(Q41930764)

14 October 2017

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

1 reference

14 October 2017

Thomas E. Cheatham, III

series ordinal

2

object named as

Thomas E Cheatham

1 reference

14 October 2017

In Suk Joung

1

1 reference

PMCID

2652252

14 October 2017

language of work or name

English

0 references

publication date

2 July 2008

1 reference

Journal of Physical Chemistry B

14 October 2017

1 reference

14 October 2017

112

1 reference

14 October 2017

30

1 reference

14 October 2017

9020-9041

1 reference

Measurement of the effect of monovalent cations on RNA hairpin stability

14 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Dioldehydrase: an essential role for potassium ion in the homolytic cleavage of the cobalt-carbon bond in adenosylcobalamin

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Distinct reaction pathway promoted by non-divalent-metal cations in a tertiary stabilized hammerhead ribozyme

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Structural roles of monovalent cations in the HDV ribozyme

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Single-ion solvation free energies and the normal hydrogen electrode potential in methanol, acetonitrile, and dimethyl sulfoxide.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Electrostatic, steric, and hydration interactions favor Na(+) condensation around DNA compared with K(+).

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Salt-induced formation of the A-state of ferricytochrome c--effect of the anion charge on protein structure.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Comparison of multiple Amber force fields and development of improved protein backbone parameters

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

MD simulation of the Na+-phenylalanine complex in water: competition between cation-pi interaction and aqueous solvation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Conductimetric determination of thermodynamic pairing constants for symmetrical electrolytes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

A structural perspective on enzymes activated by monovalent cations

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Scalable molecular dynamics with NAMD

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

The Amber biomolecular simulation programs

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

The contribution of metal ions to the structural stability of the large ribosomal subunit

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

The effect of water on protein dynamics

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Empirical force fields for biological macromolecules: overview and issues.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Molecular dynamics simulation study of oriented polyamine- and Na-DNA: sequence specific interactions and effects on DNA structure

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Molecular dynamics simulation of a palmitoyl-oleoyl phosphatidylserine bilayer with Na+ counterions and NaCl.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

A guide to ions and RNA structure

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

A molecular dynamics simulation study of oriented DNA with polyamine and sodium counterions: diffusion and averaged binding of water and cations.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

On the competition between water, sodium ions, and spermine in binding to DNA: a molecular dynamics computer simulation study

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Molecular dynamics simulation of nucleic acids: successes, limitations, and promise

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Water and monovalent ions in the minor groove of B-DNA oligonucleotides as seen by NMR.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Sequence-specific binding of counterions to B-DNA.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Molecular dynamics simulations of biomolecules: long-range electrostatic effects

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Influence of anions and cations on the dipole potential of phosphatidylcholine vesicles: a basis for the Hofmeister effect

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Insight into the stabilization of A-DNA by specific ion association: spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT]2 in the presence of hexaamminecobalt(III).

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

A molecular level picture of the stabilization of A-DNA in mixed ethanol-water solutions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Valence selectivity of the gramicidin channel: a molecular dynamics free energy perturbation study

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Biological catalysis by RNA.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Monovalent cation induced structural transitions in telomeric DNAs: G-DNA folding intermediates

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Role of divalent metal ions in the hammerhead RNA cleavage reaction

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Structural transitions of deoxyribonucleic acid in aqueous electrolyte solutions. II. The role of hydration

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Improved interaction potentials for charged residues in proteins

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Counterion-hopping along the backbone of single-stranded DNA in nanometer pores: a mechanism for current conduction.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Effective potentials for 1:1 electrolyte solutions incorporating dielectric saturation and repulsive hydration.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Molecular dynamics simulations of phospholipid bilayers: Influence of artificial periodicity, system size, and simulation time

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Steered molecular dynamics simulations of Na+ permeation across the gramicidin A channel.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Computation of methodology-independent ionic solvation free energies from molecular simulations. II. The hydration free energy of the sodium cation.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

On the Ewald artifacts in computer simulations. The test-case of the octaalanine peptide with charged termini

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Modelling of ion permeation in K+ channels by nonequilibrium molecular dynamics simulations: I. Permeation energetics and structure stability.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Monovalent cations affect the free solution mobility of DNA by perturbing the hydrogen-bonded structure of water

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Insights into the structures, energetics, and vibrations of aqua-rubidium(I) complexes: ab initio study.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Anion binding to nucleic acids.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: diffusion, free energy of hydration, and structural properties.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Ion solvation thermodynamics from simulation with a polarizable force field

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Anion concentration modulates the conformation and stability of the molten globule of cytochrome c.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Surface potential of the water liquid-vapor interface

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Structures, energetics, and spectra of aqua-cesium (I) complexes: An ab initio and experimental study

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

Aqueous Solvation Free Energies of Ions and Ion−Water Clusters Based on an Accurate Value for the Absolute Aqueous Solvation Free Energy of the Proton

2 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652252

A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat

2 December 2018

1 reference

12 December 2020

Dissolution dynamics of NaCl nanocrystal in liquid water

1 reference

12 December 2020

The Effects of Metal Ions on the Structure and Stability of the DNA Gyrase B Protein

1 reference

12 December 2020

Molecular dynamics studies of ion distributions for DNA duplexes and DNA clusters: salt effects and connection to DNA melting

1 reference

12 December 2020

Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field

1 reference

12 December 2020

Specific Ion Effects at Protein Surfaces: A Molecular Dynamics Study of Bovine Pancreatic Trypsin Inhibitor and Horseradish Peroxidase in Selected Salt Solutions

1 reference

12 December 2020

Highly compact folding of chromatin induced by cellular cation concentrations. Evidence from atomic force microscopy studies in aqueous solution

1 reference

12 December 2020

Effective interaction potentials for alkali and alkaline earth metal ions in SPC/E water and prediction of mean ion activity coefficients

1 reference

12 December 2020

Direct observation of salt effects on molecular interactions through explicit-solvent molecular dynamics simulations: differential effects on electrostatic and hydrophobic interactions and comparisons to Poisson-Boltzmann theory

1 reference

12 December 2020

Molecular force field for ionic liquids III: imidazolium, pyridinium, and phosphonium cations; chloride, bromide, and dicyanamide anions.

1 reference

12 December 2020

Multiple Time Scales in Solvation Dynamics of DNA in Aqueous Solution: The Role of Water, Counterions, and Cross-Correlations

1 reference

12 December 2020

Atomistic nature of NaCl nucleation at the solid-liquid interface

1 reference

12 December 2020

Inter-DNA electrostatics from explicit solvent molecular dynamics simulations

1 reference

12 December 2020

Quantitative characterization of ion pairing and cluster formation in strong 1:1 electrolytes

1 reference

12 December 2020

Parameters of monovalent ions in the AMBER-99 forcefield: assessment of inaccuracies and proposed improvements

1 reference

12 December 2020

Ion dynamics and water percolation effects in DNA polymorphism

1 reference

12 December 2020

Effect of NaCl and KCl on Phosphatidylcholine and Phosphatidylethanolamine Lipid Membranes: Insight from Atomic-Scale Simulations for Understanding Salt-Induced Effects in the Plasma Membrane

1 reference

12 December 2020

Ions in water: from ion clustering to crystal nucleation

1 reference

12 December 2020

Halide, Ammonium, and Alkali Metal Ion Parameters for Modeling Aqueous Solutions

1 reference

12 December 2020

Binding of alkaline-earth metal cations and some anions to phosphatidylcholine liposomes

1 reference

12 December 2020

Identifiers

DOI

10.1021/JP8001614

1 reference

14 October 2017

1 reference

14 October 2017

1 reference

PMCID

2652252