Mass Spectrometry (Measuring Atomic Mass Ch 2.

9, Composition of organic
compounds and formula (Ch 3.8)
In the electron impact mass spectrometer, molecules in the gaseous state (under low
pressure) are bombarded with a beam of very high energy (70eV) electrons. A high
energy electron may collide with a gaseous molecule and dislodge one of the
electrons in the molecule to produce a positively charged molecular ion.

M + e M + 2e
molecule molecular
ion
The molecular ion species (parent ions) are formed in the ionisation chamber and are
generally such highly energetic species that once formed (especially in the case of a
complex molecule), may undergo a series of fragmentation reactions to produce new
ions (daughter ions). The daughter ions themselves may also undergo further
fragmentation. 1
The mass spectrometer then sorts all the cationic species on the basis of their
mass/charge (m/z) ratio. In effect, the mass spectrum is a characteristic fingerprint of the
molecule and usually allows determination of the molecular mass of the molecule and,
by careful study of the fragmentation or jig saw pattern can provide structural
information or atom connectivity.

M+. =

Mass spectrum of chloroethane C2H5Cl RMM = (2x12) + (5 x 1) + (35 or 37) = 64 or 66

H H H
35 H
H C C Cl H C C Cl
37
H H
H H

~75% ~25%
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Connectivity : evidence from mass spectrometry (Ch 3.10)
From mass spectrometry we can work out that the formula for chloroethane is C2H5Cl
but how can you determine that the connectivity is CH3-CH2-Cl?
In the mass spectrum of chloroethane there are several peaks below those of the two
molecular ions at m/z 64 and 66 respectively. These are formed by various competing
fragmentations of the original molecular ion to form smaller charged daughter ions
which are also detected. Note that any neutral fragments produced cannot be
detected!
1. (64 or 66) 1 = two peaks at m/z
63 and 65 which can just be picked
out on the mas spectrum
2. (64 or 66) CH3 = two peaks at
m/z 49 and 51 which can clearly be
m/z 64 or 66 seen on the mass spectrum.

3. (64 or 66) (35 or 37 respectively) = single peak at m/z 29 due to [CH3CH2]+

From this we must deduce that CH3 and CH2 group must be bonded (connected) together!
The remaining peaks at m/z 28, 27 and 26 can be accounted for by successive losses
of H from the species [CH3CH2]+ 3
 Connectivity : Evidence from Infrared spectroscopy (Ch 3.11)
Spectroscopy and the electromagnetic spectrum

The absorption of electromagnetic radiation causes different effects on molecular

structure, depending upon the energy (frequency) of the radiation and the structure of
the molecule under investigation.
When a molecule is irradiated with electromagnetic radiation with a certain range of
frequencies then the molecule will absorb some (or all) of certain frequencies but
transmit radiations of others. Various types of spectrometer can detect the
transmitted radiation and produce a graphical representation, called a spectrum that is
usually characteristic (a fingerprint) of a particular pure molecule. 4
A brief introduction to infrared and NMR spectroscopy will be given here because,
together with mass spectrometry, they provide valuable evidence of molecular structure.
These techniques are at their most powerful when used together in conjoint analysis to
work out the structure of an unknown organic compound. Although these are not the
only techniques that can be used they are the most common.

Infrared spectroscopy is particularly useful for providing information regarding the

types of functional group present in a pure organic molecule.

Molecules are not static species, as a paper representation might suggest. They are
very dynamic and bonds are continually vibrating (stretching, bending see below, etc).
If a molecule is irradiated with infrared radiation then, because the various vibrations
are quantised, it causes those frequencies of energy that exactly match the energy of
the vibration mode to be absorbed. This causes the molecule to undergo that
particular vibration faster and the machine can produce a spectrum of those
frequencies that have not been absorbed but have been transmitted to the detector.

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Each type of functional group in a molecule has vibrational modes that usually differ from
other functional groups, which means that the relative positions of transmitttance
peaks in the spectrum can tell us (once you are practiced) which functional groups are
likely to be present.

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Nuclear Magnetic Resonance Spectroscopy (NMR) (Ch 9.4)

The nuclei of certain atoms, for example hydrogen atoms (protons) and C13 nuclei
behave as small bar magnets and they have a magnetic moment (magnetic spin).
When placed in a magnetic field these magnetic spins will orientate themselves into
one of two ways, either parallel to the external magnetic field or anti-parallel to the
external field.

a) Sample not placed in a

magnetic field
b) Sample placed in a magnetic
field (Bo)

If the sample is placed in the NMR machine and exposed to external magnetic field it
can then be irradiated with a range of frequencies of electromagnetic radiation that
corresponds to the radiofrequency range. This will cause some of those nuclei
orientated with (parallel) the external field (currently at a lower energy) to flip and
become aligned against the external field, i.e., antiparallel. These nuclei are now at a
slightly higher energy level.
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Simple representation of an NMR spectrometer

Only those frequencies that exactly correspond to the particular electronic/magnetic

micro environment of a particular type of atom (bonded to other atoms in their
particular magnetic environment) can be absorbed.
This means that an NMR spectrum is typically characteristic of a particular pure organic
compound and contains structural information that can used to work out
connectivity.
Simplistically, NMR machines can be operated at frequencies to pick up structural
information about the carbon skeleton of a molecule, 13C-NMR, or at different
frequencies to look at the proton structure, 1H-NMR.
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ppm

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 H H CH3
C NH2 CH3 C NH2
CH3 C
H H H
propan-1-amine propan-2-amine

Propan-1-amine clearly has three different carbons in three different

electronic/magnetic environments and should be expected to produce three peaks in
different regions of the 13C-NMR spectrum, one for each of the carbon atoms present.

By comparison, propan-2-amine, although it also has three carbon atoms, two of the
carbon atoms in the methyl groups are electronically/magnetically identical (in the
same environment) and will produce ONLY one peak. Clearly each of these is different
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to the central carbon atom which produces the second peak in the 13C-NMR spectrum
1H-NMR spectroscopy (Ch 19.5)

When used in conjunction with 13C-NMR spectroscopy we have a powerful system for
providing a map of the carbon-hydrogen framework (skeletal structure) of an organic
molecule. The same instrument is used but it is operated at a different frequency
range to collect the 1H-NMR spectrum.

As with 13C-NMR a lot of structural information is given but this time about the
different types of proton present in the molecule. Different regions of the spectrum
tell you the type of proton that caused the signal.

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1H-NMR spectra tend to be a little more complicated than 13C-NMR spectra but they give
extremely useful information regarding the connectivity and also the number of protons
present.

The machine will integrate the areas under the peaks and the ratios of these areas
corresponds to the ratio of each of the protons in the different groups in the molecule.

Each of these analytical techniques will be covered in much more detail in other modules.
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