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.

The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal-organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface.

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 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.

The number of structures in the Cambridge Structural Database (CSD) has increased by an order of magnitude since the preparation of two major compilations of standard bond lengths in mid-1985. It is now of interest to examine whether this huge increase in data availability has implications for the mean bond-length values published in the late 1980s. Those compilations reported mean X-H bond lengths derived from rather sparse information and for rather few chemical environments. During the intervening years, the number of neutron studies has also increased, although only by a factor of around 2.25, permitting a new analysis of X-H bond-length distributions for (a) organic X = C, N, O, B, and (b) a variety of terminal and homometallic bridging transition metal hydrides. New mean values are reported here and are compared with earlier results. These new overall means are also complemented by an analysis of X-H distances at lower temperatures (T < or = 140 K), which indicates the general level of librational effects in X-H systems. The study also extends the range of chemical environments for which statistically acceptable mean X-H bond lengths can be obtained, although values from individual structures are also collated to further extend the chemical range of this compilation. Updated default 'neutron-normalization' distances for use in hydrogen-bond and deformation-density studies are also proposed for C-H, N-H and O-H, and the low-temperature analysis provides specific values for certain chemical environments and hybridization states of X.

Crystallographic and theoretical (ab initio) data on intermolecular nonbonded interactions have been gathered together in a computerised library ('IsoStar'). The library contains information about the nonbonded contacts formed by some 250 chemical groupings. The data can be displayed visually and used to aid protein-ligand docking or the identification of bioisosteric replacements. Data from the library show that there is great variability in the geometrical preferences of different types of hydrogen bonds, although in general there is a tendency for H-bonds to form along lone-pair directions. The H-bond acceptor abilities of oxygen and sulphur atoms are highly dependent on intramolecular environments. The nonbonded contacts formed by many hydrophobic groups show surprisingly strong directional preferences. Many unusual nonbonded interactions are to be found in the library and are of potential value for designing novel biologically active molecules.

A collection of new software tools is presented for the analysis of geometrical, chemical and crystallographic data from the Cambridge Structural Database (CSD). This software supersedes the program Vista. The new functionality is integrated into the program Mercury in order to provide statistical, charting and plotting options alongside three-dimensional structural visualization and analysis. The integration also permits immediate access to other information about specific CSD entries through the Mercury framework, a common requirement in CSD data analyses. In addition, the new software includes a range of more advanced features focused towards structural analysis such as principal components analysis, cone-angle correction in hydrogen-bond analyses and the ability to deal with topological symmetry that may be exhibited in molecular search fragments.

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.