The development of versions 3 and 4 of the Cambridge Structural Database System

Allen, Frank H.; Davies, John E.; Galloy, J.; Johnson, Owen; Kennard, Olga; Macrae, Clare F.; Mitchell, Eleanor M.; Mitchell, Gary F.; Smith, Jeremy M.; Watson, David

doi:10.1021/ci00002a004

Cited by 1,367 publications

(830 citation statements)

References 30 publications

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“…The atomic coordinates of C7ADP and C8ADP, as well as UiJU~.q, are given in Tables 3 and 4, respectively. The relevant atomic distances and angles are listed in Tables 5 and 6.t The geometric features of the dihydrogen phosphates compared with the structures with R < 0.05 found in the ICSD (ICSD, 1990;Bergerhoff, Hundt, Sievers & Brown, 1983) and the CSD (Cambridge Structural Database, 1995;Allen, Davies, Galloy, Johnson, Kennard, Macrae, Mitchell, Mitchell, Smith & Watson, 1991) are normal. The corresponding interatomic distances of the crystallographically independent molecules are in accordance with C7ADP as well as in C8ADP (see also Tables 5 and 6).…”

Section: Discussionmentioning

confidence: 99%

Revision of Ferroelastic Structures of n-Heptyl- and n-Octylammonium Dihydrogen Phosphate Crystals

Fábry¹,

Petřı́ček²,

Cı́sařová³

et al. 1997

Acta Crystallogr Sect B

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This study deals with the structure determination of C7HIsNH~.H2PO 4 (C7ADP) and CsH17NH~.H2PO 4 (C8ADP). The samples used in this study were not subjected to a phase transition after they had been crystallized. Unlike a previous structure determination, weak reflections, now with indices h = 2n + 1, were included. This means that both structures are described in unit cells with the lattice parameters a twice as long as given previously. Both structures are quite similar; two double layers of dihydrogen phosphates, which are interconnected by hydrogen bonds (2.52-2.62A,), pass through each unit cell. Alkylammonium groups interact with these dih~cdrogen phosphates via longer hydrogen bonds (>2.75 A), while the rest of the aliphatic chains interact via van der Waals contacts. All H atoms were localized and no disorder of the H atoms was detected. Both structures described in the space group P12~/nl exhibit a reproducible ferroelastic switching.The hypothetical prototypic phase is orthorhombic with the space group number 60 P2/b21/n21/a. All atoms except two hydrogen species exist in pairs linked by the lost symmetry operations derived from the prototypic space group and are brought close to each other -up to 0.25/~ -under the action of them. Each of these two different hydrogens is involved in an asymmetric hydrogen bond between an oxygen pair. Under the action of a lost symmetry operation each of these hydrogens is displaced from one oxygen towards the other. Therefore, it is asssumed that during the ferroelastic switching the jumps of these two hydrogen species take place between the pertinent hydrogen-bond acceptor and donor oxygens. Hence, these oxygens reverse their role as hydrogen-bond donors and acceptors during the ferroelastic switching.

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Section: Discussionmentioning

confidence: 99%

Revision of Ferroelastic Structures of n-Heptyl- and n-Octylammonium Dihydrogen Phosphate Crystals

Fábry¹,

Petřı́ček²,

Cı́sařová³

et al. 1997

Acta Crystallogr Sect B

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“…Indeed, the two most cited articles in the history of JCICS (Warr, 2005) come into this category, these being the standard references for the database searching systems used by the Cambridge Crystallographic Data Centre (Allen et al, 1991) and by the Daresbury Chemical Database Service (Fletcher et al, 1996); both of these pre-date our 1998 starting point and are not included in Table 4 only because they have insufficient citations in the period 1998-2006. Review articles -denoted by "(R)" in Table 4 often attract large numbers of citations, e.g., from the introductory sections of subsequent papers, and there are two reviews here -those by Willett et al (1998) and by Taylor et al (2002). Of the remaining 12 articles in the table, no less than four discuss the characteristics that differentiate drugs from other, non-drug molecules (Oprea et al, 2001;Hann et al, 20001;Oprea, 2000;Gillet et al, 1998), and there are two on the calculation of binding energies (i.e., the strength with which a drug molecule attaches itself to a biological receptor) (Bohm, 1998;Wang et al, 2002).…”

