Molecular dynamics simulations of ionic liquids and electrolytes using polarizable force fields

D Bedrov, JP Piquemal, O Borodin… - Chemical …, 2019 - ACS Publications
Many applications in chemistry, biology, and energy storage/conversion research rely on
molecular simulations to provide fundamental insight into structural and transport properties …

Recent applications of Kirkwood–Buff theory to biological systems

V Pierce, M Kang, M Aburi, S Weerasinghe… - Cell biochemistry and …, 2008 - Springer
The effect of cosolvents on biomolecular equilibria has traditionally been rationalized using
simple binding models. More recently, a renewed interest in the use of Kirkwood–Buff (KB) …

Simulation of osmotic pressure in concentrated aqueous salt solutions

Y Luo, B Roux - The journal of physical chemistry letters, 2010 - ACS Publications
Accurate force fields are critical for meaningful simulation studies of highly concentrated
electrolytes. The ion models that are widely used in biomolecular simulations do not …

A GROMOS-compatible force field for small organic molecules in the condensed phase: The 2016H66 parameter set

BAC Horta, PT Merz, PFJ Fuchs, J Dolenc… - Journal of chemical …, 2016 - ACS Publications
This article reports on the calibration and validation of a new GROMOS-compatible
parameter set 2016H66 for small organic molecules in the condensed phase. The …

Convergence of sampling Kirkwood–Buff integrals of aqueous solutions with molecular dynamics simulations

P Ganguly, NFA van der Vegt - Journal of chemical theory and …, 2013 - ACS Publications
We discuss two methods for calculating Kirkwood–Buff integrals (KBIs) of aqueous cosolvent
solutions from molecular simulations. The first method is based on computing running …

A Kirkwood-Buff derived force field for aqueous alkali halides

MB Gee, NR Cox, Y Jiao, N Bentenitis… - Journal of chemical …, 2011 - ACS Publications
A classical nonpolarizable force field is presented for the simulation of aqueous alkali halide
solutions (MX), where M= Li+, Na+, K+, Rb+, and Cs+ and X= F–, Cl–, Br–, and I–, and their …

Kirkwood-Buff integrals from molecular simulation

N Dawass, P Krüger, SK Schnell, JM Simon… - Fluid Phase …, 2019 - Elsevier
Abstract The Kirkwood-Buff (KB) theory provides a rigorous framework to predict
thermodynamic properties of isotropic liquids from the microscopic structure. Several …

Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions

J Chen, CL Brooks Iii - Physical Chemistry Chemical Physics, 2008 - pubs.rsc.org
Accurate description of the solvent environment is critical in computer simulations of protein
structure and dynamics. An implicit treatment of solvent aims to capture the mean influence …

Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field

Y Luo, W Jiang, H Yu, AD MacKerell, B Roux - Faraday discussions, 2013 - pubs.rsc.org
The accuracy of empirical force fields is critical for meaningful molecular dynamics
simulations of concentrated ionic solutions. Current models are typically developed on the …

Revisiting the carboxylic acid dimers in aqueous solution: Interplay of hydrogen bonding, hydrophobic interactions, and entropy

J Chen, CL Brooks, HA Scheraga - The Journal of Physical …, 2008 - ACS Publications
Carboxylic acid dimers are useful model systems for understanding the interplay of
hydrogen bonding, hydrophobic effects, and entropy in self-association and assembly …