Journal Of Computational Chemistry
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- Wiley from 1980
Continuous symmetry measures for complex symmetry group.
We present a methodology for calculating the CSM of any complex point group, including the dihedral, tetrahedral, octahedral, and icosahedral symmetry groups. We present the method and analyze its performances and errors. We also introduce an analytical method for calculating the CSM of the linear s...
Decoding the components of dynamics in three-domain proteins.
We examine the feasibility and limitations of describing the motional behavior of three-domain proteins in which the domains are linearly connected. In addition to attempting the determination of the internal and overall reorientational correlation times, we investigate the existence of correlations...
A QM/MM study on the reaction pathway leading to 2-Aceto-2-hydroxybutyrate in the catalytic cycle of AHAS.
The reaction between the intermediate 2-hydroxyethyl-thiamin diphosphate (HEThDP(-) ) and 2-ketobutyrate, in the third step of the catalytic cycle of acetodydroxy acid synthase, is addressed from a theoretical point of view by means of hybrid quantum/molecular mechanical calculations. The QM region...
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,...