Introduction to Structural Databases

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Introduction to Structural Databases

Structural databases are essential tools for all crystallographic work and often need to be consulted at several stages of the process of producing, solving, refining and publishing the structure of a new material. Examples of such uses are:

1. Before deciding to synthesise a new compound the database could be used to check how many compounds with a particular chemical composition have been reported.
2. After synthesising and indexing the unit cell of a material the database can be searched to see if a material with the same or a similar unit cell is already known.
3. If a material is found in the database with a similar unit cell to the new material then its structure may be close enough (i.e. same symmetry and similar unit cell contents) to be used as the starting model for the Rietveld refinement of the new material.
4. To verify the results of a structure refinement the database can be consulted to find structures that have comparable bond distances, bond angles or coordination environments to the new structure.

The common information found in a structural database for each entry is:

1. bibliographic information - author(s) names, journal reference
2. the chemical compound name, formula and oxidation states of the elements present
3. the contents (number of formula units per unit cell), dimensions and symmetry (crystal system and space group) of the unit cell
4. the symmetry of the structure, atomic coordinates, occupancies and thermal parameters (isotropic or anisotropic)
5. comments on any special features of the experiment to collect the diffraction data, for example, the temperature, and on any problems found in the structure itself.

Not all the above information is found in each database for all entries, but all databases contain the information listed in points (1) to (3). All the above data for each entry is explicit. The explicit data can be used to generate data that is implicit in this stored information but that must be calculated from the stored data. Implicit data includes such things as, interatomic distances, bond angles, torsion angles, coordination numbers and structural representations that are generated by software within the database suites.

The structures in the databases have been solved using X-ray, neutron and electron diffraction techniques on samples that are generally single crystals, but with the advances in structural solution using powder diffraction data, may be powders. There are some entries whose structures are predicted from computational modelling and some determined using NMR spectroscopy, these entries generally occur for protein samples.

One important point to note is the difference between these structural databases and the database of powder diffraction files (ICDD-PDF). The latter contains the "fingerprint" powder diffraction pattern of crystalline materials whose structure may or may not be known. The structural databases contain structural information for each material (the unit cell at least) derived from analysis of diffraction data.

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