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Accelrys is a software company headquartered in the United States, with representation in Europe and Asia. It provides software for chemical, materials and bioscience research for the pharmaceutical, biotechnology, consumer packaged goods, aerospace, energy and chemical industries.It is a wholly owned subsidiary of Dassault Systèmes after an April 2014 acquisition. Wikipedia.


Rogers D.,3429 North Mountain View Drive | Hahn M.,Accelrys
Journal of Chemical Information and Modeling | Year: 2010

Extended-connectivity fingerprints (ECFPs) are a novel class of topological fingerprints for molecular characterization. Historically, topological fingerprints were developed for substructure and similarity searching. ECFPs were developed specifically for structure-activity modeling. ECFPs are circular fingerprints with a number of useful qualities: they can be very rapidly calculated; they are not predefined and can represent an essentially infinite number of different molecular features (including stereochemical information); their features represent the presence of particular substructures, allowing easier interpretation of analysis results; and the ECFP algorithm can be tailored to generate different types of circular fingerprints, optimized for different uses. While the use of ECFPs has been widely adopted and validated, a description of their implementation has not previously been presented in the literature. © 2010 American Chemical Society. Source


Friedrich A.,Goethe University Frankfurt | Winkler B.,Goethe University Frankfurt | Refson K.,Rutherford Appleton Laboratory | Milman V.,Accelrys
Physical Review B - Condensed Matter and Materials Physics | Year: 2010

We report the elastic, electronic, and vibrational properties of hexagonal Re3 N rhenium nitride from experiment and theory using density-functional-theory-based atomistic model calculations. Re3 N was formed at 12 and 20 GPa at about 2000 K in a laser-heated diamond-anvil cell and recovered at ambient conditions. The structural model proposed recently is confirmed by a comparison of the vibrational properties obtained from Raman spectroscopy and from theory, which are in very good agreement. The mode Grüneisen parameters are reported from the pressure-dependent shift of the vibrational modes. The calculated density of electronic states at the Fermi level shows that Re3 N is metallic in the pressure range 0-20 GPa. © 2010 The American Physical Society. Source


Carlsson J.M.,Accelrys | Carlsson J.M.,Fritz Haber Institute | Ghiringhelli L.M.,Fritz Haber Institute | Fasolino A.,Radboud University Nijmegen
Physical Review B - Condensed Matter and Materials Physics | Year: 2011

Several experiments have revealed the presence of grain boundaries in graphene that may change its electronic and elastic properties. Here, we present a general theory for the structure of [0001] tilt grain boundaries in graphene based on the coincidence site lattice (CSL) theory. We show that the CSL theory uniquely classifies the grain boundaries in terms of the misorientation angle θ and periodicity d using two grain-boundary indices (m,n), similar to the nanotube indices. The structure and formation energy of a large set of grain boundaries generated by the CSL theory for 0<θ<60 (up to 15 608 atoms) were optimized by a hierarchical methodology and validated by density functional calculations. We find that low-energy grain boundaries in graphene can be identified as dislocation arrays. The dislocations form hillocks like those observed by scanning tunneling microscopy in graphene grown on Ir(111) for small θ that flatten out at larger misorientation angles. We find that, in contrast to three-dimensional materials, the strain created by the grain boundary can be released via out-of-plane distortions that lead to an effective attractive interaction between dislocation cores. Therefore, the dependence on θ of the formation energy parallels that of the out-of-plane distortions, with a secondary minimum at θ=32.2 where the grain boundary is made of a flat zigzag array of only 5 and 7 rings. For θ>32.2, other nonhexagonal rings are also possible. We discuss the importance of these findings for the interpretation of recent experimental results. © 2011 American Physical Society. Source


Haider M.K.,University of York | Bertrand H.-O.,Accelrys | Hubbard R.E.,University of York | Hubbard R.E.,Vernalis
Journal of Chemical Information and Modeling | Year: 2011

Improved methods are required to predict the position and orientation (pose) of binding to the target protein of low molecular weight compounds identified in fragment screening campaigns. This is particularly important to guide initial chemistry to generate structure - activity relationships for the cases where a high resolution structure cannot be obtained. We have assessed the benefit of an implicit solvent method for assessment of fragment binding poses generated by the Multiple Copy Simultaneous Search (MCSS) method in CHARMm. Additionally, the effect of using multiple receptor structures for a flexible receptor is investigated. The original MCSS performance -50% of fragment positions accurately predicted and scored - was increased up to 67% by scoring MCSS energy minima with a Molecular Mechanics Generalized Born approach with molecular volume integration and Surface Area model (MM-GBSA). The same increase in performance (but occasionally for different targets) was observed when using the docking program GOLD followed by MM-GBSA rescoring. The combined results from both methods resulted in a higher success rate emphasizing that a comparison of different docking methods can increase the correct identification of binding poses. For a receptor where multiple structures are available, Hsp90, the average performance on randomly adding receptor structures was also investigated. The results suggest that predictions using these docking methods can be used with some confidence to guide chemical optimization, if the structure of the target either remains relatively fixed on ligand binding, or if a number of crystal structures are available with diverse ligands bound and there is information on the positions of key water molecules in the binding site. (Figure presented). © 2011 American Chemical Society. Source


Bjork J.,Linkoping University | Hanke F.,Accelrys
Chemistry - A European Journal | Year: 2014

The covalent molecular assembly on metal surfaces is explored, outlining the different types of applicable reactions. Density functional calculations for on-surface reactions are shown to yield valuable insights into specific reaction mechanisms and trends across the periodic table. Finally, it is shown how design rules could be derived for nanostructures on metal surfaces. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source

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