Quantifying the Mechanism of Phosphate Monoester Hydrolysis in Aqueous Solution by Evaluating the Relevant Ab Initio QM/MM Free-Energy Surfaces

Nikolay V. Plotnikov; B. Ram Prasad; Suman Chakrabarty; Zhen T. Chu; Arieh Warshel

doi:10.1021/jp4020146

Quantifying the Mechanism of Phosphate Monoester Hydrolysis in Aqueous Solution by Evaluating the Relevant Ab Initio QM/MM Free-Energy Surfaces

The Journal of Physical Chemistry B ◽

10.1021/jp4020146 ◽

2013 ◽

Vol 117 (42) ◽

pp. 12807-12819 ◽

Cited By ~ 45

Author(s):

Nikolay V. Plotnikov ◽

B. Ram Prasad ◽

Suman Chakrabarty ◽

Zhen T. Chu ◽

Arieh Warshel

Keyword(s):

Aqueous Solution ◽

Free Energy ◽

Ab Initio ◽

Energy Surfaces

Download Full-text

Potential energy and free energy surfaces of the formic acid dimer: Correlated ab initio calculations and molecular dynamics simulationsElectronic supplementary information (ESI) available: Optimised geometries of the structures in Tables 1 and 2. See http://www.rsc.org/suppdata/cp/b1/b110872g/

Physical Chemistry Chemical Physics ◽

10.1039/b110872g ◽

2002 ◽

Vol 4 (11) ◽

pp. 2119-2122 ◽

Cited By ~ 39

Author(s):

Jana Chocholoušová ◽

Jaroslav Vacek ◽

Pavel Hobza

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Potential Energy ◽

Formic Acid ◽

Ab Initio Calculations ◽

Ab Initio ◽

Supplementary Information ◽

Energy Surfaces

Download Full-text

Molecular Clusters: Potential Energy and Free Energy Surfaces. Quantum Chemical ab initio and Computer Simulation Studies

Atomic clusters and nanoparticles. Agregats atomiques et nanoparticules - Les Houches - Ecole d’Ete de Physique Theorique ◽

10.1007/3-540-45621-x_12 ◽

2007 ◽

pp. 565-584

Author(s):

P. Hobza

Keyword(s):

Computer Simulation ◽

Free Energy ◽

Potential Energy ◽

Ab Initio ◽

Quantum Chemical ◽

Molecular Clusters ◽

Simulation Studies ◽

Computer Simulation Studies ◽

Energy Surfaces

Download Full-text

Hybrid ab Initio Quantum Mechanics/Molecular Mechanics Calculations of Free Energy Surfaces for Enzymatic Reactions: The Nucleophilic Attack in Subtilisin

The Journal of Physical Chemistry B ◽

10.1021/jp973480y ◽

1998 ◽

Vol 102 (12) ◽

pp. 2293-2301 ◽

Cited By ~ 115

Author(s):

J. Bentzien ◽

R. P. Muller ◽

J. Florián ◽

A. Warshel

Keyword(s):

Free Energy ◽

Quantum Mechanics ◽

Ab Initio ◽

Molecular Mechanics ◽

Nucleophilic Attack ◽

Enzymatic Reactions ◽

Molecular Mechanics Calculations ◽

Energy Surfaces

Download Full-text

Reaction path optimization and vibrational frequency analysis via ab initio QM/MM free energy gradient (FEG) method: application to isomerization process of glycine in aqueous solution

Theoretical Chemistry Accounts ◽

10.1007/s00214-011-0962-4 ◽

2011 ◽

Vol 130 (2-3) ◽

pp. 215-226 ◽

Cited By ~ 26

Author(s):

Norio Takenaka ◽

Yukichi Kitamura ◽

Yoshiyuki Koyano ◽

Toshio Asada ◽

Masataka Nagaoka

Keyword(s):

Aqueous Solution ◽

Free Energy ◽

Ab Initio ◽

Frequency Analysis ◽

Vibrational Frequency ◽

Reaction Path ◽

Path Optimization ◽

Isomerization Process ◽

Energy Gradient

Download Full-text

Ab Initio Evaluation of the Free Energy Surfaces for the General Base/Acid Catalyzed Thiolysis of Formamide and the Hydrolysis of Methyl Thiolformate: A Reference Solution Reaction for Studies of Cysteine Proteases

