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Mass spectrometry
Mass spectrometry is an analytical technique that can be used
to deduce the molecular formula of an unknown compound.
Gaseous molecules of the compound are bombarded with
high-speed electrons from an electron gun.

These knock out an

electron from some of
the molecules, creating
molecular ions (M+),
which travel to the
detector plates: M(g) + e-  M+(g) + 2e-

The relative abundances of the detected ions form a

mass spectrum: a kind of molecular fingerprint that can
be identified by computer using a spectral database.
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 The molecular ion peak
The peak with the highest mass-to-charge ratio (m/z) is
formed by the heaviest ion that passes through the
spectrometer. This value of m/z is equal to the relative
molecular mass of the compound.
molecular High resolution
100 ion peak mass spectrometry
can be used to
abundance (%)

80
determine the
60 molecular formula
of a compound
40 from the accurate
mass of the
20 molecular ion.
0
0 40 80 120 160 m/z
mass spectrum of paracetamol
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What is fragmentation?
A molecular ion is a positively-charged ion, which is also a
radical as it contains a single unpaired electron. It is
therefore sometimes represented as M+•.
During mass spectroscopy, the molecular ion can fragment
into a positive ion and a radical:

M+• → X+ + Y•
NB: Only the
For example, in the case of propane: ions are
detected by
CH3CH2CH3+• → CH3CH2+ + CH3• the mass
or spectrometer.
CH3CH2CH3+• → CH3CH2• + CH3+

This fragmentation process gives rise to characteristic

peaks on a mass spectrum that can give information
about the structure of the molecule.
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Fragmentation and molecular structure

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Fragmentation of carbonyl compounds

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Interpreting mass spectra
Origins of some common peaks in mass spectra:

loss of a
methyl ion
methyl phenyl
positive positive ion
ion (15) (77)

Mass differences between peaks indicate the loss of groups

of atoms (fragments). For example, loss of a methyl group
leads to a mass difference of 15 between peaks.

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Interpreting mass spectra activity

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Uses of mass spectrometry
Some uses of mass spectrometry:
 Identifying elements in new or foreign substances, for
example analysing samples from the Mars space probe.
 Monitoring levels of environmental pollution, for example
amounts of lead or pesticide in a sample.

 In biochemical
research, for example
determining the
composition of a
protein by comparing it
against a database of
known compounds.

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Infrared spectroscopy
Infrared spectroscopy is an analytical technique that
provides information about the functional groups present in
a compound.
Certain groups of atoms absorb characteristic frequencies of
infrared radiation as the bonds between them undergo
transitions between different vibrational energy levels.
Infrared energy is only transferred to a bond if the bond
contains a dipole that changes as it vibrates. Symmetrical
molecules such as O2 or H2, are therefore IR inactive.
The particular wavelengths
absorbed are specific to
that particular configuration
of bonds and atoms
bonds absorb (functional group).
IR energy
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Infrared spectra
An infrared spectrum is a plot of transmission of infrared
radiation against wavenumber (1 / wavelength).
Any wavelength that is absorbed by the sample will transmit
less than the others, forming a dip in the graph.

The pattern in the

fingerprint region
transmission (%)

(1500-400 cm-1) is
unique to each
molecule, and so
can be used for
identification
purposes.
wavenumber (cm-1)
IR absorption spectrum for chloroethane
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IR spectra of different functional groups

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Interpreting IR spectra activity

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Uses of IR spectroscopy
Some uses of infrared spectroscopy:
 Use of IR spectra to follow the progress of a reaction
involving change of functional groups (e.g. in the chemical
industry to determine the extent of the reaction).
 Use of IR spectra to assess the purity of a compound.

 Breathalyzers:
modern breathalyzers
calculate the percentage
of ethanol in the breath
by looking at the size of
the absorption caused by
the C–H bond stretch in
the alcohol.

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How does NMR spectroscopy work?

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What does an NMR spectrum tell us?
Different chemical environments (bonds and atoms
surrounding a nucleus) affect the strength of magnetic field
that must be applied to a nucleus in order for it to enter the
resonance state.
By measuring the strength of magnetic field that must be
applied, NMR spectroscopy gives us information about the
local environment of specific atoms in a molecule. This can
be used to deduce information about molecular structure.
The environments of 13C and 1H atoms are most commonly
studied in NMR spectroscopy.

