[HTML][HTML] A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization

E Duboue-Dijon, M Javanainen, P Delcroix… - The Journal of …, 2020 - pubs.aip.org
Molecular simulations can elucidate atomistic-level mechanisms of key biological
processes, which are often hardly accessible to experiment. However, the results of the …

Simulation and theory of ions at atmospherically relevant aqueous liquid-air interfaces

DJ Tobias, AC Stern, MD Baer, Y Levin… - Annual review of …, 2013 - annualreviews.org
Chemistry occurring at or near the surface of aqueous droplets and thin films in the
atmosphere influences air quality and climate. Molecular dynamics simulations are …

Tinker 8: software tools for molecular design

JA Rackers, Z Wang, C Lu, ML Laury… - Journal of chemical …, 2018 - ACS Publications
The Tinker software, currently released as version 8, is a modular molecular mechanics and
dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with …

Scaled charges for ions: An improvement but not the final word for modeling electrolytes in water

S Blazquez, MM Conde, C Vega - The Journal of Chemical Physics, 2023 - pubs.aip.org
In this work, we discuss the use of scaled charges when developing force fields for NaCl in
water. We shall develop force fields for Na+ and Cl− using the following values for the …

[HTML][HTML] Revisiting the hydration structure of aqueous Na+

M Galib, MD Baer, LB Skinner, CJ Mundy… - The Journal of …, 2017 - pubs.aip.org
A combination of theory, X-ray diffraction (XRD) and extended x-ray absorption fine structure
(EXAFS) are used to probe the hydration structure of aqueous Na+. The high spatial …

Accurate binding of sodium and calcium to a POPC bilayer by effective inclusion of electronic polarization

J Melcr, H Martinez-Seara, R Nencini… - The Journal of …, 2018 - ACS Publications
Binding affinities and stoichiometries of Na+ and Ca2+ ions to phospholipid bilayers are of
paramount significance in the properties and functionality of cellular membranes. Current …

A holistic approach for elucidating local structure, dynamics, and speciation in molten salts with high structural disorder

S Roy, Y Liu, M Topsakal, E Dias… - Journal of the …, 2021 - ACS Publications
To examine ion solvation, exchange, and speciation for minority components in molten salts
(MS) typically found as corrosion products, we propose a multimodal approach combining …

Toward a first-principles framework for predicting collective properties of electrolytes

TT Duignan, SM Kathmann, GK Schenter… - Accounts of Chemical …, 2021 - ACS Publications
Conspectus Given the universal importance of electrolyte solutions, it is natural to expect
that we have a nearly complete understanding of the fundamental properties of these …

Effects of alkali cations and halide anions on the DOPC lipid membrane

R Vácha, SWI Siu, M Petrov… - The journal of …, 2009 - ACS Publications
By means of molecular dynamics simulations with an all-atom force field, we investigated the
affinities of alkali cations and halide anions for the dioleoylphosphatidylcholine lipid …

Spontaneous formation of KCl aggregates in biomolecular simulations: a force field issue?

P Auffinger, TE Cheatham… - Journal of Chemical Theory …, 2007 - ACS Publications
Realistic all-atom simulation of biological systems requires accurate modeling of both the
biomolecules and their ionic environment. Recently, ion nucleation phenomena leading to …