Journal of Computational Chemistry

Cover image for Vol. 35 Issue 30

Early View (Online Version of Record published before inclusion in an issue)

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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  1. Full Papers

    1. Molecular dynamics simulation of configurational ensembles compatible with experimental FRET efficiency data through a restraint on instantaneous FRET efficiencies

      Maria M. Reif and Chris Oostenbrink

      Article first published online: 22 OCT 2014 | DOI: 10.1002/jcc.23756

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      This work describes how a special restraint potential energy term can be used in molecular dynamics simulations of a system undergoing Förster resonance energy transfer (FRET) to bring the simulated FRET efficiency in agreement with the FRET efficiency measured in experiment. Thus, the methodology allows the generation of configurational ensembles that may not be accessible with unrestrained simulations, and thereby supports a meaningful interpretation of experimental FRET results in terms of the underlying molecular degrees of freedom (interchromophore distances and orientations).

    2. A comprehensive DFT investigation of bulk and low-index surfaces of ZrO2 polymorphs

      Chiara Ricca, Armelle Ringuedé, Michel Cassir, Carlo Adamo and Frederic Labat

      Article first published online: 21 OCT 2014 | DOI: 10.1002/jcc.23761

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      Zirconia is one of the most studied ceramic materials, because of the wide range of its technological applications, including Solid Oxide Fuel Cells (SOFCs). Indeed, yttria-stabilized zirconia is the most used electrolyte in high-temperature SOFC. Density functional theory (DFT) calculations are presented on the bulk structures of three ambient pressure polymorphs of zirconia. Calculations were carried out with different DFT models, from which a computational protocol is applied to selected low-index surfaces.

    3. Computing pKA values of hexa-aqua transition metal complexes

      Gegham Galstyan and Ernst-Walter Knapp

      Article first published online: 19 OCT 2014 | DOI: 10.1002/jcc.23764

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      Aqueous pKA values for hexa-aqua complexes of first and second row transition metals were computed using a combination of quantum chemical and electrostatic methods. Computed pKA values show very good agreement with measured pKA values with a root mean square deviation of 1 pH unit. Compared to previous approaches from the same lab, the precision of the method was systematically improved.

    4. From orientation disordered to ordered—An ab initio simulation on ammonia borane phase transition within Van Der Waals corrections

      Qi Song, Zhenyi Jiang, Zhiyong Zhang, Yuqing Hou and Xiaodong Zhang

      Article first published online: 18 OCT 2014 | DOI: 10.1002/jcc.23762

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      The phase transition of ammonia borane (NH3BH3), from a tetragonal I4mm ( inline image) phase with disordered orientation of hydrogen to an orthorhombic phase with Pmn21 ( inline image) symmetry, is investigated as a function of temperature, based on density functional theory calculations with semi-empirical dispersion potential correction. A series of substructures are defined and the partially occupied high temperature state can be described as a continuous transformation between these substructures. The total energies with phonon spectrum of each substructure allow the minimal free energy structure at each temperature to be determined explicitly.

    5. Lightweight object oriented structure analysis: Tools for building tools to analyze molecular dynamics simulations

      Tod D. Romo, Nicholas Leioatts and Alan Grossfield

      Article first published online: 18 OCT 2014 | DOI: 10.1002/jcc.23753

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      LOOS is a software library designed to facilitate making novel tools for analyzing molecular dynamics simulations using C++ or Python. LOOS supports reading the native file formats of most common biomolecular simulation packages. A dynamic atom selection language is included and is easily accessible to the tool-writer. LOOS is bundled with over 140 tools. Through modern C++ design, LOOS is both simple to develop with and is easily extensible

  2. Feature Articles

    1. Scents and sense: In silico perspectives on olfactory receptors

      Charleen G. Don and Sereina Riniker

      Article first published online: 18 OCT 2014 | DOI: 10.1002/jcc.23757

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      G protein-coupled receptors (GPCRs) compose one of the largest protein membrane family in our body. These refined receptors have a critical function in many essential regulation pathways and thus are involved in several severe diseases. Therefore, many studies are focus to gain insight in their functioning. In this review, Olfactory receptors (ORs), the largest GPCR subfamily, are discussed with main focus on their structural characteristics and the computational techniques that can be used to broaden our current knowledge regarding both GPCRs-malfunctioning diseases and human odor perception.

