+
R–OH
O=C=CH2
(–42)
CH2
H
O
CH3
H
17
H
.+
Organic Spectra
Mass Spectrometry
H. D. Roth
c) from β-bromo-β-phenylpropionic acid
O=C=CH2
O
O
H Br
.+
C6H5
+
O C C6H5
H
H
O
O
+
C6H5
O
H
+
H
18
O
C6H5
Organic Spectra
Mass Spectrometry
H. D. Roth
GCMS - a tool for following reactions
In a GCMS experiment the eluent of a GC is partitioned so that a
small fraction is introduced to the MS through an appropriate interface; mass
spectra are taken repeatedly; spectra associated with a particular peak can
then be examined.
Schematic of the mass selective detection unit
Example: conversion of a diketone into a bis-methylene compound by a
Wittig reaction
CH2
O
O
O
C10H14O2
166
CH2
C11H16O
164
19
CH2
C12H18
162
Organic Spectra
Mass Spectrometry
H. D. Roth
Common Fragment Ions (all EE)
Mass
29
Structure
+
H–C≡O
from aldehydes
+
30
H2C=NH2
31
H2C=O–H
39
from 1° amines
+
from 1° alcohols
cyclo-C3H3
+
from cyclopropenes
41
CH2=CH-CH2
43
CH3-C≡O
47
49/51
59
91
CH2=SH
CH2=C–Cl
from allyl halides
from ketones
+
from 1° thiols
+
from 1° chloroalk.
+
CH3–O-C≡O
CH3-O-C-CHNH2
C6H5-CH2
or c-C7H7
105
+
+
||
88
Source
+
+
from methyl esters
O
from methyl esters
of amino acids
from benzyl
+
compounds
+
C6H5–C≡O
20
from benzoyl cpds
Organic Spectra
Mass Spectrometry
H. D. Roth
Common Fragments Lost (OE or EE)
Mass
Fragment
1
15
18
H•
CH3•
H2O
19
26
F•
•C≡N
27
28
29
HC≡N
C=O
or CH2=CH2
C2H5•
or HC≡CH
35/37
36/38
41
42
Cl•
HCl
C3H5• allyl
CH2=C=O
49/51
54
CH2=C–Cl•
C4H6
59
CH3–O–C=O
79/81
77
78
Br•
C6H5•
C6H6
21
Organic Spectra
Mass Spectrometry
H. D. Roth
MS SUMMARY
•
Obtain molecular ion
•
High resolution MS → exact mass → molecular composition
and formula.
•
Readily recognized fragment ions provide structural
information.
•
Mass differences are important as they identify unobserved
neutral fragments
•
Final confirmation of structure by assigning fragment
structures. [Presence of a fragment gives positive information.
Failure to observe a fragment is just one more fact one needs
to explain.]
•
Molecular ion (M•+) is largest for straight chains, decreases
with increasing MW, and branching.
•
Cleavage occurs at 4° and 3° carbons (cation stability); largest
R• eliminated.
•
Rings and aromatics favor M•+.
•
Double bonds and aromatics favor allylic and benzylic
cleavages.
•
Cyclohexene derivatives undergo retro Diels-Alder reactions.
•
Halogen atoms are lost readily, particularly the high congeners.
•
C–C bonds next to heteroatoms are cleaved readily.
•
“Metastable” ions provide insights into fragmentation pathways.
22