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
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
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
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
Consistent gaussian basis sets of double‐ and triple‐zeta valence with polarization quality of the fifth period for solid‐state calculations
Journal of Computational Chemistry - Tập 39 Số 19 - Trang 1285-1290 - 2018
Joachim Laun, Daniel Vilela Oliveira, Thomas Bredow
Consistent basis sets of double‐ and triple‐zeta valence with polarization quality for the fifth period have been derived for periodic quantum‐chemical solid‐state calculations with the crystalline‐orbital program CRYSTAL. They are an extension of the pob‐TZVP basis sets, and are based on the full‐relativistic effective core potentials (ECPs) of the Stuttgart/Cologne group and on the def2‐...... hiện toàn bộ
TmoleX—A graphical user interface for TURBOMOLE
Journal of Computational Chemistry - Tập 31 Số 16 - Trang 2967-2970 - 2010
Claudia Steffen, Klaus Thomas, Uwe Huniar, Arnim Hellweg, Oliver Rubner, Alexander Schroer
AbstractWe herein present the graphical user interface (GUI) TmoleX for the quantum chemical program package TURBOMOLE. TmoleX allows users to execute the complete workflow of a quantum chemical investigation from the initial building of a structure to the visualization of the results in a user friendly graphical front end. The purpose of TmoleX is to make TURBOMOL...... hiện toàn bộ
Empirical force fields for biological macromolecules: Overview and issues
Journal of Computational Chemistry - Tập 25 Số 13 - Trang 1584-1604 - 2004
Alexander D. MacKerell
AbstractEmpirical force field‐based studies of biological macromolecules are becoming a common tool for investigating their structure–activity relationships at an atomic level of detail. Such studies facilitate interpretation of experimental data and allow for information not readily accessible to experimental methods to be obtained. A large part of the success of ...... hiện toàn bộ
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