Searching the Cambridge Structural Database

Although the Cambridge Structural Database does not contain (at present) any information of the type discussed in this chapter (Schafli notation, Vertex symbols, three letter codes) it is appropriate to mention it here as we are briefly dealing with information retrieval [21-25]. 

Coordination polymers are easily detected by specifying the metal - donor atom bond as polymeric in ConQuest. The problem is then to weed out the ID and 2D structures from the 3D-nets. 

In both cases the crystallographic data can easily be extracted and analysed by many different commercial available or free software, but perhaps easiest as a first option is Mercury (that works directly with ConQuest), [12] obtainable free of charge for academic users from the Cambridge Crystallography Data Centre (CCDC), the providers of the CSD. From the identification of a candidate structure in the CSD, the determination of its dimensionality using Mercury is often a matter of a few minutes (per compound A systematic study will take many hours). See further Chapter 13. 

Having said all this, we would like to alert the reader to the fact that the CCDC, is not a simply a body devoted to the permanent storage of crystallographic data but also very much an active research organisation, both in the analysis of structural data and in the development of new research and search tools for the CSD. Thus, for example, it is likely that we in the future will see search tools that can automatically recognise such features as nets, dimensionality and interpenetration. CCDC also have some more recent products called knowledge bases , IsoStar and Mogul, that may be quite useful as well. 

---

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... 

Figure 8 Aminoribofuranoside fragment whose conformations were determined by searching the Cambridge Structural Database.

Bruno, LJ, Cole, J.C. Edgington, P.R. Kessler, M. Macrae, C.F. McCabe, P. Pearson, J. Taylor, R. New software for searching the Cambridge Structural Database and visualising crystal structures. Acta Crystallogr. 2002. 

J. van de Streek and W. D. S. Motherwell, New software for searching the Cambridge Structural Database for solvated and unsolvated crystal structures applied to hydrates, CrystEngComm, 9, 55-64 (2007). 

J. van de Streek, Searching the Cambridge Structural Database for the best representative of each unique polymorph, Acta Cryst., B62, 567-579 (2006). 

The preferred geometry of a building block can be analysed by searching the Cambridge Structural Database, as shown in Figure 6.3 covering compounds of type A and B. Tliese results indicate that these nodes will essentially have to... 

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. 

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. 

Studied the orientations of groups near the C-S-C group in a variety of crystal structures containing it the Cambridge Structural Database (Allen et al., 1979) was searched for this information. Not only did these investigators find that the sulfur atom appeared to have a different radius in different directions but they found that nucleophiles and electrophiles approach it from different directions (Fig. 9). 

F.H. Allen, O. Kennard, 3D search and research using the Cambridge Structural Database. Chem. Des. Autom. News 8, 31-37 (1993)... 

Overall, the formation of pentacoordinated complexes is favored by chelating and particularly by polydentate macrocyclic ligands. A search in the Cambridge Structural Database reveals that many of the structurally characterized five-coordinated Pd(II) compounds contain macrocyclic or rigid polydentate ligands, S, N, and P donor atoms being dominant. Complexes (23), (24) and (25) are typical examples. 

---