Journal ArticleDOI
COSMO : a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient
Andreas Klamt,Gerrit Schüürmann +1 more
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TLDR
In this paper, an algorithm for the accurate calculation of dielectric screening effects in solvents is presented, which leads to rather simple expressions for the screening energy and its analytic gradient with respect to the solute coordinates.Abstract:
Starting from the screening in conductors, an algorithm for the accurate calculation of dielectric screening effects in solvents is presented, which leads to rather simple explicit expressions for the screening energy and its analytic gradient with respect to the solute coordinates. Thus geometry optimization of a solute within a realistic dielectric continuum model becomes practicable for the first time. The algorithm is suited for molecular mechanics as well as for any molecular orbital algorithm. The implementation into MOPAC and some example applications are reported.read more
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Journal ArticleDOI
Quantum mechanical continuum solvation models.
TL;DR: This paper presents a meta-modelling procedure called "Continuum Methods within MD and MC Simulations 3072", which automates the very labor-intensive and therefore time-heavy and expensive process of integrating discrete and continuous components into a discrete-time model.
Journal ArticleDOI
Chemistry with ADF
G. te Velde,F.M. Bickelhaupt,Evert Jan Baerends,C. Fonseca Guerra,S. J. A. van Gisbergen,J.G. Snijders,T. Ziegler +6 more
TL;DR: The “Activation‐strain TS interaction” (ATS) model of chemical reactivity is reviewed as a conceptual framework for understanding how activation barriers of various types of reaction mechanisms arise and how they may be controlled, for example, in organic chemistry or homogeneous catalysis.
Journal ArticleDOI
Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model
Vincenzo Barone,Maurizio Cossi +1 more
TL;DR: In this paper, a new implementation of the conductor-like screening solvation model (COSMO) in the GAUSSIAN94 package is presented, which allows Hartree−Fock (HF), density functional (DF) and post-HF energy, and HF and DF gradient calculations: the cavities are modeled on the molecular shape, using recently optimized parameters, and both electrostatic and nonelectrostatic contributions to energies and gradients are considered.
Journal ArticleDOI
CHARMM: the biomolecular simulation program.
Bernard R. Brooks,Charles L. Brooks,Alexander D. MacKerell,Lennart Nilsson,Robert J. Petrella,Benoît Roux,Youngdo Won,Georgios Archontis,Christian Bartels,Stefan Boresch,Amedeo Caflisch,Leo S. D. Caves,Qiang Cui,Aaron R. Dinner,Michael Feig,Stefan Fischer,Jiali Gao,Milan Hodošček,Wonpil Im,K. Kuczera,Themis Lazaridis,Jianpeng Ma,V. Ovchinnikov,Emanuele Paci,Richard W. Pastor,Carol Beth Post,Jingzhi Pu,M. Schaefer,Bruce Tidor,Richard M. Venable,H. L. Woodcock,Xiongwu Wu,Wei Yang,Darrin M. York,Martin Karplus,Martin Karplus +35 more
TL;DR: An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.
Journal ArticleDOI
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.
Yong Duan,Chun Wu,Shibasish Chowdhury,Mathew C. Lee,Guoming Xiong,Wei Zhang,Rong Yang,Piotr Cieplak,Piotr Cieplak,Ray Luo,Tai-Sung Lee,Tai-Sung Lee,James W. Caldwell,Junmei Wang,Peter A. Kollman +14 more
TL;DR: A third‐generation point‐charge all‐atom force field for proteins is developed and initial tests on peptides demonstrated a high‐degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace‐Gly‐nme and Ace‐Ala‐Nme di‐peptides.