KHS Chemistry Unit 3.4 Structural Analysis 1

StructuralStructuralAnalysis 1Analysis 1

Adv Higher Unit 3 Topic 4Adv Higher Unit 3 Topic 4

Gordon WatsonGordon Watson

Chemistry Department, Kelso High SchoolChemistry Department, Kelso High School

KHS Chemistry Unit 3.4 Structural Analysis 2

IntroductionIntroduction

This topic explores various methods used in the Structural AnalysisStructural Analysis of organic molecules starting with Elemental AnalysisElemental Analysis and Mass Mass SpectrometrySpectrometry.

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KHS Chemistry Unit 3.4 Structural Analysis 3

Elemental Analysis 1Elemental Analysis 1

Empirical formulas are determined by combustion combustion analysisanalysis:

CarbonCarbon, HydrogenHydrogen, Sulphur & Nitrogen can all be determined by combustion analysiscombustion analysis.

Other elements can be determined by other methods.

KHS Chemistry Unit 3.4 Structural Analysis 4

Elemental Analysis 2Elemental Analysis 2

Calculation is same as taught at Standard Grade.

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Empirical Formula 1Empirical 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

KHS Chemistry Unit 3.4 Structural Analysis 6

Empirical Formula 2Empirical Formula 2

Ratio of C:H:N:O is 3.97: 4.76: 1.59: 1.59

Divide by smallest number to simplifyDivide by smallest number to simplify

Simplifying ratio: 2.5: 2.99: 1: 1

Whole number ratioWhole number ratio is 5: 6: 2: 2

Empirical formulaEmpirical formula is C5H6N2O2

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Mass SpectrometryMass Spectrometry

A mass spectrometer does three things

vaporisesvaporises a minute sampleminute sample of compound (10-10 g)

ionisesionises the vaporised molecules

separatesseparates and analysesanalyses the ions, produced when the molecules molecules fall apartfall apart, according to their mass/charge ratio, giving a mass spectrum

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Mass SpectrometerMass Spectrometer

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Molecular IonMolecular IonA high-energy electron can dislodge an electron from a bond,

creating a radical cation (a positive ionpositive ion with an unpaired e-).

e- + H C

H

H

C

H

H

H

Molecular Molecular ionion

m1+ + m2

. M M+.

m1

. + m2

+

m1+ + m2

FragmentationFragmentation then occurs.

KHS Chemistry Unit 3.4 Structural Analysis 10

Common FragmentsCommon Fragments

Fragment m or m/z

H2O 18

CH3+ 15

CH3CH2+ 29

CH3CO+ 43

91C7H7+

H

H

H

H

H

H H

+

Some fragments are more stablemore stable and, therefore, more likelymore likely

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Tropylium IonTropylium Ion

91C7H7+

H

H

H

H

H

H H

+

This ion is a particularly stableparticularly stable ion and is often the most abundant peak (Base PeakBase Peak).

Its presence indicates that the original molecule contained a benzene ring with a carbonbenzene ring with a carbon attached - often a very useful aid to the identification of the overall molecule.

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The Mass SpectrumThe Mass Spectrum

Masses are graphed or tabulated according to their relative abundance.

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Example 1aExample 1a

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H3C CH CH2 CH3CH2

CH3

2-METHYLPENTANE

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Example 1bExample 1b

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H3C CH CH2 CH3CH2

CH3

86

M+.

The main use of a mass spectrum (at Advanced Higher ) is to identify the Molecular ionMolecular ion.

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Example 1cExample 1c

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71 H3C CH CH2 CH3CH2

CH3

15

CH3+ C5H11

+

Occasionally you can be asked to identify possible fragmentsfragments.

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Example 1dExample 1d

Unstable fragments will often rearrangerearrange themselves to form more stable molecules.

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H3C CH CH2 CH3CH2

CH3

5729

C4H9+ C2H5

+

CH CH2C2H3+

27

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Example 1eExample 1e

The detailed analysis of a mass spectrum is best left to experienced operators with years of experience.

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H3C CH CH2 CH3CH2

CH3

C3H7+ C3H7

+ C3H5+

H2C C

CH3

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Use of Mass SpectraUse of Mass SpectraAt Advanced Higher, the main (only?) use of mass spectra is to determine the molecular formulamolecular formula of the molecule.

IR Spectroscopy IR Spectroscopy and NMR SpectroscopyNMR Spectroscopy will be used to identify the actual structure of the molecule.

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H3C CH CH2 CH3CH2

CH3

86

M+.

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High Resolution Mass SpectrometerHigh Resolution Mass SpectrometerSome 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’‘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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End of Topic 4End of Topic 4

StructuralStructuralAnalysis 1Analysis 1