Ms interpretation

MASS SPECTROMETRY

INTERPRETATION

BYK RAKESH GUPTA

INTERPRETATION

* Mass of M+•- most abundant isotope masses of each element in the molecule

* MS have unit mass resolution-atomic mass- nominal mass

* M+•-identified as the ion with highest m/z ratio

* But with caution- may be an impurity/ an isotope of M+•

* Many compounds- no M+• - Low energy EI or CI for confirmn.

* Base peak- Ion with greatest abundance-need not be M+•

* Mass Spectrum- finger print of molecular structure

* Computer data bases can be used to identify unknown compounds

Characteristics of Molecular Ions

* Most compounds have an even molecular mass-exception is ‘N’ rule

* Nitrogen rule: Compound with an odd number of ‘N’ –odd M +•

* Compounds with even or zero number –even molecular mass

* CH4 (16), NH3 (17), C9H7N (129), N2H4 (32), C27H46O (386)

* Nitrogen- odd valence and even mass

•M +•, the next highest mass fragment-loss of a neutral fragment

•Look for the ratio of M+. to M+2 peak- 3:1-Cl and 1:1 -Br

M- Ion

1 H

3-14 None

15 CH3

16 O, NH2

17 OH, NH3

18 H2O

21-25 None

26 C2H4

Reasonable Losses due to Fragmentation

OH NH2

C6 H12 O C6 H14 N

MW→100100/13 = 7C+0→C7H16

1 O: C7 H16 -CH4 +O

MW →99 odd!99/13 = 7C→ C7H16

1 N: C7 H16 -CH2 +N

Nitrogen Rule

m/z 57 (100), m/z 43 (2), m/z 42 (2), m/z 41 (50), m/z 29 (45)

CH3CH=CH-NH2 (M+. m/z 57)

m/z 42 (M-CH3); m/z 41 (M-NH2); m/z 43 (-14 units) Loss of CH2 is rare and unlikely- so m/z 57 is not M+.

It may be fragment ion- CH3-C(CH3)3+.

Natural Abundances of the Isotopes

C13, N15, S33- contribute to M+1; O18, S34 Cl35, Br81to M+2

CH4, M+1, 1.1%; C2H6- 2.2%

Mass and Relative Abundance of Organic Elements

Elements containing only one isotopic form : Element Mass H(A) 1 F(A)    19 Elements containing two isotopic forms : Element Mass % Abundance Mass % Abundance C (A + 1) 12 100 13 1.10 O (A + 2) 16 100 18 0.20

Elements containing three isotopic forms : Element Mass % Abundance Mass % Abundance Mass

% Abundance S (A + 2) 32 100 33 0.80 34

4.4 Si (A + 2) 28 100 29 5.10

30 3.4

Molecular Formula from Mass Spectra

Inferences from graph :

m/z Relative abundance

(x) (y)

64 100.0

65     0.9

66     5.0

With the error limits,

m/z Relative abundance (x) (y)

64 100.0

65     0.9 ± 0.20

66     5.0 ± 0.50

m/z Relative abundance S O2

64 100.0 100.0 100.0

65     0.9 ± 0.20     0.8        0.08

66     5.0 ± 0.5     4.4        0.4

Conclusions :

Presence of an sulfur atom and O2 due to (A+2) pattern and from the peaks in the corresponding spectra.

(a+b)n ; a=3, b=1 for Cl; for Br a=2 and b=2

M+. Cl35, Br79; =3x2=6M+2 Cl37, Br79 & Cl35, Br81= 8M+4 Cl37, Br81=2

Mass spectral reactions:Unimolecular, competitive and consecutiveIons with wide range of internal energy

ABCD + e- ABCD +• + 2e ABCD + e- A +• + BCD•

AB+ + CD• A+ + B AB• + CD+ C+ + D (I)

AD+ + BC• (II)

ABCD +• + ABCD [ ABCD ABCD ]+ ABCDA+(III)

“Cool ions” appear as M +•

(I) Simple cleavages(II) Rearrangements(III) ion-molecule reactions

MS FRAGMENTATION OF HYPOTHETICAL MOLECULE

Abundance of ions depends on:

Stability of the +ve charge in the cation or +.

ion stabilization- e- sharing –hetero atoms nonbonding orbital CH3-C + =O CH3-CO +

Resonance stabilization:CH2=CH-CH2+ +CH2-CH=CH2

Stability of radical or neutral species

Steric arrangements of atoms or groups of atoms- favoring Rearrangements

Stevenson Rule: ABCD+. A + + BCD• or A . + BCD+

Radical of high IE, Ion of low IE

Loss of largest alkyl group-most abundance ion-exception C2H5CH(CH3)-C4H9

+ [C2H5CH(CH3)+] >[CH(CH3)-C4H9+ ]

> [C2H5CH-C4H9+] > [C2H5C(CH3)-C4H9

+ ]

---- C – C ---- ---- C

+ . C ----+

---- C – Z ---- ---- C + .

Z ----+

At heteroatom

+ .

+ .

a to heteroatom

---- C - C – Z ---- C=Z +

---- C . +

+ .

---- C - C – Z ---- Z + . ---- C = C +

+ .

Fragmentation process

Cleavage of s bond

+ .

---- HC – C – Z ---- ---- C=C + HZ+

Retro Diels-alder

+ .

CH2

CH2

CH2

CH2++ . + .

McLafferty

ZH

Z R

CH2

CH2

ZH

Z R

+ .

Fragmentation processCleavage of 2 s bond (rearrangements)

RR

CH+ < C+

R

R

R

RR”

CHR’

Loss of Largest Subst. Is most favored

Alkanes Intensity of M.+ is Larger for linear chain than for

branched compound

Intensity of M.+ decrease with Increasing M.W. (fatty acid is an exception)

Cleavage is favored at branching reflecting the Increased stability of the ion

Stability order: CH3+ < R-CH2

+ <

Molecular ion peaks are present, possibly with low intensity.  The fragmentation pattern contains clusters of peaks 14 mass units apart (which represent loss of (CH2)nCH3).

Alkane

Illustration of first 3 rules (large MW)

CH3

CH3

CH3CH3

CH3CH3

CH3

MW=170

M.+ is absent with heavy branchingFragmentation occur at branching: largest fragment loss

Branched alkanes

Molecular ion is stronger than in previous sample

Molecular ion smaller than linear alkane

Cleavage at branching is favored

43

(Branched alkane with Smaller MW)

Alkanes

Cleavage Favored at branching

Loss of Largest substituentFavored

intensity of M.+

is smaller with branching

CH2+ CH CH2 R

- R.

CH2+

CH CH2

CH2 CH CH2+

Aromatic Rings, Double bond, Cyclic

structures stabilize M.+

Double bond favors Allylic Cleavage Resonance – Stabilized Cation

Aromatic ring has stable M.+

Cycloalkane ring has stable M.+

R

+ . +

-R.

CH2

CH2

CH2

CH2++ . + .

Saturated Rings lose a Alkyl Chain (case of branching)

Unsaturated Rings Retro-Diels-Alder

+ . + .Retro Diels-Alder

-and -ionones-different spectra-position of db--ionone-RDA frgment m/z 136-abundant -ionone-RDA not favorable-unsubstituted olefin

C

CH+

R

-R. CH

+

CH2 CH2+

+

m/z 91O CH2+

O+

Aromatic Compounds Cleave in b Resonance Stabilized Tropylium

Tropylium ion

+

+

Tropylium ion

R CH2 CH2 Y Rx CH2 Y R

+

CH2+

Y R

x

R2

C

R1

O

C

R1

O+

C+

R1

O

- [RCH2]

- [R2]

larger

C-C Next to Heteroatom cleave leaving the charge on the Heteroatom

Esters lose a molecule of acid- similar to loss of H2O from alcs.

