4.9 spectroscopy and chromatography

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Mass spectrometry
Gaseous molecules of the compound are bombarded with
high-speed electrons from an electron gun.
M(g) + e-
→ M+
(g) + 2e-
These knock out an
electron from some of
the molecules, creating
molecular ions (M+
),
which travel to the
detector plates:
Mass spectrometry is an analytical technique that can be used
to deduce the molecular formula of an unknown compound.
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.

The molecular ion peak
molecular
ion peak
mass spectrum of paracetamol
40 80 120 160
20
40
60
80
100
0
0
abundance(%)
m/z
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.
High resolution
mass spectrometry
can be used to
determine the
molecular formula
of a compound
from the accurate
mass of the
molecular ion.

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+•
.
M+•
→ X+
+ Y•
NB: Only the
ions are
detected by
the mass
spectrometer.CH3CH2CH3
+•
→ CH3CH2
•
+ CH3
+
CH3CH2CH3
+•
→ CH3CH2
+
+ CH3
•
For example, in the case of propane:
During mass spectroscopy, the molecular ion can fragment
into a positive ion and a radical:
This fragmentation process gives rise to characteristic
peaks on a mass spectrum that can give information
about the structure of the molecule.
or

Fragmentation and molecular structure

Fragmentation of carbonyl compounds

Interpreting mass spectra
phenyl
positive ion
(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.
Origins of some common peaks in mass spectra:
methyl
positive
ion (15)
loss of a
methyl ion

Interpreting mass spectra activity

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

Infrared spectroscopy
Certain groups of atoms absorb characteristic frequencies of
infrared radiation as the bonds between them undergo
transitions between different vibrational energy levels.
Infrared spectroscopy is an analytical technique that
provides information about the functional groups present in
a compound.
The particular wavelengths
absorbed are specific to
that particular configuration
of bonds and atoms
(functional group).
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.
bonds absorb
IR energy

Infrared spectra
An infrared spectrum is a plot of transmission of infrared
radiation against wavenumber (1 / wavelength).
wavenumber (cm-1
)
transmission(%)
Any wavelength that is absorbed by the sample will transmit
less than the others, forming a dip in the graph.
IR absorption spectrum for chloroethane
The pattern in the
fingerprint region
(1500-400 cm-1
) is
unique to each
molecule, and so
can be used for
identification
purposes.

IR spectra of different functional groups

Interpreting IR spectra activity

Uses of IR 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.
Some uses of infrared spectroscopy:

How does NMR spectroscopy work?

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 13
C and 1
H atoms are most commonly
studied in NMR spectroscopy.

Carbon-13 NMR spectroscopy

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

Interpreting 13
C NMR spectra activity

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.
The signal from the carbon atoms in TMS is defined as having
a chemical shift of 0.
Si
C
C
C
C
H
H
H
H
H
H
H
H
H
H H
H
TMS (tetramethylsilane) is
universally used as the reference
compound for NMR as its methyl
groups are particularly well
shielded and so it produces a
strong, single peak at the far right
of an NMR spectrum.

13
C NMR chemical shift assignment
The chemical shift values of peaks on the 13
C 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.
5–40
20–50
190–220
Type of
carbon
δ/ppm
chemical shift

13
C NMR chemical shift activity

Proton NMR spectroscopy

Interpreting 1
H NMR spectra activity

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

Spin coupling

Splitting pattern activity

1
H NMR chemical shift assignment
The chemical shift values of peaks on an 1
H NMR spectrum
give information about the likely types of proton environment
in a compound.
0.7–1.2
2.1–2.6
9.0–10.0
Type of
proton
δ/ppm

1
H NMR chemical shift assignment activity

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.

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.
 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.
In all forms of chromatography, a mobile phase moves
through or across a stationary phase.
 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.

Thin layer chromatography

Column chromatography

Gas–liquid chromatography

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

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

Chromatography: true or false?

Glossary

What’s the keyword?

Multiple-choice quiz

4.9 spectroscopy and chromatography

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