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