Chemguide: Support for CIE A level Chemistry

This statement is about the use of NMR and X-ray crystallography in determining the structure of big molecules such as proteins.

Before you go on, you should find and read the statement in your copy of the syllabus.

This statement simply asks you for an "awareness" of the uses of NMR and X-ray crystallography. The second edition of the Applications Support Booklet makes it clear: "Students do not need to know anything about the principles or the methods of X-ray crystallography."

What follows is based on the (fairly frequent) exam questions which are asked about this topic.

X-ray crystallography

X-ray crystallography works by shining X-rays onto a very pure crystal of the substance you are interested in. The X-rays are diffracted (bent from their original path) when they interact with regions of high electron density.

The result is a diffraction pattern made up of lots of spots of varying intensities.

You will find an example of a diffraction pattern by following this link.

Measurements of patterns like this lead to electron density maps like the one you will find from the same site by following this link.

Interpretation of these enables you to see where the main atoms are to be found in the molecule, and to measure bond lengths and angles. This is useful in looking at the geometry of active sites in enzyme molecules, for example.

What a map like this doesn't show are the positions of hydrogen atoms. There isn't enough electron density around a hydrogen atom for it to have any effect on the X-rays.

Key things to remember

• X-ray crystallography needs very pure crystals to work with.

• X-ray crystallography detects positions of high electron density in a structure.

• Electrons cause diffraction of the X-rays which results in a pattern of spots.

• The pattern of spots can be used to produce an electron density map which allows you to work out the positions of various atoms, and the shapes of important features like active sites in enzymes.

• X-ray crystallography won't detect the positions of hydrogen atoms.

• If you are asked which element would show up most strongly during the X-ray crystallography of a particular substance, choose the one with the most electrons because that is where the highest electron density will be.

NMR

All you need to realise here is that:

• NMR is carried out in solution.

• NMR tells you about the position of hydrogen atoms because it affects the protons in the nuclei of hydrogen atoms.

• NMR works because of the two possible magnetic orientations of the protons - aligned with or against an applied magnetic field. The energy gap between these corresponds with energies in radio frequencies.

MRI and X-rays in medicine

This is another example of CIE at its irritating worst. There is no mention of either MRI scans or the use of medical X-rays in the syllabus, and a literal reading of syllabus statement 11.2(e) couldn't possibly be taken to imply that either are wanted, even if you trace the links back to the other statements mentioned.

There is a brief mention of MRI scans in the Applications Support Booklet. This seems, therefore, to have been arbitrarily introduced by an author of the Support Booklet - bearing no relationship to what the syllabus is asking.

CIE have asked about this twice in the 13 exam sessions up to June 2013, each time implying in the Examiner's Reports that students didn't know enough about this. Why should they?

The following is written to give you enough to be able answer a question on this non-syllabus material.

First, you must realise that medical use of X-rays has nothing whatsoever to do with X-ray crystallography.

• Medical X-rays show up bones because bones are more opaque to X-rays than soft tissue, but are not so good at identifying soft tissue.

• Medical X-rays are harmful (causing tissue damage) if over-used.

Secondly, although MRI (Magnetic Resonance Imaging) scans rely on the same sort of energy gaps between the two magnetic states of protons in hydrogen nuclei, the way this is used, and what the results show, bears no resemblance to NMR as used in chemistry or biochemistry.

You need to know that:

• Unlike X-rays, MRI doesn't cause any tissue damage.

• Unlike X-rays, MRI isn't obscured by bones.

• MRI picks up particular concentrations of hydrogen nuclei in different tissues - for example, in water or fat molecules.

• MRI can be fine-tuned to pick out particular tissue types which can be shown on a scan as different shades of grey. This includes the ability to distinguish between cancerous or normal tissue.

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