Introduction to Structure Determination  
Crystallography: Introduction  
Introduction   Infrared   Ultraviolet   Mass Spectrometry   NMR   Crystallography   Combined  
  • Introduction
  • X-ray crystallography

    X-ray diffraction, in principle, provides full structural information on the position and identity of each atom in the crystal of a compound. A beam of X-rays is passed through a crystal and the beam is diffracted in a way which depends on the position and electron density of the atoms. Computer analysis of the diffraction pattern allows for the atom types to be identified alongside their positions and hence the bond lengths and angles can be calculated.

    X-ray diffraction is used to determine the structures of thousands of new inorganic, organic and biological compounds each year. The coordinates are held in electronic databases and are available for use by researchers throughout the world. The structures of proteins and biomolecules, for example, are used to understand enzyme receptor interactions and hence to develop new drugs. The online databases include: Clearly, a crystal structure of a compound gives the most complete structural information that can be obtained. However, it has some limitations:
    • It is limited to crystalline samples of high quality and sufficient size. Growing such crystals is often very difficult, especially for biomolecules.
    • It provides information on the structure of the compound in the crystal. The 3-dimensional structure of a protein obtained in the crystal may be quite different to that in solution. As the latter is more relevent to biology, it is important to also use IR and NMR as well to establish whether the structure is the same.
    • X-rays are diffracted by the interaction with electrons on the atoms and in the bonds. X-ray diffraction is able to pick up the position of the atoms as the electron cores (i.e. the non-valence electrons) have a very high density. Unfortunately, hydrogen has no core electrons and so it is often very difficult to detect the position the H atoms. In many crystal structures, the positions of the hydrogen atoms are not known very accurately or their positions have been estimated.

    Neutron crystallography

    Neutron diffraction uses high energy neutrons instead of X-rays. The major difference is that the neutrons are diffracted by the atomic nuclei rather than the electrons. This has the advantage that the diffraction by hydrogen atoms is strong and these atoms can be located much more accurately than in X-ray diffraction.

    Note that neutron diffraction requires a nuclear reactor as a source of neutrons. It is thus only available at specialised centres, such as the ANSTO facility at Lucas Heights in NSW.

     © Prof Adam Bridgeman, School of Chemistry, The University of Sydney, 2020