The Cambridge Structural Database

For application (and indeed the first realisation ) of the supramolecular synthon approach, one requirement is a comprehensive and accessible collection of molecular crystal structures that can be used to identify robust supramolecular 

Motif searches, defined by specific interactions between particular functional groups, are conceptually based on the supramolecular aspects of crystal packing. They permit examination of potential crystal packing features on the basis of the chemical groups present in the molecules before any (co-)crystallisation is carried out. For an established crystal structure. 

Screenshot taken from the Materials Mercury program during a motif search for synthon III. The selection of pre-defined motifs is visible on the left, one structure with the identified motif highlighted is visible in the middle and the full list of search results is kj visible on the right, with accompanying frequency of observation for the motif. Reproduced by permission of the Cambridge Crystallographic Data Centre. 

Taylor, R., Research applications of the Cambridge Structural Database , Chem. Soc. Rev. 2004,33, 463-475 Allen, F. H., The Cambridge Structural Database a quarter of a million crystal structures and rising , Acta Crystallogr, Sect. B 2002, 58, 380-388. 

The CSD has been used to classify the occurrence and connectivity of crystal hydrates (Section 8.6.3), symmetry and space group frequency (as in the sub-database CSDSymmetry), frequencies of Tow symmetry packing where there is more then one molecule in the asymmetric unit (Section 8.7) and the occurrence of polymorphism (Section 8.5), CSD-based tables for bond length distributions for organic and coordination compounds have been derived - and efforts are currently underway to develop an automated library of such parameters called Mogul ° The CSD was controversially used by Braga et in conjunction with ab initio calculations to call into 

Much earlier in the history of the CSD in 1979, with a follow-up in 1985, a cautionary note on short inter-molecular interactions was also sounded by Stan Nyburg. Analysis of non-bonded, non-hydrogen-bonded 

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Typical numeric databases are Beilstein, Speclnfo, DETHERM, and the Cambridge Structural Database. 

The two major databases containing information obtained from X-ray structure analysis of small molecules are the Cambridge Structural Database (CSD) [25] and the Inorganic Crystal Structure Database (ICSD) [26] both are available as in-house versions. CSD provides access to organic and organometallic structures (mainly X-ray structures, with some structures from neutron diffraction), data which are mostly unpublished. The ICSD contains inorganic structures. 

The Cambridge Structural Database (CSD) contains crystal structure information... 

The Cambridge Structural Database (C5D) and the Inorganic Crystal Structure Database (ICSD) contain information obtained from X-ray structure analysis. 

We can contrast these methods using the data shown in Figure 9.30, which were obtained by searching the Cambridge Structural Database for the ribose phosphate fragment also shown... 

Definitive proof of the structure of porphine in the solid state awaits a variable-temperature crystallographic (X-ray or neutron diffraction) study the analysis of the anisotropic displacement factors (ADP) should disclose any rotational motion or its absence as well as determine the positions of the inner hydrogens. A search in the September 1998 version of the Cambridge Structural Database [CSD (91MI187)] showed that the only structures of porphine (codename PORPIN) were obtained in 1965 and 1972. 

In the Cambridge Structural Database [39] only two macrocyclic molecules with transition metals, in which the metal ions are joined only by imidazolyl units, have been reported. One structure is trimetallic and contains plati-num(II) [40a] and the second one is tetrametallic with copper(II) ions [40b]. 

Some similar bimetallic acylamino complexes are also known with transition metal ions, e.g., with vanadium(II) [67], palladium(II) [68], and especially platinum(II) [69]. In the Cambridge Structural Database [39] only one trimetallic structure is found in which three iron(II) ions are bridged by a total number of six acylamino ligands [70]. 

Two new computer-based resources were launched in the 1970s. One was the Cambridge Structural Database (CSD) [55], and the other was the Protein... 

Allen FH. The Cambridge Structural Database a quarter of a million crystal structures and rising. Acta Cryst B 2002 B58 380-8. 

