Structural Analysis
AH Chemistry Unit 3(d)
Overview
• Elemental microanalysis
• Mass spectroscopy
• Infra-red spectroscopy
• NMR spectroscopy
• X-ray crystallography
Elemental mircoanalysis
• Sometimes called “combustion analysis”.
• Is used to determine the masses of C, H, O, S
and N in a sample of an organic compound in
order to find the empirical formula.
• The masses of other elements in the compound
have to be determined by other methods.
Empirical formula practice
1. A sample of an organic compound with
a mass of 1.224g was completely burned in
oxygen and found to produce 2.340g of
CO2 and 1.433g of water only.
Calculate the empirical formula of the
organic compound.
Empirical formula practise
2. Oxalic acid is found in rhubarb and contains
only the elements carbon, hydrogen and oxygen.
When 1.540g of oxalic acid was burned in oxygen,
1.504g of CO2 and 0.310g of water were formed.
(a) Calculate the empirical formula for oxalic
acid.
(b) If the molecular mass of oxalic acid is 90.0,
what is its molecular formula?
Empirical formula practice
3. An organometallic compound known as
ferrocene contains only the elements Fe, C
and H. When 1.672g of ferrocene was
combusted in oxygen, 3.962g of CO2 and
0.810g of water were formed.
Calculate the empirical formula of
ferrocene.
Mass spectroscopy
What is it used for?
• To determine the accurate molecular
mass and structural features of an
organic compound.
How does it work?
1. The sample is vaporised and then ionised by being
bombarded with electrons.
2. Fragmentation can occur when the energy available is
greater than the molecular ionisation energy.
3. The parent ion and ion fragments are accelerated by an
electric field and then deflected by a magnetic field.
4. The strength of the magnetic field is varied to enable the ions
of all the different mass/charge ratios to be detected in turn.
A mass spectrum is obtained.
Mass spectra: boron
Mass spectra: zirconium
• Zirconium has five isotopes as follows:
– zirconium-90 (51.5%)
– zirconium-91 (11.2%)
– zirconium-92 (17.1%)
– zirconium-94 (17.4%)
– zirconium-96 (2.8%)
• Sketch a diagram of the mass spectrum
you would expect to be produced.
Mass spectra: zirconium
Mass spectra: chlorine
• Chlorine has two isotopes: chlorine-35
and chlorine-37 in a relative abundance
of 3 atoms to 1 atom.
• Sketch a diagram of the mass spectra
you would expect to be produced.
Mass spectra: chlorine
Why?
Mass spectra: pentane
Mass spectra: pentan-3-one
Infra-red spectroscopy
What is it used for?
• To identify specific functional groups in
organic compounds.
How does it work?
• Infra-red radiation is made up of a continuous
range of frequencies.
• By shining these at an organic compound,
some are absorbed and some are not.
• Those absorbed cause parts of the molecule to
vibrate.
• The wavelengths which are absorbed depend
on the type of chemical bond and the groups
or atoms at the ends of these bonds.
• A detector measures the intensity of the
transmitted radiation at different
wavelengths.
• A spectrum is produced.
• Infra-red spectra are expressed in terms
of wavenumber.
• The unit of measurement of
wavenumber which is the reciprocal of
wavelength, is cm-1.
Types of bond vibration
• Bond bending
• Bond stretching
Bond stretching
C
O
• Energy of the bond vibration depends on bond
length, mass of atoms etc...
• Therefore different bonds vibrate in different
ways, with different energies.
• By shining radiation with exactly the right
frequency on the bond, you can kick it into a
higher energy state.
Bond bending
O
H
H
• The same principle applies, but the
frequencies of the absorbed radiation
differ from that of bond stretching.
Fingerprint region
• This is the complicated region due to a
wide variety of bond bending vibrations
in the molecule.
• Different molecules have unique
fingerprint regions.
Similar in this
area.
Different in this
area.
Indicates –OH
group and that
the compound
is an alcohol.
By comparing
to known
spectra, you
can identify
which alcohol
you have.
Some useful pointers
• C-C bonds have vibrations which occur
over a range of wavelengths in the
finger print region – difficult to pick out.
• C-O bonds are also very difficult to
detect in this region.
• Other useful detectable bonds usually
occur outside the fingerprint region.
• Ignore the trough just below 3000 cm-1 –
this is the C-H bond.
Thoughts on this molecule?
NMR spectroscopy
What is it used for?
• To gain information about the chemical
environment of hydrogen atoms in
organic molecules.
Hydrogen nuclei spin on their own axis, either clockwise or
anti-clockwise.
They behave like tiny magnets.
(high energy)
Energy
(low energy)
strong
magnetic
field
Absorption of radiation in the radio frequency region causes
the low energy nuclei to flip to the high energy orientation.
The radiation emitted when the nuclei relax back to the low
energy orientation is detected and plotted as a spectrum of
lines.
CH3
H3C
Si
CH3
CH3
10
5
0
Chemical shift ()
The lines on the spectrum are positioned relative to a standard
substance, typically tetramethylsilane (TMS):
The line (peak) produced by the 12 H atoms in TMS is set at zero.
The position of other H atoms away from this peak is known as the
chemical shift ( ).
There are 3 pieces of information given in a spectrum:
1. The number of different hydrogen environments
CH4
CH3CH3
1 hydrogen environment
1 hydrogen environment
CH3CH2CH3
2 hydrogen environments
CH3CH2OH
3 hydrogen environments
Each hydrogen environment produces a peak at a different chemical
shift.
A chart of environments and chemical shifts is shown on page 15 of the
data booklet.
2. The number of hydrogen atoms in each environment.
The area under the peaks of each environment gives the
ratio of the number of hydrogen atoms present.
CH3CH2CH3
3 2 3
2 hydrogen environments
Ratio - 3:1
3. The number of hydrogen atoms on adjacent carbon atoms.
n+1 rule (where n = H atoms):
Number of adjacent
H atoms
Shape of line
0
singlet
1
doublet
2
triplet
3
quartet
Spectrum A:
3
H H
H C C OH c
aH bH
2
1
b
c
a
Spectrum B:
H
H
H
H
C
C
C
dH c H bH
3
OH a
2
2
1
b
a c
d
X-Ray Crystallography
What is it used for?
• To determine the precise 3D structure of
an organic compound.
• A single crystal of an organic compound is
exposed to X-rays of a single wavelength.
• Inter-atomic distances in the compound are
similar to the wavelength of X-rays.
• The crystal acts as a diffraction grating.
• The X-rays are scattered by electrons in the
crystal, producing a diffraction pattern.
• From this, an electron density map can be
produced.