Journal of Computational Chemistry
Copyright © 2013 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
- 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.
- Comparing distance metrics for rotation using the k-nearest neighbors algorithm for entropy estimation
David J. Huggins
Article first published online: 5 DEC 2013 | DOI: 10.1002/jcc.23504
Computing the distance between two different orientations of a molecule is useful for statistical mechanical applications. A number of distance metrics have been used, and this study considers the utility of different distance metrics in entropy estimation using the k-nearest neighbors algorithm. The results identify quaternion metrics as superior to a metric based on the Euler angles and demonstrate their superiority over a histogram method.
- Multireference space without first solving the configuration interaction problem
Vitaly N. Glushkov and Xavier Assfeld
Article first published online: 3 DEC 2013 | DOI: 10.1002/jcc.23502
A method is presented for generating a compact multireference space for the ground and excited states without first solving the configuration interaction problem. The proposed scheme is applied to small molecules to illustrate and calibrate calculations. The expressions for the second-order corrections of many-body perturbation theory based on this multireference space keep the computational advantages of the genuine Møller–Plesset scheme.