A-level Spectroscopy

An image of a human brain from a live patient recorded using magnetic

resonance imaging - a 3D form of n.m.r. spectroscopy
Introduction

Spectroscopy is a collective name for the various techniques that use the
interaction between molecules and electromagnetic radiation to elucidate the
structure of molecules. Spectroscopic methods are fundamental to the study of
Chemistry, Molecular Biology, Medicine and Astrophysics.

This booklet covers the following techniques:-

A) Infrared Spectroscopy - from ‘What’s in a Medicine?’

• Describe how infrared spectroscopy (i.r.) can be used for the elucidation
of molecular structure;
• Interpret infrared spectra for salicylic acid and simple compounds
containing a limited range of functional groups (hydroxyl, carbonyl,
carboxylic acid and ester) given relevant information.

B) Mass Spectrometry - from ‘What’s in a Medicine?’

• Describe how mass spectrometry (m.s.) can be used for the elucidation
of molecular structure;
• Interpret mass spectra (molecular ion and significance of the
fragmentation pattern) for salicylic acid and simple compounds containing
a limited range of functional groups (hydroxyl, carbonyl, carboxylic acid
and ester) given relevant information.

C) Nuclear Magnetic Spectroscopy - from ‘Engineering Proteins’

• Describe how nuclear magnetic resonance spectroscopy (n.m.r.) can be

used for the elucidation of molecular structure;
• Interpret nuclear magnetic resonance spectra for simple compounds
given relevant information (reference to splitting on the resonances is
not required)

This work builds on AS topics of:-

• Interaction of radiation with matter (‘Elements of Life’ and ‘Atmosphere’);

• Mass spectrometry (‘Elements of Life’).
 A) Infrared (i.r.) spectroscopy

• Used to identify bonds / functional groups

• Can only identify the exact molecule by comparison with library
spectra

Experiment 1 RSC Video

• Infrared radiation is passed simultaneously through the sample and a

reference cell.
• The reference ensures that peaks due to water or carbon dioxide in the
air can be cancelled out.
• The frequencies of i.r. radiation absorbed are determined by passing
through a rotating prism to focus one frequency at a time onto the
detector.
-1
• The spectrum shows the ________________ (cm ) on the x axis
(which is 1/λ ) and the ____________________ on the y-axis.

Calculations

1) c = λ υ 2) Wavenumber = 1/λ (cm)

e.g. What wavenumber would appear on an i.r. spectrum if the frequency of

radiation absorbed by a molecule was 2.5 x 1013 Hz?
Theory

• IR radiation corresponds to the energy required to make chemical bonds

vibrate more / move to a higher vibrational energy level.
• Therefore, energy of certain wavelengths is absorbed by molecules.
• The actual energy depends on the mass of the atoms and the strength of
the bond, so different bonds will absorb at different frequencies.

c.f.
spring
oscillations

• Stronger bonds need more energy to make them vibrate, so absorb a

higher frequency of i.r. radiation (higher wavenumber)
e.g. hydrogen halides

• Molecules with more than 2 atoms can vibrate in different ways

e.g. sulphur dioxide

• So these spectra will contain more absorptions

 • Most organic molecules contain a number of types of bond, so
characteristic absorptions will be seen for each bond.
e.g. ethanol

The following types of bond need to be recognised:-

Bond Functional group Absorbance (cm-1)

O–H Alcohols 3200 – 3600 / strong and broad*

O–H Carboxylic acids 2500 – 3200 / medium and very

broad*
C=O Aldehydes / ketones / 1680 – 1750 / strong and sharp
carboxylic acids/ esters

C-O Alcohols / esters / ethers 1050 – 1300 / medium

C-H Alkanes / alkenes etc 2850 – 3100 / medium

*Broad due to Hydrogen Bonding between O-H groups

i.r. bands.ppt
Examples of infrared spectra

1) ethanol (CH3CH2OH)

displayed
formula

i.r. spectrum

Bond / (Functional group) Absorption / cm-1

2) ethanoic acid (CH3COOH)

displayed
formula

i.r. spectrum

Bond / (Functional group) Absorption / cm-1

3) Ethyl Ethanoate (CH3COOCH2CH3)

H O H H

H C C O C C H

H H H

i.r. spectrum

Bond / (Functional group) Absorption / cm-1

1750

1250

3000
4) a) i.r. spectrum of an alcohol with molecular formula C3H8O.

