Key Stage 4 -Crystal Quest

Pupil worksheet

X-ray crystallography

Why are metals strong? Why is diamond hard? How are the atoms arranged in cholesterol? Before 1914, no one could answer these questions. They did not know the structure – the exact arrangement of atoms – of any substance.

Scientists, including father and son W.L. Bragg and W.H. Bragg, worked hard to develop a new technique: X-ray crystallography. This was an enormous breakthrough. Since 1914 scientists have used the technique to work out the structures of more than half a million substances.

Your task

You are a group of research chemists in a university in an African country. The International Union of Crystallography supports X-ray crystallography in Africa. It will give you part of the equipment needed for X-ray crystallography, a diffractometer, worth £120,000.

You want to take up the offer. But can you persuade university leaders to pay for the vital extra equipment you need for X-ray crystallography research?

Preparation

Plan a presentation to persuade university leaders to pay for an x-ray tube and computer so that you can do X-ray crystallography research. Explain:

What X-ray crystallography is and how it works. What scientists have already learnt from X-ray crystallography. What you would use the X-ray crystallography equipment for.

Presentation

Give your presentation. Be prepared to answer questions.

How X-ray crystallography works

To find out how the atoms are arranged in a substance, follow these steps:

1 Make a crystal of the substance. The crystal must be pure and perfect. This is not easy!

2 Fire X-rays at the crystal. The X-rays change direction as they bounce off layers of atoms in the crystal. This is diffraction. Diffraction produces a pattern of spots. Some spots are more intense (darker) than others. Every type of crystal makes its own pattern of spots.

3 Continue to fire X-rays at the crystal whilst rotating the crystal a small amount, say 1º. Repeat until the crystal has turned through at least 180º. This results in up to 180 diffraction pattern images of the crystal.

4 With the help of a computer program, create a 3D picture of the electron density in the crystal from all the 2D patterns of spots.

5 Use computer graphics software to build a model of the atomic structure of the crystal into the 3D electron density picture.

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Key Stage 4 -Crystal Quest

First discoveries

The structure of sodium chloride (salt) was the first to be determined by X-ray crystallography, in 1914.

X-ray crystallography showed that the compound is not made up of atoms joined by covalent bonds. It consists of positive and negative ions.

In the same year, W. L. and W.H. Bragg also discovered the structure of diamond. Its

atoms are joined together by strong covalent bonds in a tetrahedral pattern.

Also in 1914, the Braggs used X-ray crystallography to work out the structure of a metal – copper. Solid copper is made up of positively charged atoms, arranged in rows.

For every copper atom there are two negatively charged electrons, which are free to move. This explains why copper conducts electricity.

Key Stage 4 -Crystal Quest

Revealing life’s mysteries

Most biological substances do not exist naturally as crystals. But the best method of finding out their structure is X-ray crystallography. It may take weeks to obtain

perfect crystals of biological substances. Their atoms are not arranged in straight lines, so it is not easy to interpret their X-ray diffraction patterns. And, of course, the scientists who first worked out the structures of these molecules had no computers.

Dorothy Hodgkin overcame these challenges. She worked patiently for many years to find out how the atoms are

arranged in cholesterol, penicillin, and vitamin B12. She also discovered the structure of insulin. She won the Nobel Prize for Chemistry in 1964.

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This is a model of cholesterol. The black spheres represent carbon atoms. White spheres are hydrogen atoms, and the red one is oxygen.

Below is a model of an insulin molecule. Insulin is a protein. It is a hormone that controls glucose levels in your blood.

In this model, carbon atoms are green, hydrogen atoms are white, oxygen atoms are red, and nitrogen atoms are blue.

Key Stage 4 -Crystal Quest

Designer medicines

Many viruses and bacteria cause disease. Their proteins attack human cells. If scientists know the exact shape of an attacking protein they can design medicines to stop its harmful activity.

HIV

The human immunodeficiency virus (HIV) causes AIDS. The virus includes an enzyme called HIV-1 protease. This protein is vital in the life-cycle of HIV. If the virus does not have working HIV-1 protease, it cannot be infectious.

Scientists made crystals of HIV-1 protease. They used X-ray crystallography to discover its structure. The diagram shows this structure. Its individual atoms are not shown. The molecule in the black oval is not part of HIV-1 protease.

Like all enzymes, HIV-1 protease has an active site. This is where chemical reactions that are vital to the life cycle of the virus take place.

Scientists have developed drugs that join to the active site. The drugs stop the HIV-1 protease doing its job. The molecule shown in the black oval is one of these

drugs. If HIV-1 protease stops working, the virus perishes.

Other diseases

All over the world, X-ray crystallographers work out the structures of proteins from viruses and bacteria. This helps in developing drugs to stop them working.

Key Stage 4 -Crystal Quest

The future

Mars rocks

Could there be life on Mars? In 2013 scientists moved closer to finding out. The Mars rover, Curiosity, scooped up a sample of soil. Its on-board X-ray crystallography apparatus produced this diffraction pattern.

Scientists have interpreted the pattern. They have discovered that the soil sample is similar to volcanic soils in Hawaii.

Solving problems – food, water, energy, and pollution

X-ray crystallography can contribute to finding cures and vaccines for plant and animal diseases, such as tomato canker, bird flu, and swine flu.

X-ray crystallography can help improve water quality in poor communities by identifying new materials to purify water, for example nanosponges.

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X-ray crystallography can help develop new products to reduce home energy consumption, for example insulating materials. It can also identify materials to reduce the cost of solar panels and batteries.

X-ray crystallography can help to reduce mining waste by improving methods of extracting metals from ores, for example.

Key Stage 4 -Crystal Quest

Help sheet

Question What we will say

What is X-ray crystallography?

How does X-ray crystallography work?

What have scientists already learnt from X-ray crystallography?

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What would we use the X-ray crystallography equipment for?

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