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. 313-314

Section 3.7.3. Cambridge Structural Database (CSD)

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

3.7.3. Cambridge Structural Database (CSD)

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Some features of the Cambridge Structural Database system (CSD; https://www.ccdc.cam.ac.uk ; Groom et al., 2016[link]) are described in Chapter 22.5[link] of International Tables for Crystallography Volume F (Allen et al., 2011[link]). The CSD contains X-ray and neutron diffraction analyses of carbon-containing molecules with up to 1000 atoms (including hydrogens), including organic compounds, compounds of the main-group elements, organometallic compounds and metal complexes. The CSD covers peptides of up to 24 residues; higher polymers are covered by the Protein Data Bank. The CSD also covers mononucleotides, dinucleotides and trinucleotides; higher oligo­mers are covered by the Nucleic Acid Database (http://ndbserver.rutgers. edu ). There is a small overlap between the CSD and the Inorganic Crystal Structure Database in the area of molecular inorganics.

Capabilities particularly useful for structure validation are covered in Chapter 4.9[link] of this volume. This discussion will not attempt a comprehensive description of the capabilities of the CSD, but will concentrate on features that are particularly relevant to powder diffraction.

The principal interface to the CSD is the program ConQuest (Bruno et al., 2002[link]). Its most distinctive feature is the ability to draw molecular structures and fragments and carry out substructure searches. Such searches eliminate the ambiguities that can arise when searching by compound name or other text-based properties. These chemical-connectivity searches can include the number of H atoms bonded to a particular atom, the charge, the number of bonded atoms and whether the atom is part of a ring. In addition, three-dimensional quantities can be defined, tabulated and analysed. These quantities can be analysed in Mercury (Macrae et al., 2008[link]) and Mogul (Bruno et al., 2004[link]). Such analyses are useful for defining geometrical restraints in a Rietveld refinement. A general practice is to use the mean and standard deviations directly output by Mogul for the restraints. It is important to understand the CSD conventions for defining bond types to obtain successful results.

In ConQuest, searches can be carried out on author and/or journal name, as well as the normal bibliographic characteristics. Compounds can be located by chemical and/or common names, but such searches should be complemented by chemical-connectivity searches. It is possible to limit the search universe by chemical class, including carbohydrates, nucleosides and nucleotides, amino acids, peptides and complexes, porphyrins, corrins and complexes, steroids, terpenes, alkaloids and organic polymers. Searches on elements and formulae are possible, as well as searches on space groups and crystal systems. Particularly useful in searching for structure analogues are reduced-cell searches. Queries on Z, Z′ and density are useful in data mining. A wide variety of searches on experimental parameters are possible; there is an option to exclude powder structures. Searches on both pre-defined terms and general text searches are possible. Particularly convenient for users of the PDF-4/Organics database is the retrieval of individual refcodes; the refcode from the PDF entry can be input directly into ConQuest. Starting with the 2013 release of the PDF-4/Organics database this link is live; the display of a PDF entry will result in import of the coordinates from the CSD entry. Boolean operations can be used to combine search queries in many flexible ways.

In recent years, many (if not most) single-crystal structures have been determined at low temperatures, while most powder-diffraction measurements are made under ambient conditions. Thermal expansion (often anisotropic) can result in differences between the observed peak positions and those in a PDF-4/Organics entry calculated from a CSD entry. For successful phase identification, larger than default tolerances must often be used in the search/match process. Transparency effects in pure organic compounds can also lead to significant peak shifts to lower angles, as well as significant asymmetry, so wider search windows may be necessary for phase identification.

3.7.3.1. Mercury

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The structure-visualization program Mercury (Macrae et al., 2008[link]) is available as a free version and as a version with the CSD which has additional capabilities that are useful for powder diffraction. Mercury reads and writes a variety of molecular and crystal structure file formats, but is most commonly used with CIFs. Structures can be edited, and among the edit options is Normalize Hydrogens. This is particularly useful to improve the approximate H-atom positions that are often used in the early and intermediate stages of a Rietveld refinement. It is always worth including the H atoms in the structure model (in at least approximate positions) because better residuals and improved molecular geometry are obtained.

The Display Symmetry Elements tool is particularly useful for teaching symmetry. The Display Voids tool is useful in validating structures after solution. For most materials (zeolites and metal–organic frameworks are notable exceptions) we do not expect empty spaces in the crystal structure, so the presence of voids suggests the presence of an incomplete structure model and/or errors.

Among the options in the Calculate menu is Powder Pattern. The calculation can be customized by the user to match the desired instrumental configuration. The calculated pattern can be saved in several formats for comparison in the user's instrument software. Mercury expects the displacement coefficients to be given as U values. CIFs can come from many sources and can use different conventions for the displacement coefficients or may be missing them entirely. Manual editing of the input CIF is often required, otherwise strange powder patterns can be calculated.

Among the CSD-Materials/Calculations options is BFDH morphology (Bravais, 1866[link]; Friedel, 1907[link]; Donnay & Harker, 1937[link]). Although a simple calculation, it is often realistic enough to suggest the likelihood of profile anisotropy and preferred orientation, along with expected directions. The calculation can thus save guessing about preferred directions.

The Structure Overlay and Molecule Overlay options are very useful for comparing structures quantitatively. There is also an interface to the semi-empirical code MOPAC, which can also be a useful tool for assessing structural reasonableness. The H-­Bonds and Short Contacts options are useful in completing a structure solved using powder data, as often the `interesting' H-atom positions have to be deduced. There is a relatively new Solid Form menu, which contains several tools for analysing crystal structures.

References

Allen, F. H., Cole, J. C. & Verdonk, M. L. (2011). The relevance of the Cambridge Structural Database in protein crystallography. International Tables for Crystallography, Vol. F, 2nd ed., edited by E. Arnold, D. M. Himmel & M. G. Rossmann, pp. 736–748. Chichester: Wiley.Google Scholar
Bravais, A. (1866). Etudes Cristallographiques. Paris: Gathier Villars.Google Scholar
Bruno, I. J., Cole, J. C., Edgington, P. R., Kessler, M., Macrae, C. F., McCabe, P., Pearson, J. & Taylor, R. (2002). New software for searching the Cambridge Structural Database and visualizing crystal structures. Acta Cryst. B58, 389–397.Google Scholar
Bruno, I. J., Cole, J. C., Kessler, M., Luo, J., Motherwell, W. D. S., Purkis, L. H., Smith, B. R., Taylor, R., Cooper, R. I., Harris, S. E. & Orpen, A. G. (2004). J. Chem. Inf. Comput. Sci. 44, 2133–2144.Google Scholar
Donnay, J. D. H. & Harker, D. (1937). A new law of crystal morphology extending the law of Bravais. Am. Mineral. 22, 463–467.Google Scholar
Friedel, G. (1907). Etudes sur la loi de Bravais. Bull. Soc. Fr. Miner. 30, 326–455.Google Scholar
Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). The Cambridge Structural Database. Acta Cryst. B72, 171–179.Google Scholar
Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). Mercury CSD 2.0 – new features for the visualization and investigation of crystal structures. J. Appl. Cryst. 41, 466–470.Google Scholar








































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