Journal of Computational Chemistry

Cover image for Vol. 38 Issue 3

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

Impact Factor: 3.648

ISI Journal Citation Reports © Ranking: 2015: 41/163 (Chemistry Multidisciplinary)

Online ISSN: 1096-987X

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

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  1. Nuclear-relaxed elastic and piezoelectric constants of materials: Computational aspects of two quantum-mechanical approaches

    Alessandro Erba, Dominique Caglioti, Claudio Marcelo Zicovich-Wilson and Roberto Dovesi

    Version of Record online: 9 DEC 2016 | DOI: 10.1002/jcc.24687

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    Two alternative approaches for the quantum-mechanical determination of the nuclear-relaxation term of elastic and piezoelectric tensors of materials are illustrated and compared. The computational advantages of a quasi-analytical scheme based on the internal-strain tensor with respect to a numerical scheme based on geometry optimizations are documented both in terms of accuracy and efficiency.

  2. The GPU-enabled divide-expand-consolidate RI-MP2 method (DEC-RI-MP2)

    Dmytro Bykov and Thomas Kjaergaard

    Version of Record online: 7 DEC 2016 | DOI: 10.1002/jcc.24678

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    We report porting of the divide-expand-consolidate resolution of the identity second-order Møller–Plesset perturbation (DEC-RI-MP2) method to the graphic processing units (GPUs) using OpenACC compiler directives. The OpenACC-based implementation efficiently accelerates the rate-determining step of the DEC-RI-MP2 method with minor implementation effort. Moreover, the GPU acceleration results in a better load balance and thus in an overall scaling improvement of the DEC algorithm. The resulting cross-platform hybrid MPI/OpenMP/OpenACC implementation has scalable and portable performance on heterogeneous HPC architectures. The GPU-enabled code was benchmarked using a reduced version of the S12L test set.

  3. You have full text access to this OnlineOpen article
    Electronic absorption spectra of pyridine and nicotine in aqueous solution with a combined molecular dynamics and polarizable QM/MM approach

    Marco Pagliai, Giordano Mancini, Ivan Carnimeo, Nicola De Mitri and Vincenzo Barone

    Version of Record online: 2 DEC 2016 | DOI: 10.1002/jcc.24683

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    The electronic absorption spectrum of nicotine in aqueous solution has been computed with an integrated protocol, performing time-dependent density functional theory calculations with a polarizable QM/MM scheme on a series of configurations extracted from molecular dynamics simulations. The protocol has been preliminary verified calculating the electronic absorption spectrum of the rigid aromatic moiety of nicotine (i.e., pyridine) in water.

  4. Residue-centric modeling and design of saccharide and glycoconjugate structures

    Jason W. Labonte, Jared Adolf-Bryfogle, William R. Schief and Jeffrey J. Gray

    Version of Record online: 30 NOV 2016 | DOI: 10.1002/jcc.24679

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    Carbohydrates are present everywhere in nature, possessing a vast array of structural diversity, yet historically, they have been challenging to model. RosettaCarbohydrate is a new tool for researchers studying the form and function of carbohydrate structures. The framework integrates with Rosetta's successful modeling and design suite and addresses challenges unique to glycans. This article describes the development of the framework and highlights its applications, including loop modeling and glyco-ligand docking.

  5. Anomerization reaction of bare and microhydrated d-erythrose via explicitly correlated coupled cluster approach. Two water molecules are optimal

    Marek Szczepaniak and Jerzy Moc

    Version of Record online: 29 NOV 2016 | DOI: 10.1002/jcc.24680

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    This comprehensive benchmark computational study has explored a complete path of the anomerization reaction of bare d-erythrose relating a pair of the low-energy α- and β-furanose anomers, the former of which was recently observed spectroscopically. The issue of the number of water molecules (n) required for optimal stabilization of the erythrose anomerization reaction rate-determining transition state is addressed by a systematic exploration of the potential energy surface of the ring opening in the α-anomer-(H2O)n and various β-anomer-(H2O)n (n = 1–3) clusters. The lowest free energy barrier of the erythrose ring opening is predicted for the doubly hydrated α-anomer.

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