NB: This Alcohol is oxidised to compound 4)b) when heated under distillation
with acidified potassium dichromate and 4)c) when heated to reflux with
acidified potassium dichromate.

Clue?

Bond / (Functional group) Absorption / cm-1

Displayed Formula of 4a
4) b) i.r. spectrum of the compound with molecular formula C3H6O
obtained by distilling compound 4)a) with acidified potassium
dichromate

Bond / (Functional group) Absorption / cm-1

Displayed Formula of compound 4b

4)c) i.r. spectrum of the compound with molecular formula C3H6O2 formed
when compound 4a is heated to reflux with acidified potassium
dichromate

Bond / (Functional group) Absorption / cm-1

Displayed Formula of Compound 4c

5)a) i.r. spectrum of an isomer of 4a which forms the same product 5)b)
whether it is heated to distil or reflux with acidified potassium
dichromate

Bond / (Functional group) Absorption / cm-1

Displayed Formula of Compound 5a

5)b) i.r. spectrum of the product of the reaction of 5a with acidified
potassium dichromate when heated to reflux or distillation.

Bond / (Functional group) Absorption / cm-1

Displayed Formula of Compound 5b

6) Salicylic Acid (2-hydroxybenzoic acid - (HOC6H4COOH))

displayed
formula

i.r. spectrum

Bond / (Functional group) Absorption / cm-1

7) Aspirin (CH3COOC6H4COOH)

i.r. spectrum

Bond / (Functional group) Absorption / cm-1

2900 v. broad

1750

1700

1200
 B) Mass Spectrometry

• Use M+ (molecular ion) to measure Mr

• Use M+2 isotope peaks to identify Cl or Br
• Use fragmentation pattern to confirm structure of molecule

Experiment 2 – RSC video

AS-level

• Vaporisation of atoms or molecules;

• Ionisation of atoms or molecules;
• Acceleration of ions;
• Deflection of ions;
• Detection of ions.
A2-level

• The atoms or molecules are ionised by bombarding with high energy

electrons:-

- + -
e.g. CH3COCH3 + e [CH3COCH3] + 2e
M+

• Usually, the resulting molecular ion has such high energy that it splits up
into a smaller ion and an uncharged molecule (fragmentation)

+ +
e.g. [CH3COCH3] [CH3CO] + CH3
M+m/e = 58 43

+ +
or [CH3COCH3] CH3CO + [CH3]
58 15

NB The first fragmentation route is more likely because fragments containing

+
the [R-C=O] group (acylium cations) are particularly stable.

• The following peaks are often seen in the fragmentation patterns of mass
spectra – the highlighted peaks usually provide very useful clues in
determining the structure of a molecule

fragment m/e
CH3 15
CH3CH2 or CHO 29
CH2NH2 30
CH2OH 31
CH3CO or C3H7 43
CONH2 44
COOH 45
C6H5 77
C6H5CH2 91
C6H5CO 105
Examples of fragmentation and the interpretation of mass spectra

1) Propanone (CH3COCH3)

displayed
formula

mass spectrum

m/z Formula m/z lost Group lost

58

43

15
2) Propanal (CH3CH2CHO)

displayed
formula

mass spectrum

m/z Formula m/z lost Group lost

58

57

29
3) Methyl Benzoate (C6H5COOCH3)

O H

C O C H

mass spectrum

m/z Formula m/z lost Group lost

136

105

77
4) Ethyl Ethanoate (CH3COOCH2CH3)

H O H H

H C C O C C H

H H H

mass spectrum

m/z Formula m/z lost Group lost

88

73

43

29

15
5) Salicylic Acid (2-hydroxybenzoic acid - (HOC6H4COOH))

displayed
formula

mass spectrum

m/z Formula m/z lost Group lost

138

*
120

92

* NB 3- or 4- hydroxybenzoic acid isomers cannot eliminate water –why not?

