Quantum mechanics/molecular mechanics dual Hamiltonian free energy perturbation

Iakov Polyak; Tobias Benighaus; Eliot Boulanger; Walter Thiel

doi:10.1063/1.4817402

Quantum mechanics/molecular mechanics dual Hamiltonian free energy perturbation

The Journal of Chemical Physics ◽

10.1063/1.4817402 ◽

2013 ◽

Vol 139 (6) ◽

pp. 064105 ◽

Cited By ~ 28

Author(s):

Iakov Polyak ◽

Tobias Benighaus ◽

Eliot Boulanger ◽

Walter Thiel

Keyword(s):

Free Energy ◽

Quantum Mechanics ◽

Molecular Mechanics ◽

Free Energy Perturbation ◽

Energy Perturbation

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Studies on the binding of pepstatin and its derivatives to Rhizopus pepsin by quantum mechanics, molecular mechanics, and free energy perturbation methods

Journal of the American Chemical Society ◽

10.1021/ja00018a004 ◽

1991 ◽

Vol 113 (18) ◽

pp. 6735-6750 ◽

Cited By ~ 11

Author(s):

B. G. Rao ◽

U. Chandra Singh

Keyword(s):

Free Energy ◽

Quantum Mechanics ◽

Molecular Mechanics ◽

Perturbation Methods ◽

Free Energy Perturbation ◽

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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Molecular recognition by β-cyclodextrin derivatives: molecular dynamics, free-energy perturbation and molecular mechanics/ Poisson-Boltzmann surface area goals and problems

Theoretical Chemistry Accounts ◽

10.1007/s00214-002-0384-4 ◽

2002 ◽

Vol 108 (5) ◽

pp. 286-292 ◽

Cited By ~ 14

Author(s):

Ivan Beà ◽

Carlos Jaime ◽

Peter Kollman

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Recognition ◽

Molecular Mechanics ◽

Surface Area ◽

Free Energy Perturbation ◽

Cyclodextrin Derivatives ◽

Poisson Boltzmann ◽

Energy Perturbation

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A theoretical study of tautomerism in the gas phase and aqueous solution: a combined use of state-of-the-art ab initio quantum mechanics and free energy-perturbation methods

Journal of the American Chemical Society ◽

10.1021/ja00255a010 ◽

1987 ◽

Vol 109 (21) ◽

pp. 6283-6289 ◽

Cited By ~ 109

Author(s):

Piotr Cieplak ◽

Paul Bash ◽

U. Chandra Singh ◽

Peter A. Kollman

Keyword(s):

Aqueous Solution ◽

Free Energy ◽

Quantum Mechanics ◽

Gas Phase ◽

Perturbation Methods ◽

Theoretical Study ◽

State Of The Art ◽

Free Energy Perturbation ◽

Combined Use ◽

Energy Perturbation

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Relative Binding Affinities of Fructose-1,6-Bisphosphatase Inhibitors Calculated Using a Quantum Mechanics-Based Free Energy Perturbation Method

Journal of the American Chemical Society ◽

10.1021/ja072905j ◽

2007 ◽

Vol 129 (30) ◽

pp. 9296-9297 ◽

Cited By ~ 27

Author(s):

M. Rami Reddy ◽

Mark D. Erion

Keyword(s):

Free Energy ◽

Quantum Mechanics ◽

Perturbation Method ◽

Free Energy Perturbation ◽

Binding Affinities ◽

Relative Binding ◽

Fructose 1,6 Bisphosphatase ◽

Energy Perturbation

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Application of the quantum mechanics and free energy perturbation methods to study molecular processes

International Journal of Quantum Chemistry ◽

10.1002/qua.560320811 ◽

1987 ◽

Vol 32 (S14) ◽

pp. 65-74 ◽

Cited By ~ 11

Author(s):

Piotr Cieplak ◽

U. Chandra Singh ◽

Peter A. Kollman

Keyword(s):

Free Energy ◽

Quantum Mechanics ◽

Perturbation Methods ◽

Free Energy Perturbation ◽

Molecular Processes ◽

Energy Perturbation

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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

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Characterization of the effect of functional groups substitution at the 2-position of adenine on the stability of a duplex dodecamer d(CGCGAATTCGCG)2 by molecular mechanics and free energy perturbation method

Computer Simulation of Biomolecular Systems ◽

10.1007/978-94-017-1120-3_20 ◽

1997 ◽

pp. 563-600

Author(s):

Hiroshi Kuramochi ◽

U. Chandra Singh

Keyword(s):

Free Energy ◽

Perturbation Method ◽

Molecular Mechanics ◽

Functional Groups ◽

Free Energy Perturbation ◽

Energy Perturbation ◽

The Stability

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Free energy perturbation method for chemical reactions in the condensed phase: a dynamic approach based on a combined quantum and molecular mechanics potential

Journal of the American Chemical Society ◽

10.1021/ja00260a028 ◽

1987 ◽

Vol 109 (26) ◽

pp. 8092-8094 ◽

Cited By ~ 219

Author(s):

Paul A. Bash ◽

Martin J. Field ◽

Martin Karplus

Keyword(s):

Free Energy ◽

Perturbation Method ◽

Molecular Mechanics ◽

Chemical Reactions ◽

Condensed Phase ◽

Free Energy Perturbation ◽

Dynamic Approach ◽

Energy Perturbation

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Development of a Quantum Mechanics-Based Free-Energy Perturbation Method: Use in the Calculation of Relative Solvation Free Energies

Journal of the American Chemical Society ◽

10.1021/ja049281r ◽

2004 ◽

Vol 126 (20) ◽

pp. 6224-6225 ◽

Cited By ~ 20

Author(s):

M. Rami Reddy ◽

U. C. Singh ◽

Mark D. Erion

Keyword(s):

Free Energy ◽

Quantum Mechanics ◽

Perturbation Method ◽

Free Energy Perturbation ◽

Free Energies ◽

Energy Perturbation ◽

Solvation Free Energies

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