Crystal structures database software

The inorganic equivalent of the CSD is the Inorganic Crystal Structure Database (ICSD) (FIZ 2001 Bergerhoff et al. 1983). This currently contains over 53000 entries (August 2000) with two updates per year, and may be searched in a manner similar to that used for the CSD. There are currently efforts under way to unify the searching software for these two important data bases, a move which would considerably facilitate and widen their use. Another useful source is the inorganic section of the PDF (ICDD 2001 Jenkins and Snyder 1996). For older references, the first two volumes of Groth (1906, 1908) are particularly valuable. 

Bergerhoff, G., and Brown, I. D. Inorganic crystal structure database. In Crys-tallographic Databases. Information Content, Software Applications, Scientific Applications. Section 2.2. pp. 77-95. International Union of Crystallography Bonn, Cambridge, Chester (1987). 

Peak position and intensities (or areas) can be used to identify the phases present in the material (Fig. 1.9). Those parameters are typically compared with the PDF database from the International Center of Diffraction Data (a conunercial database with entries listed as Ox-xxx-xxxx, where x are numbers) [8]. Other databases are also available (such as the RRUFF Project or the FIZ Inorganic Crystal Structure Database [4]) but the magnitude of the ICDD database, with half a million entries makes it a very popular choice. Search/match software is typically used to assist in the process. A common approach is to match at least the three strongest peaks... 

Another recent database, still in evolution, is the Linus Pauling File (covering both metals and other inorganics) and, like the Cambridge Crystallographic Database, it has a "smart software part which allows derivative information, such as the statistical distribution of structures between symmetry types, to be obtained. Such uses are described in an article about the file (Villars et al. 1998). The Linus Pauling File incorporates other data besides crystal structures, such as melting temperature, and this feature allows numerous correlations to be displayed. 

Figure 5 The crystal structures for SEB and TSST-1. These structures were constructed by using data provided by Entrez s 3-D database and software for molecular modeling. Primary references for SEB and TSST-1 crystai structures are Papageorgiou etal. and Prasad ef respectiveiy.

The vast number of crystal structures now deposited in the Cambridge Structural Database and recent software developments make systematic exploration of crystal packing trends another new, powerful tool. 

Computational results were obtained using Spartan 08 (Wavefunction Inc., Irvine, CA) and software programs from Accelrys Software Inc. with graphical displays generated by the Discovery Studio Visualizer. Where protein structures have been downloaded from the RCSB Protein Data Bank the full references and PDB IDs have been given. I wish to acknowledge the use of the Chemical Database Service at Daresbury for access to other crystal structures. Again, full primary sources can be found in the references. 

Common approaches for the tailoring of nonmetallic (ceramic) materials properties involve topochemical methods (those where the crystal structure remains largely unaffected) and the preparation of phases in which one or more sublattices are alloyed. In principle, such materials are within the realm of CALPHAD. On the other hand, as has already been stated, extrapolation does not really aid the discovery of new or novel phases, with unique crystal structures. Furthermore, assessed thermochemical data for the vast majority of ceramic systems, particularly transition metal compounds, are presently not available in commercial databases for use with phase diagram software. This does not necessarily preclude the use of the CALPHAD method on these systems However, it does require the user to carry out their own thermodynamic assessments of the (n — 1 )th-order subsystems and to import that data into a database for extrapolation to nth-order systems, which is not a trivial task. 

Since first data concerning structures of uranyl compounds with CV(U(V1)) = 5 appeared in 1999, it is of great interest to include these structures into the analysis of the characteristics of the U(V1) VD polyhedra. Initial crystal structure information was extracted from the known stmcture databases [2, 3] and analyzed using the TOPOS software [16]. Stmctures were included into consideration under conditions that crystallographic agreement index (7 i) is less than 0.10 and that there is no disorder in the U or O sites in the UO polyhedra. In total, 908 compounds were considered that contained 1465 crystallographically independent U(V1) atoms. From these atoms, 15, 306, 906, and 238 have coordination numbers of 5, 6, 7, and 8, respectively. 

Most powder diffraction databases only serve angular dispersive X-ray diffraction. Energy dispersive X-ray diffraction data can be transformed into an angular dispersive equivalent that can then be used in conventional search-match software. Users of neutron diffraction data are currently limited to performing phase identification using a list of crystal structures imported into a Rietveld program. It is wise to first run samples destined for neutron diffraction sample in a powder XRD prior to confirm phase purity, and to use calculated patterns to assist in phase identification of possible undesired phases due to ancillary equipment or sample environment. 

A special type of bond-type assignment problem concerns tautomerism. Some chemical databases provide specific tautomeric bond types, or analyse a query for either the keto or enol constructions and add the missing one (as an. OR. option) automatically. In the CSD, only the single tautomeric form identified by the crystal structure determination is encoded in the connectivity tables. The software has not yet been upgraded to accommodate searches for both forms, hence the onus is on the user to encode both representations if that is the desired goal of a query. 

Structure retrieval or generation Crystal structures of organic compounds can be found in the Cambridge Crystallographic Data Centre (CCDC) database (http //www.ccdc.cam.ac.uk/). Those that do not exist may be generated by 3D rendering software. The 3D structural coordinates of biomacromolecules can be retrieved from the Protein Data Bank (http //www.rcsb.org/pdb/). 

---