The Journal of Physical Chemistry B ◽

10.1021/jp010279l ◽

2001 ◽

Vol 105 (19) ◽

pp. 4471-4484 ◽

Cited By ~ 40

Author(s):

Marek Štrajbl ◽

Jan Florián ◽

Arieh Warshel

Keyword(s):

Free Energy ◽

Ab Initio ◽

Cysteine Proteases ◽

Reference Solution ◽

General Base ◽

Acid Catalyzed ◽

Solution Reaction ◽

Energy Surfaces ◽

Hydrolysis Of

Download Full-text

Potential Energy and Free Energy Surfaces of All Ten Canonical and Methylated Nucleic Acid Base Pairs: Molecular Dynamics and Quantum Chemical ab Initio Studies

The Journal of Physical Chemistry B ◽

10.1021/jp0104886 ◽

2001 ◽

Vol 105 (24) ◽

pp. 5804-5817 ◽

Cited By ~ 59

Author(s):

Martin Kabeláč ◽

Pavel Hobza

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Nucleic Acid ◽

Potential Energy ◽

Ab Initio ◽

Quantum Chemical ◽

Acid Base ◽

Base Pairs ◽

Nucleic Acid Base ◽

Energy Surfaces

Download Full-text

Efficient computation of free energy surfaces of chemical reactions using ab initio molecular dynamics with hybrid functionals and plane waves

Journal of Computational Chemistry ◽

10.1002/jcc.26222 ◽

2020 ◽

Vol 41 (19) ◽

pp. 1790-1797 ◽

Cited By ~ 1

Author(s):

Sagarmoy Mandal ◽

Nisanth N. Nair

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Ab Initio ◽

Chemical Reactions ◽

Plane Waves ◽

Ab Initio Molecular Dynamics ◽

Efficient Computation ◽

Hybrid Functionals ◽

Energy Surfaces

Download Full-text

Tautomerism of 1,2,3- and 1,2,4-triazole in the gas phase and in aqueous solution: a combined ab initio quantum mechanics and free energy perturbation study

The Journal of Physical Chemistry ◽

10.1021/j100377a016 ◽

1990 ◽

Vol 94 (14) ◽

pp. 5499-5501 ◽

Cited By ~ 36

Author(s):

James R. Cox ◽

Stephen. Woodcock ◽

Ian H. Hillier ◽

Mark A. Vincent

Keyword(s):

Aqueous Solution ◽

Free Energy ◽

Quantum Mechanics ◽

Ab Initio ◽

Gas Phase ◽

Free Energy Perturbation ◽

Energy Perturbation

Download Full-text

Ab Initio QM/MM Simulation with Proper Sampling: “First Principle” Calculations of the Free Energy of the Autodissociation of Water in Aqueous Solution

The Journal of Physical Chemistry B ◽

10.1021/jp021625h ◽

2002 ◽

Vol 106 (51) ◽

pp. 13333-13343 ◽

Cited By ~ 107

Author(s):

Marek Štrajbl ◽

Gongyi Hong ◽

Arieh Warshel

Keyword(s):

Aqueous Solution ◽

Free Energy ◽

Ab Initio ◽

First Principle ◽

First Principle Calculations ◽

Proper Sampling

Download Full-text

Ab initio/LD studies of chemical reactions in solution: Reference free-energy surfaces for acylation reactions occurring in serine and cysteine proteases

International Journal of Quantum Chemistry ◽

10.1002/(sici)1097-461x(2000)77:1<44::aid-qua6>3.0.co;2-a ◽

2000 ◽

Vol 77 (1) ◽

pp. 44-53 ◽

Cited By ~ 5

Author(s):

Marek ?trajbl ◽

Jan Flori�n ◽

Arieh Warshel

Keyword(s):

Free Energy ◽

Ab Initio ◽

Chemical Reactions ◽

Cysteine Proteases ◽

Energy Surfaces ◽

Acylation Reactions

Download Full-text