Journal of Computational Chemistry

Cover image for Vol. 36 Issue 17

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. Multidimensional persistence in biomolecular data

      Kelin Xia and Guo-Wei Wei

      Article first published online: 30 MAY 2015 | DOI: 10.1002/jcc.23953

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      Persistent homology has emerged as a popular technique for the topological simplification of massive biomolecular data. Resolution-based multidimensional persistent homology is introduced to bridge the gap between traditional topology and geometry. The utility, robustness, and efficiency of the proposed topological methods for protein folding, protein flexibility analysis, the topological denoising of cryo-electron microscopy data, and the scale dependence of nanoparticles are demonstrated.

    2. An analytical bond-order potential for carbon

      X. W. Zhou, D. K. Ward and M. E. Foster

      Article first published online: 27 MAY 2015 | DOI: 10.1002/jcc.23949

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      A new parameterization of Pettifor's bond order potential has been performed for carbon. The method captures the property trends of important carbon phases and passes stringent molecular dynamics simulation tests: not only allowing for the crystalline growth of graphene, graphite, and carbon nanotubes, but also the transformation of graphite to diamond at high pressure.

    3. The origins of the directionality of noncovalent intermolecular interactions#

      Changwei Wang, Liangyu Guan, David Danovich, Sason Shaik and Yirong Mo

      Article first published online: 25 MAY 2015 | DOI: 10.1002/jcc.23946

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      The block-localized wavefunction method, which can derive hypothetical structures without the charge transfer effect and conduct intermolecular energy decomposition analysis, is used to probe the origins of the directionality of weak noncovalent bonds. While the overall steric energy exhibits certain angular dependency, in all cases the charge transfer exhibits the strongest directionality, suggesting that the linearity or near linearity of noncovalent bonds is largely governed by the charge-transfer interaction whose magnitude determines the bond covalency.

    4. Structure and stability of supramolecular crown ether complexes

      Kim Julia Hintze, Arne Lützen and Thomas Bredow

      Article first published online: 22 MAY 2015 | DOI: 10.1002/jcc.23950

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      A protocol for the efficient calculation of supramolecular binding affinities of crown ether derivatives with ammonium cations is presented. The performance of various density functionals and the MP2 method is investigated and the influence of dispersion interaction is analyzed. CCSD(T) binding energies extrapolated to the basis set limit served as internal reference.

    5. Replica state exchange metadynamics for improving the convergence of free energy estimates

      Raimondas Galvelis and Yuji Sugita

      Article first published online: 19 MAY 2015 | DOI: 10.1002/jcc.23945

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      Metadynamics (MTD) is a powerful enhanced sampling method for systems with rugged energy landscapes. It constructs a bias potential in a collective variable (CV) space to overcome barriers between metastable states. In the bias-exchange MTD (BE-MTD), multiple replicas approximate the CV space by exchanging bias potentials (replica conditions). We propose the replica state exchange metadynamics (RSE-MTD), which use a more sophisticated replica-exchange scheme to improve the convergence of free energy for a given simulation time.

    6. A comparative computationally study about the defined m(II) pincer hydrogenation catalysts (m = fe, ru, os)

      Haijun Jiao, Kathrin Junge, Elisabetta Alberico and Matthias Beller

      Article first published online: 17 MAY 2015 | DOI: 10.1002/jcc.23944

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      DFT studies on the defined pincer-type catalysts M(H)2(CO)[NH(C2H4PiPr2)2] (1M) and M(H)(CO)[N(C2H4PiPr2)2] (2M) (M = Fe, Ru, Os) reveal remarkable differences in electronic structures and hydrogenation reactivity of nitriles, ester, and ketones. For acetonitrile hydrogenation, Fe- and Ru-based catalysts are best. For methyl benzoate hydrogenation and dehydrogenation of benzyl alcohol, Ru-based catalysts are best. In contrast, Os-based catalysts are least active.

    7. Quantum supercharger library: Hyper-parallelism of the Hartree–Fock method

      Kyle D. Fernandes, C. Alicia Renison and Kevin J. Naidoo

      Article first published online: 14 MAY 2015 | DOI: 10.1002/jcc.23936

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      The Quantum Supercharger Library's Hartree–Fock module completely performed on a GPU hardware accelerator in double precision yields up to a 19× speed-up over the best performing GAMESS-UK CPU software.

