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
- Sparsity-weighted outlier FLOODing (OFLOOD) method: Efficient rare event sampling method using sparsity of distribution
Ryuhei Harada, Tomotake Nakamura and Yasuteru Shigeta
Article first published online: 27 NOV 2015 | DOI: 10.1002/jcc.24255
Biologically rare events play important roles in understanding functions. To computationally reproduce them, Outlier FLOODing (OFLOOD) method is powerful, in which sparse distributions of biological states are detected as outliers and intensively resampled by MD simulations. As an extension, sparsity-weighted OFLOOD method is newly proposed, in which a hierarchical clustering defines ranks of outliers. Accordingly to the ranks, the confirmational resampling from outliers is performed, accerlarating the conformational sampling of bio-molecules.
- UV-photoexcitation and ultrafast dynamics of HCFC-132b (CF2ClCH2Cl)
Gessenildo Pereira Rodrigues, Elizete Ventura, Silmar Andrade do Monte and Mario Barbatti
Article first published online: 26 NOV 2015 | DOI: 10.1002/jcc.24260
HCFC-132b is an important industrial compound, with a strong impact on health and environment. Upon UV irradiation, it decomposes into dozens of different photoproducts. In this article, nonadiabatic dynamics simulation is used to explain how photo-decomposition takes place through the competition between diverse reaction pathways in the subpicosecond time scale.
- The barrier to the methyl rotation in Cis-2-butene and its isomerization energy to Trans-2-butene, revisited (pages 143–154)
Chérif F. Matta, Seyed Abdolreza 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.