1 of 45© boardworks ltd 2010. 2 of 45© boardworks ltd 2010

1 of 45 © Boardworks Ltd 2010


Mass spectrometry

Gaseous molecules of the compound are bombarded with high-speed electrons from an electron gun.

M(g) + e- M+(g) + 2e-

These knock out an electron from some of the molecules, creating molecular ions (M+), which travel to the detector plates:

Mass spectrometry is an analytical technique that can be used to deduce the molecular formula of an unknown compound.

The relative abundances of the detected ions form a mass spectrum: a kind of molecular fingerprint that can be identified by computer using a spectral database.


The molecular ion peak

molecular ion peak

mass spectrum of paracetamol40 80 120 160

20

40

60

80

100

00

abu

nd

ance

(%

)

m/z

The peak with the highest mass-to-charge ratio (m/z) is formed by the heaviest ion that passes through the spectrometer. This value of m/z is equal to the relative molecular mass of the compound.

High resolution mass spectrometry can be used to determine the molecular formula of a compound from the accurate mass of the molecular ion.


What is fragmentation?

A molecular ion is a positively-charged ion, which is also a radical as it contains a single unpaired electron. It is therefore sometimes represented as M+•.

M+• → X+ + Y•

NB: Only the ions are

detected by the mass

spectrometer. CH3CH2CH3+• → CH3CH2

• + CH3+

CH3CH2CH3+• → CH3CH2

+ + CH3•

For example, in the case of propane:

During mass spectroscopy, the molecular ion can fragment into a positive ion and a radical:

This fragmentation process gives rise to characteristic peaks on a mass spectrum that can give information about the structure of the molecule.

or


Fragmentation and molecular structure


Fragmentation of carbonyl compounds


Interpreting mass spectra

phenyl positive ion

(77)

Mass differences between peaks indicate the loss of groups of atoms (fragments). For example, loss of a methyl group leads to a mass difference of 15 between peaks.

Origins of some common peaks in mass spectra:

methyl positive ion (15)

loss of a methyl ion


Interpreting mass spectra activity


Uses of mass spectrometry

Identifying elements in new or foreign substances, for example analysing samples from the Mars space probe.

Monitoring levels of environmental pollution, for example amounts of lead or pesticide in a sample.

Some uses of mass spectrometry:

In biochemical research, for example determining the composition of a protein by comparing it against a database of known compounds.


Infrared spectroscopy

Certain groups of atoms absorb characteristic frequencies of infrared radiation as the bonds between them undergo transitions between different vibrational energy levels.

Infrared spectroscopy is an analytical technique that provides information about the functional groups present in a compound.

The particular wavelengths absorbed are specific to that particular configuration of bonds and atoms (functional group).

Infrared energy is only transferred to a bond if the bond contains a dipole that changes as it vibrates. Symmetrical molecules such as O2 or H2, are therefore IR inactive.

bonds absorbIR energy


Infrared spectra

An infrared spectrum is a plot of transmission of infrared radiation against wavenumber (1 / wavelength).

wavenumber (cm-1)

tran

smis

sio

n (

%)

Any wavelength that is absorbed by the sample will transmit less than the others, forming a dip in the graph.

IR absorption spectrum for chloroethane

The pattern in the fingerprint region (1500-400 cm-1) is unique to each molecule, and so can be used for identification purposes.


IR spectra of different functional groups


Interpreting IR spectra activity


Uses of IR spectroscopy

Use of IR spectra to follow the progress of a reaction involving change of functional groups (e.g. in the chemical industry to determine the extent of the reaction).

Use of IR spectra to assess the purity of a compound.

Breathalyzers: modern breathalyzers calculate the percentage of ethanol in the breath by looking at the size of the absorption caused by the C–H bond stretch in the alcohol.

Some uses of infrared spectroscopy:


How does NMR spectroscopy work?


What does an NMR spectrum tell us?

Different chemical environments (bonds and atoms surrounding a nucleus) affect the strength of magnetic field that must be applied to a nucleus in order for it to enter the resonance state.

