The Databases

The Databases

There are five established structural databases, all of which are available on CD-ROM. The one for your particular use depends heavily on the class of material you are interested in.

(i) Cambridge Structural Database (CSD)

The CSD is run by the Cambridge Structural Database System and contains detailed information on over 257000 crystal structures obtained for organic, organo-metallic compounds and metal-organic complexes. It does not include proteins, high molecular weight polymers, and purely inorganic carbide , carbonates, carbonyls and cyanates. The database is fully retrospective, including all work that has ever been reported.

Most entries contain all the information given in points (1) to (5) of the Introduction to Structural Databases except for the thermal parameters of the atoms in the structures. For each entry in the database three distinct types of information are stored. These are categorised as 1D Bibliographic Information (containing all the bibliographic material for a particular entry and summarising the structural and experimental information for the crystal structure), a conventional 2D chemical diagram of the molecular structure, and a 3D representation of the molecule and the 3D crystal structure. This database is probably the most powerful of the databases discussed.
Some of the features include:

searching the database for particular molecules in a structure or for even smaller fragments, including particular hybridisations of bonds in the fragment , for instance, a C=C-F fragment may be searched for in which the C atoms are sp² hybridised
peforming statistical analysis on particular geometrical structural features of all structures containing that feature. For instance, after obtaining all structures containing the C=C-F fragment, the structures can be compared and analysed statistically to produce information on the C(sp²)-F bond length distribution, mean, minimum and maximum over all the structures containing this fragment
seaching and assessment of intramolecular and/ or intermolecular non-bonded contacts patterns within structures in the database, for example, searching for X-H...Y configurations that might be regarded as hydrogen-bonds.

A case study of the style of a search, and the data retrieved, is given for this database in the next section.

(ii) Inorganic Crystal Structure Database (ICSD)

The ICSD is maintained in Germany, at the Fachinformationszentrum Energie Physik Mathematik, Karlsruhe and the Institute for Inorganic Chemistry of the University of Bonn and contains information on more than 61775 inorganic crystal structures. The ICSD contains information on all structures:

that have no C-C and/ or C-H bonds in any of their residues
(avoids overlap with the CSD, which has essentially the opposite criteria);
and that include at least one of the non-metallic elements H, He, B, C, N, O, F, Ne, Si, P, S, Cl, Ar, As, Se, Br, Kr, Te, I, Xe, At and Rn
(avoids most overlap with CRYSTMET (see (iii));
and whose coordinates have been fully determined (although coordinates of H atom may be missing).

Again ICSD is retrospective, back to 1912, with all information being taken from original papers and their supplementary material. Most entries contain all the information given in points (1) to (5) of the Introduction to Structural Databases.

(iii) NRCC Metals Crystallographic Data File (CRYSTMET)

This database is maintained by the National Research Council Canada and contains information on more than 52500 metal and intermetallic phases characterised since 1913. Requirements for inclusion are that the composition be clearly defined and that the space group and unit cell have be determined. A few compounds of metals with metalloids (elements lying on the border between metals and non-metals in the periodic table) are also included, as are a few metallic oxides. Most entries contain all the information given in points (1) to (5) of the Introduction to Structural Databases. The database also includes the option to produce diffractometer traces with requested resolution for each entry in the database where the structure is known.

(iv) The Protein Databank (PDB)

The PDB was established in 1971 for the structures of biological macromolecule such as proteins, nucleic acids, enzymes, viruses and polysaccharides. It now contains more than 17902 entries. All atomic coordinates are transformed to a standard orthonormal coordinate frame, so that users need not be familar with the details of crystal coordinate systems.

The sheer size and complexity of protein structures makes it unlikely that the work you will be doing with powder samples will involve use of this database, although some structures are now being solved and refined using high resolution synchrotron X-ray powder diffraction data!

(v) ICDD NIST Crystal Data File

This is not a full structural database, unlike the other databases mentioned above, however it is a valuable aid in doing structural work. The database contains more than 237671 entries for all crystalline materials except for proteins, high-molecular weight polymers and solid solutions. The primary data includes the information in points (1) to (3) of the Introduction to Structural Databases, but NO atomic coordinates are given. For each entry there are also transformation matrices provided to transform the observed unit cell to a standard unit cell if such a transformation is necessary.

Course Material Index

Section Index

Author(s): Martin Attfield