Mass spectrometry in
organic chemistry
Starter:
Use mini wipe boards
to brainstorm what
you know about mass
spectrometry
Keywords:
Molecular ion (M+)
Fragmentation
Learning Objectives
A:
Use the molecular ion peak in an organic
molecule’s mass spectrum to determine
its molecular mass.
B:
Explain that a mass spectrum is essentially
a molecule’s fingerprint that can be
identified using a spectral database.
Molecular ion (M+) – the positive ion formed
when a molecule loses an electron
Fragmentation – the process that causes a
positive ion to split into pieces, one of which is a
positive fragment ion
Mass Spectrometry
When an organic compound is placed in a mass
spectrometer, some molecules lose an electron
and are ionised. The resulting positive ion is called
the molecular ion and is given the symbol M+
Electron impact is the oldest and best established
method of ionisation. The molecules being tested
are bombarded with electrons. If an electron is
dislodged from a molecule, a positive ion is
formed.
With ethanol, a C2H5OH molecule is ionised to
form the molecular ion, C2H5OH+
C2H5OH + e-  C2H5OH (molecular ion) + 2e-
Mass Spectrometry
• The mass of the electron is negligible
• The molecular ion has a molecular mass equal
to the molecular mass of the compound
• This molecular ion can be detected and
analysed
Excess energy form the ionisation process can be
transferred to the molecular ion, making it
vibrate. This causes bonds to weaken and the
molecular ion can split into pieces by
fragmentation. Fragmentation results in a
positive fragment ion and a neutral species.
Mass Spectrometry
A possible fragmentation of an ethanol
molecular ion;
C2H5OH+  CH3 + CH2OH+ (fragment ion)
Fragment ions are often broken up further
into smaller fragments.
The molecular ion and fragment ions are
detected in a mass spectrometer.
The molecular ion (M+) produces the peak
with the highest m/z value in the mass
spectrum
Mass Spectrometry
The molecular mass of a molecule can be
determined using mass spectrometry by locating
the M+ peak
For ethanol, the
molecular ion peak is
located at a m/z ratio
of 46. this indicates
that the molecular
mass of the molecule
is 46. the other peaks
in the spectrum are a
result of
fragmentation
Mass Spectrometry
Mass spectrometry can be used to determine
the structure of an unknown compound.
• Although the molecular ion peak of 2
isomers will have the same m/z value, the
fragmentation patterns will be different
• Each organic compound produces a unique
mass spectrum, which can be used as a
fingerprint for identification
Look at the mass spectra for pentane and 2methylbutane. Identify the M+ ion peak and
fragmentation patterns
Mass Spectrometry
Mass Spectrometry
Although mass spectra can be analysed by
viewing the spectra, modern mass
spectrometers are often linked to a special
database.
When a mass spectrum for an unknown sample
is produced, the spectral database is scanned
automatically until a perfect match is found
Plenary
1. Write a
balanced
equation
showing the
ionisation for
octane. State the
likely m/z value
for the molecular
ion peak
2. In the spectra
for compounds A
and B, identify
the m/z value for
each molecular
ion peak
Mass spectrometry:
fragmentation patterns
Starter:
????
Keywords:
Fragment ion
Learning Objectives
A:
Suggest the identity of the major
fragment ions in a given mass spectrum.
B:
Use molecular ion peaks and
fragmentation peaks to identify
structures.
Fragment ion – a positive ion produced by the
splitting of a molecular ion
Mass Spectrometry
When looking at a mass spectrum, fragment peaks
appear alongside the more important molecular
ion peak. These fragment peaks give information
about the structure of the compound.
Some common peaks to look out for:
m/z value
15
17
29
43
57
Possible identity of fragment ion
CH3+
OH+
C2H5+
C3H7+
C4H9+
Mass Spectrometry
As well as being used to identify the molecular
mass of a molecule, a mass spectrum can also be
used to work out some of the molecule’s structural
detail.
Use the mass spectrum to identify the alkane
Mass Spectrometry
The equations below show how the molecular
ion could be fragmented to form fragment ions
with m/z values of 57 and 43
Plenary
1. The mass
spectrum is for
pent-1-ene.
Suggest the ions
responsible for
the peaks labelled
A, B and C.
2. Draw structures
for the fragment
ions represented
by peaks with m/z
values of 43, 57
and 71