Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations

IS Joung, TE Cheatham III - The journal of physical chemistry B, 2008 - ACS Publications
Alkali (Li+, Na+, K+, Rb+, and Cs+) and halide (F−, Cl−, Br−, and I−) ions play an important
role in many biological phenomena, roles that range from stabilization of biomolecular …

Ion pairing in molecular simulations of aqueous alkali halide solutions

CJ Fennell, A Bizjak, V Vlachy… - The Journal of Physical …, 2009 - ACS Publications
Using classical molecular dynamics simulations, we study ion− ion interactions in water. We
study the potentials of mean force (PMF) for the full set of alkali halide ion pairs, and in each …

Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems

FL Barroso daSilva, LG Dias - Biophysical reviews, 2017 - Springer
Abstract pH is a critical parameter for biological and technological systems directly related
with electrical charges. It can give rise to peculiar electrostatic phenomena, which also …

The effect of pH and ionic strength on the adsorption of glyphosate onto ferrihydrite

RC Pereira, PR Anizelli, E Di Mauro, DF Valezi… - Geochemical …, 2019 - Springer
Abstract Although, glyphosate (N-(phosphonomethyl) glycine) is one of the most widely used
herbicides in the world, its interaction with poorly crystalline iron oxides, such as ferrihydrite …

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 …

Ion hydration and structural properties of water in aqueous solutions at normal and supercooled conditions: a test of the structure making and breaking concept

P Gallo, D Corradini, M Rovere - Physical Chemistry Chemical Physics, 2011 - pubs.rsc.org
We study with the method of molecular dynamics simulation the structural properties of
aqueous solutions of NaCl, KCl and KF salts at ambient conditions and upon supercooling …

Models of protein crystal growth

AM Kierzek, P Zielenkiewicz - Biophysical chemistry, 2001 - Elsevier
The growth of large and well ordered protein crystals remains the major obstacle in protein
structure determination by means of X-ray crystallography. One of the reasons is that the …

Local order in aqueous NaCl solutions and pure water: X-ray scattering and molecular dynamics simulations study

S Bouazizi, S Nasr, N Jaîdane… - The Journal of …, 2006 - ACS Publications
The microstructures of pure water and aqueous NaCl solutions over a wide range of salt
concentrations (0− 4 m) under ambient conditions are characterized by X-ray scattering and …

Coarse-grained ions without charges: reproducing the solvation structure of NaCl in water using short-ranged potentials

RC DeMille, V Molinero - The Journal of chemical physics, 2009 - pubs.aip.org
A coarse-grained model of NaCl in water is presented where the ions are modeled without
charge to avoid computationally challenging electrostatics. A monatomic model of water [V …

Ion association in concentrated NaCl brines from ambient to supercritical conditions: results from classical molecular dynamics simulations

DM Sherman, MD Collings - Geochemical Transactions, 2002 - pubs.rsc.org
Highly concentrated NaCl brines are important geothermal fluids; chloride complexation of
metals in such brines increases the solubility of minerals and plays a fundamental role in the …