INDEX crystallographic data

Single-crystal precession data indicate orthorhombic symmetry with the crystallographic space group Fddd. This system is not isostructural with any other known metal oxyfluoride or metal dioxide. The cell dimensions, determined from Guinier data, are a = 8.370 1 A. b = 10.182 1 A. and c = 7.030 1 A. The indexed powder data are given in reference 6. 

In producing an image of molecules from crystallographic data, the computer simulates the action of a lens, computing the electron density within the unit cell from the list of indexed intensities obtained by the methods described in Chapter 4. In this chapter, I will discuss the mathematical relationships between the crystallographic data and the electron density. 

CML is most widely used to describe individual molecules, but is also capable of describing chemical reactions (Holliday et al. 2006), spectra (Kuhn et al. 2007), computational chemistry results and crystallographic data. Although only one specification of CML contains all the mentioned types of data, specific subsets of CML are informally referred to by a specific name (http //cml.sourceforge.net/wiki/index. php/FAQ), such as CMLReact for reactions or CMLSpect for spectra. 

Henceforth, crystal structure analyses of carbohydrates (class 45), amino acids (class 48), purines and pyrimidines (class 44) and nucleosides and nucleotides (class 47) are referenced by means of their Cambridge Crystallographic Data Base REFCODES. All other crystal structure analyses are referenced in the General Index. 

The Cambridge Crystallographic Data Base was an indispensible source of data and we are grateful for permission to use the Refcodes for indexing. 

The easiest way to access the crystal structure literature is through "Molecular Structures and Dimensions", which provides an up-to-date well indexed bibliography of all organic and organometallic crystal structures that are available (2). This excellent series is the work of the Cambridge Crystallographic Data Centre, established by Professor Olga Kennard in the U.K. 

So how do we know the unit cell of the crystal and its orientation The first step in the collection of crystallographic data consists of taking one or two test images, from which the spot positions are determined. Each diffraction spot is then assigned indices h,k,l based on its position on the detector. This is called indexing and the unit cell parameters and crystal orientation are determined here. Once the diffraction pattern is indexed, we can use the Ewald construction to predict where spots should be observed. The prediction is important, since some of the spots may be so faint that detection would be impossible unless we knew where to expect them. 

Fig. 14-1 Standard 3 x 5 in. JCPDS diffraction data card (card 628 from Set 5) for sodium chloride. Appearing on the card are 1 (file number), 2 (three strongest lines), 3 (lowest-angle line), 4 (chemical formula and name of substance), 5 (data on diffraction method used), 6 (crystallographic data), 7 (optical and other data), 8 (data on specimen), and 9 (diffraction pattern). Intensities are expressed as percentages of Ii, the intensity of the strongest line on the pattern. Most cards have a symbol in the upper right comer indicating the quality of the data (high quality), i (lines indexed, intensities fairly reliable), c (calculated pattern), and o (low reliability). (Courtesy of Joint Conunittee on Powder Diffraction Standards.)...

Cambridge Structural Database (CSD), Cambridge Crystallographic Data Center, 12 Union Road, Cambridge, CB2 lEZ, UK, 1995. Its URL http //www.ccdc.cam.ac.uk/index.html. 

Figure 3. The HOMA (phenol) aromaticity index vs. the /(OH) bond length for crystallographic data for ketamines. Reprinted with permission from Ref. 21. Copyright 2005 John Wiley Sons, Ltd.

Cambridge Crystallographic Data Bank http //www.ccdc.cam.ac.uk/ Glycoscience database http //www.glycosciences.de/index.php Marchessault RH, Sarko A. X-Ray structure of polysaccharides. Adv Carbo-... 

The crystallographic data will indicate the proper index k, i.e., into which site thejth is sent by the operator 0. The (+1) is a definition of phase. For example, 0 may be chosen as a two-fold screw axis, or a glide plane, and so on. Having chosen the nature of 03, the remaining operators in the factor group, the y3, behave as follows ... 

The stracture of CGZA crystal can be indexed to the cubic system. For the final acceptable refinement, which relates to a lower R factor, the Al " ions occupy the A sites, the larger Zr" ions occupy the D sites, and the largest Ca " and Gd " ions occupy the L sites with a ratio of 2 1 [16]. The crystallographic data and stracture refinement for the CGZA crystal are listed in Table 9.1 [16]. The 24c, 16a, and 24d WyckofF sites are fully occupied by Ca VGd, Zr", and Al, respectively. Based on the effective ionic radii (r) of the cations, Ce " (r = 1.14 A for CN = 8) is expected to preferably occupy the sites of Gd [16]. 

Each entry gives the formula, name, and Strukturbericht and Structure Reports references. The entries are arranged in accordance with the classification scheme based on chemical structure of the Cambridge Crystallographic Data Centre within each class the order is by formula. The formula index will help to locate a compound for which the classification is doubtful. The classification is ... 

The CSD database format is a set of proprietary binary files which contain indexes, keys and data for ID (e.g., numeric data), 2D and 3D aspects of crystallographic data. A subset of the CSD is now available from CCDC in MDLI s proprietary binary format containing only molecule (not crystallographic) data this version, covering about 80% of the CSD, represents nearly all those entries for which 2D-to-3D matching records exist. The intermediate files from this effort, in SDfile interchange format, may be used to construct 3D molecule databases under other database managers. 

These tables eontain data for approximately 2700 polymers. In general, the format and organization of the tables follows that used in the 2nd edition of the Polymer Handbook (Section B Crystallographic Data Section C Melting Points Seetion D Formula Index and Section E References). The Formula Index is included as an aid to the searcher it permits one to determine the polymer name used in these tables from the structural line formula for the polymer of interest. 

For polycrystalline materials, electron methods can be used to supplement and clarify X-ray results. For example, with X-ray powder patterns, it is often difficult or even impossible to index lines in a diffraction pattern if mixtures are present, whereas, using electron diffraction, the problem can be solved by obtaining unit cell data for each phase from selected-area diffraction patterns. Likewise, with complex powders of new materials, the indexing of X-ray patterns is especially difficult if the unit cell is large and of low symmetry. Electron diffraction patterns from small crystals reveal the reciprocal lattice, giving information on the principal axes and crystallographic symmetry. Many new materials are prepared as small samples of tiny crystals suitable only for electrons microscopy, so that electron diffraction is often the best way to obtain crystallographic data on the material. 

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