By measuring the strength of magnetic field that must be applied, NMR spectroscopy gives us information about the local environment of specific atoms in a molecule. This can be used to deduce information about molecular structure.

The environments of 13C and 1H atoms are most commonly studied in NMR spectroscopy.


Carbon-13 NMR spectroscopy


Interpreting 13C NMR spectra

The 13C NMR spectrum of ethylamine contains two peaks. This is because ethylamine has two unique 13C environments, each requiring the application of a different magnetic field strength for that carbon nucleus to enter the resonance state.

C

H

H

H

C N

H

H

H

H

One peak is due to the carbon atom with three hydrogen atoms attached to it, and the second to the carbon

atom with two hydrogen atoms and

an amine group attached to it.


Interpreting 13C NMR spectra activity


Chemical shift and TMS

The horizontal scale on an NMR spectrum represents chemical shift (δ). Chemical shift is measured in parts per million (ppm) of the magnetic field strength needed for resonance in a reference chemical called TMS.

The signal from the carbon atoms in TMS is defined as having a chemical shift of 0.

Si

C

C

C

C

H

H

HH

H

HH

H

H

H H

HTMS (tetramethylsilane) is universally used as the reference compound for NMR as its methyl groups are particularly well shielded and so it produces a strong, single peak at the far right of an NMR spectrum.


13C NMR chemical shift assignment

The chemical shift values of peaks on the 13C NMR spectrum can help us identify the types of carbon atom in a compound. The likely source of spectrum peaks can be identified using a data table of typical chemical shift values.

5–40

20–50

190–220

Type of carbon

δ/ppm

chemical shift


13C NMR chemical shift activity


Proton NMR spectroscopy


Interpreting 1H NMR spectra activity


Integration and the number of hydrogens

The height of the peaks in an NMR spectrum does not give us any useful information.

The spectrum can be integrated to find this information.

However, the area under the peaks on a 1H NMR spectrum is proportional to the number of hydrogen atoms causing the signal. The ratio of the areas under the peaks tells you the ratio of 1H atoms in each environment.

21

3


Spin coupling


Splitting pattern activity


1H NMR chemical shift assignment

The chemical shift values of peaks on an 1H NMR spectrum give information about the likely types of proton environment in a compound.

0.7–1.2

2.1–2.6

9.0–10.0

Type of proton

δ/ppm


1H NMR chemical shift assignment activity


Uses of NMR spectroscopy

NMR spectroscopy uses the same technology as magnetic resonance imaging (MRI). This is an important non-invasive method of gaining information about internal structures in the body used in diagnostic medicine and scientific research.

NMR spectroscopy is also used in the pharmaceutical industry to check the purity of compounds.

Often, a combination of mass spectrometry, infrared spectroscopy and NMR spectroscopy is used in modern analysis to elucidate the structure of organic molecules.


What is chromatography?

Chromatography is a series of analytical techniques that can be used to separate mixtures of compounds for further use or for analysis.

stationary phase – this phase does not move. Compounds in the mixture are attracted to it (adsorbed) and slowed down. Either a solid or a liquid.

In all forms of chromatography, a mobile phase moves through or across a stationary phase.

mobile phase – this phase moves. The more soluble compounds in the

mixture are carried faster as the mobile phase moves. Either a liquid or a gas.


Thin layer chromatography


Column chromatography


Gas–liquid chromatography


High performance liquid chromatography

High performance liquid chromatography (HPLC) is a development of column chromatography in which the eluent is pumped through the column at high pressure.

This results in better and faster separation than can be achieved in standard column chromatography.

components collected

eluent reservoir

pump

column

detector

data analysis

injector


Gas chromatography–mass spectroscopy

In both GL chromatography and HPLC, the output from the chromatography column can be passed through a mass spectrometer. The spectra obtained can be compared to spectra of known compounds.

Gas chromatography–mass spectroscopy (GC–MS) is used extensively in forensics, environmental monitoring and in airport security systems. It is sensitive enough to detect minute quantities of substances


Chromatography: true or false?


Glossary


What’s the keyword?


Multiple-choice quiz

1 of 45© boardworks ltd 2010. 2 of 45© boardworks ltd 2010

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