AM1/d-CB1: A Semiempirical Model for QM/MM Simulations of Chemical Glycobiology Systems (Q35774198)

10 August 2017

title

AM1/d-CB1: A Semiempirical Model for QM/MM Simulations of Chemical Glycobiology Systems (English)

1 reference

10 August 2017

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Krishna Govender

1

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Kevin J. Naidoo

object named as

Kevin J Naidoo

series ordinal

3

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author name string

Jiali Gao

series ordinal

2

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10 August 2017

publication date

1 January 2014

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Journal of Chemical Theory and Computation

10 August 2017

published in

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10 August 2017

volume

10

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10 August 2017

page(s)

4694-4707

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Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions: H, O, and P Atoms

10 August 2017

cites work

1 reference

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Ring puckering: a metric for evaluating the accuracy of AM1, PM3, PM3CARB-1, and SCC-DFTB carbohydrate QM/MM simulations

12 July 2018

1 reference

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Accurate proton affinity and gas-phase basicity values for molecules important in biocatalysis

12 July 2018

1 reference

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Glycosidase inhibition: assessing mimicry of the transition state

12 July 2018

1 reference

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12 July 2018

1 reference

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Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements

12 July 2018

1 reference

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Targeting base excision repair to improve cancer therapies

12 July 2018

1 reference

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RM1: a reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I

12 July 2018

1 reference

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Toward a detailed understanding of base excision repair enzymes: transition state and mechanistic analyses of N-glycoside hydrolysis and N-glycoside transfer

12 July 2018

1 reference

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12 July 2018

Glycosidase mechanisms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4478602

Conserved domains of glycosyltransferases

12 July 2018

1 reference

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Structure of the Fusarium oxysporum endoglucanase I with a nonhydrolyzable substrate analogue: substrate distortion gives rise to the preferred axial orientation for the leaving group

12 July 2018

1 reference

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MOPAC: a semiempirical molecular orbital program

12 July 2018

1 reference

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Evaluating AM1/d-CB1 for Chemical Glycobiology QM/MM Simulations

12 July 2018

1 reference

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Interpreting medium ring canonical conformers by a triangular plane tessellation of the macrocycle.

25 September 2018

1 reference

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Substrate-assisted and nucleophilically assisted catalysis in bovine α1,3-galactosyltransferase. Mechanistic implications for retaining glycosyltransferases.

25 September 2018

1 reference

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Promiscuity in alkaline phosphatase superfamily. Unraveling evolution through molecular simulations.

25 September 2018

1 reference

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A PM3/d specific reaction parameterization for iron atom in the hydrogen abstraction catalyzed by soybean lipoxygenase-1.

25 September 2018

1 reference

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QCRNA 1.0: a database of quantum calculations for RNA catalysis

25 September 2018

1 reference

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Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4478602

Basicity of nucleophilic carbenes in aqueous and nonaqueous solvents-theoretical predictions.

25 September 2018

1 reference

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Hybrid QM/MM study of thio effects in transphosphorylation reactions: the role of solvation

25 September 2018

1 reference

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First-principle predictions of absolute pKa's of organic acids in dimethyl sulfoxide solution

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4478602

Hybrid QM/MM study of thio effects in transphosphorylation reactions

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4478602

Theoretical evaluation of pK(a) in phosphoranes: implications for phosphate ester hydrolysis

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4478602

Retaining Glycosyltransferase Mechanism Studied by QM/MM Methods: Lipopolysaccharyl-α-1,4-galactosyltransferase C Transfers α-Galactose via an Oxocarbenium Ion-like Transition State

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4478602

6 December 2018

Glycosidase mechanisms

1 reference

12 December 2020

The structure and stability of biological metaphosphate, phosphate, and phosphorane compounds in the gas phase and in solution

1 reference

12 December 2020

Multilevel and density functional electronic structure calculations of proton affinities and gas-phase basicities involved in biological phosphoryl transfer

1 reference

12 December 2020

Kinetic isotope effect studies of the reaction catalyzed by uracil DNA glycosylase: evidence for an oxocarbenium ion-uracil anion intermediate

1 reference

12 December 2020

Catalytic Itinerary in 1,3-1,4-β-Glucanase Unraveled by QM/MM Metadynamics. Charge Is Not Yet Fully Developed at the Oxocarbenium Ion-like Transition State

1 reference

12 December 2020

Identifiers

DOI

10.1021/CT500372S

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10 August 2017

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10 August 2017

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