Journal of Computational Chemistry
Copyright © 2014 Wiley Periodicals, Inc., A Wiley Company
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
Recently Published Articles
- 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
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).
- 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
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.
- 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
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.
- A spherical harmonic transform spectral analysis of a localized surface plasmon on a gold nano shell (pages 2225–2230)
Dan Berco and Chin-Kun Hu
Article first published online: 18 OCT 2014 | DOI: 10.1002/jcc.23741
The localized surface plasmon (LSP) modes of a gold nano shell (AuNS) having a silica core by means of discrete dipole approximation (DDA) and spherical harmonics transform for selected wavelengths is studied. An efficient solution is demonstrated for the near and intermediate field terms by the dyadic green function approach and determine the optical extinction efficiency by the far field term. The advantages of a spectral analysis are combined with DDA flexibility to solve an arbitrary-shaped model and demonstrate the LSP dominant mode wavelength dependency.
- 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
The phase transition of ammonia borane (NH3BH3), from a tetragonal I4mm ( ) phase with disordered orientation of hydrogen to an orthorhombic phase with Pmn21 ( ) 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.