Journal of Computational Chemistry
© Wiley Periodicals, Inc.
Edited By: Charles L. Brooks III, Masahiro Ehara, Gernot Frenking, and Peter R. Schreiner
Impact Factor: 3.589
ISI Journal Citation Reports © Ranking: 2014: 36/157 (Chemistry Multidisciplinary)
Online ISSN: 1096-987X
Recently Published Articles
- The Cu2O2 torture track for a real-life system: [Cu2(btmgp)2O2]2+ oxo and peroxo species in density functional calculations†
Martin Rohrmüller, Alexander Hoffmann, Christian Thierfelder, Sonja Herres-Pawlis and Wolf Gero Schmidt
Article first published online: 7 JUL 2015 | DOI: 10.1002/jcc.23983
Density functional theory calculations of the equilibrium geometry, vibrational modes, ionization energies, electron affinities, and optical response of [Cu2(btmgp)2(μ-O)2]2+ (oxo) and [Cu2(btmgp)2(μ-η2:η2-O2)]2+ (peroxo) are presented. Particular attention is paid to the modification of the electronic structure, optical transitions, and excited-state energies along the transition path between the oxo and peroxo species. Charge decomposition and natural transition orbital analyses are used for obtaining microscopic insight into the molecular orbital interactions.
- Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis
Junchao Xia, William F. Flynn, Emilio Gallicchio, Bin W. Zhang, Peng He, Zhiqiang Tan and Ronald M. Levy
Article first published online: 7 JUL 2015 | DOI: 10.1002/jcc.23996
We present the ASyncRE methodology to perform large-scale replica exchange molecular dynamics (REMD) simulations asynchronously on grid computing networks consisting of heterogeneous and distributed computing environments as well as on homogeneous high-performance clusters, such as NSF XSEDE clusters and BOINC distributed computing networks at Temple University and Brooklyn College at CUNY. We also propose several ways to improve the efficiency of REMD simulations in the context of the ASyncRE methodology.
- A theoretical study of imine hydrocyanation catalyzed by halogen-bonding
Norah Heinz, Michael Dolg and Albrecht Berkessel
Article first published online: 7 JUL 2015 | DOI: 10.1002/jcc.23999
A mechanistic description of an organocatalysis based on halogen-bonding: Possible reaction pathways of the hydrocyanation of an imine species catalyzed by CN activation by four different monodentate halogen-bond donors. The mechanism is evaluated and discussed in detail at the level of scalar-relativistic gradient-corrected density functional theory.
- Atomic-resolution dissection of the energetics and mechanism of isomerization of hydrated ATP-Mg2+ through the SOMA string method
Davide Branduardi, Fabrizio Marinelli and José D. Faraldo-Gómez
Article first published online: 7 JUL 2015 | DOI: 10.1002/jcc.23991
The mechanisms of isomerization of ATP-Mg2+ in solution are examined with three complementary enhanced-sampling simulation methods. The recently developed String Method with Optimal Molecular Alignment is used to identify and characterize the minimum free-energy paths for the major conformational transitions of the complex, in a 48-dimensional space. This analysis reveals the driving forces controlling these isomerization mechanisms at single-atom resolution.
- Orthogonal sampling in free-energy calculations of residue mutations in a tripeptide: TI versus λ-LEUS
Noah S. Bieler and Philippe H. Hünenberger
Article first published online: 7 JUL 2015 | DOI: 10.1002/jcc.23984
λ-LEUS, a combination of λ-dynamics and local-elevation umbrella-sampling, is more efficient than thermodynamic integration, because the dynamical variation of the alchemical variable λ opens up pathways to circumvent barriers in the orthogonal space.