(Q33892565)

29 July 2017

title

Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions (English)

1 reference

29 July 2017

2

William L Jorgensen

1 reference

29 July 2017

Orlando Acevedo

1

1 reference

29 July 2017

language of work or name

English

0 references

publication date

1 January 2010

1 reference

Accounts of Chemical Research

29 July 2017

published in

1 reference

29 July 2017

volume

43

1 reference

29 July 2017

issue

1

1 reference

29 July 2017

page(s)

142-151

1 reference

Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria

29 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

QM/MM methods for biomolecular systems

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Origin of the activity drop with the E50D variant of catalytic antibody 34E4 for Kemp elimination

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Extension of the PDDG/PM3 Semiempirical Molecular Orbital Method to Sulfur, Silicon, and Phosphorus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Kemp elimination catalysts by computational enzyme design

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Why urea eliminates ammonia rather than hydrolyzes in aqueous solution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

New algorithms and an in silico benchmark for computational enzyme design

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Mechanisms and free energies of enzymatic reactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Asymmetric catalysis by chiral hydrogen-bond donors

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Potential energy functions for atomic-level simulations of water and organic and biomolecular systems

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Evidence for distinct roles in catalysis for residues of the serine-serine-lysine catalytic triad of fatty acid amide hydrolase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Insight into a natural Diels-Alder reaction from the structure of macrophomate synthase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Structural adaptations in a membrane enzyme that terminates endocannabinoid signaling

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Molecular dynamics simulations of biological reactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Molecular characterization of an enzyme that degrades neuromodulatory fatty-acid amides

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Understanding Rate Accelerations for Diels-Alder Reactions in Solution Using Enhanced QM/MM Methodology.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Computation of Accurate Activation Barriers for Methyl-Transfer Reactions of Sulfonium and Ammonium Salts in Aqueous Solution

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

NO-MNDO: Reintroduction of the Overlap Matrix into MNDO.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Multidimensional exploration of valley-ridge inflection points on potential-energy surfaces

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

The putative Diels-Alderase macrophomate synthase is an efficient aldolase

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

A new solvent-dependent mechanism for a triazolinedione ene reaction

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Elucidation of hydrolysis mechanisms for fatty acid amide hydrolase and its Lys142Ala variant via QM/MM simulations.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Monte Carlo simulations of biomolecules: The MC module in CHARMM.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Influence of inter- and intramolecular hydrogen bonding on kemp decarboxylations from QM/MM simulations

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Macrophomate synthase: QM/MM simulations address the Diels-Alder versus Michael-Aldol reaction mechanism

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Positional ordering of reacting groups contributes significantly to the efficiency of proton transfer at an antibody active site

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Steric retardation of SN2 reactions in the gas phase and solution

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Accuracy of free energies of hydration using CM1 and CM3 atomic charges

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

PDDG/PM3 and PDDG/MNDO: improved semiempirical methods.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Parameterization of charge model 3 for AM1, PM3, BLYP, and B3LYP

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880334

Solvent effects and mechanism for a nucleophilic aromatic substitution from QM/MM simulations

29 October 2018

1 reference

12 December 2020

Medium effects on the decarboxylation of a biotin model in pure and mixed solvents from QM/MM simulations

1 reference

12 December 2020

Performance of B3LYP Density Functional Methods for a Large Set of Organic Molecules

1 reference

12 December 2020

Extension of the PDDG/PM3 and PDDG/MNDO semiempirical molecular orbital methods to the halogens

1 reference

12 December 2020

Cope elimination: elucidation of solvent effects from QM/MM simulations

1 reference

12 December 2020

Elucidation of Rate Variations for a Diels-Alder Reaction in Ionic Liquids from QM/MM Simulations

1 reference

12 December 2020

Comparison of SCC-DFTB and NDDO-based semiempirical molecular orbital methods for organic molecules

1 reference

12 December 2020

Identifiers

DOI

10.1021/AR900171C

1 reference

29 July 2017

1 reference

29 July 2017

1 reference