  3. Full Papers

    1. Why it is sometimes difficult to determine the accurate position of a hydrogen atom by the semiexperimental method: Structure of molecules containing the OH or the CH3 group

      Natalja Vogt, Jean Demaison, Jürgen Vogt and Heinz Dieter Rudolph

      Article first published online: 18 OCT 2014 | DOI: 10.1002/jcc.23758

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      The semiexperimental (SE) technique has the reputation to be one of the most accurate methods to determine an equilibrium structure. However, in some cases, it cannot accurately determine the position of the hydrogen atoms in a methyl or hydroxyl group. To investigate the origins of this difficulty, the SE structures of several molecules containing either the OH or the CH3 group are determined and compared to their best ab initio counterparts.

    2. Enhanced sampling simulations of DNA step parameters

      Aleksandra Karolak and Arjan van der Vaart

      Article first published online: 9 OCT 2014 | DOI: 10.1002/jcc.23751

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      A simplified method for the calculation of DNA step parameters and their Cartesian derivatives is introduced. Using three atoms per base and no structure overlays, the method is highly efficient for use in free energy simulations while retaining good accuracy. The method is illustrated by calculating the flexibility of the central CG step in methylated and unmethylated DNA strands.

    3. van der Waals corrected density functional calculations of the adsorption of benzene on the Cu (111) surface

      Damien J. Carter and Andrew L. Rohl

      Article first published online: 6 OCT 2014 | DOI: 10.1002/jcc.23745

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      The performance of several van der Waals (vdW) functionals at calculating the interactions between benzene and the copper (111) surface was investigated. Local orbital methods using appropriate basis sets combined with a vdW functional can successfully model adsorption between metal surfaces and organic molecules.

    4. Structural evolution of small gold clusters doped by one and two boron atoms

      Rafael Grande-Aztatzi, Paulina R. Martínez-Alanis, José Luis Cabellos, Edison Osorio, Ana Martínez and Gabriel Merino

      Article first published online: 3 OCT 2014 | DOI: 10.1002/jcc.23748

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      The potential energy surfaces of gold clusters doped with one and two boron atoms have been explored in detail using a stochastic search algorithm. DFT computations show that these gold-boron clusters have well-defined growth patterns.

    5. 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.

    6. 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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    7. Impact of Mn on the solution enthalpy of hydrogen in austenitic Fe-Mn alloys: A first-principles study

      Jörg von Appen, Richard Dronskowski, Aurab Chakrabarty, Tilmann Hickel, Robert Spatschek and Jörg Neugebauer

      Article first published online: 24 SEP 2014 | DOI: 10.1002/jcc.23742

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      Adding a substantial amount of manganese to steels yields a material with extraordinary mechanical properties. A tiny amount of hydrogen in high-Mn steels, however, is already suffcient for the onset of devastating embrittlement effects. Using first-principles methods, an attraction of both elements is revealed, providing a complete analysis of the elastic, chemical, and magnetic origin of this phenomenon. These insights contribute to strategies to better control the hydrogen distribution in steels.

    8. Melting of icosahedral nickel clusters under hydrostatic pressure

      Bing Fu, Li Chen, Feifei Wang, Yiqun Xie and Xiang Ye

      Article first published online: 21 SEP 2014 | DOI: 10.1002/jcc.23739

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      Since nickel–iron mixture is one kind of dominant components in terrestrial planet lower mantle, melting of nickel under hydrostatic pressure is always an interesting topic. In this work, the melting behaviors of icosahedral nickel clusters under hydrostatic pressure have been studied by constant-pressure molecular dynamic simulation. This work is intended to provide a better understanding for the thermal properties of nickel cluster and will help to develop new nanomaterials under hydrostatic pressure.

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