In mass spectrometry, fragmentation is the dissociation of energetically unstable molecular ions formed from passing the molecules in the ionization chamber of a mass spectrometer. The fragments of a molecule cause a unique pattern in the mass spectrum.

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