Journal of Computational Chemistry
© Wiley Periodicals, Inc.
Edited By: Charles L. Brooks III, Masahiro Ehara, Gernot Frenking, and Peter R. Schreiner
Impact Factor: 3.648
ISI Journal Citation Reports © Ranking: 2015: 41/163 (Chemistry Multidisciplinary)
Online ISSN: 1096-987X
Recently Published Articles
- On the formation of smaller p-block endohedral fullerenes: Bonding analysis in the E@C20 (E = Si, Ge, Sn, Pb) series from relativistic DFT calculations
Alvaro Muñoz-Castro and R. Bruce King
Version of Record online: 20 APR 2017 | DOI: 10.1002/jcc.24809
The plausible encapsulation of main-group element in the smaller fullerene is evaluated, discussing electronic, bonding, and spectroscopic characteristics.
- Are induced fit protein conformational changes caused by ligand-binding predictable? A molecular dynamics investigation
Cen Gao, Jeremy Desaphy and Michal Vieth
Version of Record online: 16 APR 2017 | DOI: 10.1002/jcc.24714
Conventional MD was run on 39 apo structures (no ligand), and the resulting trajectories were compared to a set of 147 holo X-ray structures (ligand-bound). The simulation results did not perform better than using the normalized crystallographic structural factors as predictors of active-site rigid residues (87% predictive power) and mobile residues (47% predictive power). These results suggest potential issues in the use of unligated simulation frames directly for drug design applications such as ligand docking.
- A rapid solvent accessible surface area estimator for coarse grained molecular simulations
Shuai Wei, Charles L. Brooks III and Aaron T. Frank
Version of Record online: 16 APR 2017 | DOI: 10.1002/jcc.24709
A fast and straightforward method is developed that predicts residue-wise solvent accessible surface areas (SASAs) from coordinates of protein structures. The method, Protein-CSolvent Accessibilities or PCASA, should find utility as a tool for energetic and structural analysis of coarse-grained protein models. To ensure that the method was not biased toward native-like (folded) structures, PCASA is trained on a large dataset containing both folded and unfolded protein conformations. The resulting model is found to accurately recapitulate all-atom reference SASAs.
- Comparing the performance of TD-DFT and SAC-CI methods in the description of excited states potential energy surfaces: An excited state proton transfer reaction as case study (pages 1084–1092)
Marika Savarese, Umberto Raucci, Ryoichi Fukuda, Carlo Adamo, Masahiro Ehara, Nadia Rega and Ilaria Ciofini
Version of Record online: 13 APR 2017 | DOI: 10.1002/jcc.24780
The performances, in the description of excited state potential energy surfaces, of several density functional approximations representative of the currently most applied exchange correlation functionals’ families have been tested with respect to post Symmetry Adapted Cluster-Configuration Interaction results. An experimentally well-characterized intermolecular excited state proton transfer reaction has been considered as test case showing the delicate balance between solvent effects and electronic structure description needed for the correct recovering of excited states ordering.
- Density functional theory study of mechanism of epoxy-carboxylic acid curing reaction (pages 1093–1102)
Uyen Q. Ly, My-Phuong Pham, Maurice J. Marks and Thanh N. Truong
Version of Record online: 13 APR 2017 | DOI: 10.1002/jcc.24779
Epoxy-based polymers with an imperative set of physical properties has established billion-USD business whereas curing by carboxylic acid forms an important class of these materials. Despite its importance, fundamental understanding of its mechanism at the molecular level is rather limited. This study provides for the first time a full underlying atomistic detailed picture of epoxy-carboxylic acid curing reactions from first principles.