This document provides an overview of mass spectrometry, including its basic principles, fragmentation patterns, and interpretation of mass spectra. It discusses the formation of molecular ions and their fragments, different cleavage mechanisms, and key rearrangement reactions relevant to mass spectrometry. Additionally, it addresses the isotopic effects and the nitrogen rule related to molecular weight determination.

1. Dr. Ashwani Dhingra
Associate Professor
GGSCOP, Yamunanagar

2. Basic concepts
• Mass spectrometry (Mass Spec
or MS) uses high energy
electrons to break a molecule
into fragmentation.
• A beam of high-energy electrons
breaks the moleculeapart.
• The masses of the fragments
and their relative abundance
reveal information about the
structure of the molecule.
• Separation and analysis of the
fragments provides information
about:
– Molecular weight
– Structure

3. • Massspectrometryis
the mostaccurate
methodfor determining
the molecularmassof
the compoundand its
elemental composition.
• It is alsocalledas
positiveionspectraor
line spectra.

4. Background
• The impact of a stream of high energy
electrons causes the molecule to lose an
electron forming a radical cation.
– A species with a positive charge and one
unpaired electron
+ e
-
C H
H
H
H H
H
H
H
C + 2 e
-
Molecular ion (M+)
m/z = 16

5. Background
• The impact of the stream of high energy
electrons can also break the molecule or the
radical cation into fragments.
(not detected by MS)
m/z = 29
molecular ion (M
+
) m/z = 30
+ C
H
H
H
+ H
H
H C
H
H
C
H
H
H C
H
H
C
H
H
H C
H
H
+ e
-
H C
H
H
C
H
H
H

6. Background
• Molecular ion (parent ion):
– The radical cation corresponding to the
mass of the original molecule
• The molecular ion is usually the highest mass
in the spectrum
– Some exceptions w/specific isotopes
– Some molecular ion peaks are absent.
H
H
H
H
C H C
H
H
C
H
H
H

7. Background
SDBSWeb : http://riodb01.ibase.aist.go.jp/sdbs/ (National Institute of Advanced Industrial
Science and Technology, 11/1/09)
• Mass spectrum of ethanol (MW = 46)
M+

8. Background
• The resulting mass spectrum is a graph of the
mass of each cation vs. its relative abundance.
• The peaks are assigned an abundance as a
percentage of the base peak.
• the most intense peak in the spectrum
• The base peak is not necessarily the same as
the parent ion peak.

9. Background
The mass spectrum of ethanol
SDBSWeb : http://riodb01.ibase.aist.go.jp/sdbs/ (National Institute of Advanced
Industrial Science and Technology, 11/1/09)
base peak
M+

10. Fragmentation Patterns
• The impact of the stream of high
energy electrons often breaks the
molecule into fragments, commonly a
cation and a radical.
– Bonds break to give the most stable
cation.
– Stability of the radical is less
important.

11. Fragmentation Patterns
• Alkanes
– Fragmentation often splits off simple alkyl
groups:
• Loss of methyl M+ - 15
• Loss of ethyl M+ - 29
• Loss of propyl M+ - 43
• Loss of butyl M+ - 57
– Branched alkanes tend to fragment forming
the most stable carbocations.

12. Fragmentation Patterns
Mass spectrum of 2-methylpentane

13. • degreeofunsaturation
• Structuresandfunctional groups
Connectivityof structures
• Referencespectraand
comparison to
possible structures where
uniqueidentification is
not possible

14. Fragmentation
Pattern
Simple Cleavage
• Stevenson’s Rule
• Homolytic Cleavage
• Heterolytic Cleavage
• Retro Diels Alder Reaction
Rearrangement accompanied
by Transfer of atoms
• Mc-Lafferty rearrangement
• H transfer reaction
• Scrambling
• Ortho effect
Skeletal Rearrangement

15. Fragmentation Pattern-Stevenson’s rule

16. Homolytic cleavage – Radical Site Driven
• Cleavage is caused when an electron from a bond to an
atom adjacent to the charge site pairs up with the
radical
• Weakened α-sigma bond breaks
• This mechanism is also called α-cleavage
• The charge does not move in this reaction.
• Charged product is an even electron species.
• α-cleavage directing atoms: N > S, O, π, R• > Cl, Br > H
• Loss of longer alkyl chains is often favored
• Energetics of both products (charged and neutral)
are important

