Literature DB >> 21197980

A smooth, nonsingular, and faithful discretization scheme for polarizable continuum models: the switching/Gaussian approach.

Adrian W Lange1, John M Herbert.   

Abstract

Polarizable continuum models (PCMs) are a widely used family of implicit solvent models based on reaction-field theory and boundary-element discretization of the solute/continuum interface. An often overlooked aspect of these theories is that discretization of the interface typically does not afford a continuous potential energy surface for the solute. In addition, we show that discretization can lead to numerical singularities and violations of exact variational conditions. To fix these problems, we introduce the switching/Gaussian (SWIG) method, a discretization scheme that overcomes several longstanding problems with PCMs. Our approach generalizes a procedure introduced by York and Karplus [J. Phys. Chem. A 103, 11060 (1999)], extending it beyond the conductor-like screening model. Comparison to other purportedly smooth PCM implementations reveals certain artifacts in these alternative approaches, which are avoided using the SWIG methodology. The versatility of our approach is demonstrated via geometry optimizations, vibrational frequency calculations, and molecular dynamics simulations, for solutes described using quantum mechanics and molecular mechanics.

Year:  2010        PMID: 21197980     DOI: 10.1063/1.3511297

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  18 in total

1.  Mechanisms of the Formation of Adenine, Guanine, and Their Analogues in UV-Irradiated Mixed NH3:H2O Molecular Ices Containing Purine.

Authors:  Partha P Bera; Tamar Stein; Martin Head-Gordon; Timothy J Lee
Journal:  Astrobiology       Date:  2017-07-14       Impact factor: 4.335

2.  Chemoselective Carbonyl Allylations with Alkoxyallylsiletanes.

Authors:  Paul Spaltenstein; Elizabeth J Cummins; Kelly-Marie Yokuda; Tim Kowalczyk; Timothy B Clark; Gregory W O'Neil
Journal:  J Org Chem       Date:  2019-03-13       Impact factor: 4.354

3.  VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions.

Authors:  Erich R Kuechler; Timothy J Giese; Darrin M York
Journal:  J Chem Phys       Date:  2016-04-28       Impact factor: 3.488

4.  Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions.

Authors:  Xiaoliang Pan; Junjie Yang; Richard Van; Evgeny Epifanovsky; Junming Ho; Jing Huang; Jingzhi Pu; Ye Mei; Kwangho Nam; Yihan Shao
Journal:  J Chem Theory Comput       Date:  2021-09-01       Impact factor: 6.578

5.  O-Acetyl Migration within the Sialic Acid Side Chain: A Mechanistic Study Using the Ab Initio Nanoreactor.

Authors:  Lisa Oh; Yang Ji; Wanqing Li; Ajit Varki; Xi Chen; Lee-Ping Wang
Journal:  Biochemistry       Date:  2022-09-02       Impact factor: 3.321

6.  Progress in developing Poisson-Boltzmann equation solvers.

Authors:  Chuan Li; Lin Li; Marharyta Petukh; Emil Alexov
Journal:  Mol Based Math Biol       Date:  2013-03-01

7.  Theoretical study of methyl group transfer assisted by proton transfer reaction in the N-acylated imidates.

Authors:  Rezika Larabi; Soraya Abtouche; Meziane Brahimi
Journal:  J Mol Model       Date:  2014-05-31       Impact factor: 1.810

8.  Efficient Computation of Geometries for Gold Complexes.

Authors:  Isaac F Leach; Leonardo Belpassi; Paola Belanzoni; Remco W A Havenith; Johannes E M N Klein
Journal:  Chemphyschem       Date:  2021-05-28       Impact factor: 3.102

9.  Consistent inclusion of continuum solvation in energy decomposition analysis: theory and application to molecular CO2 reduction catalysts.

Authors:  Yuezhi Mao; Matthias Loipersberger; Kareesa J Kron; Jeffrey S Derrick; Christopher J Chang; Shaama Mallikarjun Sharada; Martin Head-Gordon
Journal:  Chem Sci       Date:  2020-11-27       Impact factor: 9.825

10.  Densely Functionalized 2-Methylideneazetidines: Evaluation as Antibacterials.

Authors:  Giovanni Petrillo; Cinzia Tavani; Lara Bianchi; Alice Benzi; Maria Maddalena Cavalluzzi; Lara Salvagno; Laura Quintieri; Annalisa De Palma; Leonardo Caputo; Antonio Rosato; Giovanni Lentini
Journal:  Molecules       Date:  2021-06-25       Impact factor: 4.411

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.