James A. Chisholm

Mercury CSD 2.0 – new features for the visualization and investigation of crystal structures

The program Mercury, developed by the Cambridge Crystallographic Data Centre, is designed primarily as a crystal structure visualization tool. A new module of functionality has been produced, called the Materials Module, which allows highly customizable searching of structural databases for intermolecular interaction motifs and packing patterns. This new module also includes the ability to perform packing similarity calculations between structures containing the same compound. In addition to the Materials Module, a range of further enhancements to Mercury has been added in this latest release, including void visualization and links to ConQuest, Mogul and IsoStar.

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.

Supramolecular synthon competition in organic sulfonates: A CSD survey

The hydrogen bonding motifs seen in sulfonate salts have been examined using the CSD. In a total sample of 1069 sulfonate salts, 594 structures contain NH-donors, and this subset of structures has been investigated in detail. Several robust hydrogen-bonding motifs have been identified. A particularly robust R(2,2)8 motif, here called the bidentate motif, has been investigated in more detail. This motif occurs with a probability of 75.4% in the CSD, and 78.6% in the sulfonate salts. A set of rules for the prediction of the occurrence of the bidentate motif in sulfonate salts has been developed.

A molecular dynamics simulation of the melting points and glass transition temperatures of myo- and neo-inositol

The heat of sublimation, density, melting point, and glass transition temperature are calculated for myo- and neo-inositol, using the condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field and molecular dynamics techniques. Our results show that the calculated heats of sublimation and density are very close to the experimental values for both compounds. Furthermore, our simulated melting temperatures for myo- and neo-inositol also compare very well to the experimentally obtained data. The glass transition temperatures for myo- and neo-inositol have been calculated to be ca. 494 K and ca. 518 K, respectively, and the shape of the volume versus temperature plots produced are typical for a glass transition. As a result, it is our view that the COMPASS force field suitably describes these two compounds in molecular simulations and that molecular dynamics techniques, combined with this force field, can be used to simulate the melt and glass transitions for such molecules.

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.

Classical simulations of the properties of group-III nitrides

Abstract:The spin magnetic susceptibility of the p-d model is calculated by means of a perturbation theory in the hybridization term V through a generalized cumulant expansion (GCE). The analysis is approached from the paramagnetic metallic phase. The results qualitatively reproduce some unusual magnetic properties in the normal state of the hole-doped cuprates, supporting the scenario of a Van Hove singularity near the Fermi level.We present interatomic pair potential parameters derived for the GaInAlN system. Potentials are fitted to bulk material properties, such as lattice constants and elastic and dielectric constants, and are then employed to calculate Schottky and Frenkel defect energies in GaN, InN and AlN. Schottky defects are found to be lower in energy than Frenkel defects, suggesting that vacancies are more readily formed in the group-III nitrides. The formation energies of both Schottky and Frenkel defects in all the nitrides are found to depend on the size of the cation. Solution energies indicate that InN readily dissolves in both GaN and AlN, at least at low concentration.

Carbonyl⋯carbonyl interactions in first-row transition metal complexes

Carbonyl⋯carbonyl interactions involving Tr–CO moieties (Tr = first-row transition element) have been studied using crystal structure data retrieved from the Cambridge Structural Database and by use of DFT calculations. By comparison with organic ketones, Tr–CO systems show an increased tendency to form close CO⋯CO interactions, with 45% of these forming pairwise interactions in a sheared antiparallel dimer motif and 55% having a perpendicular (single interaction) geometry. The bulky Tr and steric hindrance arising from other ligands at Tr play a significant role in the formation and geometry of the interactions. DFT calculations for the antiparallel dimer indicate that interaction energies for Tr–CO systems are slightly stronger than for organic ketones, and there is evidence of a stronger CO bond dipole in Tr–CO systems. With interaction energies comparable to those for medium strength hydrogen bonds, we conclude that CO⋯CO interactions in Tr–CO species may have a role to play in the design of novel carbonyl-containing inorganic and metal–organic structures.

Hydrogen-bond coordination in organic crystal structures: statistics, predictions and applications

Statistical models to predict the number of hydrogen bonds that might be formed by any donor or acceptor atom in a crystal structure have been derived using organic structures in the Cambridge Structural Database. This hydrogen-bond coordination behaviour has been uniquely defined for more than 70 unique atom types, and has led to the development of a methodology to construct hypothetical hydrogen-bond arrangements. Comparing the constructed hydrogen-bond arrangements with known crystal structures shows promise in the assessment of structural stability, and some initial examples of industrially relevant polymorphs, co-crystals and hydrates are described.