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 …

Charge Separation in Molecular Clusters:  Dissolution of a Salt in a Salt−(Solvent)n Cluster

C Dedonder-Lardeux, G Grégoire, C Jouvet… - Chemical …, 2000 - ACS Publications
The related subject of intermolecular charge transfer in van der Waals complexes (donor-
acceptor complexes excited on the one part (A*-D or AD*) where the electron is transferred …

Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM

P Banáš, P Jurečka, NG Walter, J Šponer, M Otyepka - Methods, 2009 - Elsevier
Hybrid QM/MM methods combine the rigor of quantum mechanical (QM) calculations with
the low computational cost of empirical molecular mechanical (MM) treatment allowing to …

Low-noise nanopore enables in-situ and label-free tracking of a trigger-induced DNA molecular machine at the single-molecular level

Z Zhu, X Duan, Q Li, R Wu, Y Wang… - Journal of the American …, 2020 - ACS Publications
Solid-state nanopores have shown special high potential in a label-free molecular assay,
structure identification, and target-index at the single-molecular level, even though …

Water and ion binding around RNA and DNA (C, G) oligomers

P Auffinger, E Westhof - Journal of molecular biology, 2000 - Elsevier
The dynamics, hydration, and ion-binding features of two duplexes, the A (r (CG) 12) and the
B (d (CG) 12), in a neutralizing aqueous environment with 0.25 M added KCl have been …

Ions and counterions in a biological channel: a molecular dynamics simulation of OmpF porin from Escherichia coli in an explicit membrane with 1 M KCl aqueous salt …

W Im, B Roux - Journal of molecular biology, 2002 - Elsevier
A 5ns all-atom molecular dynamics trajectory of Escherichia coli OmpF porin embedded in
an explicit dimyristoyl-phosphatidylcholine (DMPC) bilayer bathed by a 1M [KCl] aqueous …

Computation of methodology-independent single-ion solvation properties from molecular simulations. IV. Optimized Lennard-Jones interaction parameter sets for the …

MM Reif, PH Hünenberger - The Journal of chemical physics, 2011 - pubs.aip.org
A companion article has been published: Computation of methodology-independent single-
ion solvation properties from molecular simulations. III. Correction terms for the solvation free …

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 …

Unexpected solute aggregation in water on dilution

S Samal, KE Geckeler - Chemical Communications, 2001 - pubs.rsc.org
Studies on cluster–cluster aggregation phenomena in aqueous solutions of fullerene–
cyclodextrin conjugates, β-cyclodextrin, sodium chloride, sodium guanosine …

Potentials of mean force of simple ions in ambient aqueous solution. II. Solvation structure from the three-dimensional reference interaction site model approach, and …

A Kovalenko, F Hirata - The Journal of Chemical Physics, 2000 - pubs.aip.org
Understanding the behavior of ions in solution is of fundamental importance for a wide
variety of chemical problems, including chemical reaction rates and organic reaction …