The document discusses fragmentation patterns in mass spectra, including how molecular ions are formed when organic samples are bombarded by electrons in a mass spectrometer. It explains that molecular ions may break up into smaller fragment ions and describes factors that affect fragmentation, such as stability of bonds and functional groups. Furthermore, it provides examples of mass spectral fragmentation patterns for different organic compounds like alkanes, alcohols, ketones, amines, and bromides.

1. Samrat Prithviraj Chauhan Government College
Ajmer
2021-2022
Department Of Chemistry
Fragmentation Pattern in Mass Spectra
Submitted By: Sakshi Arora
M.Sc.(Chemistry) Semester III

2. Index
1. Formation of Molecular Ion
2. Fragmentation
3. Factors affecting Fragmentation
4. Mass Spectral Fragmentation of Organic
Compounds
5. Reference

3. • When the vaporised organic sample passes into the ionisation chamber
of a mass spectrometer, it is bombarded by a stream of electrons of 9 to
15eV energy the molecular ion is produced, by loss of single electron.
• These electrons have a high enough energy to knock an electron off an
organic molecule to form a positive ion. This ion is called the molecular
ion or the parent ion (𝑀+ 𝑜𝑟 𝑀+.).
M + e⁻  𝑀+. + 2e⁻
Neutral High energy Radical cation
molecule electron (Molecular ion)
• The molecular ions are energetically unstable, and some of them will
break up into smaller pieces.
Formation of Molecular Ion

4. • It is break-up process of the molecular ion into smaller ions(fragment ions) if the
energy of the bombarding electron is around 70eV, the additional energy is
consumed in fragmenting the parent ion. It gives further information about the
structure of the compound.
• If the lifetime of the molecular ion is greater than 10−6seconds, a peak
corresponding to the molecular ion will appear in the mass spectrum. However,
molecular ions with lifetimes less than 10−6 seconds break apart into fragments
before they are accelerated within the ionization chamber and enter the mass
analyzer.
• A bond is cleaved in a way that the positive charge remains with one fragment
while the odd electron goes with the other.
Molecular Ion Cation Radical
Fragmentation

5. • The uncharged free radical will not produce a line on the mass spectrum. Only
charged particles will be accelerated, deflected and detected by the mass
spectrometer.
• The greater the fragmentation of the molecular ion the greater is the loss of
intensity of molecular ion peak.
Fragmentation of the molecular ion
A• B⁺
[A-B]⁺• Radical Cation
Molecular ion
(a radical cation) A⁺ •B
Cation Radical

6. • Preferred pathway is (I) since positive charge is on the fragment containing the
heteroatom(oxygen) whose non bonding electrons provide resonance
stabilisation.

7.  The Mass spectrum of a compound is a record constructed by plotting
mass/charge vs relative abundance.
 The base peak is the most intense peak in the spectrum.
 The m/z value of parent ion is equal to the molecular mass of the
compound.
 The more stable an ion is, the more likely it is to form and the higher will
be its peak height.
 The intensity of fragment ions in the mass spectrum reflect on the
stability of the ion and the energy relationships of the bonds broken and
formed during the reaction leading to the ion.
Mass Spectrum

8. 1. Number of fragment peaks
• The number of abundant ions and their distribution in the mass
spectrum gives good information about the type of the molecule.
• The molecular ion peak in aromatic compounds is relatively much
intense due to the presence of π electron system.
• Example- Aromatic molecules give abundant molecular ion of high
stability(few fragment peaks) while aliphatic structure display many
fragment ions(increasing in abundance towards low m/z values).
Factors Affecting Fragmentation

9. Naphthalene
Molecular ion is highly abundant.
Due to absence of an easily
cleaved group it give abundant
molecular ion of high stability.
Toluene

10. n-Butane
It gives a series of ions separated by
14 mass units.
15(𝐶𝐻3
+
), 29(𝐶2𝐻5
+
), 43(𝐶3𝐻7
+
)
2,3-Butanedione
It shows only two prominent peaks in
addition to molecular ion peaks

11. 2. Common fragment ions and structure
• The presence of an ion at m/z=43 is
often an evidence for the presence of a
methyl ketone group(𝐶𝐻3CO).
• The presence of an ion at m/z=91 is
characteristic to show the presence of a
benzylic residue in a compound.
• The presence of an ion at m/z=105 is
characteristic to show the presence of
𝐶6𝐻5𝐶𝑂+
in mass spectrum of
benzophenone.
• The most intense ion at m/z=30 strongly
indicates a primary amine while
secondary at m/z=44 and tertiary at
m/z=58.

12. 3. Characteristic m/z values
due to functional groups
• The fragmentation pathway
characteristic of a functional groups
may provide distinction among
isomeric alcohols.
• Primary and secondary alcohols
usually give weak molecular ions and
for tertiary alcohols, the molecular ion
is either very weak or absent.
• Prominent base peaks in 1°
alcohol is
at m/z=31, 2° alcohol at m/z=45 and
for 3°alcohol is at m/z=59 due to
loss of largest alkyl group.

13. Fragmentation of Alkanes
 The relative abundance of saturated hydrocarbons is more than the
corresponding branch chain compound with the same number of carbon atoms.
Order of stability of carbocations: primary < secondary < tertiary
A regular series of fragment peaks separated by 14(𝐶𝐻2) mass units are observed.
There is loss of 𝐶𝐻2 units in series M-14, M-28, M-42 etc.
The intensity of molecular ion is low with increase in branching due to rapid and
extensive fragmentation.
Mass Spectral Fragmentation of Organic
Compounds

14. n-Pentane
The peak with the highest m/z 72
value is called molecular ion peak and
it is equal to molecular mass of
pentane.

15. 2-Methylbutane
Bond cleavage takes place preferably
at the site of branching.
Loss of 𝐶𝐻3 radical gives a secondary
carbocation.

16. Fragmentation of 2-Hexanol
Absence of molecular ion peak in the mass
spectrum means that the compound is highly
branched or 3o alcohols whereas 2o and
1oalcohols give very small molecular ion
peaks.
Base peak is at m/z=45 due to loss of larger
alkyl group. A peak at 𝑀+
−18 is due to loss
of water.

17. Fragmentation of 2-Pentanone
The larger group on either side of the ketone is preferably lost by an α
cleavage.
The major fragmentation peak is due to formation of resonance
stabilized acylium ion.

18. Fragmentation of 2-Bromopropane
Isotopic peaks are also formed along with the molecular ion peak, in case of
bromo compounds M+ and (M+ + 2) peaks are formed in the intensity ratio 1 : 1.
(M+2) peak is of same intensity compared to the parent peak.

19. Fragmentation of Ethylamine
If the 𝑀+ is formed at the odd mass number,
then the molecule carries an odd number of
nitrogen atoms.
The base peak is formed at m/z =30 for
primary amines due to 𝐶𝐻2 = 𝑁𝐻2
+
(iminium ion) which results from α-cleavage
of molecular ion.
Loss of largest branch from the α-carbon is
preferred.

20. REFERENCE
Spectroscopy of Organic Compounds(Sixth Edition) by P.S. Kalsi
Elementary Organic Spectroscopy((Fifth Edition) by Y.R. Sharma