International
Tables for
Crystallography
Volume H
Powder diffraction
Edited by C. J. Gilmore, J. A. Kaduk and H. Schenk

International Tables for Crystallography (2018). Vol. H, ch. 3.7, pp. 319-321

Section 3.7.8. Crystallography Open Database (COD) (with Saulius Gražulis)

J. A. Kaduka,b,c*

aDepartment of Chemistry, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, IL 60616, USA,bDepartment of Physics, North Central College, 131 South Loomis Street, Naperville, IL 60540, USA, and cPoly Crystallography Inc., 423 East Chicago Avenue, Naperville, IL 60540, USA
Correspondence e-mail: kaduk@polycrystallography.com

3.7.8. Crystallography Open Database (COD) (with Saulius Gražulis)

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The Crystallography Open Database (COD) project (http://www.crystallography.net/cod/ ; Gražulis et al., 2009[link], 2012[link]) aims at collecting in a single open-access database all organic, inorganic and organometallic structures, except for the structures of biological macromolecules, which are available in the Protein Data Bank (Berman et al., 2003[link], 2011[link]). The database was founded by Armel Le Bail, Lachlan Cranswick, Michael Berndt, Luca Lutterotti and Robert M. Downs in February 2003 as a response to Michael Berndt's letter published on the Structure Determination by Powder Diffractometry (SDPD) mailing list (Berndt, 2003[link]). Since December 2007, the main database server has been maintained and new software has been developed by Saulius Gražulis and Andrius Merkys at the Institute of Biotechnology of Vilnius University (VU). Currently, the database includes more than 376 000 entries describing structures of small molecules and small-to-medium-sized unit-cell materials as published in IUCr journals and other major crystallographic and peer-reviewed journals, as well as contributions by crystallographers from major laboratories. Most of the mineral data are obtained from the American Mineralogist Structure Database (Rajan et al., 2006[link]) and are donated by its maintainer and COD co-founder Robert M. Downs.

The database is an internet resource (Fig. 3.7.15[link]) with data-search and download capabilities designed by Armel Le Bail and Michael Berndt. In addition, registered users may deposit new data, whether from previous publications or as personal communications, using the deposition web site designed at VU by Saulius Gražulis, Justas Butkus and Andrius Merkys. The deposition software performs rigorous checks of syntax and semantics.

[Figure 3.7.15]

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(a) The website and search interface of the Crystallography Open Database (COD) permits searches of crystallographic data by a range of parameters and unrestricted retrieval of the found data. (b) Data can be viewed online in the interactive Jmol applet (Hanson, 2010[link], 2013[link]) or downloaded for further processing either one record at a time or in bulk.

The COD website allows searching on COD numerical identifier, unit-cell parameters, chemical composition and bibliographic data. Substructure searches using SMILES and SMARTS strings have been implemented. The free software package OpenBabel (O'Boyle et al., 2011[link]; Hutchison, 2007[link]) is used for both the CIF-to-SMILES transformation and the actual search.

The retrieved records can be viewed online or downloaded for further processing. For massive data mining, COD permits downloads and updates of the whole database using Subversion, Rsync or http protocols. The ease of access to the COD data and its open nature has spurred the use of this resource for software testing (Grosse-Kunstleve & Gildea, 2011[link]), teaching (Moeck, 2004[link]) and research (First & Floudas, 2013[link]). Multiple mirrors around the globe (Quirós-Olozábal, 2006[link]; Gražulis, 2007[link]; Moeck, 2007a[link]; Chateigner, 2010[link]) ensure data preservation, provide off-site backups, offer improved search interfaces (Moeck, 2007b[link]) and increase reliability.

For the powder-diffraction community, the COD is interesting not only as an archive of structures solved by powder-diffraction methods, but also as a possibility for use in search/match procedures to identify crystalline compounds. Recently, the development of an open full-pattern search/match internet tool was launched by the COD developers. It allows phase quantifications from X-ray, neutron and electron powder patterns (with high- or medium-resolution instruments) provided that the structures are already in the COD. This tool is particularly suited to nanocrystalline powders, in which severe line broadening appears, precluding phase identification from only peak positions (Lutterotti et al., 2012[link]). COD-derived databases are also offered for software produced by several diffractometer vendors (Rigaku, 2011[link]; PANalytical, 2012a[link],b[link]; Bruker, 2013[link]). In addition to the COD, searches and matches can be performed against its sister database, the PCOD, which contains structures predicted by the GRINSP program (Le Bail, 2005[link]) and hypothetical zeolites (Pophale et al., 2013[link]). The power of such an approach is demonstrated by PCOD entry 3102887 (formulated as SiO2). It was recently identified as corresponding structurally to a new phosphorus(V) oxonitride polymorph δ-PON (Baumann et al., 2012[link]).

References

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