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Mass spectrometry
(about the theory and applications)
Lecture-2
By
Dr. Ahmed M. Metwaly
Objectives Nitrogen rule
Mechanisms of fragmentation
• Sigma bond cleavage [σ]
• Charge site initiation
• Radical site initiation [α-cleavage]
Application of MS to organic compounds
The Nitrogen Rule - Compound containing C, H, O, and an even number of
nitrogens (or no nitrogen) will have an even molecular weight.
- Compound containing C, H, O, and an odd number of
nitrogens will have an odd molecular weight. Why???
Problem
• Which of the following ions will appear at an even
mass number?
▫ NH3
▫ C4H9N
▫ C5H6N2
▫ C2H5NH2
Mechanisms of fragmentation
Sigma bond cleavage [σ]
• The higher molecular weight carbocation able to
stabilize the positive charge.
-e-
C
H3C
H3C
H3C
C CH2CH3
H3C
H3C
H3C
C
H3C
H3C
H3C
++CH2CH3
m/z = 86m/z = 57
CH2CH3
C2H5 S C2H5C2H5 S C2H5
C2H5S+
+ C2H5-e-
Let's have another look at the mass spectrum
for pentane
• In the stick diagram showing the mass spectrum of pentane,
the line produced at m/z = 72 is due to the molecular ion.
• What causes the line at m/z = 57? (How about C4H9+)
• C4H9+ would be [CH3CH2CH2CH2]+, and this would be
produced by the following fragmentation:
• The methyl radical produced will simply get lost in the
machine.
• The tallest line in the stick diagram at m/z = 43 is
called the base peak can be worked out similarly.
• If you play around with the numbers, you will find
that this corresponds to a break producing a 3-
carbon ion:
• The line at m/z = 29 is typical of an ethyl ion,
[CH3CH2]+:
Charge site initiation [ί]
• Charge site initiation [ί] through inductive effect
C2H5 O C2H5i C2H5
++ C2H5OC2H5 O C2H5
-e-
Application of radical site initiation
Allylic cleavage
CH3-CH2-CH = CH2-e-
CH3 - CH2 - CH - CH2
CH2 = CH - CH2+
+ CH3
m/z = 41
Radical site initiation [α-cleavage]
CH3-CH2 O CH2CH3-e-
H2C=OC2H5+
+ CH3CH3-CH2 O CH2CH3
Retro Diels Alder fragmentation [RDA]
• RDA fragmentation may be simplified as:
-e-
+ =
m/z = 55
+RDA
Hydrogen rearrangement; rH
[McLafferty rearrangement]
• For unsaturated compounds.
• Six-membered transition state.
• This method used for compounds having a carbonyl
group and containing Gamma-hydrogen, e.g.
carboxylic acids (e.g. R-CH2-CH2-CH2COOH).
C
O
H2C OH
R CH
H
CH2
-e-
C
O
H2C OH
R CH
H
CH2
rH
C
O
H2C OH
R CH
CH2
H
C
O
H2C OH
R CH
CH2
H
+
m/z = 60
Therefore, long chain carboxylic acids usually
yield peak at m/z 60 in their mass spectra.
Molecular ion abundance
• Abundance reflects the stability of molecular ions formed.
• Increased unsaturation and number of rings, increases the
stability and abundances.
• Resonances will increase abundances.
• Branching and increased chain length up to C6 or C8,
decrease stability and abundances.
Probability of ionization [I]
1. [I] value of a π-bond is lower than that of σ-bond.
2.[I] value of conjugated π-bond is lower than that of
unconjugated.
3.[I] value of non-bonding electrons on a heteroatom
is lower than of π-bond.
Common MS fragments of organic compounds
m/z lost Moiety Compounds exhibiting loss
1 H aldehydes
15 CH3 branched sites
16 O sulfoxides, nitro compounds
16 NH2 amides, aromatic amines
17 OH acids
18 H2O alcohols, aldehydes, ketones, ethers
m/z lost Moiety Compounds exhibiting loss
26 CN alkylcyanides
29 C2H5 or CHO alcohols
31 OCH3 or CH2OH methyl esters, alcohols
35 Cl halide-containing
45 OC2H5 or COOH ethyl esters or carboxylic
acids
Application of MS to organic compounds
• Saturated hydrocarbons - regularly spaced clusters separated by 14 mass
units
• Cleavage favored at branched C atoms:
▫ Tertiary > secondary > primary
▫ Positive charge on branched C (carbonium ion).
• More stable carbocations will be more abundant.
• Ring compounds have strong parent ions. Intensity related to stability
of ring.
• Compounds with carbonyl break at this group
• m/z 16 large for primary amines.
Mass spectra of alkanes
More stable carbocations will be more abundant
Mass Spectra of Alkenes
Resonance-stabilized cations favored
Application of MS to natural products
Fatty acids
• Molecular ion peak of a straight chain monocarboxylic acid
is weak but usually discernible.
• The most characteristic peak (sometimes the base peak) is at
m/e 60 due to McLafferty rearrangement.
MS spectrum of stearic acid
Methyl ester of fatty acids
• The mass spectrum of a methyl - ester is very
similar to that of corresponding carboxylic acid.
• The methyl ester is more volatile than the free fatty
acids and therefore the easier to examine.
• m/e 74; corresponding to the m/e 60 peak of fatty
acid is usually base peak or predominant.
MS spectrum of methyl stearate
Alkaloids (Papaverine)
• Using radical site initiation [α-cleavage]:
N
H3CO
H3CO
H3CO
H3CO
-e-
N
H3CO
H3CO
H3CO
H3CO
N+
H3CO
H3CO
H3CO
H3CO
+
Volatile oils (Limonene)
Using RDA fragmentation.
+ =
m/z = 68
m/z = 68
+RDA
or
RDA-e-
Volatile oils (Menthone)
• Using rH (McLafferty rearrangement):
O O
-e-
H
OH OH
+
m/z = 112
rH
Flavonoids (Kampferol)
• Using RDA fragmentation.
• The both ions are stable and positively charged.
OOH
HO O
OH
OH
OOH
HO O
OH
OH
HO
OH
O
OH
OH
O
-e- m/z = 152
m/z = 134
m/z = 286
Summary Nitrogen rule
Mechanisms of fragmentation
• Sigma bond cleavage [σ]
• Charge site initiation
• Radical site initiation [α-cleavage]
Application of MS to organic compounds
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