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
- Grid-based algorithm to search critical points, in the electron density, accelerated by graphics processing units (pages 2272–2278)
Raymundo Hernández-Esparza, Sol-Milena Mejía-Chica, Andy D. Zapata-Escobar, Alfredo Guevara-García, Apolinar Martínez-Melchor, Julio-M. Hernández-Pérez, Rubicelia Vargas and Jorge Garza
Article first published online: 25 OCT 2014 | DOI: 10.1002/jcc.23752
Grid-based methods are quite convenient to search for critical points on systems that exhibit non-nuclear attractors. However, these methods are computationally expensive. An efficient algorithm with good scaling on central processing units is proposed. The algorithm has better performance when implemented on graphics processing units (GPUs), even in GPUs not dedicated for high-performance computing.
- 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.