1. Unit 3.4 Structural Analysis
Adv Higher Unit 3 Topic 4
Unit 3.4 Structural Analysis 1 1 1 1

2. Unit 3.4 Structural Analysis
Introduction
This topic explores various methods used in the Structural Analysis of organic molecules starting with Elemental Analysis and Mass Spectrometry.
Unit 3.4 Structural Analysis

3. Unit 3.4 Structural Analysis
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.
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Unit 3.4 Structural Analysis

4. Unit 3.4 Structural Analysis
Elemental Analysis 2
Calculation is same as taught at Standard Grade.
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5. Unit 3.4 Structural Analysis
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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6. Unit 3.4 Structural Analysis
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: : 2.99: 1: 1
Whole number ratio is 5: 6: 2: 2
Empirical formula is C5H6N2O2
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Unit 3.4 Structural Analysis

7. Unit 3.4 Structural Analysis
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
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Unit 3.4 Structural Analysis

8. Unit 3.4 Structural Analysis
Mass Spectrometer
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9. Unit 3.4 Structural Analysis
Molecular Ion
A high-energy electron can dislodge an electron from a bond,
creating a radical cation (a positive ion with an unpaired e-).
Molecular ion
m1+ + m2.
M M+.
m1. + m2+
m1+ + m2
Fragmentation then occurs.
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Unit 3.4 Structural Analysis

10. Unit 3.4 Structural Analysis
Common Fragments
Some fragments are more stable and, therefore, more likely
Fragment m or m/z
H2O CH
CH3CH
CH3CO
C7H7+ + 91
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Unit 3.4 Structural Analysis

11. Unit 3.4 Structural Analysis
Tropylium Ion
C7H7+ + 91
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.
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The Mass Spectrum
Masses are graphed or tabulated according to their relative abundance.
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13. Unit 3.4 Structural Analysis
Example 1a
m/z 80 60
100 40 20
rel abundance
H3C CH
CH2
CH3
2-METHYLPENTANE
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14. Unit 3.4 Structural Analysis
Example 1b
m/z 80 60
100 40 20
rel abundance
H3C CH
CH2
CH3 86
M+.
The main use of a mass spectrum (at Advanced Higher ) is to identify the Molecular ion.
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Example 1c
m/z 80 60
100 40 20
rel abundance 71
H3C CH
CH2
CH3 15
CH3+
C5H11+
Occasionally you can be asked to identify possible fragments.
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16. Unit 3.4 Structural Analysis
Example 1d
m/z 80 60
100 40 20
rel abundance
H3C CH
CH2
CH3 57 29
C4H9+
C2H5+
C2H3+ 27
Unstable fragments will often rearrange themselves to form more stable molecules.
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17. Unit 3.4 Structural Analysis
Example 1e
The detailed analysis of a mass spectrum is best left to experienced operators with years of experience.
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Use of Mass Spectra
At Advanced Higher, the main (only?) use of mass spectra is to determine the molecular formula of the molecule.
m/z 80 60
100 40 20
rel abundance
H3C CH
CH2
CH3 86
M+.
IR Spectroscopy and NMR Spectroscopy will be used to identify the actual structure of the molecule.
Unit 3.4 Structural Analysis

19. 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 CO or CN2H4
A more accurate measurement of mass from the spectrometer could be
C3H8 C2H4O CO2 CN2H4
Unit 3.4 Structural Analysis