(Q35029322)

5 August 2017

title

A combined experimental and theoretical study of ion solvation in liquid N-methylacetamide (English)

1 reference

5 August 2017

A Combined Experimental and Theoretical Study of Ion Solvation in Liquid N-Methylacetamide (English)

1 reference

15 June 2024

1

Haibo Yu

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20681718

15 June 2024

3

Troy W. Whitfield

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20681718

15 June 2024

4

Roger E. Koeppe

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20681718

15 June 2024

author name string

Benoît Roux

6

1 reference

5 August 2017

Christopher L. Mazzanti

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20681718

15 June 2024

Olaf S. Andersen

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20681718

15 June 2024

language of work or name

English

0 references

publication date

1 August 2010

1 reference

5 August 2017

11 August 2010

1 reference

National Center for Biotechnology Information

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=20681718

full work available at URL

15 June 2024

https://europepmc.org/articles/pmc3109503?pdf=render

file format

Portable Document Format

online access status

open access

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20681718

https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20681718/?tool=EBI

15 June 2024

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20681718

https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20681718/pdf/?tool=EBI

15 June 2024

file format

Portable Document Format

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20681718

https://europepmc.org/articles/PMC3109503

15 June 2024

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20681718

https://europepmc.org/articles/PMC3109503?pdf=render

15 June 2024

file format

Portable Document Format

online access status

open access

content deliverer

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20681718

https://doi.org/10.1021/ja103270w

15 June 2024

online access status

open access

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20681718

https://pubs.acs.org/doi/pdf/10.1021/ja103270w

15 June 2024

1 reference

Journal of the American Chemical Society

15 June 2024

published in

1 reference

5 August 2017

volume

132

1 reference

5 August 2017

issue

31

1 reference

5 August 2017

page(s)

10847-10856

1 reference

All-atom empirical potential for molecular modeling and dynamics studies of proteins

5 August 2017

cites work

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On the origin of the electrostatic potential difference at a liquid-vacuum interface

8 July 2018

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Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy

8 July 2018

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Structural transitions in ion coordination driven by changes in competition for ligand binding

8 July 2018

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

8 July 2018

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8 July 2018

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Geometry and Excitation Energy Fluctuations of NMA in Aqueous Solution with CHARMM, AMBER, OPLS, and GROMOS Force Fields: Implications for Protein Ultraviolet Spectra Simulation

8 July 2018

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Understanding the dielectric properties of liquid amides from a polarizable force field.

8 July 2018

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The predominant role of coordination number in potassium channel selectivity

8 July 2018

1 reference

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Selectivity in K+ channels is due to topological control of the permeant ion's coordinated state

8 July 2018

1 reference

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Tuning ion coordination architectures to enable selective partitioning

8 July 2018

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Polarizable empirical force field for aromatic compounds based on the classical drude oscillator

8 July 2018

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Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels

8 July 2018

1 reference

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Ion selectivity in potassium channels

8 July 2018

1 reference

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Biomolecular modeling: Goals, problems, perspectives

8 July 2018

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Molecular dynamics: survey of methods for simulating the activity of proteins

8 July 2018

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Potential energy functions for atomic-level simulations of water and organic and biomolecular systems

8 July 2018

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Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands.

8 July 2018

1 reference

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A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

8 July 2018

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CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.

8 July 2018

1 reference

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CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations.

8 July 2018

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8 July 2018

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Molecular dynamics simulations of biomolecules

8 July 2018

1 reference

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Computational studies of the gramicidin channel

8 July 2018

1 reference

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Structures of gramicidins A, B, and C incorporated into sodium dodecyl sulfate micelles

8 July 2018

1 reference

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Unified Approach for Molecular Dynamics and Density-Functional Theory

8 July 2018

1 reference

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Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density

8 July 2018

1 reference

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Density-functional exchange-energy approximation with correct asymptotic behavior

8 July 2018

1 reference

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Canonical dynamics: Equilibrium phase-space distributions

8 July 2018

1 reference

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The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity

8 July 2018

1 reference

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High-resolution polypeptide structure in a lamellar phase lipid environment from solid state NMR derived orientational constraints

8 July 2018

1 reference

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3109503

High-resolution conformation of gramicidin A in a lipid bilayer by solid-state NMR.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3109503

Cooperative effects in water-biomolecule crystal systems

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3109503

Calculations of electrostatic properties in proteins. Analysis of contributions from induced protein dipoles

8 July 2018

1 reference

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A Functional Connection Between the Pores of Distantly Related Ion Channels as Revealed by Mutant K + Channels

8 July 2018

1 reference

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Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model.

