All matter in the universe, from your shoes to the most distant stars, is made up of atoms. But how are atoms packed together to form all of the structure of our world? In this activity we will explore several techniques that are used in the field of X-ray crystallography, many pioneered by women, to see inside matter and take pictures of the atoms themselves.
Inside the atom
Figure 1 shows two different pictures of what an atom looks like. The central region is called the nucleus of the atom. It has a positive electric charge and is thousands of times heavier than the electrons that make up the outer part of the atom. Electrons are negatively charged particles (particles are the smallest amount of a thing that can exist; no matter how hard you try, they cannot be cut into smaller amounts). The Bohr model of the atom (shown on the left side of Figure 1) was one of the first models of the atom. It was developed in 1911 and it shows the electrons orbiting around the nucleus of the atom much like the planets in our solar system orbit around the sun. This simple model explains many of the properties of atoms, but it is incomplete.
A better model, the Schrodinger picture, is shown to the right in Figure 1. In this (quantum) model, the electrons are like a cloud that spreads out and surrounds the nucleus. The electron has a probability of being found at each location in the cloud. In quantum physics, the electrons only appear to be particles when we take a picture of them, or observe them. If we leave them alone they will spread out like a wave. If you are interested you can learn more about the quantum properties of electrons in the extension activity 4; in this activity we will instead study the atom as a whole.
X-ray crystallography
In order to study how atoms are arranged in a material, scientists can shine an X-ray beam on a sample of that material. When the beam passes through the sample it will scatter (deflect or bounce) off of the atoms. By studying the pattern the scattered beams make on a detector scientists can work out how the atoms are arranged in the sample. For this to work the atoms must be arranged in a periodic/repeating pattern (as you’ll see during the activity).
When the atoms are arranged in a repeating pattern, the sample is called a crystal, and the technique of shining X-rays on it to determine its atomic structure is called X-ray crystallography. This technique has many applications;biologists use it to design more effective drugs, and engineers use it to develop new materials, technology and sources of renewable energy! Much of the early X-ray crystallography discoveries were made by women such as Kathleen Lonsdale and Isabel Knaggs (structure of benzene), Isabella Karle (analyzing crystals and helped revolutionize drug design), Elizabeth Wood (crystal’s electric, magnetic and superconductive properties), Dorothy Hodgkin (Nobel Prize-winning chemist -determine the molecular structure of penicillin, vitamin B12, and insulin) and perhaps most famously, Rosalind Franklin’s (demonstrated the double helix structure of DNA).
Wave interference
To understand how crystallography works, we first need to talk about the fact that light is a wave (X-rays are one type of light). You may be more familiar with ocean waves, where water moves up and down in a repeating pattern (in physics we would say that the water is oscillating up and down). This is generally true: in all types of waves, something is oscillating up and down or back and forth.
To see what happens when we shine X-ray photons (which are waves) on atoms, look at Figure 2. In the picture, the X-rays are the dark lines that are going up and down repeatedly, similar to what an ocean wave looks like. The distance between the peaks of the wave is called the wavelength. For ocean waves it’s about 160 ft, and in the figure the X-ray photons have a wavelength of about 1.1 inches (in reality X-ray photons have a wavelength of around one millionth of a millimeter, but this is just a model).
In Figure 2 you can see the waves are scattering off of two atoms (the black and blue balls) in the sample. When the scattered waves reach the detector they will interfere (combine with each other). This means that at each point in space the heights of the two waves are added together. On the left side of Figure 2, the peaks of the two waves add together, which creates an extra large wave. This is called constructive interference. On the right side of Figure 2, however, the peaks of the first wave overlap with the low points of the second wave, so when they’re added together you just get a flat line. This is called destructive interference.
In X-ray crystallography, the conditions for constructive and destructive interference are determined by the wavelength of the X-rays, the angle the X-ray beam hits the sample, and by the spacing between the atoms in the sample. In Figure 2, the only difference between the constructive and destructive interference examples is that the atoms in the crystal on the right are closer together than the atoms in the crystal on the left. This is also why we can’t use visible light to do crystallography: the distance between atoms in most solids is similar to the wavelength of X-rays, but visible light has a wavelength that is usually thousands of times longer, so the interference pattern you’d see with visible light wouldn’t tell you anything about the arrangement of the atoms. Scientists observe what X-ray wavelengths and beam angles lead to constructive or destructive interference, and from that data determine how the atoms are arranged in the sample.
