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
- Energy exchange network of inter-residue interactions within a thermally fluctuating protein molecule: A computational study
Takakazu Ishikura, Yuki Iwata, Tatsuro Hatano and Takahisa Yamato
Article first published online: 6 JUL 2015 | DOI: 10.1002/jcc.23989
The “crosstalk” among interacting residues in a small globular protein, PDZ3 (right bottom), was represented as a graph of energy exchange network (EEN). The removal of its C-terminal helix (red cartoon) is known to significantly decrease ligand affinity without changing the overall protein structure; nevertheless, the helix constitutes an essential part of the graph (black rounded rectangles), indicating that the EEN graph captured key features of the physical properties of PDZ3.
- Constrained numerical gradients and composite gradients: Practical tools for geometry optimization and potential energy surface navigation
Michael Stenrup, Roland Lindh and Ignacio Fdez. Galván
Article first published online: 3 JUL 2015 | DOI: 10.1002/jcc.23987
Geometry optimization, a central problem in computational chemistry, is ideally performed using analytical gradients. However, for many high-level methods such gradients are not available and one has to resort to more expensive numerical differentiation. In this work, it is shown how constraints used to simplify the optimization problem can also be used to speed-up an underlying numerical gradient calculation. In addition, a method to combine numerical and analytical differentiation is proposed, allowing efficient, unconstrained optimization.
- Benchmark calculations of the adsorption of aromatic molecules on graphene
Weizhou Wang, Tao Sun, Yu Zhang and Yi-Bo Wang
Article first published online: 2 JUL 2015 | DOI: 10.1002/jcc.23994
M05-2X, M06-2X, M11-L, and N12 significantly underestimate the strengths of the adsorption of aromatic molecules on graphene. The best performing functionals are B97-D, B-LYP-D3, and ωB97X-D. The combination of SCS-SAPT0 and aug-cc-pVDZ performs very well for the energy component analysis of the adsorption of aromatic molecules on graphene.
- Structure and stability of noble gas bound EX3+ compounds (E = C, Ge, Sn, Pb; X = H, F, Cl, Br)
Sudip Pan, Diego Moreno, Sreyan Ghosh, Pratim K. Chattaraj and Gabriel Merino
Article first published online: 1 JUL 2015 | DOI: 10.1002/jcc.23986
Making a bond: (E = C-Pb; X = H, F-Br) could bind noble gas atoms, particularly Ar to Rn, quite effectively. The π back-bonding causing X E electron transfer plays an important role in deciding their noble gas binding ability.
- Four-component relativistic DFT calculations of 77Se NMR chemical shifts: A gateway to a reliable computational scheme for the medium-sized organoselenium molecules
Yury Yu. Rusakov and Leonid B. Krivdin
Article first published online: 1 JUL 2015 | DOI: 10.1002/jcc.23993
A versatile high-accuracy computational scheme for the 77Se NMR chemical shifts of the medium-sized organoselenium compounds is suggested within a framework of a full four-component relativistic density functional theory. The main accuracy factors (functionals, basis sets, relativistic geometry, vibrational corrections, and solvent effects) are addressed.