Journal of Computational Chemistry

Cover image for Vol. 35 Issue 13

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: 3.835

ISI Journal Citation Reports © Ranking: 2012: 34/152 (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. Using operators to expand the block matrices forming the Hessian of a molecular potential

      Martin Carlsen

      Article first published online: 16 APR 2014 | DOI: 10.1002/jcc.23609

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      Compact expressions for the derivatives of a molecular potential are important for use in theoretical and practical applications. In this work, the second-order derivatives are expanded in terms of operators. This leads to a new set of formulas that can be implemented efficiently in high-level programming languages.

    2. SN1-SN2 and SN2-SN3 mechanistic changes revealed by transition states of the hydrolyses of benzyl chlorides and benzenesulfonyl chlorides

      Shinichi Yamabe, Guixiang Zeng, Wei Guan and Shigeyoshi Sakaki

      Article first published online: 14 APR 2014 | DOI: 10.1002/jcc.23607

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      Transition states of hydrolysis reactions Z[BOND]C6H4[BOND]X[BOND]Cl are investigated with specific water molecules (n = 6, 9, 11, 17, 23, and 29), where X = CH2, and SO2 and Z = O2N, Cl, H, H3C, and H3CO. In the case of a large n value and an electron-donating Z group, the hydrolysis reaction occurs through a SN2 mechanism. However, the combination of a small n value and an electron-withdrawing Z group converts the reaction mechanism to SN3.

    3. gWEGA: GPU-accelerated WEGA for molecular superposition and shape comparison

      Xin Yan, Jiabo Li, Qiong Gu and Jun Xu

      Article first published online: 11 APR 2014 | DOI: 10.1002/jcc.23603

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      A graphic processing unit (GPU)-accelerated weighted Gaussian algorithm for shape and/or pharmacophore features-based molecular superimposing is reported. The algorithm can search more than 55 million three-dimensional structures per second with multiple GPU nodes.

  2. Software News and Updates

    1. ALMOST: An all atom molecular simulation toolkit for protein structure determination

      Biao Fu, Aleksandr B. Sahakyan, Carlo Camilloni, Gian Gaetano Tartaglia, Emanuele Paci, Amedeo Caflisch, Michele Vendruscolo and Andrea Cavalli

      Article first published online: 27 MAR 2014 | DOI: 10.1002/jcc.23588

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      Almost” (all atom molecular simulation toolkit) is an open source computational package for the structure determination and analysis of biomolecules. Almost provides tools for the molecular structure determination using various types of experimental measurements as conformational restraints and methods for the analysis of structural and dynamical properties of complex molecular systems.

  3. Full Papers

    1. Analyzing the electric response of molecular conductors using “electron deformation” orbitals and occupied-virtual electron transfer

      Marcos Mandado and Nicolás Ramos-Berdullas

      Article first published online: 27 MAR 2014 | DOI: 10.1002/jcc.23595

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      Electron deformation orbitals and occupied-virtual electron transfer induced by a constant external electric perturbation provide an orbital picture of the charge transfer process. The proposed methodology is qualitatively related to the band model of conductivity and allows discernment between good and poor unimolecular conductors in terms of their electronic structure.

    2. A multiple time step scheme for multiresolved models of Macromolecules

      Nicodemo Di Pasquale, Richard J. Gowers and Paola Carbone

      Article first published online: 26 MAR 2014 | DOI: 10.1002/jcc.23594

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      In the dual-resolved model, bead–bead and atom–atom interactions are sampled with two different timestep values. For k timesteps, bead–bead forces are approximated with their Taylor expansion:

    3. Assessment of the orbital-optimized coupled-electron pair theory for thermochemistry and kinetics: Improving on CCSD and CEPA(1)

      Emine Soydaş and Uğur Bozkaya

      Article first published online: 25 MAR 2014 | DOI: 10.1002/jcc.23592

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      An assessment of the orbital-optimized coupled-electron pair theory [or simply “optimized CEPA(0)”, OCEPA(0)] [Bozkaya and Sherrill, J. Chem. Phys., 2013, 139, 054104] for thermochemistry and kinetics is presented. Our results demonstrate that the OCEPA(0) method is quite helpful for problematic open-shell systems and transition-states as well as for closed-shell molecules.

