Peter A. Wood

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.

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.

High-pressure polymorphism in amino acids

Pressure up to 10 GPa is a powerful method for studying polymorphism in organic crystal structures, and this review surveys work carried out on high-pressure polymorphism in amino acids. High-pressure polymorphs have been established crystallographically for glycine, alanine, serine, cysteine and leucine. Phase transitions can be driven by the avoidance of very short intermolecular contacts or by promotion of a more stable molecular conformation. Experimental methods are also briefly surveyed, along with three methods that have proved very helpful in the analysis of high-pressure polymorphs, namely the PIXEL method for calculation of intermolecular energies, topological analysis with Voronoi–Dirichlet partitioning and Hirshfeld surfaces for gaining a graphical overview of intermolecular interactions.

Orthogonal dipolar interactions between amide carbonyl groups

Orthogonal dipolar interactions between amide C=O bond dipoles are commonly found in crystal structures of small molecules, proteins, and protein–ligand complexes. We herein present the experimental quantification of such interactions by employing a model system based on a molecular torsion balance. Application of a thermodynamic double-mutant cycle allows for the determination of the incremental energetic contributions attributed to the dipolar contact between 2 amide C=O groups. The stabilizing free interaction enthalpies in various apolar and polar solvents amount to −2.73 kJ mol−1 and lie in the same range as aromatic-aromatic C–H⋯π and π–π interactions. High-level intermolecular perturbation theory (IMPT) calculations on an orthogonal acetamide/N-acetylpyrrole complex in the gas phase at optimized contact distance predict a favorable interaction energy of −9.71 kJ mol−1. The attractive dipolar contacts reported herein provide a promising tool for small-molecule crystal design and the enhancement of ligand–protein interactions during lead optimization in medicinal chemistry.

New software for statistical analysis of Cambridge Structural Database data

A new piece of software for statistical analysis of geometrical, chemical and crystallographic data within the Cambridge Structural Database System is described. This software has been written specifically to deal with chemical structure data and crucially provides simultaneous visualization of the three-dimensional structural information.

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.

Interaction geometries and energies of hydrogen bonds to C=O and C=S acceptors: a comparative study

The occurrence, geometries and energies of hydrogen bonds from N-H and O-H donors to the S acceptors of thiourea derivatives, thioamides and thiones are compared with data for their O analogues - ureas, amides and ketones. Geometrical data derived from the Cambridge Structural Database indicate that hydrogen bonds to the C[double bond]S acceptors are much weaker than those to their C[double bond]O counterparts: van der Waals normalized hydrogen bonds to O are shorter than those to S by approximately 0.25 A. Further, the directionality of the approach of the hydrogen bond with respect to S, defined by the C[double bond]S...H angle, is in the range 102-109 degrees , much lower than the analogous C[double bond]O...H angle which lies in the range 127-140 degrees . Ab initio calculations using intermolecular perturbation theory show good agreement with the experimental results: the differences in hydrogen-bond directionality are closely reproduced, and the interaction energies of hydrogen bonds to S are consistently weaker than those to O, by approximately 12 kJ mol(-1), for each of the three compound classes. There are no CSD examples of hydrogen bonds to aliphatic thiones, (Csp(3))(2)C=S, consistent with the near-equality of the electronegativities of C and S. Thioureas and thioamides have electron-rich N substituents replacing the Csp(3) atoms. Electron delocalization involving C[double bond]S and the N lone pairs then induces a significant >C(delta+)[double bond]S(delta-) dipole, which enables the formation of the medium-strength C[double bond]S...H bonds observed in thioureas and thioamides.

Effect of pressure on the crystal structure of salicylaldoxime‐I, and the structure of salicylaldoxime‐II at 5.93 GPa

The effect of pressure on the crystal structure of salicylaldoxime has been investigated. The ambient-pressure phase (salicylaldoxime-I) consists of pairs of molecules interacting through oximic OH...O hydrogen bonds; taken with phenolic OH...N intramolecular hydrogen bonds, these dimers form a pseudo-macrocycle bounded by an R4 4(10) motif. The dimers interact principally via pi...pi stacking contacts. Salicylaldoxime derivatives are used industrially as selective solvent extractants for copper; the selectivity reflects the compatibility of the metal ion with the pseudo-macrocycle cavity size. On increasing the pressure to 5.28 GPa the size of the cavity was found to decrease by an amount comparable to the difference in hole sizes in the structures of the Cu2+ salicylaldoximato complex and its Ni2+ equivalent. On increasing the pressure to 5.93 GPa a new polymorph, salicylaldoxime-II, was obtained in a single-crystal to single-crystal phase transition. PIXEL calculations show that the phase transition is driven in part by relief of intermolecular repulsions in the dimer-forming OH...O-bonded ring motif, and the ten-centre hydrogen-bonding ring motif of the phase I structure is replaced in phase II by a six-centre ring formed by oximic OH...N hydrogen bonds. The transition also relieves repulsions in the pi...pi stacking contacts. The intramolecular OH...N hydrogen bond of phase I is replaced in phase II by a intermolecular phenolic OH...O hydrogen bond, but the total interaction energy of the pairs of molecules connected by this new contact is very slightly repulsive because the electrostatic hydrogen-bond energy is cancelled by the repulsion term. The intra- to intermolecular hydrogen-bond conversion simply promotes efficient packing rather than contributing to the overall lattice energy.

Evaluation of molecular crystal structures using Full Interaction Maps

The specific crystalline form of a compound has a significant impact on its solid state properties. A key requirement for chemists developing crystalline materials is therefore to understand and evaluate the crystal form under investigation. We show here how the visualisation of molecular interaction maps within the context of a crystal structure can be used to evaluate the stability of polymorphic structures, assess multiple types of non-covalent interactions and provide a platform for crystal morphology analysis. Examples of three industrially-relevant compounds – sulfathiazole, anastrozole and cipamfylline – illustrate this well. A qualitative agreement with experimental stability data is observed for the five sulfathiazole crystal forms. The anastrozole crystal structure is demonstrated to optimise interactions to the strongest acceptor sites even though there are no conventional hydrogen-bond donors in the structure. Finally, the fastest growing plane of the needle-like morphology of cipamfylline is shown to have more H-bond donor and acceptor interactions per surface area than the slower growing planes.