6) Aspirin (CH3COOC6H4COOH)

mass spectrum

m/z Formula m/z lost Group lost

180

138

120

43
7) ethanamide (CH3CONH2)

displayed
formula

mass spectrum

m/z Formula m/z lost Group lost

59

44

43
8) paracetamol (4-hydroxyphenylethanamide) (HOC6H4NHCOCH3)

displayed
formula

mass spectrum

m/z Formula m/z lost Group lost

151

109

108

43
 C) Nuclear Magnetic Resonance (n.m.r.) spectroscopy

• The number of peaks – number of proton types

• The chemical shift (δ) – what are the proton types
• The integration – how many protons of each type

Experiment 3 – RSC video

• Sample is placed in a very strong magnetic field

• A pulse of radiofrequency radiation is applied
• Radiofrequency signal emitted from sample is detected

Theory
• Nuclei have a property called nuclear spin which generates a tiny
magnetic field. The nuclei therefore behave like tiny bar magnets.

• When such nuclei are placed in a large magnetic field they will become
aligned with or against the direction of the external field.
• The nuclei lined up with the field are slightly more stable (lower energy)
than those that oppose the external field.

• The energy gap between these two states corresponds to radiofrequency

radiation.

• If the sample is irradiated with a pulse of radio waves, the nuclei in the
lower energy state may be promoted to the higher energy state (the tiny
bar magnets ‘flip’ from being aligned with to against the external field).

• The excited nuclei will then return to the ground state releasing fixed
quanta of energy which will be detected.
 • The energy gap depends on the chemical environment of the nuclei and can be
used to deduce the exact structure of the molecule.

• Ethanal has two proton types, so produces 2 signals in the n.m.r. spectrum.

The important features of the spectrum are:-

• The number of peaks – number of proton types
• The integration – how many protons of each type
• The chemical shift (δ) – what are the proton types

The following table can be used to link the chemical shift to the proton type (chemical
environment of H atom):-

type of proton chemical shift δ / ppm

RCH3 / RCH2R (alkane) 0.8 - 1.4
RCOCH3 (carbonyls, esters) 1.8 - 2.2
RCH2Hal 3.2 - 4.6
ROCH3 (esters, ethers) 3.2 - 3.5
ROH (alcohol) 1.0 - 6.0
RC6H4H (arenes) 6.0 - 9.0
RC6H4CH3 (methylarene) 2.2 - 2.4
RCONHR (amides) 7.0 - 10.0
RCHO (aldehydes) 9.7 - 9.8
RCOOH (carboxylic acids) 9.0 - 12.0
RC6H4OH (phenols) variable
RNHR (amines) variable

[R represents an alkyl group]

Examples of the interpretation of n.m.r spectra

1) propanone (CH3COCH3)

displayed
formula

nmr spectrum

Proton integration inference δ / ppm inference

Ha

2) propanal (CH3CH2CHO)
 displayed
formula

nmr spectrum

Proton integration inference δ / ppm inference

Ha 9.7

Hb 2.4

Hc 1.1
3) ethyl ethanoate (CH3COOCH2CH3)

Ha O
Hb Hc
C C O C C
Ha Hc

Ha Hb Hc

nmr spectrum

Proton integration inference δ / ppm inference

Ha 2.1

Hb 4.1

Hc 1.2
4) Salicylic Acid (2-hydroxybenzoic acid - (HOC6H4COOH))

displayed
formula

nmr spectrum

Proton integration inference δ / ppm inference

Ha 8.0

Hb 7.6

Hc 7.0

Where are the O-H groups?

 5) Aspirin (CH3COOC6H4COOH)

H
H

H
H

nmr spectrum

Proton integration inference δ / ppm inference

Ha 1 11.3

Hb 4x1 7-8

Hc 3 2.1
6) Mystery compound – “Why are there no aspirin in the jungle?”

n.m.r. spectrum

Proton integration inference δ / ppm inference

Ha 1 9.7

Hb 1 9.1

Hc 2 7.4

Hd 2 6.7

He 3 2.0

Structure
Combined Spectral Techniques

1) Predict the ir, nmr and mass spectra of propanal

a) IR spectroscopy

Bond / (Functional group) Absorption / cm-1

b) Nmr spectroscopy

Proton integration inference δ / ppm inference

c) Mass Spectrometry

m/z Formula m/z lost Group lost

Deduce the structure of the molecule from these spectra

a) ir spectrum

b) nmr spectrum

c) mass spectrum

45

60