Journal of Computational Chemistry

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Vectorization of the general Monte Carlo classical trajectory program VENUS
Journal of Computational Chemistry - Tập 12 Số 8 - Trang 1014-1024 - 1991
Xiche Hu, William L. Hase, Tony Pirraglia
AbstractThe general chemical dynamics computer program VENUS is used to perform classical trajectory simulations for large polyatomic systems, with many atoms and complicated potential energy functions. To simulate an ensemble of many trajectories requires a large amount of CPU time. Since each trajectory is independent, it is possible to parallel process a large s...... hiện toàn bộ
Ability of the PM3 quantum‐mechanical method to model intermolecular hydrogen bonding between neutral molecules
Journal of Computational Chemistry - Tập 14 Số 1 - Trang 89-104 - 1993
Marcus W. Jurema, George C. Shields
AbstractThe PM3 semiempirical quantum‐mechanical method was found to systematically describe intermolecular hydrogen bonding in small polar molecules. PM3 shows charge transfer from the donor to acceptor molecules on the order of 0.02–0.06 units of charge when strong hydrogen bonds are formed. The PM3 method is predictive; calculated hydrogen bond energies with an ...... hiện toàn bộ
The Computer System G R A P H: A Useful Tool in Chemical Graph Theory
Journal of Computational Chemistry - Tập 7 Số 5 - Trang 640-644 - 1986
Dragoš Cvetković, Iván Gutman
AbstractThe interactive programming system GRAPH, implemented at the Faculty of Electrical Engineering in Belgrade, is described. This system has been designed to treat a great variety of problems of graph theory. In the present article we point out the applicability of the system GRAPH in chemical investigations and illustrate it by two examples.
Coarse‐graining: A procedure to generate equilibrated and relaxed models of amorphous polymers
Journal of Computational Chemistry - Tập 28 Số 12 - Trang 1929-1935 - 2007
David Curcó, Carlos Alemán
AbstractWe present a coarse‐graining procedure to construct models of amorphous polymers. The method, which was applied to polyethylene, is based on a generation–relaxation strategy previously developed to provide independent atomistic microstructures. The coarse‐graining was performed by assigning positions to mesoscopic particles denoted blobs, which represent gr...... hiện toàn bộ
KiSThelP: A program to predict thermodynamic properties and rate constants from quantum chemistry results†
Journal of Computational Chemistry - Tập 35 Số 1 - Trang 82-93 - 2014
Sébastien Canneaux, Frédéric Bohr, Éric Hénon
Kinetic and Statistical Thermodynamical Package (KiSThelP) is a cross‐platform free open‐source program developed to estimate molecular and reaction properties from electronic structure data. To date, three computational chemistry software formats are supported (Gaussian, GAMESS, and NWChem). Some key features are: gas‐phase molecular thermodynamic properties (offering hindered rotor treat...... hiện toàn bộ
Accurate description of van der Waals complexes by density functional theory including empirical corrections
Journal of Computational Chemistry - Tập 25 Số 12 - Trang 1463-1473 - 2004
Stefan Grimme
AbstractAn empirical method to account for van der Waals interactions in practical calculations with the density functional theory (termed DFT‐D) is tested for a wide variety of molecular complexes. As in previous schemes, the dispersive energy is described by damped interatomic potentials of the form C6R...... hiện toàn bộ
An efficient algorithm for multistate protein design based on FASTER
Journal of Computational Chemistry - Tập 31 Số 5 - Trang 904-916 - 2010
Benjamin D. Allen, Stephen L. Mayo
AbstractMost of the methods that have been developed for computational protein design involve the selection of side‐chain conformations in the context of a single, fixed main‐chain structure. In contrast, multistate design (MSD) methods allow sequence selection to be driven by the energetic contributions of multiple structural or chemical states simultaneously. Thi...... hiện toàn bộ
Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
Journal of Computational Chemistry - Tập 13 Số 8 - Trang 952-962 - 1992
Shuichi Miyamoto, Peter A. Kollman
AbstractAn analytical algorithm, called SETTLE, for resetting the positions and velocities to satisfy the holonomic constraints on the rigid water model is presented. This method is still based on the Cartesian coordinate system and can be used in place of SHAKE and RATTLE. We implemented this algorithm in the SPASMS package of molecular mechanics and dynamics. Sev...... hiện toàn bộ
Update of the AIM2000‐Program for atoms in molecules
Journal of Computational Chemistry - Tập 23 Số 15 - Trang 1489-1494 - 2002
Friedrich Biegler‐König, Jens Schönbohm
AbstractThe second version of the program package AIM2000 is presented. AIM2000 makes use of the well established theory of atoms in molecules. AIM2000 analyzes the molecular structure and calculates properties of atoms in molecules as well as properties of interatomic surfaces. The program has an interactive, context‐sensitive help component and extensive 2D and 3...... hiện toàn bộ
Optimization of parameters for semiempirical methods. III Extension of PM3 to Be, Mg, Zn, Ga, Ge, As, Se, Cd, In, Sn, Sb, Te, Hg, Tl, Pb, and Bi
Journal of Computational Chemistry - Tập 12 Số 3 - Trang 320-341 - 1991
James J. P. Stewart
AbstractUsing a recently developed procedure for optimizing parameters for semiempirical methods,1 PM3 has been extended to a total of 28 elements. Average ΔHf errors for the newly parameterized elements are Be: 8.6, Mg: 8.4, Zn: 5.8, Ga: 14.9, Ge: 11.4, As: 8.5, Se: 11....... hiện toàn bộ
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