Cambridge structural data base

Recent research on the Cambridge structural data base shows139 11 alkenes (and 2 alkynes) which are involved in interactions with the —OH group, with distance H- C of olefin <2.4 A. 66 is an instance of intramolecular hydrogen bonding interactions140. Intermolecular hydrogen bonds can be observed in 67141 and 68142. 

Cambridge Structural Data Base (CSD). Cambridge Crystallographic Data Centre, University Chemical Laboratory, Cambridge, England. 

Experimental structures are often the basis for computational studies they are used as input structures for structure optimizations and conformational searches, for the parameterization and validation of force fields and for analyzing the effects of crystal lattices. More than 200,000 experimental structures have been reported, and the majority are found in the Cambridge Structural Data Base (CSD, small molecular structures which include carbon atoms) the Inorganic Crystals Structure Database (ICSD) and the Protein Data Base (PDB this database includes X-ray as well as optimized structures based on NMR data). 

A simultaneously performed search in the Cambridge Structural Data Base revealed that expanded X-C-C bond angles are more or less common (see Table 1) [13-15]. 

The possibility of errors in deposited structures must be considered. Errors in chirality may be prevalent in high resolution small molecule structures. For example, the small molecule structure of streptogramin A is represented by its enantiomer in the Cambridge Structural Data Base. The effort to solve the structure of streptogramin A bound to the ribosome was initially hindered by relying on that incorrect small molecule structure. Likewise, the structure of anisomycin is incorrectly diagrammed as its enantiomer in most of the ribosomal literature. Fortunately, these chirality errors were identified when solving structures of these antibiotics bound to macromolecules. In fact, the identification of these errors may increase confidence in the reliability of these structures of complexes between ribosomes and antibiotics. 

Bond distances are influenced by coordination environment and, secondarily, by the nature of the substituents (electronegativity and size). A least-squares analysis of approximately two-hundred silicon compounds taken from the Cambridge structural data base has provided a consistent set of reference values for bonds between silicon and various nonmetals and these values are shown in Table 3, as well as the values expected for single bonds to silicon corrected for electronegativity differences. 

The crystallinity of mannitol batches was examined by X-ray powder diffraction (XRPD) patterns, which were then compared to pure mannitol polymorphs gained from the Cambridge structural data base [38]. An X-ray diffractometer (Stadi P, Stoe Cie GmbH, Darmstadt, Germany) equipped with a CuKaj radiation source was used for this task. The patterns were recorded at a voltage of 40 kV and a current strength of 30 mA. The bended radiation was detected by a rotating proportional counter from 5° to 40° 26 to obtain the XRPD pattern. 

Crystallographic coordinates of Me-BPh were obtained from the Cambridge structural data base [14]. The Me-BPh crystal is triclinic, space group PI, a=7.184 A, b=8.073 A, c=17.071 A, a = 91.04 j3 = 93.50 7 = 110.06 [4]. The crystal was simulated by replicating the unit cell using periodic boundary conditions. In the crystal the Me-BPh associates in one dimensional chains by stacking of rings 1 and 3. 

Figure 2. Schematic diagram of the hydrogen-bond structure in the crystal structure of gentiobiose (GENTOSOl REFCODE in Cambridge Crystallographic Data Base). The arrows indicate infinite chains. Distances are H—O in A, angles are 0-H—O in degrees. The covalent 0-H bond lengths have been normalized to 0.97 A.

Molecular structure data bases are particularly useful in the analysis and engineering of zinc coordination polyhedra, and statistical results from the Brookhaven Protein Data Bank (Bernstein et al., 1977) and the Cambridge Structural Database (Allen et al., 1983) are presented... 

The text has been substantially revised, many new examples incorporated and errors corrected. A substantial new chapter dealing with supramolecular chemistry has been incorporated. Once again, a deliberate decision was made to try to limit references to the secondary rather than the primary literature. Where structural data have been presented, the use of the files of the Cambridge Crystallographic Data Centre and the Brookhaven Protein Structure Data Base are gratefully acknowledged. 

Kovari, Z., Bocskei, Zs., Kassai, Cs., Fogassy, E., and Kozma, D. Investigation of the structural background of stereo- and enantioselectivity of 0,0 -dibenzoyl-(2/ ,3R)-tartaric acid-alcohol supramolecular compound formation, Chirality 2003, submitted for publication. Crystal data are deposited at the Cambridge Crystal Structure Data Base under the following numbers CCDC 181497, 181498, 181499,181500, 181501, 181502, 181503, 181504,181505. 

Since this structural data consists of atomic parameters which describe the interatomic vectors in three dimensions, the simultaneous evolvement of computer graphics has played an important role in the way the data can be used. The data base which is the particular source for the hydrogen bond data analyzed in this monograph is the Cambridge Crystallographic Structure Data Base [39, 40]. There is also a vast amount of structural information in the protein and nucleic acid data... 

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. 

Of all the physical sciences, Crystallography has benefited the most from the spectacular advances in computer technology in the past decade. The Cambridge Crytallographic Crystal Structure Data Base contains the results of the published crystal structure analyses of organic and organo-metallic compounds. The Protein... 

I should like to thank Dr. Sharon Bellard of the Cambridge Crystallographic Data Base and Dr. Paul Raithby for their invaluable assistance in obtaining structural data, and Dr. Ken Seddon for kindling and nurturing an interest in these ligands. 

This chapter is concerned with the solid state structures of arsenic, antimony and bismuth compounds, which in general contain at least one bond between carbon and the Group 15 element. In selecting material for discussion, I have been greatly aided by the availability of the Cambridge Crystallographic Data Base. The period under consideration covers effectively the years between 1981 and 1992. 

The 3D-molecular structures the book have been drawn using atomic coordinates accessed from the Cambridge Crystallographic Data Base and implemented through the ETH in Zurich, or from the Protein Data Bank (http //www/rcsb.org/pdb). 

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