Journal of Computational Chemistry

Cover image for Vol. 35 Issue 9

5 April 2014

Volume 35, Issue 9

Pages i–vi, 683–764

  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 9 (pages i–ii)

      Article first published online: 25 FEB 2014 | DOI: 10.1002/jcc.23571

      Thumbnail image of graphical abstract

      Classical and ab initio molecular dynamics in the presence and absence of the explicit tetrahydrofuran (THF) solvent, and associated continuum methods, have shown the importance of explicit solvation in accurately modeling the structural, energetic, and dynamical properties of a chemical-hydrogen storage catalyst. The cover shows the bi-functional Ru catalyst surrounded by THF molecules from classical MD, as presented by Sateesh Bandaru, Niall J. English, and J. M. D. MacElroy on page 683.

    2. You have free access to this content
      Cover Image, Volume 35, Issue 9 (pages iii–iv)

      Article first published online: 25 FEB 2014 | DOI: 10.1002/jcc.23572

      Thumbnail image of graphical abstract

      On page 692, Hugh S. C. Martin, Shantenu Jha, and Peter V. Coveney explore the use of two popular free energy calculation methodologies in a nucleotide–nanopore translocation system, using the α-hemolysin nanopore. The cover shows a cross-section of the protein pore αHL (green) with key features inside the pore interior including the wide inner chamber, a constriction about half way down the pore, followed by the transmembrane barrel that spans the lipid bilayer. The translocating molecule, in this example a polynucleotide (pink), is positioned being led down by the 3'-end.

    3. You have free access to this content
      Cover Image, Volume 35, Issue 9 (pages v–vi)

      Article first published online: 25 FEB 2014 | DOI: 10.1002/jcc.23573

      Thumbnail image of graphical abstract

      The cover shows the conversion between different states by the minimum energy crossing point (MECP). For studies of the organometallic chemistry involving different spin states, MECPs are often considered to be a critical point in dynamics simulations and reaction path computations. On page 703, Kun Liu, Yu-Xue Li, Jia-Ling Su, and Bin Wang report on the reliability of DFT methods to predict electronic structures and MECPs for the [FeIVO] unit by taking the multiconfiguration quasidegenerate perturbation theory (MCQDPT) method as a reference.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Implicit and explicit solvent models for modeling a bifunctional arene ruthenium hydrogen-storage catalyst: A classical and ab initio molecular simulation study (pages 683–691)

      Sateesh Bandaru, Niall J. English and J. M. D. MacElroy

      Article first published online: 4 JAN 2014 | DOI: 10.1002/jcc.23514

      Thumbnail image of graphical abstract

      Classical and ab initio molecular dynamics in the presence and absence of an explicit tetrahydrofuran solvent, and associated continuum methods, have shown the importance of explicit solvation in accurately modeling the structural, energetic, and dynamical properties of a chemical-hydrogen storage catalyst. This is particularly the case for capturing the rich tapestry of hydrogen-bonding interactions. The image shows a gas-phase-optimized configuration on the left, and solvent-distorted examples on the right.

    2. You have full text access to this OnlineOpen article
      Comparative analysis of nucleotide translocation through protein nanopores using steered molecular dynamics and an adaptive biasing force (pages 692–702)

      Hugh S. C. Martin, Shantenu Jha and Peter V. Coveney

      Article first published online: 9 JAN 2014 | DOI: 10.1002/jcc.23525

      Thumbnail image of graphical abstract

      The translocation of nucleotide molecules across nanopores has attracted attention as a next-generation technique for sequencing DNA. Computer simulations can provide atomistic-level insight of important states and processes. Two computational methodologies in a nucleotide–nanopore translocation system are compared using the α-hemolysin nanopore. The first uses constant velocity-steered molecular dynamics with Jarzynski's equality; the second applies an adaptive biasing force, which has not previously been applied to the nucleotide–nanopore system.

