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.

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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.

Two new programs have been developed for searching the Cambridge Structural Database (CSD) and visualizing database entries: ConQuest and Mercury. The former is a new search interface to the CSD, the latter is a high-performance crystal-structure visualizer with extensive facilities for exploring networks of intermolecular contacts. Particular emphasis has been placed on making the programs as intuitive as possible. Both ConQuest and Mercury run under Windows and various types of Unix, including Linux.

The conclusions derived from systematic analyses of intermolecular contact distances in organic crystals may be affected by the values assumed for van der Waals radii. The most widely used tabulations of van der Waals radii date back 30 years or more. Moreover, many of the tabulated values were chosen to reproduce volumes, not contact distances in crystals. Literally millions of nonbonded contact distances have been characterized by crystallography since the tabulations were compiled. A study has therefore been performed to establish the degree of consistency between these accumulated crystallographic data and the van der Waals radii of the common nonmetallic elements, as compiled by Pauling and Bondi. For halogens and sulfur, the results show a remarkable agreement between observed contact distances and the Bondi radii. Agreement is slightly less good for carbon, nitrogen, and oxygen, but discrepancies are still only about 0.05 Å. However, there is a significant difference for hydrogen, where the Bondi value of 1.2 Å is probably too high by about 0.1 Å.

A survey of 113 published neutron diffraction crystal structures is described. The major results are as follows. Hydrogen atoms that are covalently bonded to carbon have a statistically significant tendency to form short intermolecular contacts to oxygen atoms rather than to carbon or hydrogen atoms. This phenomenon is probably due to electrostatic stabilization of the short C-H-O contacts. The proton in the majority of short C-H-O contacts lies within 30°of the plane containing the lone-pair orbitals of the oxygen atom. C-H groups that are adjacent to nitrogen atoms are particularly likely to participate in short C-H-O interactions, but the environment of the oxygen atom is unimportant. The crystal structures also contain several short, intermolecular C--N and C-H-Cl contacts. It is concluded that the C-H-O, C--N, and C-H-Cl 3 Acetamide (ACEMID03)

The crystallographically determined bond length, valence angle, and torsion angle information in the Cambridge Structural Database (CSD) has many uses. However, accessing it by means of conventional substructure searching requires nontrivial user intervention. In consequence, these valuable data have been underutilized and have not been directly accessible to client applications. The situation has been remedied by development of a new program (Mogul) for automated retrieval of molecular geometry data from the CSD. The program uses a system of keys to encode the chemical environments of fragments (bonds, valence angles, and acyclic torsions) from CSD structures. Fragments with identical keys are deemed to be chemically identical and are grouped together, and the distribution of the appropriate geometrical parameter (bond length, valence angle, or torsion angle) is computed and stored. Use of a search tree indexed on key values, together with a novel similarity calculation, then enables the distribution matching any given query fragment (or the distributions most closely matching, if an adequate exact match is unavailable) to be found easily and with no user intervention. Validation experiments indicate that, with rare exceptions, search results afford precise and unbiased estimates of molecular geometrical preferences. Such estimates may be used, for example, to validate the geometries of libraries of modeled molecules or of newly determined crystal structures or to assist structure solution from low-resolution (e.g. powder diffraction) X-ray data.

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