Section: The Core Literaturementioning

confidence: 99%

A bibliometric analysis of the literature of chemoinformatics

Willett

2008

Aslib Proceedings

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Abstract.Purpose: To analyse the literature of chemoinformatics, a subject that has arisen over the last few years and that draws on techniques from a range of disciplines, most notably chemistry (particularly computational and medicinal chemistry), computer science and information science. Method: Subject, author and citation searches of (principally) the Web of Knowledge database. Findings:The Journal of Chemical Information and Modeling (previously the Journal of Chemical Information and Computer Sciences) is the core journal for the subject, but with many significant papers being published in journals whose principal focus is molecular modelling, quantitative structure-activity relationships or more general aspects of chemistry. The discipline is international in scope, and many of the most cited papers describe software packages that play a key role in modern chemoinformatics research Originality: This is the first bibliometric study of chemoinformatics, and one of only a very few that consider the bibliometrics of computational chemistry more generally. Paper Type Research paper KeywordsAuthor productivity, Bibliometrics, cheminformatics, chemoinformatics, citation analysis INTRODUCTION Chemical information has been processed and exploited for many years, first in printed (Cooke, 2004) and then in computer form Hann and Green 1999). It is now, under the name of chemoinformatics, a key component of modern chemical research (Gasteiger and Engels, 2003;Leach and Gillet, 2003). Chemoinformatics' enhanced role has come about principally from the vast increase that has occurred in the volumes of data that need to be stored, searched and mined in research programmes for the discovery of biologically active molecules, most obviously but not exclusively in the pharmaceutical and agrochemical industries. These programmes involve the synthesis of large numbers of In this paper, we shall take 1998 as the starting point for our analysis, as this was when Brown's first formal definition of chemoinformatics appeared. That said, many of the basic techniques in chemoinformatics were developed prior to that date; indeed, the title of the paper by Hann and Green (1999) is "Chemoinformatics -a new name for an old problem".The 1998 starting point is thus rather arbitrary in nature and the interested reader is referred to several accounts (Chen 2006;Engel 2006;Willett 2003) that describe the historical development of the subject and of its core technologies, e.g., the use of graph, statistical and expert-system methods for searching chemical structure databases, for predicting biological activity, and designing synthetic pathways, respectively.

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“…27 The initial partial charges for the solute were computed from the crystal geometry. In a typical simulation, the methyl glycoside was solvated by 270 TIP3P water molecules in a theoretical box with approximate dimensions 23 × 23 × 20 Å.…”

Section: Computational Detailsmentioning

confidence: 99%

Solvated ensemble averaging in the calculation of partial atomic charges

Basma¹,

Sundara²,

Çalgan³

et al. 2001

J Comput Chem

139

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In the calculation of partial atomic charges, for use in molecular mechanics or dynamics simulations, it is common practice to select only a single conformation for the molecule of interest. For molecules that contain rotatable bonds, it is preferable to compute the charges from several relevant conformations. We present here results from a charge derivation protocol that determines the partial charges by averaging charges computed for conformations selected from explicitly solvated MD simulations, performed under periodic boundary conditions. This approach leads to partial charges that are weighted by a realistic population of conformations and that are suitable for condensed phase simulations. This protocol can, in principle, be applied to any class of molecule and to nonaqueous solvation. Carbohydrates contain numerous hydroxyl groups that exist in an ensemble of orientations in solution, and in this report we apply ensemble averaging to a series of methyl glycosides. We report the extent to which ensemble averaging leads to charge convergence among the various monosaccharides and among the constituent atoms within a given monosaccharide. Due to the large number of conformations (200) in our ensembles, we are able to compute statistically relevant standard deviations for the partial charges. An analysis of the standard deviations allows us to assess the extent to which equivalent atom types may, nevertheless, require unique partial charges. The configurations of the hydroxyl groups exert considerable influence on internal energies, and the limits of ensemble averaged charges are discussed in terms of these properties.

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The development of versions 3 and 4 of the Cambridge Structural Database System

Cited by 1,367 publications

References 30 publications

Revision of Ferroelastic Structures of n-Heptyl- and n-Octylammonium Dihydrogen Phosphate Crystals

Revision of Ferroelastic Structures of n-Heptyl- and n-Octylammonium Dihydrogen Phosphate Crystals

A bibliometric analysis of the literature of chemoinformatics

Solvated ensemble averaging in the calculation of partial atomic charges

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