    3. The reliability of DFT methods to predict electronic structures and minimum energy crossing point for [FeIVO](OH)2 models: A comparison study with MCQDPT method (pages 703–710)

      Kun Liu, Yu-Xue Li, Jia-Ling Su and Bin Wang

      Article first published online: 4 FEB 2014 | DOI: 10.1002/jcc.23535

      Thumbnail image of graphical abstract

      Due to the balance between speed and accuracy, DFT methods have been the most useful electronic structure methods for treating large organometallic systems. The reliability of DFT methods for predicting electronic structures and the minimum energy crossing point for the [FeIVO] unit are reported, taking the multiconfiguration quasidegenerate perturbation theory method as a reference. This work provides a basis for the further study of [FeIVO] chemistry.

    4. Microsecond simulations of DNA and ion transport in nanopores with novel ion–ion and ion–nucleotides effective potentials (pages 711–721)

      Pablo M. De Biase, Suren Markosyan and Sergei Noskov

      Article first published online: 12 FEB 2014 | DOI: 10.1002/jcc.23544

      Thumbnail image of graphical abstract

      Rapid DNA sequencing with biological nanopores is a technology with potential to revolutionize medical genomics. The rational design of nanopores with computational methods is hindered by the complexity of captured DNA dynamics. Presented here is an efficient algorithm for the development of effective potentials that can be used to directly study DNA and ion transport in nanopores. The algorithm performs on par with all-atom molecular dynamics simulations, while predicting experimentally measured residual currents and their nucleotide depends.

    5. The effect of the intermolecular potential formulation on the state-selected energy exchange rate coefficients in N2–N2 collisions (pages 722–736)

      Alexander Kurnosov, Mario Cacciatore, Antonio Laganà, Fernando Pirani, Massimiliano Bartolomei and Ernesto Garcia

      Article first published online: 17 FEB 2014 | DOI: 10.1002/jcc.23545

      Thumbnail image of graphical abstract

      The figure shows the quasiclassical trajectory probability of the (25, 25|26, 24) transition at T = 2000 K plotted as a function of the Jacobi angles θ1 and θ2 at the distance of maximum closeness between the two N2 molecules obtained both on the potential energy surface (PES)0 (lhs panel) and PES2 (rhs panel). The values obtained on PES2 show the dominance of I-like configurations resulting from the innermost location of the repulsive wall of INTERPOT-II (the intermolecular component of PES2) as typical of lower impact parameter collisions. This is less the case for collisions occurring on PES0 (with an intermolecular component of INTERPOT-I), which have a long-range attractive tail as typical of larger impact parameter collisions.

    6. Accessing the applicability of polarized protein-specific charge in linear interaction energy analysis (pages 737–747)

      Xiangyu Jia, Juan Zeng, John Z. H. Zhang and Ye Mei

      Article first published online: 5 FEB 2014 | DOI: 10.1002/jcc.23547

      Thumbnail image of graphical abstract

      The applicability of a new polarized charge model, termed delta restrained electrostatic potential, in predicting the protein–ligand binding affinity is investigated. In this charge model, a perturbation term is added to the mean-field library charge (e.g., AMBER charge) to capture the system dependence. Results from linear interaction energy studies of two systems show that this charge model can provide satisfactory binding free energies that are in high correlation with experimental measurements.

    7. Continuous symmetry measures for complex symmetry group (pages 748–755)

      Chaim Dryzun

      Article first published online: 6 FEB 2014 | DOI: 10.1002/jcc.23548

      Thumbnail image of graphical abstract

      The continuous symmetry measures methodology enables the estimation of symmetry contents of structures and relates them with other physical properties. A new approach allows the symmetry measure of any complex point group to be estimated. Error factors of the new approach are analyzed, and it is applied for the study of the symmetry of several simple systems.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Integrating open-source software applications to build molecular dynamics systems (pages 756–764)

      Bruce M. Allen, Paul K. Predecki and Maciej Kumosa

      Article first published online: 4 FEB 2014 | DOI: 10.1002/jcc.23537

      Thumbnail image of graphical abstract

      Molecular Dynamics Studio is a collection of integrated open-source software applications working together to aid researchers and students with molecular dynamics simulations. The integrated applications allow the researcher or student to draw three-dimensional molecules, to type atoms using the CFF91 force field, to generate an initial molecular dynamics cell, and to generate the large-scale atomic/molecular massively parallel simulator geometry input file. All three applications are integrated through the enhanced molecular machine part file created in this research.

SEARCH

SEARCH BY CITATION