Elna Pidcock

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.

Mercury: visualization and analysis of crystal structures

Since its original release, the popular crystal structure visualization program Mercury has undergone continuous further development. Comparisons between crystal structures are facilitated by the ability to display multiple structures simultaneously and to overlay them. Improvements have been made to many aspects of the visual display, including the addition of depth cueing, and highly customizable lighting and background effects. Textual and numeric data associated with structures can be shown in tables or spreadsheets, the latter opening up new ways of interacting with the visual display. Atomic displacement ellipsoids, calculated powder diffraction patterns and predicted morphologies can now be shown. Some limited molecular-editing capabilities have been added. The object-oriented nature of the C++ libraries underlying Mercury makes it easy to re-use the code in other applications, and this has facilitated three-dimensional visualization in several other programs produced by the Cambridge Crystallographic Data Centre.

DASH : a program for crystal structure determination from powder diffraction data

DASH is a user-friendly graphical-user-interface-driven computer program for solving crystal structures from X-ray powder diffraction data, optimized for molecular structures. Algorithms for multiple peak fitting, unit-cell indexing and space-group determination are included as part of the program. Molecular models can be read in a number of formats and automatically converted to Z-matrices in which flexible torsion angles are automatically identified. Simulated annealing is used to search for the global minimum in the space that describes the agreement between observed and calculated structure factors. The simulated annealing process is very fast, which in part is due to the use of correlated integrated intensities rather than the full powder pattern. Automatic minimization of the structures obtained by simulated annealing and automatic overlay of solutions assist in assessing the reproducibility of the best solution, and therefore in determining the likelihood that the global minimum has been obtained.

Hydrogen-bond directionality at the donor H atom—analysis of interaction energies and database statistics

A thorough analysis has been performed on the effects of varying the angle at the donor hydrogen in hydrogen bonds using database studies and ab initio intermolecular interaction energy calculations. Non-activated C–H⋯acceptor interactions are seen to have a weak energy dependence on the D–H⋯A angle, but for all of the conventional hydrogen-bonds studied the D–H⋯A angle has a range of 40–65° within an energy penalty of RT (2.5 kJ mol−1). Interactions with D–H⋯A angle in the range 120–140° are seen to have substantially reduced stabilisation energies and angles below 120° are generally unlikely to correspond to significant interactions.

WebCSD: the online portal to the Cambridge Structural Database

The new web-based application WebCSD is introduced, which provides a range of facilities for searching the Cambridge Structural Database within a standard web browser. Search options within WebCSD include two-dimensional substructure, molecular similarity, text/numeric and reduced cell searching.

Solving molecular crystal structures from laboratory X-ray powder diffraction data with DASH: the state of the art and challenges

The crystal structures of 35 molecular compounds have been redetermined from laboratory monochromatic capillary transmission X-ray powder diffraction data using the simulated-annealing approach embodied within the DASH structure solution package. The compounds represent industrially relevant areas (pharmaceuticals; metal coordination compounds; nonlinear optical materials; dyes) in which the research groups in this multi-centre study are active. The molecules were specifically selected to form a series within which the degree of structural complexity (i.e. degrees of freedom in the global optimization) increased systematically, the degrees of freedom increasing with increasing number of optimizable torsion angles in the structural model and with the inclusion of positional disorder or multiple fragments (counterions; crystallization solvent; Z′ > 1). At the lower end of the complexity scale, the structure was solved with excellent reproducibility and high accuracy. At the opposite end of the scale, the more complex search space offered a significant challenge to the global optimization procedure and it was demonstrated that the inclusion of modal torsional constraints, derived from the Cambridge Structural Database, offered significant benefits in terms of increasing the frequency of successful structure solution by restricting the magnitude of the search space in the global optimization.

Quantifying Homo‐ and Heteromolecular Hydrogen Bonds as a Guide for Adduct Formation

An investigation into the predictability of molecular adduct formation is presented by using the approach of hydrogen bond propensity. Along with the predictions, crystallisation reactions (1a-1j) were carried out between the anti-malarial drug pyrimethamine (1) and the acids oxalic (a), malonic (b), acetylenedicarboxylic (c), adipic (d), pimelic (e), suberic (f), azelaic acids (g), as well as hexachlorobenzene (h), 1,4-diiodobenzene (i), and 1,4-diiodotetrafluorobenzene (j); seven (1a to 1g) of these successfully formed salts. Five of these seven salts were found to be either hydrated or solvated. Hydrogen bond propensity calculations predict that hydrogen bonds between 1 and acids a-g are more likely to form rather than the H bonds involved in self-association, providing a rationale for the observation of the seven new salts. In contrast, propensity of hydrogen bonds between 1 and h-j is much smaller as compared to other bonds predicted for self-association/solvate formation, in agreement with the observed unsuccessful reactions.

A database survey of molecular and crystallographic symmetry.

The point of contact between molecular and crystallographic symmetries is that of the Wyckoff position, the position at which a molecule resides in a crystal structure. These Wyckoff positions may have the same symmetry as the molecules, some symmetry in common with the molecules or no symmetry at all. Using CSDSymmetry [Yao et al. (2002). Acta Cryst. B58, 640-646], a relational database containing information pertaining to the symmetry of molecules and the crystal structures that play host to them, the distribution of molecules over Wyckoff positions and the occupancy of Wyckoff positions in crystal structures is presented. Analysis of these data has led to the characterization of some relationships between molecular and crystallographic symmetry.

Knowledge-based hydrogen bond prediction and the synthesis of salts and cocrystals of the anti-malarial drug pyrimethamine with various drug and GRAS molecules

We have previously reported on hydrogen bond propensity calculations for the potential formation of adducts between pyrimethamine and dicarboxylic acids. Here we extend the range of potential synthon interactions using a variety of potential coformers. Specifically calculations were performed to predict the possibility of the formation of molecular adducts, 1a–1h, between the anti-malarial drug pyrimethamine (1) and (a) carbamazepine, (b) theophylline, (c) aspirin, (d) α-ketoglutaric acid, (e) saccharin, (f) p-coumaric acid, (g) succinimide and (h) L-isoleucine. The bonds of highest propensity were predicted between 1 and coformers (b–h), indicating a high probability of formation of adducts between 1 and b–h. In contrast the bonds of highest propensity were between reactants and the solvent for the adduct 1a, indicating either a high probability of the reactants crystallizing as solvates or incorporation of solvent into the adduct lattice. Experimental results agreed with the propensity calculations with the formation of a solvated cocrystal (1a·CH3OH). The successful application of hydrogen bond propensity calculations to the prediction of likely outcomes of these cocrystallization reactions suggests that this may be a useful tool in designing more targeted screening experiments.

Knowledge-based approaches to co-crystal design

The use of knowledge-based methods has been intimately connected with the field of co-crystal design since the seminal papers of Etter and Desiraju in the 1990s. Here we explain and exemplify how rational co-crystal design has been carried out in the past using crystal structure knowledge as well as presenting emerging methodologies for knowledge-based co-former selection.