Deuterium expts- ‘H’ comes from -position

When -H not available- a ketene is eliminated

Rearrangement reactions in OMS involve ‘H’ atom transfer

x

CH2

CH2

H

CH2

O

CY

x

CH2

CH2

H

CH2

O

CY

McLafferty

Y H, R, OH, NR2Ion Stabilized by resonance

- CH2=CH2

x

CH2

O

CY

H

Cleavage of small neutral molecules(CO2, CO, olefins, H2O ….)Result often from rearrangement

McLafferty Rearrangement: Involves -H migration to a d.b-6TS

Requires- multiple bond. C=O, C=C, C=S, C=N, CC, CN and a -HInteratomic distance of 1.8 A between -H and acceptor

Enol form is retained before fragmentation

Neutral species like H2O, NH3, ROH etc.-eliminated from orthoDisubstituted aromatic compounds- Ortho effectDifferentiation of Ortho- from meta- and para- isomers

-Et

-29

Most intense peaks are often:

m/z 41, 55, 69

Double Bond Stabilize M+

Double Bond favor Allylic cleavage

CH2 CH CH+ Et

EtMe

+CH2 CH CH

EtMe

CH2 CH CH +

EtMe

M+ = 112 m/z = 83

Alcohol

An alcohol's molecular ion is small or non-existent.  Cleavage of the C-C bond next to the oxygen usually occurs.  A loss of H2O may

occur as in the spectra below.

16

Mass Spectral Cleavage Reactions of Alcohols Alcohols undergo -cleavage (at the bond next to the

C-OH) as well as loss of H-OH to give C=C

Alcohols

Phenol

H3C CH

NH2

CH2

NH2

m/z30m/z443:1

H3C C

OH

CH2

NH2

CH3

m/z59 m/z30

2:1

H3C C

OH

CH2

NH2

CH3

m/z58 m/z31

17:1

C6H5 CH2 CH2 OH

91 31

15:1

C6H5 CH2 CH2 NH2

91 30

1:10

CH3 C CH2

CH3

CH3

OH57 31

3:1

R CH2

OH

CH2+

OH+.

R CH2

NH2

CH2

NH2+

+.m/z 31 m/z 30

R CH R

OH

CH+

R'

OHm/z 30+R'

' "'R C R'

OH

R"-R"' C R'

OH

R"

+

m/z 29+R'+R"

+.C

R

X

+ C

R

X

+R C

X

R R.

:+

X= N,S,O,cl

Molecular ion is prominent

1)

Cleavage in b of aromatic ring

Rearrangement

2)

xO

R

O+

C5H5

-CO

m/z 93 m/z 65

O

H

- CH2=CH2 x

O

H

H

x

O

H

H

m/z 94

- R

Aromatic Ether

• +

B

CH3 —CH2 —O—CH2 —CH2 —CH2 —CH3 CH3 —CH2 —O+ =CH2

CH3 —CH2 —O —CH2+

Cleavage of C-C next to OxygenLoss of biggest fragment

m/z 59

Aliphatic Ether

m/z 73

m/z 45B

CH3 —CH2—CH —O —CH2 —CH3

CH3

CH =O+ —CH2

CH3

H— CH2

Box rearr.

CH =O+ H

CH3

1- Cleavage of C-C next to Oxygen

m/z 73

m/z 45

M·+

2- Cleavage of C-O bond: charge on alkyl

Ether Rearrangement

Ether

Fragmentation tends to occur alpha to the oxygen atom

Aldehyde

Cleavage of bonds next to the aldehyde group results in the loss of hydrogen (molecular ion less 1) or the loss of CHO.

Major fragmentation peaks result from cleavage of the C-C bonds adjacent to the carbonyl

Ketone

Carboxylic Acid

In short chain acids, peaks due to the loss of OH (molecular ion less 17) and COOH (molecular ion less 45) are prominent due to cleavage of bonds next to C=O.

Ester

Fragments appear due to bond cleavage next to C=O (alkoxy group loss, -OR) and hydrogen rearrangements

Amide

Primary amides show a base peak due to the McLafferty rearrangement

Amine

Molecular ion peak is an odd number.  Alpha-cleavage dominates

aliphatic amines.

The base peak is from the C-C cleavage adjacent to the C-N bond.

Halide

The presence of chlorine or bromine atoms is usually recognizable from isotopic peaks