Journal of Computational Chemistry

Cover image for Vol. 35 Issue 29

Edited By: Charles L. Brooks III, Masahiro Ehara, Gernot Frenking, and Peter R. Schreiner

Impact Factor: 3.601

ISI Journal Citation Reports © Ranking: 2013: 36/148 (Chemistry Multidisciplinary)

Online ISSN: 1096-987X

Associated Title(s): International Journal of Quantum Chemistry, Wiley Interdisciplinary Reviews: Computational Molecular Science

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Recently Published Articles

  1. Efficient calculation of relative binding free energies by umbrella sampling perturbation

    Fabian Zeller and Martin Zacharias

    Article first published online: 29 SEP 2014 | DOI: 10.1002/jcc.23744

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    The change of a potential of mean force upon the modification of a system can be estimated by an umbrella sampling perturbation method that does not require additional simulations. Application to computational alanine-scanning of a peptide-protein complex by means of relative separation PMFs resulted in accurate free energy estimates for a series of peptide modifications. The method yields rigorously derived free energy changes under the condition of sufficiently small perturbations.

  2. Controlling the oxidative addition of aryl halides to Au(I) (pages 2140–2145)

    Israel Fernández, Lando P. Wolters and F. Matthias Bickelhaupt

    Article first published online: 26 SEP 2014 | DOI: 10.1002/jcc.23734

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    The oxidative addition of aryl halides to Au(I) complexes is considered a kinetically sluggish reaction. By combining the Activation Strain Model and Energy Decomposition Analysis methods, the factors causing this reaction to be slow are been identified. Based on this new insight, we suggest the best combination of gold(I) complex and aryl halide to turn this process into a feasible, low-barrier transformation.

  3. GneimoSim: A modular internal coordinates molecular dynamics simulation package

    Adrien B. Larsen, Jeffrey R. Wagner, Saugat Kandel, Romelia Salomon-Ferrer, Nagarajan Vaidehi and Abhinandan Jain

    Article first published online: 26 SEP 2014 | DOI: 10.1002/jcc.23743

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  4. Geometrical and optical benchmarking of copper(II) guanidine–quinoline complexes: Insights from TD-DFT and many-body perturbation theory (part II) (pages 2146–2161)

    Alexander Hoffmann, Martin Rohrmüller, Anton Jesser, Ines dos Santos Vieira, Wolf Gero Schmidt and Sonja Herres-Pawlis

    Article first published online: 25 SEP 2014 | DOI: 10.1002/jcc.23740

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    Ground- and excited-state properties of copper(II) charge-transfer systems have been investigated starting from density-functional calculations with particular emphasis on the role of the exchange and correlation functional, the basis set, solvent effects, and the treatment of dispersive interactions. Furthermore, the applicability of TD-DFT to excitations of copper(II) bis(chelate) charge-transfer systems was explored by performing many-body perturbation theory (GW + BSE), independent-particle approximation (IPA) and ΔSCF calculations for a small model system that contains simple guanidine and imine groups.

  5. Bayesian inference of conformational state populations from computational models and sparse experimental observables

    Vincent A. Voelz and Guangfeng Zhou

    Article first published online: 24 SEP 2014 | DOI: 10.1002/jcc.23738

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    We present a Bayesian inference approach to estimating conformational state populations from a combination of molecular modeling and sparse experimental data. Unlike alternative approaches, our method is designed for use with small molecules and emphasizes high-resolution structural models, using inferential structure determination with reference potentials, and MCMC to sample the posterior distribution of conformational states. As an application of the method, we determine solution-state conformational populations of the 14-membered macrocycle cineromycin B, using a combination of previously published sparse NMR observables and REMD/QM-refined conformational ensembles. Our results agree better with experimental data compared to previous modeling efforts. Bayes factors are calculated to quantify the consistency of computational modeling with experiment, and the relative importance of reference potentials and other model parameters.