Journal Of Computational Chemistry
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- Wiley from 1980
Drug release by pH-responsive molecular tweezers: Atomistic details from molecular modeling.
We performed a computational study of a pH-responsive molecular tweezer using ab initio quantum chemistry in the gas-phase and molecular dynamics (MD) simulations in solution. The binding free energy in solution was calculated using steered MD. We observe, in atomistic detail, the pH-induced conform...
Cover image, volume 33, issue 26.
A HOBDI (4-hydroxybenzylidene-1,2-dimethylimidazolinone) solute molecule in aqueous solution was used as one of the test systems to validate the newly implemented quantum-chemical/molecular-mechanical (QM/MM) functionality of the GROMOS (Groningen Molecular Simulation) software for (...
Inside cover, volume 33, issue 24.
As presented by Chuan Li, Lin Li, Jie Zhang, and Emil Alexov on page 1960, the image shows the distribution of electrostatic field mapped onto the surface of the adeno-associated virus, PDB ID 3KIC. The structural file, after a standard protonation, contains approximately 484,500 ato...
A simplified homology-model builder toward highly protein-like structures: an inspection of restraining potentials.
A homology model builder using simple restraining potentials based on spline-interpolated quadratic functions is developed and interfaced with CHARMM package. The continuity and stability of the potential function were validated, and the parameters were optimized using the CASP7 targ...
Assessment of TD-DFT- and TD-HF-based approaches for the prediction of exciton coupling parameters, potential energy curves, and electronic ...
The reliability of linear response approaches such as time-dependent Hartree-Fock (TD-HF) and time-dependent density functional theory (TD-DFT) for the prediction of the excited state properties of 3,4;9,10-tetracarboxylic-perylene-bisimide (PBI) aggregates is investigated. A dimer m...
Accurate bond dissociation enthalpies by using doubly hybrid XYG3 functional.
We examine the performance of XYG3, a newly developed doubly hybrid density functional (Zhang, Xu, and Goddard III, Proc Natl Acad Sci USA 2009, 106, 4963), to calculate covalent bond dissociation enthalpy (BDE). We use 5 atoms, 32 molecular radicals, and 116 closed-shell molecules to set up 142 bon...
Performance enhancements for GROMACS nonbonded interactions on BlueGene.
Several improvements to the previously optimized GROMACS BlueGene inner loops that evaluate nonbonded interactions in molecular dynamics simulations are presented. The new improvements yielded an 11% decrease in running time for both PME and other kinds of GROMACS simulations that use nonbonded table...
Alkali metal atom-aromatic ring: a novel interaction mode realizes large first hyperpolarizabilities of M@AR (M=Li, Na, and K, AR=pyrrole, i...
Several new electride compounds M@pyrrole (M = Li, Na, and K), Li@AR (AR = indole, thiophene, and benzene), Li@tryptophan and Li@serotonin were designed and investigated, which exhibit considerably large first hyperpolarizabilities (β(0) ) (6705, 1116, 11399, 5781, 4808, 1536, 8106,...
Automatic analysis of computed catalytic cycles.
We present the AUTOF program that allows the user to apply the complete model in a black box fashion. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011. Copyright © 2010 Wiley Periodicals, Inc....
Structural stability and phase transition in OsC and RuC.
The structural stability and phase transition of osmium and ruthenium carbides (OsC and RuC) were investigated by first principles. Nine structures were considered for each carbide. Zinc blende structure has the lowest energy among the considered structures at ambient conditions for both carbides. F...