(Q33893615)

29 July 2017

title

Multiscale Reactive Molecular Dynamics for Absolute pKa Predictions and Amino Acid Deprotonation (English)

1 reference

29 July 2017

J Gard Nelson

1

1 reference

29 July 2017

Yuxing Peng

series ordinal

2

1 reference

29 July 2017

Daniel W Silverstein

series ordinal

3

1 reference

29 July 2017

Jessica M J Swanson

series ordinal

4

1 reference

29 July 2017

publication date

6 May 2014

1 reference

Journal of Chemical Theory and Computation

29 July 2017

published in

1 reference

29 July 2017

volume

10

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29 July 2017

issue

7

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29 July 2017

page(s)

2729-2737

1 reference

Defining Condensed Phase Reactive Force Fields from ab Initio Molecular Dynamics Simulations: The Case of the Hydrated Excess Proton

29 July 2017

cites work

1 reference

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Absolute pKa Values and Solvation Structure of Amino Acids from Density Functional Based Molecular Dynamics Simulation

5 July 2018

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Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data

5 July 2018

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Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel

5 July 2018

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Computationally Efficient Multiconfigurational Reactive Molecular Dynamics

5 July 2018

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

5 July 2018

1 reference

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Multiscale reactive molecular dynamics

5 July 2018

1 reference

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An accurate density functional theory based estimation of pK(a) values of polar residues combined with experimental data: from amino acids to minimal proteins

5 July 2018

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Insights into the mechanism of proton transport in cytochrome c oxidase

5 July 2018

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Progress in the prediction of pKa values in proteins

5 July 2018

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Intricate role of water in proton transport through cytochrome c oxidase

5 July 2018

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Elucidation of the proton transport mechanism in human carbonic anhydrase II.

5 July 2018

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Role of charge transfer in the structure and dynamics of the hydrated proton

5 July 2018

1 reference

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Revisiting the carboxylic acid dimers in aqueous solution: interplay of hydrogen bonding, hydrophobic interactions, and entropy

5 July 2018

1 reference

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Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations

5 July 2018

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Computer simulation of proton solvation and transport in aqueous and biomolecular systems

5 July 2018

1 reference

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Adding explicit solvent molecules to continuum solvent calculations for the calculation of aqueous acid dissociation constants

5 July 2018

1 reference

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The statistical-thermodynamic basis for computation of binding affinities: a critical review

5 July 2018

1 reference

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On the origin of proton mobility suppression in aqueous solutions of amphiphiles

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4095931

Direct absolute pKa predictions and proton transfer mechanisms of small molecules in aqueous solution by QM/MM-MD.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4095931

A reliable and efficient first principles-based method for predicting pK(a) values. III. Adding explicit water molecules: can the theoretical slope be reproduced and pK(a) values predicted more accurately?

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4095931

A refined MS-EVB model for proton transport in aqueous environments.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4095931

Empirical valence bond models for reactive potential energy surfaces: a parallel multilevel genetic program approach.

29 October 2018

1 reference

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Enhancement of proton conductance by mutations of the selectivity filter of aquaporin-1.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4095931

A computational study of ultrafast acid dissociation and acid-base neutralization reactions. I. The model

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4095931

On the formation of proton-shared and contact ion pair forms during the dissociation of moderately strong acids: an Ab initio molecular dynamics investigation

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4095931

A reliable and efficient first principles-based method for predicting pK(a) values. 2. Organic acids

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4095931

Improving the point-charge description of hydrogen bonds by adaptive force matching.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4095931

Developing ab initio quality force fields from condensed phase quantum-mechanics/molecular-mechanics calculations through the adaptive force matching method.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4095931

Eigen and Zundel forms of small protonated water clusters: structures and infrared spectra.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4095931

Relative pKa values from first-principles molecular dynamics: the case of histidine deprotonation.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4095931

A multistate empirical valence bond description of protonatable amino acids

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4095931

Deprotonation of a histidine residue in aqueous solution using constrained ab initio molecular dynamics

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4095931

Concerted and Sequential Proton Transfer Mechanisms in Water-Separated Acid-Base Encounter Pairs

29 October 2018

1 reference

12 December 2020

Separable dual-space Gaussian pseudopotentials

1 reference

12 December 2020

Dissociation mechanism of acetic acid in water

1 reference

12 December 2020

An improved multistate empirical valence bond model for aqueous proton solvation and transport

1 reference

12 December 2020

Identifiers

DOI

10.1021/CT500250F

1 reference

29 July 2017

1 reference

29 July 2017

1 reference