8 July 2018

1 reference

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Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3109503

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

25 October 2018

1 reference

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Computation of methodology-independent ionic solvation free energies from molecular simulations. I. The electrostatic potential in molecular liquids.

25 October 2018

1 reference

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Structural properties of liquid N-methylacetamide via ab initio, path integral, and classical molecular dynamics

25 October 2018

1 reference

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Structure and hydrogen bonding in neat N-methylacetamide: classical molecular dynamics and Raman spectroscopy studies of a liquid of peptidic fragments

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3109503

Experimental validation of theoretical potassium and sodium cation affinities of amides by mass spectrometric kinetic method measurements

25 October 2018

1 reference

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Ion solvation thermodynamics from simulation with a polarizable force field

25 October 2018

1 reference

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On the potential functions used in molecular dynamics simulations of ion channels

25 October 2018

1 reference

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Acceleration schemes for ab initio molecular-dynamics simulations and electronic-structure calculations.

25 October 2018

1 reference

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Charge-on-spring polarizable water models revisited: From water clusters to liquid water to ice

25 October 2018

1 reference

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Estimating entropies from molecular dynamics simulations

9 December 2018

1 reference

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Atomic Level Anisotropy in the Electrostatic Modeling of Lone Pairs for a Polarizable Force Field Based on the Classical Drude Oscillator

9 December 2018

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12 December 2020

Efficient pseudopotentials for plane-wave calculations

1 reference

12 December 2020

Special Issue on Polarization

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12 December 2020

Separable dual-space Gaussian pseudopotentials

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12 December 2020

Absolute hydration entropies of alkali metal ions from molecular dynamics simulations

1 reference

12 December 2020

1H-NMR study of gramicidin A transmembrane ion channel. Head-to-head right-handed, single-stranded helices

1 reference

12 December 2020

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

1 reference

12 December 2020

Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator

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

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

8

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Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids

15 June 2024

11

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Comparison of simple potential functions for simulating liquid water

15 June 2024

20

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Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations

15 June 2024

22

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Accounting for polarization in molecular simulation

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Cooperative effects in simulated water

15 June 2024

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Fluctuating Charge Study of Polarization Effects in Chlorinated Organic Liquids

15 June 2024

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Effective field of a dipole in non-polar polarizable fluids

15 June 2024

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Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm

15 June 2024

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A simple polarizable model of water based on classical Drude oscillators

15 June 2024

61

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Development of a simple, self-consistent polarizable model for liquid water

15 June 2024

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A polarizable model of water for molecular dynamics simulations of biomolecules

15 June 2024

78

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Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations

15 June 2024

84

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Constant pressure molecular dynamics algorithms

15 June 2024

87

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A unified formulation of the constant temperature molecular dynamics methods

15 June 2024

88

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A smooth particle mesh Ewald method

15 June 2024

90

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Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

15 June 2024

91

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Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations

15 June 2024

93

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THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

15 June 2024

94

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Multidimensional free-energy calculations using the weighted histogram analysis method

15 June 2024

95

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The calculation of the potential of mean force using computer simulations

15 June 2024

96

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Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations

15 June 2024

97

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Absolute hydration free energies of ions, ion–water clusters, and quasichemical theory

15 June 2024

100

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The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors

15 June 2024

108

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Nosé–Hoover chains: The canonical ensemble via continuous dynamics

15 June 2024

117

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15 June 2024

Identifiers

DOI

10.1021/JA103270W

1 reference

5 August 2017

1 reference

5 August 2017

1 reference