# TEACHER NOTES X-RAY DIFFRACTION

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```					                      TEACHER NOTES
X-RAY DIFFRACTION
crystal
glass
fibre

X-ray            monochromator
source                               sample
detector
holder

HOW DOES IT WORK?

X-rays are diffracted by electron clouds. Firing x-rays at electron clouds that are around
ordered atoms (in crystals) gives a diffraction pattern. We can interpret the diffraction
pattern to calculate the 3-dimensional position of the atoms in the crystals. There is a good
tutorial that explains x-ray diffraction at a second-year university level at
http://www.matter.org.uk/diffraction/introduction/default.htm

We get a good diffraction pattern by placing a large crystal made of a perfectly ordered
arrangement of atoms in front of an intense x-ray source. Typical crystals analysed in the
School of Chemistry's diffractometer have dimensions of around 0.5mm.

The x-rays are fired in bursts of 10-30 seconds, the diffraction pattern is collected by the
detector, and then the crystal is rotated by 0.3o before the x-rays are fired again. This
firing-rotating-firing continues for 8-12 hours until we have collected the full 3-dimensional
x-ray diffraction pattern.

WHAT CAN IT TELL US?

Crystal structures are calculated from diffraction patterns. If we had collected diffraction
data on a caffeine crystal, we would end up with the picture in Figure 1 after we had
processed the data. This picture shows the sites where the clouds of electrons that
diffracted the x-rays are located. The next job of the crystallographer is to work out what
type of atoms are surrounded by the electrons, and then play join-the-dots to work out
where the bonds are.
CAFFEINE.

The crystal and molecular structures of caffeine are below. Small atoms (with a small
electron cloud) often don't diffract enough electrons to appear in the structure, so it is
unusual for all the hydrogen atoms to be visible (as they are here). We can tell the
difference between single, double and triple bonds by looking at the bond length – multiple
bonds are shorter. We determine the identity of the atoms by looking at the amount of
electron density they have around them. It is easy to distinguish a copper from carbon in
diffraction data but telling nitrogen from oxygen is more difficult – x-ray analysis is always
combined with other analyses to make sure that the identity is correct.

CH3
O       N     N

N         N
H3C
O      CH3

WHAT IS X-RAY CRYSTALLOGRAPHY USED FOR?

X-ray crystal structures of proteins and viruses are studied in attempts to identify sites that
are vulnerable to attack by drugs. X-ray diffraction is also useful in materials science. For
example, I identified the 0.5nm channels in zinc glucarate (below) using x-ray
http://www.scienceinpublic.com/sciencenow/2003/mick_moylan.htm

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