    8. Quantum supercharger library: Hyper-parallel integral derivatives algorithms for ab initio QM/MM dynamics

      C. Alicia Renison, Kyle D. Fernandes and Kevin J. Naidoo

      Article first published online: 14 MAY 2015 | DOI: 10.1002/jcc.23938

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      Complete parallelization of the one and two integral derivatives for GPU accelerators provides high speed ab initio QM/MM simulations of 10ps/day for single off-the-shelf GPU cards.

    9. Calculation of the stability of nonperiodic solids using classical force fields and the method of increments: N2o as an example

      Carsten Müller and Daniel Spångberg

      Article first published online: 14 MAY 2015 | DOI: 10.1002/jcc.23939

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      This study demonstrates a statistical approach to the calculation of temperature-dependent cohesive energies of randomly disordered molecular crystals such as nitrous oxide (N2O) at sophisticated levels of post-Hartree-Fock theory.

  2. Software News and Updates

    1. Pteros 2.0: Evolution of the fast parallel molecular analysis library for C++ and python

      Semen O. Yesylevskyy

      Article first published online: 14 MAY 2015 | DOI: 10.1002/jcc.23943

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      Pteros 2.0 is the high-performance open-source library for molecular modeling and analysis of molecular dynamics trajectories in C++ and Python languages. Pteros is suitable for writing complex reusable programs in C++ and simple interactive scripts in Python. The new version improves the facilities for asynchronous trajectory reading and parallel execution of analysis tasks by introducing analysis plug-ins, which could be written in either C++ or Python in a completely uniform way. The high level of abstraction provided by analysis plug-ins greatly simplifies prototyping and implementation of complex analysis algorithms.

  3. Full Papers

    1. First-principle modelling of forsterite surface properties: Accuracy of methods and basis sets

      Raffaella Demichelis, Marco Bruno, Francesco R. Massaro, Mauro Prencipe, Marco De La Pierre and Fabrizio Nestola

      Article first published online: 14 MAY 2015 | DOI: 10.1002/jcc.23941

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      This article presents an accurate assessment of methods for the study of forsterite surface properties and reactivity. The ability to build a realistic model for such system is essential to understand the fundamental interactions responsible for a variety of natural phenomena happening on Earth and in space.

    2. A rigorous and optimized strategy for the evaluation of the Boys function kernel in molecular electronic structure theory

      Alexander K. H. Weiss and Christian Ochsenfeld

      Article first published online: 13 MAY 2015 | DOI: 10.1002/jcc.23935

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      This work is focused on the efficient evaluation of the Boys function located at the heart of Coulomb and exchange type electron integrals. Different evaluation strategies for individual orders and arguments of the Boys function are used to achieve a minimal number of floating-point operations. Two similar algorithms are derived by amplifying the benefits of two strategies previously proposed by other groups (Gill et al., Int. J. Quantum Chem. 1991, 40, 745 and Ishida, Int. J. Quantum Chem. 1996, 59, 209).

  4. Software News and Updates

    1. Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model

      Justin A. Lemkul, Benoît Roux, David van der Spoel and Alexander D. MacKerell Jr.

      Article first published online: 12 MAY 2015 | DOI: 10.1002/jcc.23937

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      Polarizable force fields represent the new generation in biomolecular simulation. In the Drude oscillator model, additional particles are attached to atoms in the system to represent electronic degrees of freedom. These simulations are more expensive than those done with traditional force fields, and to this end the powerful GROMACS software package has been extended to include algorithms necessary to efficiently simulate polarizable systems, enabling long-scale simulations of increasingly informative and accurate biomolecular models.

