A-level Chemistry/AQA/Module 4/Structure Determination

There are three different techniques for structural determination on the module 4 syllabus - mass spectroscopy, infrared spectroscopy and nuclear magnetic resonance (usually n.m.r.) spectroscopy. Each has its own purpose and all are valuable in identifying compounds - the three put together are usually enough to give a strong conclusion so long as the relevant data is provided.

Mass spectrometry

Much of the theory behind mass spec. is covered at AS level - but aimed at atomic rather than molecular identification. To summarize, the sample chemical to be tested is vaporized and then ionized by an electron beam. The resultant positive ions are then accelerated by charged plates in the spectroscope and deflected by an electromagnet of variable strength. When the magnet is adjusted correctly, the ions are detected electrically by plates which accept the charge dissipated when sample ions collide with them to produce a measurable (but very small) current. The relative current is recorded as the electromagnet strength is varied to produce a mass to charge ratio usually represented as "m/z".

The general idea behind use with molecules is the same - a mass to charge ratio is produced and peaks can appear at varying values of m/z either by way of secondary ionization or isotopic variance of component atoms. However, the matter is complicated by fragmentation of the molecule on ionization - where groups break off the molecule to produce many more peaks of varying mass on the resulting reading.

This bond fission produces a mixture of fragment ions which can sometimes be used to identify functional groups in a compound - though not always reliably - and makes for a much more complex result than for atomic tests.

The main features to watch out for are:

• The highest major peak caused by the whole molecular ion
• A small peak one value above this caused by Carbon-13 inclusion in some molecules for organic samples
• Major peaks at values for known functional group masses - e.g. 77 almost always represents a phenyl group (with 5 hydrogens rather than 6)

Remember that when the molecular ion is produced, two species are formed - an ion and a radical. Only the ion is detected by the spectroscope, but for any given split species of both kinds will be produced so both groups will likely be detected to some extent.

Infrared spectroscopy

All molecules are able to convert energy supplied from electromagnetic radiation into vibrations in the bonds between their constituent atoms. Different bonds vibrate at different frequencies and therefore by passing infrared radiation through a sample of a substance it can be observed which wavelengths are absorbed. When compared to known data, these drops in transmittance (or rises in absorption, if you prefer) can be used to analyze the functional groups present in a compound.

The process produces an output graph with (usually) percentage transmittance on the y axis and "wave number" - related to the frequency of the supplied radiation - along the x axis. The trace is high and dips where an area of high absorption is present, and data is supplied on the exam paper for the given patterns over which each group causes a drop in transmittance as a range - for example the N-H bond in amines forms a trough from around 3100 – 3500 cm⁻¹.

Below around 1500 cm⁻¹, most graphs become very complex and with a lot of interacting troughs - this is known as the fingerprint region and is unique for any compound. This is the region used to conclusively identify a sample if it is pure and fingerprint region data is available.

Nuclear Magnetic Resonance Spectroscopy

This is perhaps the most complex information you will be required to interpret in the exam - the basic principle goes that, as all Hydrogen nuclei (i.e. protons) have a magnetic spin and can absorb energy from radio frequency radiation to move into higher energy states, resonance can occur when the nuclei oscillate between states. As the nucleus moves into a higher energy state, its spin will cease to be parallel to the applied magnetic field and so will drop back down - and this process will be repeated giving absorption peaks in the spectrum.

Electrons around a proton shield it from the applied field and so the frequencies of absorption vary depending on the environment that the proton is in. This is affected by even small variances in electronegativity of nearby atoms in the molecule, and this is measured in terms of 'chemical shift' (usually represented by δ) - the standard n.m.r spectrum appears as a trace with absorption on the y axis and decreasing δ on the x axis, with spikes at points of high absorption where resonance occurs.

As with IR spec, data is supplied on your test paper for chemical shifts relating to specific chemical groups.