Ian J. Bruno

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.

The Cambridge Structural Database

This paper is the definitive article describing the creation, maintenance, information content and availability of the Cambridge Structural Database (CSD), the world’s repository of small molecule crystal structures.

Retrieval of Crystallographically-Derived Molecular Geometry Information

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.

IsoStar: A library of information about nonbonded interactions

Crystallographic and theoretical (ab initio) data on intermolecular nonbondedinteractions have been gathered together in a computerised library(’IsoStar‘). The library contains information about the nonbonded contactsformed by some 250 chemical groupings. The data can be displayed visually andused to aid protein–ligand docking or the identification of bioisostericreplacements. Data from the library show that there is great variability inthe geometrical preferences of different types of hydrogen bonds, although ingeneral 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 dependenton intramolecular environments. The nonbonded contacts formed by manyhydrophobic groups show surprisingly strong directional preferences. Manyunusual nonbonded interactions are to be found in the library and are ofpotential value for designing novel biologically active molecules.

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.

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.

One in half a million: a solid form informatics study of a pharmaceutical crystal structure

We introduce a knowledge-based approach to the evaluation, analysis and prediction of the properties of a crystal form; described inclusively as Solid Form Informatics. This approach is exemplified using the recently published crystal structure of the drug lamotrigine in the context of the Cambridge Structural Database (CSD). Analysis at the molecular, intermolecular and supramolecular level is carried out using the range of software available in the CSD System alongside new research applications. This work provides a template for the thorough analysis of any crystal structure and paves the way toward a fully automated structural analysis for the drug formulation scientist, with the aim to better provide answers to the fundamental questions raised during the drug development process. To conclude, the knowledge gained about the structure is applied to predict the potential for a co-crystal formulation of the drug and to automatically select optimal co-crystal formers. The crystal structure of lamotrigine was the half-millionth structure to enter the CSD. We demonstrate how the 499,999 structures that preceded it are central to the analyses presented.

Factors affecting d-block metal-ligand bond lengths: toward an automated library of molecular geometry for metal complexes.

Metal-ligand (M-L) bond lengths for a range of ligands (carboxylates, chlorides, pyridines, water, tertiary phosphines, and alkenes) and a variety of metals have been retrieved from the Cambridge Structural Database, CSD. Analysis of the factors which affect M-L bond lengths (for example, ligand coordination mode, oxidation state, metal coordination number and geometry, spin and Jahn-Teller effects, and ligand trans to M-L bond) shows that it is generally possible to subdivide the M-L data sets systematically to obtain better defined, unimodal, bond length distributions with means and sample standard deviations (SSDs) which reflect the nature of the bond in question. Typically, the SSDs for the M-L data sets can be reduced to 0.04-0.05 A by these methods. This work is an extension to tables of bond lengths in organometallic compounds and coordination complexes published in 1989. The importance of the factors which affect M-L bond lengths for particular metal-ligand groups are discussed. From the case studies reported, an algorithm is proposed by which compilation of a library of molecular geometry for metal complexes may be automated. The points that need to be considered to produce such a molecular library from the data stored in the CSD are discussed. The development of such a library would allow users to retrieve chemically well-defined geometric data rapidly and accurately. This should be of use, for example, to crystallographers and molecular modelers.

Deducing chemical structure from crystallographically determined atomic coordinates

An improved algorithm has been written for assigning chemical structures to incoming entries to the Cambridge Structural Database.

Crystallography and Databases

Crystallographic databases have existed as electronic resources for over 50 years, and have provided comprehensive archives of crystal structures of inorganic, organic, metal–organic and biological macromolecular compounds of immense value to a wide range of structural sciences. They thus serve a variety of scientific disciplines, but are all driven by considerations of accuracy, precise characterization, and potential for search, analysis and reuse. They also serve a variety of end-users in academia and industry, and have evolved through different funding and licensing models. The diversity of their operational mechanisms combined with their undisputed value as scientific research tools gives rise to a rich ecosystem. A session at SciDataCon2016 gave an overview of the largest extant crystallographic databases and their current activities and plans for the future. This review summarizes these presentations and considers them alongside other players in the field, demonstrating their variety, versatility and focus on quality and usefulness.