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Carbon-13 NMR spectroscopy

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Interpreting 13C NMR spectra
The 13C NMR spectrum of ethylamine contains two peaks.
This is because ethylamine has two unique 13C environments,
each requiring the application of a different magnetic field
strength for that carbon nucleus to enter the resonance state.
H H One peak is due to
H
the carbon atom with
H C C N
three hydrogen atoms
H attached to it, and the
H H
second to the carbon
atom with two
hydrogen atoms and
an amine group
attached to it.

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Interpreting 13C NMR spectra activity

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Chemical shift and TMS
The horizontal scale on an NMR spectrum represents
chemical shift (δ). Chemical shift is measured in parts per
million (ppm) of the magnetic field strength needed for
resonance in a reference chemical called TMS.
H
TMS (tetramethylsilane) is
universally used as the reference H C H
H H
compound for NMR as its methyl
groups are particularly well H C Si C H
shielded and so it produces a H H
strong, single peak at the far right H C H
of an NMR spectrum. H

The signal from the carbon atoms in TMS is defined as having

a chemical shift of 0.

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13C NMR chemical shift assignment
The chemical shift values of peaks on the 13C NMR spectrum
can help us identify the types of carbon atom in a compound.
The likely source of spectrum peaks can be identified using a
data table of typical chemical shift values.
Type of
δ/ppm
carbon

5–40

20–50

190–220

chemical shift
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13C NMR chemical shift activity

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Proton NMR spectroscopy

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Interpreting 1H NMR spectra activity

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Integration and the number of hydrogens
The height of the peaks in an NMR spectrum does not give
us any useful information.
However, the area
under the peaks on
a 1H NMR spectrum
is proportional to the
number of hydrogen
atoms causing the 3
signal. The ratio of
2
the areas under the
peaks tells you the 1
ratio of 1H atoms in
each environment.

The spectrum can be integrated to find this information.

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Spin coupling

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Splitting pattern activity

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1H NMR chemical shift assignment
The chemical shift values of peaks on an 1H NMR spectrum
give information about the likely types of proton environment
in a compound.
Type of
δ/ppm
proton

0.7–1.2

2.1–2.6

9.0–10.0

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1H NMR chemical shift assignment activity

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Uses of NMR spectroscopy
NMR spectroscopy uses the same
technology as magnetic resonance
imaging (MRI). This is an important
non-invasive method of gaining
information about internal structures in
the body used in diagnostic medicine
and scientific research.

NMR spectroscopy is also used in

the pharmaceutical industry to
check the purity of compounds.

Often, a combination of mass spectrometry, infrared

spectroscopy and NMR spectroscopy is used in modern
analysis to elucidate the structure of organic molecules.
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What is chromatography?
Chromatography is a series of analytical techniques that
can be used to separate mixtures of compounds for further
use or for analysis.
In all forms of chromatography, a mobile phase moves
through or across a stationary phase.
 stationary phase – this phase does not
move. Compounds in the mixture are
attracted to it (adsorbed) and slowed
down. Either a solid or a liquid.
 mobile phase – this phase moves.
The more soluble compounds in the
mixture are carried faster as the mobile
phase moves. Either a liquid or a gas.

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Thin layer chromatography

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Column chromatography

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Gas–liquid chromatography

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High performance liquid chromatography
High performance liquid chromatography (HPLC) is a
development of column chromatography in which the eluent is
pumped through the column at high pressure.

pump
injector This results in
better and faster
eluent separation than
reservoir can be achieved
in standard
data analysis column
column chromatography.

detector
components collected

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Gas chromatography–mass spectroscopy
In both GL chromatography and HPLC, the output from the
chromatography column can be passed through a mass
spectrometer. The spectra obtained can be compared to
spectra of known compounds.

Gas chromatography–
mass spectroscopy
(GC–MS) is used
extensively in forensics,
environmental monitoring
and in airport security
systems. It is sensitive
enough to detect minute
quantities of substances

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Chromatography: true or false?

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Glossary

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What’s the keyword?

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Multiple-choice quiz

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