18. Homolytic
cleavage-
Alpha
Cleavage

19. Alpha cleavage

20. beta Cleavage

21. Heterolytic
Cleavage:
Charge
Driven
• Attraction of an electron pair by an
electronegative atom that ends up as a
radical or as closed shell neutral
molecule or Transfer a pair of
electrons from an adjacent bond or
atom to Charged site
• This breaks a sigma bond
• Also called Charge site-initiated
cleavage or inductive cleavage
• The charge migrates to the electron
pair donor
• The electron pair neutralizes the
original charge
• Even electron fragments can further
dissociate by this mechanism
• Inductive cleavage directing
atoms: Halogens > O, S, >> N, C

22. Inductive cleavage ‘i’

23. Inductive Cleavage

24. Two bond
Cleavage
 Cleavage of two bonds
simultaneously
 In this process, an
elimination occurs
 The odd electron
molecular ion yields an
OD+
and an even
electron neutral
fragment N (usually a
stable small molecule of
some type:H2O, a
hydrogen halide or an
alkene

26. Mc-Lafferty rearrangements
• First described by Fred Mc Lafferty in 1956.
• In this rearrangement, a gamma hydrogen (from a carbon
which is 3 atom away from radical cation) is transferred
to a charged site via a six membered transition state with
concurrent cleavage of sigma bond between alpha and
beta carbons.
• This results in a new radical cation and an alkene with a pi
bond between original beta and gamma carbons.

27. Mc-Lafferty
Rearrangement
• The “1,5 shift” in carbonyl-containing ions is
called the McLafferty rearrangement
• Creates a distonic radical cation (charge and
radical separate)
• 6-membered intermediate is sterically
favorable
• Such rearrangements are common
• Once the rearrangement is complete, molecule can
fragment by any previously described mechanism

29. Rearrangements-transfer of atoms
• H-transfer rearrangements:
• involves transfer of a H atom from one
carbon to another over a pi bond sysytem
during fragmentation
or
• “INTRAMOLECULAR HYDROGEN TRANSFER
REARRANGEMENTS”

30. Rearrangements-
transfer of atoms
• Scrambling:
• imp type of H-transfer reaction
is scrambling. It takes place by
rupture and reformation of c-c bonds
and involves equilibrium of identity.
• e.g. Formation of tropylium ion from
benzyl derivative is a good ex of this
fragmentation.

31. Ortho
effect
• Ortho Effect:
• In a suitably substituted
compounds or cis-olefins, the
substituent and a hydrogen can
come in close proximity so as to
help the elimination of a neutral
molecule. This effect is known as
ortho effect.

32. • In order to interpret the mass
spectrum , one should attain an
understanding of the ionization
process.
• Toobserve fragmentation pattern.
• Theexact molecular weight: The
molecular weight of apure compound
from the identification of the
parent peak. Themolecular weight
one candetermine molecular formula.
• Theisotope effects : Heavy
isotopes will exhibit peaksin a
massspectrum at m/e one or more
units higher than normal. i.e.,
there will be small peaksatM+1 and
M+2.

33. • In organiccompounds,is a
relationship between thevalanceand the
mass of the most common isotope for
mostelements.
• Evenelements havean evenvalance.
• Odd elements havean oddvalance.
• Thisleads to the‘nitrogenrule.’Itassumes
• That wearelimitingourelements toC,
H, halogens, O andN.

34. • AcompoundcontainingonlyC, H
,OorXwillhaveaneven molecul
ar weight.
• Acompoundwithanoddnumber
of nitrogenswillhaveanoddmole
cularweight.
• Acompoundwith aneven
numberof nitrogens willhavean
evenmolecular weight.

35. Logical losses

36. General steps in
mass spectral interpretation

37. What is a mass spectrum

38. RELATIVE ABUNDANCE
• It is a method of reporting the amount of
each mass to charge measurement after
assigning the most abundant ion 100%.
Abundance:
• . The amount of an isotope of an
element that exists in nature , usually
expressed as a percentage of the total
amount of all isotopes of the element.

39. A simple mass spectrum

40. A simple mass spectrum

41. A simple mass spectrum

42. A simple mass spectrum

43. A simple mass spectrum

44. A simple mass spectrum

46. ASPIRIN (or) SALICYLICACID
(m.wt-180)

47. Mass spectra of toulene : (m/z=91)

48. Thank you