Journal of Computational Chemistry

Cover image for Vol. 35 Issue 6

5 March 2014

Volume 35, Issue 6

Pages i–vi, 415–505

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. You have free access to this content
      Cover Image, Volume 35, Issue 6 (pages i–ii)

      Version of Record online: 4 FEB 2014 | DOI: 10.1002/jcc.23540

      Thumbnail image of graphical abstract

      The problem of the electrostatic potential is present in chemical and atomic/molecular simulations. On page 427, Pablo García-Risueño et al. present an analysis of different methods to calculate the classical electrostatic Hartree potential created by charge distributions. This work may enable more accurate and efficient simulations, helping scientists to tackle many new systems. The cover illustrates the performance competition of Poisson solvers. The image is courtesy of Forschungzentrum Jülich, and provided by Pablo García-Risueño, Joseba Alberdi-Rodriguez, and Jesús Pérez-Amor. The velocimeter creative commons is by Anderson Mancini.

    2. You have free access to this content
      Cover Image, Volume 35, Issue 6 (pages iii–iv)

      Version of Record online: 4 FEB 2014 | DOI: 10.1002/jcc.23541

      Thumbnail image of graphical abstract

      The cover shows the bimolecular substitution (SN2) reaction of CH3F + OH in an aqueous solution along its reaction pathway. The purple curve represents the free energy reaction pathway in a water solution. Structures of the reactant complex, transition state, and product complex in water are shown along the reaction pathway from left to right. The transition state is the highest point on the curve. On page 445, Jie Chen et al. present a system containing 1418 water molecules in the solution environment.

    3. You have free access to this content
      Cover Image, Volume 35, Issue 6 (pages v–vi)

      Version of Record online: 4 FEB 2014 | DOI: 10.1002/jcc.23532

      Thumbnail image of graphical abstract

      A polarizable dipole–dipole interaction model is established to estimate the hydrogen bond distances and interaction energies for hydrogen-bonded complexes containing N[BOND]H···O=C and C[BOND]H···O=C hydrogen bonds. The chemical bonds N[BOND]H, C=O, and C[BOND]H are regarded as bond dipoles. The dipole–dipole interaction may be attractive or repulsive depending on the relative orientation of the two bond dipoles. The calculations by Shu-Shi Li et al. on page 415 show that this model can accurately and efficiently yield hydrogen bond distances and interaction energies for N[BOND]H···O=C and C[BOND]H···O=C hydrogen-bonded complexes.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. A polarizable dipole–dipole interaction model for evaluation of the interaction energies for N[BOND]H···O[DOUBLE BOND]C and C[BOND]H···O[DOUBLE BOND]C hydrogen-bonded complexes (pages 415–426)

      Shu-Shi Li, Cui-Ying Huang, Jiao-Jiao Hao and Chang-Sheng Wang

      Version of Record online: 30 OCT 2013 | DOI: 10.1002/jcc.23473

      Thumbnail image of graphical abstract

      A polarizable dipole–dipole interaction model is established to estimate the hydrogen bond distances and interaction energies for hydrogen-bonded complexes containing the N[BOND]H···O[DOUBLE BOND]C and C[BOND]H··· O[DOUBLE BOND]C hydrogen bonds.

    2. A survey of the parallel performance and accuracy of Poisson solvers for electronic structure calculations (pages 427–444)

      Pablo García-Risueño, Joseba Alberdi-Rodriguez, Micael J. T. Oliveira, Xavier Andrade, Michael Pippig, Javier Muguerza, Agustin Arruabarrena and Angel Rubio

      Version of Record online: 19 NOV 2013 | DOI: 10.1002/jcc.23487

      Thumbnail image of graphical abstract

      The calculation of the electrostatic Hartree potential is nearly ubiquitous in computational chemistry and physics. Although there are a number of methods to efficiently carry out this calculation, the advantages of these methods are often unclear, which can lead to serious bottlenecks when many cores are used for the calculation. To clarify their features, some of the most popular Hartree potential solvers are examined in terms of accuracy and efficiency, with a special emphasis on massive parallel scaling performance.

