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
- Transferability and additivity of dihedral parameters in polarizable and nonpolarizable empirical force fields
Marie Zgarbová, Andreana M. Rosnik, F. Javier Luque, Carles Curutchet and Petr Jurečka
Article first published online: 30 JUL 2015 | DOI: 10.1002/jcc.24012
Explicit inclusion of polarization in empirical force fields may improve transferability of dihedral angle parameters between molecules and different environments and also additivity of the dihedral terms in larger molecules. However, treatment of the short range polarization interactions between close neighbors, that is, the 1–2 and 1–3 interactions, seems to be crucial in achieving the desired effects.
- Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP reductase (FabI)
Pin-Chih Su, Cheng-Chieh Tsai, Shahila Mehboob, Kirk E. Hevener and Michael E. Johnson
Article first published online: 27 JUL 2015 | DOI: 10.1002/jcc.24011
Computation prediction on ligand-protein binding activities (Molecular Mechanics Poisson-Boltzmann surface area (MM-PBSA), (Quantum Mechanics/) MM-Generalized Born surface area ((QM/)MM-GBSA), has gained attention in the pharmaceutical community due to its efficiency and accuracy. However, the effect of radii sets, GB methods, QM Hamiltonians, sampling protocols, and simulation length on the MM-PBSA and (QM/)MM-GBSA performance has not been extensively studied. The article highlights the importance of these factors in the MM-PBSA and (QM/)MM-GBSA performance using the bacterial enoyl-ACP reductase and benzimidazole inhibitors as a test case.
- Bis(azulene) “submarine” metal dimer sandwich compounds (C10H8)2M2 (M = Ti, V, Cr, Mn, Fe, Co, Ni): Parallel and opposed orientations
Hongyan Wang, Hui Wang, R. Bruce King and Henry F. Schaefer III
Article first published online: 27 JUL 2015 | DOI: 10.1002/jcc.24013
The lowest energy (C10H8)2M2 submarine sandwich structures of the early transition metals Ti, V, Cr, and Mn have the azulene units functioning as bis(pentahapto) ligands to each metal atom. For the later transition metals Fe, Co, and Ni the lowest energy (C10H8)2M2 structures contain pentahapto-trihapto azulene ligands with an uncomplexed CC double bond
- A new QM/MM method oriented to the study of ionic liquids
M. Luz Sánchez, José C. Corchado, M. Elena Martín, Ignacio Fdez. Galván, Rute Barata-Morgado and Manuel A. Aguilar
Article first published online: 24 JUL 2015 | DOI: 10.1002/jcc.24023
A new quantum mechanic/molecular mechanic method, related to the average solvent electrostatic potential/molecular dynamics methodology, is presented to the study of pure ionic liquids. The method permits, through an iterative procedure, the full coupling between the polarized charge distribution of the ions and the liquid structure around them. The procedure has been tested with 1-ethyl-3-methylimidazolium tetrafluoroborate.
- A deeper insight into strain for the sila-biprismane ( Si18H12) cluster with its endohedrally trapped silicon atom, Si19H12
Holger Vach, Lena V. Ivanova, Qadir K. Timerghazin, Fatme Jardali and Ha-Linh Thi Le
Article first published online: 24 JUL 2015 | DOI: 10.1002/jcc.24009
Formation of overcoordinated silicon hydride nanoclusters with nontetrahedral atomic configurations is the result of a self-assembly process in a silane/hydrogen plasma reactor operated close to dusty plasma conditions as shown in our ab initio molecular dynamics simulations. Both symmetric and asymmetric Si19H12 isomers are ultrastable and exhibit aromatic-like behavior. Ultrastability results from extensive electron delocalization that is induced by electron-deficient bonds.