Sam Motherwell

Extended motifs from water and chemical functional groups in organic molecular crystals

The probability of organic compounds crystallising as hydrates increases with increasing number of polar chemical groups in the molecule. The extended patterns of H-bonding involving chemical groups and water molecules have been studied and classified. The most frequent ring, chain, tape and layer patterns displayed between the water molecules alone in organic molecular crystals are also predominant patterns in the larger H-bond network when other donor/acceptors are included.

COMPACK: a program for identifying crystal structure similarity using distances

A method is presented for comparing crystal structures to identify similarity in molecular packing environments. The relative position and orientation of molecules is captured using interatomic distances, which provide a representation of structure that avoids the use of space-group and cell information. The method can be used to determine whether two crystal structures are the same to within specified tolerances and can also provide a measure of similarity for structures that do not match exactly, but have structural features in common. Example applications are presented that include the identification of an experimentally observed crystal structure from a list of predicted structures and the process of clustering a list of predicted structures to remove duplicates. Examples are also presented to demonstrate partial matching. Such searches were performed to analyse the results of the third blind test for crystal structure prediction, to identify the frequency of occurrence of a characteristic layer and a characteristic hydrogen-bonded chain.

New software for searching the Cambridge Structural Database for solvated and unsolvated crystal structures applied to hydrates

In this paper we describe several new pieces of software that allow the Cambridge Structural Database (CSD) to be searched for solvated and unsolvated crystal structures. One program finds all pairs of solvated and unsolvated crystal structures of the same chemical compound for a given solvent; another program finds all crystal structures that were grown from a particular solvent. In addition, an algorithm was implemented to determine the stereochemistry of a crystal structure from its 3-D atomic coordinates. Results for water as the solvent molecule are presented. It is found that about 25% of all crystal structures grown from water form hydrates. If a chemical compound is soluble in water, it seems almost impossible to predict if it will form a hydrate or not, although presence of both donors and acceptors in the host compound appears to be required. Chiral molecules produce significantly more hydrates, presumably including water to achieve close packing in spite of the lack of inversion centres.

Knowledge-based approaches to crystal design

The 365 000 crystal structures recorded so far in the Cambridge Structural Database (CSD) have already been used extensively in the study of intermolecular interactions and crystal packing, providing fundamental knowledge that can be applied in crystal engineering and crystal design. However, as the scientific problems posed to the CSD become more sophisticated, there is a need to develop more extensive software facilities for database searching and for analysing search results. In this Highlight, we review a number of novel informatics approaches to the CSD, including derivative databases and new research software, and exemplify their use in providing further knowledge that is important in the design of novel crystalline materials.

A new algorithm for performing three-dimensional searches of the Cambridge Structural Database

A search algorithm, 3DSEARCH, is presented that can readily identify challenging extended chemical queries from three-dimensional molecular crystal structure information. The program combines substructure search and distance search techniques within a depth-first backtracking algorithm. Performance metrics are presented for example searches composed of several substructures and several intermolecular connections. It is shown that such searches, which are outside the capabilities of current search engines, can now be performed on the entire Cambridge Structural Database with search times of around half an hour.

Searching the Cambridge Structural Database for polymorphs.

In order to identify all pairs of polymorphs in the Cambridge Structural Database (CSD), a method was devised to automatically compare two crystal structures. The comparison is based on simulated powder diffraction patterns, but with special provisions to deal with differences in unit-cell volumes caused by temperature or pressure. Among the 325,000 crystal structures in the Cambridge Structural Database, 35,000 pairs of crystal structures of the same chemical compound were identified and compared. A total of 7300 pairs of polymorphs were identified, of which 154 previously were unknown.

GRX: a program to search the CSD for functional group exchanges

In order to establish the effect of exchanging one functional group by another on the crystal structure, one would like to be able to search the Cambridge Structural Database for all pairs of crystal structures where this substitution has been made. A program called GRX (group exchange) was written for that purpose.

Prediction of H-Bonding Motifs for Pyrazoles and Oximes Using the Cambridge Structural Database

H-bonding motifs for pyrazoles and oximes have been examined in the Cambridge Structural Database. The accessible surface of the N atoms has been found to be useful as a discriminator to divide structures into dimer and catemer motifs for both pyrazoles and oximes. Low accessibility favors dimers and tetramers and high values favor catemers and trimers. Total molecular volume shows some correlation for oximes, while high values favor dimers. Empirical rules were successfully applied to predict the motifs of eight new structures in the subsequent release of the CSD.

CCDC 198894: Experimental Crystal Structure Determination

Related Article: A.Sanchez-Migallon, A.de la Hoz, C.Lopez, R.M.Claramunt, L.Infantes, S.Motherwell, K.Shankland, H.Nowell, I.Akorta, J.Elguero|2003|Helv.Chim.Acta|86|1026|doi:10.1002/hlca.200390091