Analysis of polarization in QM/MM modelling of biologically relevant hydrogen bonds (Q42276982)

19 October 2017

Analysis of polarization in QM/MM modelling of biologically relevant hydrogen bonds (English)

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19 October 2017

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19 October 2017

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19 October 2017

Adrian J Mulholland

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Kittusamy Senthilkumar

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Kittusamy Senthilkumar

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1

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Jeremy N. Harvey

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Jeremy N Harvey

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6

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Frederick Manby

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object named as

Frederick R Manby

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19 October 2017

1 December 2008

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Journal of the Royal Society Interface

19 October 2017

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19 October 2017

5 Suppl 3

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19 October 2017

S207-16

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

19 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2585273

Chemical accuracy in QM/MM calculations on enzyme-catalysed reactions.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2585273

Modelling enzyme reaction mechanisms, specificity and catalysis.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2585273

Generalized hybrid-orbital method for combining density functional theory with molecular mechanicals

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2585273

Force fields for protein simulations

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2585273

Peripheral heme substituents control the hydrogen-atom abstraction chemistry in cytochromes P450.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2585273

Development and current status of the CHARMM force field for nucleic acids.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2585273

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

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2585273

High-accuracy computation of reaction barriers in enzymes.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2585273

The Fe-CO bond energy in myoglobin: a QM/MM study of the effect of tertiary structure

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2585273

A regularized and renormalized electrostatic coupling Hamiltonian for hybrid quantum-mechanical-molecular-mechanical calculations

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2585273

QM/MM studies of the electronic structure of the compound I intermediate in cytochrome c peroxidase and ascorbate peroxidase

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2585273

Multiple high-level QM/MM reaction paths demonstrate transition-state stabilization in chorismate mutase: correlation of barrier height with transition-state stabilization

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2585273

Lennard-Jones parameters for the combined QM/MM method using the B3LYP/6-31G*/AMBER potential

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2585273

Differential transition-state stabilization in enzyme catalysis: quantum chemical analysis of interactions in the chorismate mutase reaction and prediction of the optimal catalytic field.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2585273

Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2585273

Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method

17 August 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSIF.2008.0243.FOCUS

A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSIF.2008.0243.FOCUS

Calibration of the Quantum/Classical Hamiltonian in Semiempirical QM/MM AM1 and PM3 Methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSIF.2008.0243.FOCUS

Frontier Bonds in QM/MM Methods: A Comparison of Different Approaches

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSIF.2008.0243.FOCUS

AddRemove: A new link model for use in QM/MM studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSIF.2008.0243.FOCUS

Adjusted Connection Atoms for Combined Quantum Mechanical and Molecular Mechanical Methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSIF.2008.0243.FOCUS

Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree−Fock Wave Functions with Molecular Mechanics

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSIF.2008.0243.FOCUS

Description of Electron Delocalization via the Analysis of Molecular Fields

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSIF.2008.0243.FOCUS

Importance of van der Waals Interactions in QM/MM Simulations

21 January 2018

1 reference

12 December 2020

Acetyl-CoA enolization in citrate synthase: a quantum mechanical/molecular mechanical (QM/MM) study

1 reference

12 December 2020

Conceptual Density Functional Theory

1 reference

12 December 2020

On the electron leak problem in orbital-free embedding calculations

1 reference

12 December 2020

Spin-forbidden CO ligand recombination in myoglobin

1 reference

12 December 2020

Electronic Structure of Compound I in Human Isoforms of Cytochrome P450 from QM/MM Modeling

1 reference

12 December 2020

Energy decomposition in molecular complexes: Implications for the treatment of polarization in molecular simulations

1 reference

12 December 2020

10.1098/RSIF.2008.0243.FOCUS

Identifiers

DOI

1 reference

19 October 2017

1 reference

19 October 2017

1 reference

PMCID

2585273