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 barrier to the methyl rotation in Cis-2-butene and its isomerization energy to Trans-2-butene, revisited
Chérif F. Matta, SeyedAbdolreza Sadjadi, Dale A. Braden and Gernot Frenking
Article first published online: 18 NOV 2015 | DOI: 10.1002/jcc.24223
Atomic origin of the locally stabilizing H⋯H contact in cis-2-butene from virial QTAIM atomic energies along the potential energy surface of methyl rotation, i.e., in terms of atomic sub-potential energy surfaces.
- A highly efficient hybrid method for calculating the hydration free energy of a protein
Hiraku Oshima and Masahiro Kinoshita
Article first published online: 17 NOV 2015 | DOI: 10.1002/jcc.24253
Although the hydration free energy (HFE) is one of the most important factors in studies on the structural stability of a protein, its calculation is significantly difficult in computational cost and accuracy. We develop a new method for calculating the HFE by combining the generalized Born model and the morphometric approach. Our method gives almost the same result as that from the three-dimensional reference interaction site model (3D-RISM) theory with drastic reduction of computational cost.
- Shift-and-invert parallel spectral transformation eigensolver: Massively parallel performance for density-functional based tight-binding
Murat Keçeli, Hong Zhang, Peter Zapol, David A. Dixon and Albert F. Wagner
Article first published online: 17 NOV 2015 | DOI: 10.1002/jcc.24254
Massively parallel supercomputers can extend the size of systems that we can study with quantum chemistry methods. However, the eigenvalue problem remains the bottleneck of scalability for density-functional based tight-binding (DFTB) or semi-empirical molecular orbital methods. We present a sparse eigensolver that enables DFTB calculations for systems with more than 100,000 atoms utilizing more than 200,000 CPU cores.
- Revisiting the concept of the (a)synchronicity of diels-alder reactions based on the dynamics of quasiclassical trajectories
Miguel A. F. de Souza, Elizete Ventura, Silmar A. do Monte, José M. Riveros and Ricardo L. Longo
Article first published online: 17 NOV 2015 | DOI: 10.1002/jcc.24245
Model Diels-Alder cycloaddition reactions were studied by static and dynamics approaches to establish the (a)synchronous character of the concerted mechanism. The use of static criteria, such as the asymmetry of the TS geometry, for classifying and quantifying the (a)synchronicity of the concerted reaction mechanism provides contradictory results and conclusions when compared to the dynamics approach.
- Self-consistent field for fragmented quantum mechanical model of large molecular systems
Yingdi Jin, Neil Qiang Su, Xin Xu and Hao Hu
Article first published online: 17 NOV 2015 | DOI: 10.1002/jcc.24252
Fragment-based, linear-scaling, quantum chemistry methods hold great potential for application in accurate simulations of complex molecular systems. Because of the coupled inter-fragment interactions, however, conventional fragment methods often employ a dual-layer SCF scheme to converge both the intra- and inter-fragment interactions. The total number of fragment SCF iterations displays a size-dependence to the target molecule. A new global SCF scheme developed here shows excellent performance over a broad range of molecular sizes and is applicable to other fragment methods.