Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method (Q37330110)

19 August 2017

Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method (English)

1 reference

19 August 2017

Xiancheng Zeng

1

1 reference

19 August 2017

Hao Hu

series ordinal

2

1 reference

19 August 2017

Xiangqian Hu

series ordinal

3

1 reference

19 August 2017

Weitao Yang

series ordinal

4

1 reference

19 August 2017

language of work or name

English

0 references

publication date

1 April 2009

1 reference

Journal of Chemical Physics

19 August 2017

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19 August 2017

130

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19 August 2017

16

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19 August 2017

164111

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A molecular dynamics study of the hydroxyl radical in solution applying self-interaction-corrected density functional methods.

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

QM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate Isomerase

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

Mechanism of OMP decarboxylation in orotidine 5'-monophosphate decarboxylase

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: fractional electron approach.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

Combined quantum mechanical and molecular mechanical simulations of one- and two-electron reduction potentials of flavin cofactor in water, medium-chain acyl-CoA dehydrogenase, and cholesterol oxidase

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: the case of histone lysine methyltransferase SET7/9.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

Role of protein frame and solvent for the redox properties of azurin from Pseudomonas aeruginosa.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

Calculating potentials of mean force from steered molecular dynamics simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

Free energy reconstruction from nonequilibrium single-molecule pulling experiments

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

Unified Approach for Molecular Dynamics and Density-Functional Theory

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

Absolute standard hydrogen electrode potential measured by reduction of aqueous nanodrops in the gas phase

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

Free energies for biological electron transfer from QM/MM calculation: method, application and critical assessment.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

Insights into current limitations of density functional theory.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

A classical point charge model study of system size dependence of oxidation and reorganization free energies in aqueous solution

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

Calculation of redox properties: understanding short- and long-range effects in rubredoxin

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

Diabatic free energy curves and coordination fluctuations for the aqueous Ag+Ag2+ redox couple: a biased Born-Oppenheimer molecular dynamics investigation.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

Catalytic mechanism and product specificity of the histone lysine methyltransferase SET7/9: an ab initio QM/MM-FE study with multiple initial structures.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

Density-functional molecular-dynamics study of the redox reactions of two anionic, aqueous transition-metal complexes.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

Simulating redox coupled proton transfer in cytochrome c oxidase: looking for the proton bottleneck.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

The protein backbone makes important contributions to 4-oxalocrotonate tautomerase enzyme catalysis: understanding from theory and experiment

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

Electronic structure and solvation of copper and silver ions: a theoretical picture of a model aqueous redox reaction.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautomerase

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

Frozen Density Functional Free Energy Simulations of Redox Proteins: Computational Studies of the Reduction Potential of Plastocyanin and Rusticyanin

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

Ab initio molecular dynamics for molecules with variable numbers of electrons.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736613

On the Theory of Oxidation‐Reduction Reactions Involving Electron Transfer. I

2 September 2018

1 reference

Electrostatic Free Energy and Other Properties of States Having Nonequilibrium Polarization. I

21 January 2018

1 reference

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

The missing term in effective pair potentials

21 January 2018

1 reference

First Principles Study of Alkali-Tyrosine Complexes: Alkali Solvation and Redox Properties.

21 January 2018

1 reference

QM/MM Free-Energy Perturbation Compared to Thermodynamic Integration and Umbrella Sampling: Application to an Enzymatic Reaction

21 January 2018

1 reference

Computational Electrochemistry: The Aqueous Ru3+|Ru2+Reduction Potential

21 January 2018

1 reference

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

21 January 2018

1 reference

Molecular Theories and Simulation of Ions and Polar Molecules in Water

21 January 2018

1 reference

Transmission coefficient calculation for proton transfer in triosephosphate isomerase based on the reaction path potential method

21 January 2018

1 reference

12 December 2020

Unexpected deacetylation mechanism suggested by a density functional theory QM/MM study of histone-deacetylase-like protein

1 reference

12 December 2020

Nuclear quantum effects on an enzyme-catalyzed reaction with reaction path potential: proton transfer in triosephosphate isomerase

1 reference

12 December 2020

Ab initio molecular dynamics simulation of the aqueous Ru2+/Ru3+ redox reaction: the Marcus perspective

1 reference

12 December 2020

Realistic quantitative descriptions of electron transfer reactions: diabatic free-energy surfaces from first-principles molecular dynamics

1 reference

12 December 2020

Localization and delocalization errors in density functional theory and implications for band-gap prediction

1 reference

12 December 2020

Cu(aq)+/Cu(aq)2+ redox reaction exhibits strong nonlinear solvent response due to change in coordination number

1 reference

12 December 2020

Fitting Molecular Electrostatic Potentials from Quantum Mechanical Calculations

1 reference

12 December 2020

Identifiers

DOI

10.1063/1.3120605

1 reference

19 August 2017

1 reference

19 August 2017

PubMed publication ID

19405565

1 reference