Showing papers by "Colin R. Groom published in 2011"

Identification, classification and relative stability of tautomers in the cambridge structural database

Abstract: Families of tautomers in the Cambridge Structural Database (CSD) have been identified, analysed and classified. We identified 108 molecules that crystallise in two different tautomeric forms. Most commonly, pairs of tautomers crystallise together in the same crystal structure. Tautomeric polymorphs—pairs of tautomers crystallising in different crystal structures with no other or identical components—are very rare. The calculation of the relative stabilities of the different pairs of tautomers mirrors the relative frequencies with which tautomeric forms are observed in the CSD. Our improved understanding of the factors influencing tautomeric preferences in crystal structures may allow the prediction and design of crystal structures containing tautomeric forms that are, as yet, unobserved in the solid state.

The Cambridge Structural Database: experimental three-dimensional information on small molecules is a vital resource for interdisciplinary research and learning

Abstract: Crystal structure determination is the method of choice for the analysis of novel chemical compounds from monatomic metals to proteins and viruses, with some 700,000 crystal structures published so far. Of these, over 500,000 (70%) are carbon-containing organic and metal-organic small molecules, for which experimental three-dimensional (3D) numerical results are stored in the Cambridge Structural Database (CSD), together with two-dimensional chemical structure information and text and numerical fields that record chemical and physical properties. The CSD is fully searchable using an Internet search engine or specialist-distributed software that provides advanced facilities for structure display and data analysis, including many special features for understanding molecular recognition processes such as protein–ligand interactions. Two knowledge bases derived from the CSD provide immediate access to information on intramolecular geometry and intermolecular interactions. CSD information is heavily used in academic and industrial research that relies on knowledge of 3D molecular geometry and intermolecular interactions, for example, in structural chemistry and biology, drug discovery, materials design and development, and in crystallography itself. As a teaching tool, the CSD has a fundamental role to play in illustrating the 3D chemical concepts that are essential for those who study chemistry as a principal or subsidiary subject. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 368–376 DOI: 10.1002/wcms.35

Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress. A response from the Cambridge Crystallographic Data Centre.

Abstract: S expressed in the paper “Data-Driven HighThroughput Prediction of the 3-D Structure of Small Molecules: Review and Progress”, recently published in the Journal of Chemical Information and Modeling may give readers a misleading impression of important scientific resources. The authors state that “One obstacle in this area may be the closed nature of the CSD, which unlike the PDB cannot be used without severe restrictions, even for academic research purposes.”The only substantive restrictions placed on the use of the Cambridge Structural Database are that licensees will not redistribute derived data without prior permission of the CCDC and that use of the system is acknowledged appropriately. The authors do not explain how this presents an obstacle to research in this area. It seems rather ironic that the authors criticize the very resource that has made their research possible, in this way. In as much as the service described in this article uses data from the Cambridge Structural Database, express permission was immediately granted by the Cambridge Crystallographic Data Centre. The authors continue “This is yet another example of the unfortunate state of affairs in chemoinformatics, where an overly zealous culture of closeness and secrecy, sometimes related to short-term profits, have greatly hampered scientific progress.” The Cambridge Structural Database is maintained and distributed by the Cambridge Crystallographic Data Centre (CCDC). This is a not-for-profit organization, which has charitable status, conferred and overseen by a U.K. Government Commission. This is in recognition of the scientific objectives of the organization and ensures that all income earned is applied for the benefit of science. TheCSD is licensed at below cost to academic organizations in 70 countries throughout the world. However, in cases where scientists are not able to source the modest funding for the database, access is never denied. The activities of Cambridge Crystallographic Data Centre Software Limited, an organization that develops and licenses other software in the area of drug discovery, provides the additional income to the CCDC that make this possible. This self-funding mechanism has been discussed elsewhere and has allowed this comprehensive and accurate resource, which requires much effort, to be developed and maintained. In addition, the CCDC provides a completely free service whereby data associated with any specific experiment can be obtained from our Web site. The CCDC prides itself on its openness and willingness to collaborate with scientists internationally and has a strong track record in this regard. Far from hampering scientific progress, our culture does much to advance science, as evidenced from the research our tools and products have enabled and the scientific output of the organization itself.