Crystallography is the experimental science of determining the arrangement of atoms in crystalline solids. The word "crystallography" derives from the Greek words crystallon "cold drop, frozen drop", with its meaning extending to all solids with some degree of transparency, graphein "to write". In July 2012, the United Nations recognised the importance of the science of crystallography by proclaiming that 2014 would be the International Year of Crystallography. X-ray crystallography is used to determine the structure of large biomolecules such as proteins. Before the development of X-ray diffraction crystallography, the study of crystals was based on physical measurements of their geometry; this involved measuring the angles of crystal faces relative to each other and to theoretical reference axes, establishing the symmetry of the crystal in question. This physical measurement is carried out using a goniometer; the position in 3D space of each crystal face is plotted on a stereographic net such as a Wulff net or Lambert net.
The pole to each face is plotted on the net. Each point is labelled with its Miller index; the final plot allows the symmetry of the crystal to be established. Crystallographic methods now depend on analysis of the diffraction patterns of a sample targeted by a beam of some type. X-rays are most used; this is facilitated by the wave properties of the particles. Crystallographers explicitly state the type of beam used, as in the terms X-ray crystallography, neutron diffraction and electron diffraction; these three types of radiation interact with the specimen in different ways. X-rays interact with the spatial distribution of electrons in the sample. Electrons are charged particles and therefore interact with the total charge distribution of both the atomic nuclei and the electrons of the sample. Neutrons are scattered by the atomic nuclei through the strong nuclear forces, but in addition, the magnetic moment of neutrons is non-zero, they are therefore scattered by magnetic fields. When neutrons are scattered from hydrogen-containing materials, they produce diffraction patterns with high noise levels.
However, the material can sometimes be treated to substitute deuterium for hydrogen. Because of these different forms of interaction, the three types of radiation are suitable for different crystallographic studies. An image of a small object is made using a lens to focus the beam, similar to a lens in a microscope. However, the wavelength of visible light is three orders of magnitude longer than the length of typical atomic bonds and atoms themselves. Therefore, obtaining information about the spatial arrangement of atoms requires the use of radiation with shorter wavelengths, such as X-ray or neutron beams. Employing shorter wavelengths implied abandoning microscopy and true imaging, because there exists no material from which a lens capable of focusing this type of radiation can be created. Scientists have had some success focusing X-rays with microscopic Fresnel zone plates made from gold, by critical-angle reflection inside long tapered capillaries. Diffracted X-ray or neutron beams cannot be focused to produce images, so the sample structure must be reconstructed from the diffraction pattern.
Sharp features in the diffraction pattern arise from periodic, repeating structure in the sample, which are very strong due to coherent reflection of many photons from many spaced instances of similar structure, while non-periodic components of the structure result in diffuse diffraction features - areas with a higher density and repetition of atom order tend to reflect more light toward one point in space when compared to those areas with fewer atoms and less repetition. Because of their ordered and repetitive structure, crystals give diffraction patterns of sharp Bragg reflection spots, are ideal for analyzing the structure of solids. Coordinates in square brackets such as denote a direction vector. Coordinates in angle brackets or chevrons such as <100> denote a family of directions which are related by symmetry operations. In the cubic crystal system for example, <100> would mean, or the negative of any of those directions. Miller indices in parentheses such as denote a plane of the crystal structure, regular repetitions of that plane with a particular spacing.
In the cubic system, the normal to the plane is the direction, but in lower-symmetry cases, the normal to is not parallel to. Indices in curly brackets or braces such as denote a family of planes and their normals which are equivalent in cubic materials due to symmetry operations, much the way angle brackets denote a family of directions. In non-cubic materials, <hkl> is not perpendicular to. Some materials that have been analyzed crystallographically, such as proteins, do not occur as crystals; such molecules are placed in solution and allowed to crystallize through vapor diffusion. A drop of solution containing the molecule and precipitants is sealed in a container with a reservoir containing a hygroscopic solution. Water in the drop diffuses to the reservoir increasing the concentration and allowing a crystal to form. If the concentration were to rise more the molecule would precipitate out of solution, resulting in disorderly granules rather than an orderly and hence usable crystal. Once a crystal is obtained, data can be collected using a beam of radiation.
Although many universities that engage in crystallographic research have their own X-ray producing equipment, synchrotrons are used as X-ray sources, bec
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