Structural
Analysis 1
Gordon Watson
Chemistry Department, Kelso High School
Adv Higher Unit 3 Topic 4
KHS Chemistry
Unit 3.4 Structural Analysis
1
Introduction
43
rel abundance
100
80
60
41
40
20
20
40
60
80
100
m/z
This topic explores various methods used in the Structural Analysis
of organic molecules starting with Elemental Analysis and Mass
Spectrometry.
KHS Chemistry
Unit 3.4 Structural Analysis
2
Elemental Analysis 1
Empirical formulas are determined by combustion
analysis:
Carbon, Hydrogen, Sulphur & Nitrogen can all be determined
by combustion analysis.
Other elements can be determined by other methods.
KHS Chemistry
Unit 3.4 Structural Analysis
3
Elemental Analysis 2
Calculation is same as taught at Standard Grade.
KHS Chemistry
Unit 3.4 Structural Analysis
4
Empirical Formula 1
A substance was analysed and gave these results:
C 47.6% ; H 4.76% ; N 22.2% and O 25.4% by mass.
What is the empirical formula?
In 100 g there will be
47.6 / 12
moles of C
=
3.97
4.76 / 1
moles of H
=
4.76
22.2 / 14
moles of N
=
1.59
25.4 / 16
moles of O
=
1.59
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Unit 3.4 Structural Analysis
5
Empirical Formula 2
Ratio of C:H:N:O is 3.97: 4.76: 1.59: 1.59
Divide by smallest number to simplify
Simplifying ratio:
2.5: 2.99: 1: 1
Whole number ratio is 5: 6: 2: 2
Empirical formula is C5H6N2O2
KHS Chemistry
Unit 3.4 Structural Analysis
6
Mass Spectrometry
A mass spectrometer does three things
 vaporises a minute sample of compound (10-10 g)
 ionises the vaporised molecules
 separates and analyses the ions, produced when the molecules
fall apart, according to their mass/charge ratio, giving a mass
spectrum
KHS Chemistry
Unit 3.4 Structural Analysis
7
Mass Spectrometer
KHS Chemistry
Unit 3.4 Structural Analysis
8
Molecular Ion
A high-energy electron can dislodge an electron from a bond,
creating a radical cation (a positive ion with an unpaired e-).
H H
H H
H C C H
H C C+
H H
H H
e-
+
H H
Molecular
ion
H C C H
H
H H
M
M+
.
m1
m1+ + m2
H C+
.
+m
H
2
.
m +m +
1
KHS Chemistry
+
2
H
H
C H
H
Fragmentation then occurs.
Unit 3.4 Structural Analysis
9
Common Fragments
Some fragments are more stable and, therefore, more likely
Fragment
m or m/z
H2O
18
CH3+
15
CH3CH2+
29
CH3CO+
43
H
H
H
C7H7+
+
H
H
H
KHS Chemistry
91
H
Unit 3.4 Structural Analysis
10
Tropylium Ion
H
H
H
C7H7+
+
H
H
H
91
H
This ion is a particularly stable ion and is often the most
abundant peak (Base Peak).
Its presence indicates that the original molecule contained a
benzene ring with a carbon attached - often a very useful aid
to the identification of the overall molecule.
KHS Chemistry
Unit 3.4 Structural Analysis
11
The Mass Spectrum
Masses are graphed or tabulated according to their relative abundance.
KHS Chemistry
Unit 3.4 Structural Analysis
12
Example 1a
rel abundance
100
CH3
80
60
H3C
40
CH
CH2
CH2
CH3
2-METHYLPENTANE
20
20
KHS Chemistry
40
60
80
100
Unit 3.4 Structural Analysis
m/z
13
Example 1b
M+
rel abundance
100
80
.
CH3
60
H3C
40
CH
CH2
CH2
CH3
86
20
20
40
60
80
100
m/z
The main use of a mass spectrum (at Advanced Higher ) is to
identify the Molecular ion.
KHS Chemistry
Unit 3.4 Structural Analysis
14
Example 1c
rel abundance
100
CH3+
80
CH3
60
71
40
20
C5H11+
H3C
CH
CH2
CH2
CH3
15
20
40
60
80
100
m/z
Occasionally you can be asked to identify possible fragments.
KHS Chemistry
Unit 3.4 Structural Analysis
15
Example 1d
rel abundance
100
C4H9+
80
C2H5+
CH3
60
27
40
29
57
20
20
H3C
40
60
80
100
CH
m/z
CH2
CH2
CH3
C2H3+ CH
CH2
Unstable fragments will often rearrange themselves to form more
stable molecules.
KHS Chemistry
Unit 3.4 Structural Analysis
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Example 1e
43
rel abundance
100
C3H7+
C3H7+
C3H5+
CH3
CH3
80
H3C
60
CH
CH2
CH2
CH3
H2C
C
41
40
20
20
40
60
80
100
m/z
The detailed analysis of a mass spectrum is best left to experienced
operators with years of experience.
KHS Chemistry
Unit 3.4 Structural Analysis
17
Use of Mass Spectra
At Advanced Higher, the main (only?) use of mass spectra is
to determine the molecular formula of the molecule.
M+
rel abundance
100
80
.
CH3
60
H3C
40
CH
CH2
CH2
CH3
86
20
20
40
60
80
100
m/z
IR Spectroscopy and NMR Spectroscopy will be used to identify
the actual structure of the molecule.
KHS Chemistry
Unit 3.4 Structural Analysis
18
High Resolution Mass Spectrometer
Some modern Mass Spectrometers can now determine masses to
5 or 6 decimal places.
This is accurate enough to differentiate between molecules of the
‘same mass’. Eg molecules with a mass of ‘44’ could be:
C3H8
C2H4O
CO2
or CN2H4
A more accurate measurement of mass from the spectrometer
could be 44.029
C3H8
C2H4O
CO2
CN2H4
44.06260
44.02620
43.98983
44.03740
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Unit 3.4 Structural Analysis
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Structural
Analysis 1
End of Topic 4
KHS Chemistry
Unit 3.4 Structural Analysis
20