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
- Assessing the accuracy of improved force-matched water models derived from Ab initio molecular dynamics simulations
Andreas Köster, Thomas Spura, Gábor Rutkai, Jan Kessler, Hendrik Wiebeler, Jadran Vrabec and Thomas D. Kühne
Version of Record online: 27 MAY 2016 | DOI: 10.1002/jcc.24398
The accuracy of water models derived from ab initio molecular dynamics simulations by means on an improved force-matching scheme is assessed for a large variety of different thermodynamic, transport and structural properties. It is found that although the resulting force-matched water models are typically less accurate than fully empirical force fields in predicting thermodynamic properties, they are nevertheless much more accurate than generally appreciated in reproducing the structure of liquid water.
- Reformulating the entropic contribution in molecular docking scoring functions
Version of Record online: 27 MAY 2016 | DOI: 10.1002/jcc.24397
In this contribution, in the context of the Rigid Rotor Harmonic Approximation (RRHO), a general mass and Planck's constant independent expression for the dissociation free energy in ligand–receptor systems is derived. The proposed RRHO expression features a systematically additive negative (anti-binding) entropic term depending on readily available ligand–receptor quantities, allowing to straightforwardly compute the standard dissociation free energy without resorting to expensive normal mode analysis or molecular dynamics-based approaches.
- Theoretical study of lithium ionic conductors by electronic stress tensor density and electronic kinetic energy density
Hiroo Nozaki, Yosuke Fujii, Kazuhide Ichikawa, Taku Watanabe, Yuichi Aihara and Akitomo Tachibana
Version of Record online: 27 MAY 2016 | DOI: 10.1002/jcc.24409
Material characterization scheme using the stress tensor density and kinetic energy density, which are based on the quantum field theory, is applied to the chemical bonds among lithium ionic conductors. Ionicity of bonding is found to be characterized by the intermediate pattern of stress tensor between covalent and metallic bonding, and in addition, by the morphology of the zero surface of kinetic energy density, called electronic interface.
- Ranking protein–protein docking results using steered molecular dynamics and potential of mean force calculations
Laura J. Kingsley, Juan Esquivel-Rodríguez, Ying Yang, Daisuke Kihara and Markus A. Lill
Version of Record online: 27 MAY 2016 | DOI: 10.1002/jcc.24412
Predicting how two proteins will bind to one another is a challenging task. This method combines protein–protein docking, steered molecular dynamics, and potential of mean force calculations to predict and evaluate protein–protein interactions.
- pKa prediction for acidic phosphorus-containing compounds using multiple linear regression with computational descriptors
Donghai Yu, Ruobing Du and Ji-Chang Xiao
Version of Record online: 24 MAY 2016 | DOI: 10.1002/jcc.24381
The relationship between experimental pKa and structure parameters were represented with a numerical equation, which were fitted by multiple linear regression with R2 = 0.9742 in training set, and tested with R2 = 0.9663 in test set. This result indicated that our model is accurate and effective in mathematics and chemistry respectively. Consequently, the pKa of Acidic Phosphorus-Containing Compounds is described appropriately with this method. And this conclusion is useful in designing new acidic phosphorus-containing compounds for rare earth extraction.