  5. Full Papers

    1. Nucleic acid reactivity: Challenges for next-generation semiempirical quantum models

      Ming Huang, Timothy J. Giese and Darrin M. York

      Article first published online: 6 MAY 2015 | DOI: 10.1002/jcc.23933

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      A series of semiempirical models have been tested against a wide range of datasets relevant to RNA catalysis, including: proton affinities and polarizabilities, nucleobase dimers, dimethyl phosphate anion conformations, nucleoside sugar and glycosidic torsion conformations, and RNA phosphoryl transfer model reactions through comparisons with high-level benchmark calculations. The assessment of semiempirical models provides guidelines for their range of application as well as insight for their improvement.

    2. The competition of Y⋯o and X⋯n halogen bonds to enhance the group V σ-hole interaction in the NCY⋯o[DOUBLE BOND]PH3⋯NCX and O[DOUBLE BOND]PH3⋯NCX⋯NCY (X, Y[DOUBLE BOND]F, Cl, and Br) complexes

      Wei Li, Yanli Zeng, Xiaoyan Li, Zheng Sun and Lingpeng Meng

      Article first published online: 27 APR 2015 | DOI: 10.1002/jcc.23922

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      In this work, the complexes O[DOUBLE BOND]PH3⋯NCX, NCY⋯O[DOUBLE BOND]PH3⋯NCX, and O[DOUBLE BOND]PH3⋯NCX⋯NCY (X, Y[DOUBLE BOND]F, Cl, Br) were designed to investigate the enhancing effects of Y⋯O and X⋯N halogen bonds on the P⋯N Group V σ-hole interaction. The Y⋯O halogen bonds affect the σ-hole region (decreased density region) outside the phosphorus atom more than the P⋯N internuclear region (increased density region outside the nitrogen atom), while it is contrary for the X⋯N halogen bonds.

    3. Inter- and intramolecular CF···c[DOUBLE BOND]o interactions on aliphatic and cyclohexane carbonyl derivatives

      Rodrigo A. Cormanich, Roberto Rittner, David O'Hagan and Michael Bühl

      Article first published online: 23 APR 2015 | DOI: 10.1002/jcc.23918

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      Prototypical inter- and intramolecular CF···C[DOUBLE BOND]O interactions are assessed computationally at the B3LYP-D3 level. The interactions are noticeable in intermolecular complexes 1, where they can amount to stabilizations around about 1 kcal mol, however, they are not strong enough to dominate conformational preferences in organofluorine derivatives such as 2 - 4.

    4. Theoretical and experimental investigation of crown/ammonium complexes in solution

      Andreas J. Achazi, Larissa K. S. von Krbek, Christoph A. Schalley and Beate Paulus

      Article first published online: 13 APR 2015 | DOI: 10.1002/jcc.23914

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      Gibbs energies of association inline image of monovalent crown/ammonium complexes in solution are calculated with DFT-D3(BJ) and the continuum solvation model COSMO-RS. For comparison, experimental data are obtained by isothermal titration calorimetry. Calculated and measured Gibbs energies of association inline image in solution agree well.

    5. From small fullerenes to the graphene limit: A harmonic force-field method for fullerenes and a comparison to density functional calculations for Goldberg–Coxeter fullerenes up to C980

      Lukas N. Wirz, Ralf Tonner, Andreas Hermann, Rebecca Sure and Peter Schwerdtfeger

      Article first published online: 26 MAR 2015 | DOI: 10.1002/jcc.23894

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      A general force field is introduced which works for all fullerene isomers. It leads to structures and zero-point vibrational energy contributions in very good agreement to more expensive quantum theoretical calculations. The graphene limit is well represented by the growth of Goldberg-Coxeter transforms of C20.

    6. Prediction of the crystal packing of di-tetrazine-tetroxide (DTTO) energetic material

      Jose L. Mendoza-Cortes, Qi An, William A. Goddard III, Caichao Ye and Sergey Zybin

      Article first published online: 18 MAR 2015 | DOI: 10.1002/jcc.23893

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      The two most stable isomers of Di-tetrazine-tetroxide (DTTO), c1 and c2, were used to predict the most stable polymorphs of DTTO. For the c1 isomer, the most stable polymorph has P212121 space group with a density of 1.96 g/cm3. Conversely, for the c2 isomer, the most stable polymorph has Pbca space group with a density of 1.98 g/cm3. These predicted densities are among the highest of current energetic materials.

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