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: 3.835
ISI Journal Citation Reports © Ranking: 2012: 34/152 (Chemistry Multidisciplinary)
Online ISSN: 1096-987X
Recently Published Articles
- TiS2 and ZrS2 single- and double-wall nanotubes: First-principles study
Andrei V. Bandura[a] and Robert A. Evarestov[a]
Article first published online: 10 DEC 2013 | DOI: 10.1002/jcc.23508
The structure and stability of TiS2 and ZrS2 nanolayers and nanotubes are studied by hybrid DFT. A small but noticeable deviation of the cross-section of the external walls is found in the armchair-like double-wall nanotubes from the completely cylindrical shape. The comparison of sulfide-based and oxide-based nanotubes with hexagonal morphology shows that the formation energy of the disulfide nanotubes is less than the formation energy of the dioxide nanotubes.
- LEAP: Highly accurate prediction of protein loop conformations by integrating coarse-grained sampling and optimized energy scores with all-atom refinement of backbone and side chains
Shide Liang, Chi Zhang and Yaoqi Zhou
Article first published online: 10 DEC 2013 | DOI: 10.1002/jcc.23509
Loop prediction is an integral part of homolog modeling and protein structure prediction. The loop prediction by energy-assisted protocol technique combines coarse-grained scoring, backbone refinement, and all-atom minimization for improved loop prediction. © 2013 Wiley Periodicals, Inc.
- Why is N···Be distance of NH3H+···DBeH shorter than that of NH3D+···HBeH? paradoxical geometrical isotope effects for partially isotope-substituted dihydrogen-bonded isotopomers
Taro Udagawa and Masanori Tachikawa
Article first published online: 9 DEC 2013 | DOI: 10.1002/jcc.23505
Geometrical isotope effect (GIE), which is induced by isotope-substitution of hydrogen, in dihydrogen-bonded NH3X+···YBeH (X, Y = H, D, and T) systems are systematically analyzed using the ab initio multi-component MO method. Isotope effects of interaction energies and magnetic shieldings are also analyzed. Authors found that GIE of RN···Be can be explained by the cooperative effect of primary and secondary GIEs and the dihydrogen-bonded distance becomes shorter by heavier Y and lighter X isotope-substitution.
- Decoding the components of dynamics in three-domain proteins
Mateusz Maciejewski, Paul N. Barlow and Nico Tjandra
Article first published online: 9 DEC 2013 | DOI: 10.1002/jcc.23510
The feasibility and limitations of describing the motional behavior of three-domain proteins in which the domains are linearly connected are studied via Brownian dynamics simulations. Two limiting cases occur: the domain motion is independent when the domains interact via weak potentials, and interdependent when these potentials are strong. Dynamics in three-domain systems is completely described by model-free formalism.
- ChemNetworks: A complex network analysis tool for chemical systems
Abdullah Ozkanlar and Aurora E. Clark
Article first published online: 5 DEC 2013 | DOI: 10.1002/jcc.23506
ChemNetworks converts chemical systems into network graphs that can then be data-mined for short- and long-range patterns and their lifetimes. Correlations can be made between network organization/stability and the reactivity therein. This has implications for the study of a wide variety of processes, including phase changes, aggregation, interfacial structure, mixed media and so forth.