HIV Protease. Docking of the 3D structures of the Cambridge Structural Database into the HIV protease binding site, by shape and to some extent by chemical complementarity, was performed with an early version of the... 

XB is a particularly directional interaction, more directional than HB. The angle between the covalent and non-covalent bonds around the halogen in D- X-Y is approximately 180° [48]. As discussed above, the origin of this directionality is in the anisotropic distribution of electron density around the halogen atom. Figure 5 shows the Cambridge Structure Database (CSD, ver-... 

G. P. Shields, P.R. Raithby, F. H. Allen, W. D. S. Motherwell, The assignment and validation of metal oxidation states in the Cambridge Structural Database. Acta Crystallogr. B46 (2000) 244. 

Typical Ni—L bond lengths have been extracted from the Cambridge Structure Database (CSD) and listed in tabular form.321 Also, Ni11—L bond lengths from the CSD have been analyzed by the BDBO technique, which is related to the bond valence model (BVM) where the total bond order is equal to the oxidation state of any atom.322 Selected mean Ni—L distances from the CSD source are collected in Table 2. 

The Cambridge Structural Database contains many compounds treated in this chapter and only selected examples are mentioned here. 

Fabian and Kalman [5] retrieved 50 structures from the Cambridge Structural Database, including the polymorphs of 22 compounds, in order to evaluate the frequency of isostructurality among polymorphs. It was found that one-, two-, or three-dimensional isostructurality was exhibited by approximately one-half of the compounds studied. Three-dimensional isostructurality was connected to the gradual ordering of crystal structures, while one- and two-dimensional isostructurality could be related to specific packing interactions. Interestingly, conformational polymorphs were not found to exhibit isostructurality. 

Information on structure and bonding in alkali metal species with group 14, 15, and 16 ligands has been mainly focused on lithium derivatives the heavier analogs have been dealt with to a much-reduced extent. As mentioned in a 2004 review article,11 a search in the Cambridge Structural Database (CSD) revealed 778 structures with an Li-C bond, but only 197 with an Na-C, 235 with a K-C, 57 with an Rb-C, and just 31 with a Cs-C bond. 

Kahler, T. Olbrich, F. Private Communication to the Cambridge Structural Database, 2001. 

In six-membered cyclic nitronates (e.g., in (85)) adopting a half-chair conformation, the C-6 and C-5 atoms deviate from the plane of four atoms in the opposite directions, the deviation of the C-6 atom being substantially larger (the deviation of the C-5 atom. The latter is generally at most 0.05 A). It should be noted that one six-membered cyclic nitronate adopts a half-boat conformation (data from the Cambridge Structural Database, see also Fig. 3.2 and its discussion). 

The conformation B (Fig. 3.2) is a half-boat, in which the C-5 and C-6 atoms deviate in the same direction from the plane of the nitronate fragment but at different angles (01 =53.7° and 02 = —46.6°, that is, A = 7.1°). The discussion of the conformation A is valid for the conformation B. Interestingly, X-ray data for one six-membered cyclic nitronate adopting the conformation B are available in the Cambridge Structural Database. 

Gilli and coworkers57 have recognized many other examples of the RAHB phenomenon from the Cambridge Structural Database, documenting the structural correlations that strongly support the hypothesis of the covalent nature of these H-bonds. The computational examples presented in this section are fully consistent with their RAHB model, and similar NBO/NRT patterns would be expected to characterize the many interesting classes of compounds that were considered by these workers, but are beyond the scope of the present work. 

In all cases, the high degree of pyramidality attributed to the presence of two electronegative oxygen atoms at nitrogen, confirms the predictions of HF/6-31G calculations.5 On the basis of geometries for all acyclic amides in the Cambridge Structural Database in 2002,117 amides 31b and 31f are the most pyramidal amides of this type.5... 

Table 2 Comparison of average C-0 structural parameters (A) for neutral and partially deprotonated polycarboxylic acids as extracted from the Cambridge Structural Database (CSD) ...

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