    3. A multilayered representation, quantum mechanical and molecular mechanics study of the CH3F + OH reaction in water (pages 445–450)

      Jie Chen, Yulong Xu and Dunyou Wang

      Version of Record online: 25 NOV 2013 | DOI: 10.1002/jcc.23498

      Thumbnail image of graphical abstract

      The bimolecular nucleophilic substitution (SN2) reaction of CH3F + OH [RIGHTWARDS ARROW] CH3OH + F is a fundamental reaction in organic chemistry and has been extensively studied in the gas phase. However, until now there have been no theoretical calculations for this reaction in an aqueous solution. A multi-layered representation, hybrid QM, and MM method is employed to study this reaction in water.

    4. Is the DPT tautomerization of the long A·G Watson–Crick DNA base mispair a source of the adenine and guanine mutagenic tautomers? A QM and QTAIM response to the biologically important question (pages 451–466)

      Ol'ha O. Brovarets', Roman O. Zhurakivsky and Dmytro M. Hovorun

      Version of Record online: 30 DEC 2013 | DOI: 10.1002/jcc.23515

      Thumbnail image of graphical abstract

      By bridging QM calculations with the quantum theory of atoms in molecules (QTAIM), the tautomerisation of the biologically important A·G DNA base mispair (C1 symmetry) into the A*·G* DNA base mispair (C1 symmetry) proceeds through the asynchronous concerted double proton transfer (DPT) via the non-planar transition state (TSA·G[LEFT RIGHT ARROW]A*·G*) with C1 symmetry. The nine key points, two of which are accidentally degenerative, are detected and analyzed for the first time. The A*·G* DNA base mispair has a dynamically unstable structure with an extremely short lifetime of 4.8·10−14 s, obtained at the MP2/cc-pVQZ//B3LYP/6–311++G(d,p) level of theory in a vacuum.

    5. Perturbative treatment of anharmonic vibrational effects on bond distances: An extended langevin dynamics method (pages 467–478)

      Tonghao Shen, Neil Qiang Su, Anan Wu and Xin Xu

      Version of Record online: 29 DEC 2013 | DOI: 10.1002/jcc.23516

      Thumbnail image of graphical abstract

      Guided by quantum perturbative theory, the Langevin dynamics is extended to cover zero-point energy and temperature-dependent vibrational effects on molecular structures. The present method shows a substantial improvement over the classical molecular dynamics, which ceases to work for the hard mode when quantum effects are significant.

    6. Characterization of the potential energy surfaces of two small but challenging noncovalent dimers: (P2)2 and (PCCP)2 (pages 479–487)

      Eric Van Dornshuld and Gregory S. Tschumper

      Version of Record online: 9 JAN 2014 | DOI: 10.1002/jcc.23522

      Thumbnail image of graphical abstract

      Eight stationary points of the P2 dimer and six stationary points of the PCCP dimer are characterized with the second-order Møller–Plesset (MP2) electronic structure method. The canonical and explicitly correlated MP2 and CCSD(T) complete basis set limit binding energies are reported.

    7. A QM/MM study on the reaction pathway leading to 2-Aceto-2-hydroxybutyrate in the catalytic cycle of AHAS (pages 488–494)

      Leslie Sánchez, Gonzalo A. Jaña and Eduardo J. Delgado

      Version of Record online: 6 JAN 2014 | DOI: 10.1002/jcc.23523

      Thumbnail image of graphical abstract

      The reaction between the intermediate HEThDP- and 2-ketobutyrate, in the third step of the catalytic cycle of acetodydroxy acid synthase (AHAS), is addressed from a theoretical point of view by hybrid QM/MM calculations. The results show that the reaction occurs via a two-step mechanism corresponding to the carboligation and proton transfer in the first stage; and the product release in the second step.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. ChemNetworks: A complex network analysis tool for chemical systems (pages 495–505)

      Abdullah Ozkanlar and Aurora E. Clark

      Version of Record online: 5 DEC 2013 | DOI: 10.1002/jcc.23506

      Thumbnail image of graphical abstract

      ChemNetworks converts chemical systems into network graphs that can then be data-mined for short- and long-range patterns and their lifetimes. Correlations can be made between network organization/stability and the reactivity therein. This has implications for the study of a wide variety of processes, including phase changes, aggregation, interfacial structure, mixed media, and so forth.

SEARCH

SEARCH BY CITATION