    4. a new perspective of shape recognition to discover the phase transition of finite-size clusters

      Po-Jen Hsu

      Article first published online: 23 MAR 2014 | DOI: 10.1002/jcc.23593

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      An ultrafast shape recognition technique was applied to analyze the phase transition of finite-size clusters. The shape of clusters is the unique property that distinguishes clusters from bulk systems, and is comprehensive and natural for structural analysis. The probability contour and the implementation of the substructure provide insightful atom/shell-resolved perspectives. The method can considerably simplify the tedious trajectory analysis and is efficient in any type of finite-size system, including polymers and nanostructures.

    5. Oxygen adsorption characteristics on hybrid carbon and boron-nitride nanotubes

      Haining Liu and C. Heath Turner

      Article first published online: 23 MAR 2014 | DOI: 10.1002/jcc.23589

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      Hybrid carbon nanotube and boron-nitride nanotube materials have been recently synthesized in the lab. Here, DFT calculations indicate that molecular oxygen adsorption is significantly enhanced on these hybrid carbon and boron-nitride nanotube materials, versus on pristine nanotubes. Furthermore, the large change in the band gap upon oxygen adsorption may provide unique sensing capabilities, in addition to other catalytic properties, motivating further experimental investigations.

    6. Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations

      Jaewoon Jung, Takaharu Mori and Yuji Sugita

      Article first published online: 23 MAR 2014 | DOI: 10.1002/jcc.23591

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      A new hybrid (MPI+OPENMP) parallelization scheme is developed for molecular dynamics (MD) simulations introducing a cell-wise version of the midpoint method, named the “midpoint cell method.” This method retains the advantages of the original midpoint method for MPI parallelization, and it allows efficient shared memory parallelization by grouping particle data cell-wise and distributing cell pairs over OPENMP threads. The parallel performance of the midpoint cell method on a K computer shows scalability up to 32,768 cores for a system of 1 million atoms. One MD step with long-range interaction can be calculated within 4.5 ms.

    7. Identifying essential pairwise interactions in elastic network model using the alpha shape theory

      Fei Xia, Dudu Tong, Lifeng Yang, Dayong Wang, Steven C. H. Hoi, Patrice Koehl and Lanyuan Lu

      Article first published online: 19 MAR 2014 | DOI: 10.1002/jcc.23587

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      The image shows a comparison of the elastic networks generated by the conventional cutoff-based approach (top) and alpha shape theory (bottom). The protein's Protein Data Bank code is 1LTU. The figure shows the detailed spring connections for the protrusion part of the protein, as elastic network models based on cutoffs have difficulty in accurately reproducing the experimental B-factors in this region. Excellent agreement with the experimental B-factor is achieved after removing a few pairwise connections according to the alpha shape theory.

    8. Quantitative investigation of bonding characteristics in ternary Zintl anions. Charge and energy analysis of [Sn2E152(ZnPh)] (E15 = Sb, Bi) and [Sn2Sb5(ZnPh)2]3−

      Marc Raupach, Stefanie Dehnen and Ralf Tonner

      Article first published online: 24 FEB 2014 | DOI: 10.1002/jcc.23560

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      Density functional theory based analysis of the chemical bonding in ternary Sn/(Sb,Bi)/Zn Zintl anions outlines the importance of π-bonding contributions, polarized σ-bonding and significant electrostatic effects. This leads to a quantitative description of the metal–ligand interaction in this interesting compound class and has implications on ligand design for the stabilization of Zintl cages.

  4. Rapid Communication

    1. Toward product control in ring-opening oligomerization of 9H-9-borafluorenes

      Hui Zhu and Zheng-Wang Qu

      Article first published online: 7 FEB 2014 | DOI: 10.1002/jcc.23555

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      The remarkable substituent effects of the bulky tert-butyl-substitution on the ring-opening oligomerization reactivity of 9H−9-borafluorene compounds are mainly due to the evidently increased trimerization barrier from intermediate G on substitution. Both G and H are actually formed from ring-opening aryl exchange through double B[BOND]C[BOND]B bridges and, thus, cannot support the Köster's postulate. Experimentally desired polymerization channels are expected at a controlled heating, opening the way toward higher oligomers with improved thermal stability.

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