Computer software crystal structure determination

Chemists use X-ray crystallography to determine the exact structure of chemical compounds. This involves taking a solid crystal of a pure compound and diffracting X-rays off of it, which produces a complex diffraction pattern. Using computer software, the diffraction pattern can be processed to yield a structure that describes the structure of an individual molecule of the compound making up the crystal. This is a powerful technique, but it can only be used on compounds that can be crystallized. It s also worth pointing out that the solid phase structure of a molecule is not always the same as that in a solution, so caution should be used when relating crystal structures to chemical reactivity in the solution phase. 

In order to obtain detailed structure, a knowledge of diffraction intensities is essential, the intensities being related to the structure factor. Computer-controlled single-crystal X-ray diffractometers with structure (software) packages have made structure elucidation a routine matter. The availability of synchrotron X-radiation of continuously variable wavelength has made X-ray diffraction a still more powerful structural tool for the study of solids. A technique of great utility to solid state chemists is the Rietveld treatment of powder X-ray diffraction profiles (Rietveld, 1969 Manohar, 1983). Automated structure packages for the determination of unknown structures by this method are now commercially available (see section 2.2.3). In Fig. 2.1, we show a typical set of profile data. 

Perhaps the most crucial advance in recent decades has been the rapid evolution of computational methods for determining the structure from the diffraction patterns. The quality of the raw data is affected by the number of atoms in the unit cell, the temperature of the crystal, and of course imperfections in the crystal. Often this makes the pattern ambiguous enough that there is no unique solution more than one structure—often only slightly different—would result in the same pattern, to within some experimental error. Modern software solves for the set of possible solutions, using the known chemical composition of the crystal and basic rules of chemical bonding to arrive at the likeliest geometry. 

In the past, it would take months or years to determine the structure of a protein molecule now it takes a day or even a few hours. Since the wavelength can be changed easily and the intensity of an x-ray is much brighter, more data can be collected. By analyzing the diffraction pattern using software, it becomes much simpler to make a map of the electron density in the crystal. Programs are available or may be devised to have the shape and the structure displayed on a computer screen as a mass of squiggly lines, ribbons, and little balls. 

Single-crystal X-ray diffraction is the most useful experimental technique available for the determination of the three-dimensional crystal arrangement. Improvements in automated data collection methods on computer-controlled diffractometers and the development of more-robust refinement software has led to structure solution becoming almost routine. Over the past 10 years the total number of structures stored in the Cambridge Crystallographic Database (often referred to as the Cambridge Structural... 

---