(Q34267439)

1 August 2017

title

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

1 reference

1 August 2017

3

Darrin M York

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1 August 2017

Adam Moser

1

1 reference

1 August 2017

Kevin Range

series ordinal

2

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1 August 2017

language of work or name

English

0 references

publication date

1 November 2010

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Journal of Physical Chemistry B

1 August 2017

published in

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1 August 2017

volume

114

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1 August 2017

issue

43

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1 August 2017

page(s)

13911-13921

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

1 August 2017

cites work

1 reference

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Reproducing basic pKa values for turkey ovomucoid third domain using a polarizable force field

6 July 2018

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pH-dependent mechanism of nitric oxide release in nitrophorins 2 and 4

6 July 2018

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Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies

6 July 2018

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Solvent Structure and Hammerhead Ribozyme Catalysis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

Recent advances in implicit solvent-based methods for biomolecular simulations

6 July 2018

1 reference

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Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation

6 July 2018

1 reference

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Toward the accurate first-principles prediction of ionization equilibria in proteins.

6 July 2018

1 reference

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Prediction and rationalization of protein pKa values using QM and QM/MM methods.

6 July 2018

1 reference

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Phosphoryl group transfer: evolution of a catalytic scaffold

6 July 2018

1 reference

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Isotope effects in the study of phosphoryl and sulfuryl transfer reactions

6 July 2018

1 reference

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Generalized Gradient Approximation Made Simple

6 July 2018

1 reference

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

Density-functional exchange-energy approximation with correct asymptotic behavior

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

The dimensions and shapes of the furanose rings in nucleic acids

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

Bond order and charge localization in nucleoside phosphorothioates

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

Ribozyme-catalyzed and nonenzymatic reactions of phosphate diesters: rate effects upon substitution of sulfur for a nonbridging phosphoryl oxygen atom

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations.

6 July 2018

1 reference

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Molecular dynamics at constant pH and reduction potential: application to cytochrome c(3)

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

A universal approach to solvation modeling.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

Stabilization of amino acid zwitterions with varieties of anionic species: the intrinsic mechanism

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

Bond or cage effect: how nitrophorins transport and release nitric oxide.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 2. Application to transphosphorylation thio effects in solution.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 1. Implementation.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

QCRNA 1.0: a database of quantum calculations for RNA catalysis

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

A comprehensive evaluation of the kinetic method applied in the determination of the proton affinity of the nucleic acid molecules.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

The determinants of carboxyl pKa values in turkey ovomucoid third domain

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

The proton affinity of proline analogs using the kinetic method with full entropy analysis

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

The pK(a)'s of 2'-hydroxyl group in nucleosides and nucleotides.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

Ras catalyzes GTP hydrolysis by shifting negative charges from gamma- to beta-phosphate as revealed by time-resolved FTIR difference spectroscopy

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

First Principles Calculations of Aqueous pKaValues for Organic and Inorganic Acids Using COSMO−RS Reveal an Inconsistency in the Slope of the pKaScale

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2970571

Gas-phase structure of protonated histidine and histidine methyl ester: combined experimental mass spectrometry and theoretical ab initio study

28 October 2018

1 reference

12 December 2020

Pseudorotation of natural and chemically modified biological phosphoranes: implications for RNA catalysis

1 reference

12 December 2020

1 reference

12 December 2020

The pKaof the Internucleotidic 2‘-Hydroxyl Group in Diribonucleoside (3‘→5‘) Monophosphates

1 reference

12 December 2020

Explanation by a putative triester-like mechanism for the thio effects and Mn2+ rescues in reactions catalyzed by a hammerhead ribozyme

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

Structure and binding of Mg(II) ions and di-metal bridge complexes with biological phosphates and phosphoranes

1 reference

12 December 2020

Proton affinity of uracil. A computational study of protonation sites

1 reference

12 December 2020

Acidic hydrolysis of deoxycytidine and deoxyuridine derivatives. The general mechanism of deoxyribonucleoside hydrolysis

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

Accurate pK(a) calculations for carboxylic acids using complete basis set and Gaussian-n models combined with CPCM continuum solvation methods

1 reference

12 December 2020

Optimised parameters for A-DNA and B-DNA

1 reference

12 December 2020

Transesterification thio effects of phosphate diesters: free energy barriers and kinetic and equilibrium isotope effects from density-functional theory

1 reference

12 December 2020

Kinetic isotope effects on thio-substituted biological phosphoryl transfer reactions from density-functional theory

1 reference

12 December 2020

Density functional study of the in-line mechanism of methanolysis of cyclic phosphate and thiophosphate esters in solution: insight into thio effects in RNA transesterification

1 reference

12 December 2020

Pseudorotation barriers of biological oxyphosphoranes: a challenge for simulations of ribozyme catalysis

1 reference

12 December 2020

Conformational analysis of the sugar ring in nucleosides and nucleotides. New description using the concept of pseudorotation

1 reference

12 December 2020

Identifiers

DOI

10.1021/JP107450N

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1 August 2017

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1 August 2017

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