Exploring the ab initio/classical free energy perturbation method: The hydration free energy of water

Shinichi Sakane; Eric M. Yezdimer; Wenbin Liu; Jose A. Barriocanal; Douglas J. Doren; Robert H. Wood

doi:10.1063/1.1305862

Exploring the ab initio/classical free energy perturbation method: The hydration free energy of water

The Journal of Chemical Physics ◽

10.1063/1.1305862 ◽

2000 ◽

Vol 113 (7) ◽

pp. 2583-2593 ◽

Cited By ~ 21

Author(s):

Shinichi Sakane ◽

Eric M. Yezdimer ◽

Wenbin Liu ◽

Jose A. Barriocanal ◽

Douglas J. Doren ◽

...

Keyword(s):

Free Energy ◽

Perturbation Method ◽

Ab Initio ◽

Free Energy Perturbation ◽

Hydration Free Energy ◽

Energy Perturbation

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Ab initio quantum mechanics-based free energy perturbation method for calculating relative solvation free energies

Journal of Computational Chemistry ◽

10.1002/jcc.20510 ◽

2006 ◽

Vol 28 (2) ◽

pp. 491-494 ◽

Cited By ~ 24

Author(s):

M. Rami Reddy ◽

U. C. Singh ◽

Mark D. Erion

Keyword(s):

Free Energy ◽

Quantum Mechanics ◽

Perturbation Method ◽

Ab Initio ◽

Free Energy Perturbation ◽

Free Energies ◽

Energy Perturbation ◽

Solvation Free Energies

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Relative solvation free energies calculated using an ab initio QM/MM-based free energy perturbation method: dependence of results on simulation length

Journal of Computer-Aided Molecular Design ◽

10.1007/s10822-009-9300-5 ◽

2009 ◽

Vol 23 (12) ◽

pp. 837-843 ◽

Cited By ~ 2

Author(s):

M. Rami Reddy ◽

Mark D. Erion

Keyword(s):

Free Energy ◽

Perturbation Method ◽

Ab Initio ◽

Free Energy Perturbation ◽

Free Energies ◽

Energy Perturbation ◽

Solvation Free Energies

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The Hydration Free Energy of Aqueous Na+and Cl-at High Temperatures Predicted by ab Initio/Classical Free Energy Perturbation: 973 K with 0.535 g/cm3and 573 K with 0.725 g/cm3

The Journal of Physical Chemistry A ◽

10.1021/jp013568i ◽

2002 ◽

Vol 106 (7) ◽

pp. 1409-1418 ◽

Cited By ~ 23

Author(s):

Wenbin Liu ◽

Shinichi Sakane ◽

Robert H. Wood ◽

Douglas J. Doren

Keyword(s):

Free Energy ◽

Ab Initio ◽

High Temperatures ◽

Free Energy Perturbation ◽

Hydration Free Energy ◽

Energy Perturbation

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Density and Temperature Dependences of Hydration Free Energy of Na+and Cl-at Supercritical Conditions Predicted by ab Initio/Classical Free Energy Perturbation

The Journal of Physical Chemistry B ◽

10.1021/jp034226a ◽

2003 ◽

Vol 107 (35) ◽

pp. 9505-9513 ◽

Cited By ~ 9

Author(s):

Wenbin Liu ◽

Robert H. Wood ◽

Douglas J. Doren

Keyword(s):

Free Energy ◽

Ab Initio ◽

Free Energy Perturbation ◽

Hydration Free Energy ◽

Supercritical Conditions ◽

Temperature Dependences ◽

Energy Perturbation

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A free-energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): Application to highly solvent-dependent reactions

Journal of Computational Chemistry ◽

10.1002/jcc.21653 ◽

2010 ◽

Vol 32 (5) ◽

pp. 778-786 ◽

Cited By ~ 12

Author(s):

Kenji Hori ◽

Toru Yamaguchi ◽

Keita Uezu ◽

Michinori Sumimoto

Keyword(s):

Monte Carlo ◽

Free Energy ◽

Monte Carlo Simulations ◽

Perturbation Method ◽

Free Energy Perturbation ◽

Quantum Mechanical ◽

Quantum Mechanical Calculations ◽

Energy Perturbation

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Binding free energy calculation of human beta defensin 3 with negatively charged lipid bilayer using free energy perturbation method

Biophysical Chemistry ◽

10.1016/j.bpc.2021.106662 ◽

2021 ◽

pp. 106662

Author(s):

Ann Brewer ◽

Liqun Zhang

Keyword(s):

Free Energy ◽

Perturbation Method ◽

Lipid Bilayer ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Free Energy Perturbation ◽

Energy Calculation ◽

Binding Free Energy Calculation ◽

Energy Perturbation

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Achieving fast convergence of ab initio free energy perturbation calculations with the adaptive force-matching method

Highlights in Theoretical Chemistry - From Quantum Mechanics to Force Fields ◽

10.1007/978-3-642-34450-3_13 ◽

2012 ◽

pp. 149-159

Author(s):

Eric R. Pinnick ◽

Camilo E. Calderon ◽

Andrew J. Rusnak ◽

Feng Wang

Keyword(s):

Free Energy ◽

Ab Initio ◽

Fast Convergence ◽

Free Energy Perturbation ◽

Matching Method ◽

Force Matching ◽

Energy Perturbation

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Calculation of relative binding affinities of fructose 1,6-bisphosphatase mutants with adenosine monophosphate using free energy perturbation method

Journal of Computational Chemistry ◽

10.1002/jcc.20617 ◽

2007 ◽

Vol 28 (5) ◽

pp. 932-937 ◽

Cited By ~ 8

Author(s):

Ravichandra Mutyala ◽

R. N. Reddy ◽

M. Sumakanth ◽

P. Reddanna ◽

M. Rami Reddy

Keyword(s):

Free Energy ◽

Perturbation Method ◽

Adenosine Monophosphate ◽

Free Energy Perturbation ◽

Binding Affinities ◽

Relative Binding ◽

Fructose 1,6 Bisphosphatase ◽

Energy Perturbation

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Computational Prediction of Molecular Hydration Entropy with Hybrid Scaled Particle Theory and Free-Energy Perturbation Method

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.5b00325 ◽

2015 ◽

Vol 11 (10) ◽

pp. 4933-4942 ◽

Cited By ~ 9

Author(s):

Hwanho Choi ◽

Hongsuk Kang ◽

Hwangseo Park

Keyword(s):

Free Energy ◽

Perturbation Method ◽

Computational Prediction ◽

Free Energy Perturbation ◽

Scaled Particle Theory ◽

Particle Theory ◽

Energy Perturbation

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Calculation of Absolute Protein–Ligand Binding Constants with the Molecular Dynamics Free Energy Perturbation Method

Methods in Molecular Biology - Molecular Modeling of Proteins ◽

10.1007/978-1-59745-177-2_6 ◽

2008 ◽

pp. 109-120 ◽

Cited By ~ 7

Author(s):

Hyung-June Woo

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Ligand Binding ◽

Perturbation Method ◽

Binding Constants ◽

Free Energy Perturbation ◽

Energy Perturbation

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