Development of a methodology to compute solvation free energies on the basis of the theory of energy representation for solutions represented with a polarizable force field

2012 ◽  
Vol 137 (21) ◽  
pp. 214503 ◽  
Author(s):  
Daiki Suzuoka ◽  
Hideaki Takahashi ◽  
Tatsuya Ishiyama ◽  
Akihiro Morita
Keyword(s):  
Force Field ◽  
Free Energies ◽  
Polarizable Force Field ◽  
Solvation Free Energies

scholarly journals Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field

2016 ◽  
Vol 37 (32) ◽  
pp. 2749-2758 ◽  
Author(s):  
Noor Asidah Mohamed ◽  
Richard T. Bradshaw ◽  
Jonathan W. Essex
Keyword(s):  
Force Field ◽  
Small Molecules ◽  
Free Energies ◽  
Polarizable Force Field ◽  
Solvation Free Energies

scholarly journals Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field

2010 ◽  
Vol 6 (4) ◽  
pp. 1181-1198 ◽  
Author(s):  
Christopher M. Baker ◽  
Pedro E. M. Lopes ◽  
Xiao Zhu ◽  
Benoît Roux ◽  
Alexander D. MacKerell
Keyword(s):  
Force Field ◽  
Free Energies ◽  
Accurate Calculation ◽  
Polarizable Force Field ◽  
Lennard Jones

Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field

2012 ◽  
Vol 8 (8) ◽  
pp. 2553-2558 ◽  
Author(s):  
Devleena Shivakumar ◽  
Edward Harder ◽  
Wolfgang Damm ◽  
Richard A. Friesner ◽  
Woody Sherman
Keyword(s):  
Force Field ◽  
Next Generation ◽  
Free Energies ◽  
Solvation Free Energies

Prediction of Solvation Free Energies with Thermodynamic Integration Using the General Amber Force Field

2014 ◽  
Vol 10 (8) ◽  
pp. 3570-3577 ◽  
Author(s):  
Silvia A. Martins ◽  
Sergio F. Sousa ◽  
Maria João Ramos ◽  
Pedro A. Fernandes
Keyword(s):  
Force Field ◽  
Thermodynamic Integration ◽  
Free Energies ◽  
Amber Force Field ◽  
Solvation Free Energies

scholarly journals Calculating binding free energies of host–guest systems using the AMOEBA polarizable force field

2016 ◽  
Vol 18 (44) ◽  
pp. 30261-30269 ◽  
Author(s):  
David R. Bell ◽  
Rui Qi ◽  
Zhifeng Jing ◽  
Jin Yu Xiang ◽  
Christopher Mejias ◽  
...  
Keyword(s):  
Force Field ◽  
Free Energies ◽  
Polarizable Force Field ◽  
Guest Binding ◽  
Binding Free Energies

Cucurbit[7]uril host–guest binding free energies are investigated using the AMOEBA polarizable force field.

Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field

2010 ◽  
Vol 6 (5) ◽  
pp. 1509-1519 ◽  
Author(s):  
Devleena Shivakumar ◽  
Joshua Williams ◽  
Yujie Wu ◽  
Wolfgang Damm ◽  
John Shelley ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Force Field ◽  
Free Energy Perturbation ◽  
Free Energies ◽  
Energy Perturbation ◽  
Solvation Free Energies

scholarly journals Optimized Halogen Atomic Radii for PBSA Calculations Using Off-Center Point-Charges

2021 ◽  
Author(s):  
Andreia Fortuna ◽  
Paulo J. Costa
Keyword(s):  
Force Field ◽  
Free Energies ◽  
Field Methods ◽  
Amber Force Field ◽  
Center Point ◽  
Common Strategy ◽  
Poisson Boltzmann ◽  
General Force ◽  
Solvation Free Energies ◽  
Atomic Radii

<div>In force field methods, the usage of off-center point-charges, also called extra-points (EPs), is a common strategy to tackle the anisotropy of the electrostatic potential of covalently-bonded halogens (X), thus allowing the description of halogen bonds (XBs) at the molecular mechanics / molecular dynamics (MM/MD) level. Diverse EP implementations exist in the literature differing on the charge sets and/or the X–EP distances. Poisson–Boltzmann and surface area (PBSA) calculations can be used to obtain solvation free energies (∆G solv ) of small molecules, often to compute binding free energies (∆G bind ) at the MM PBSA level. This method depends, among other parameters, on the empirical assignment of atomic radii (PB radii). Given the multiplicity of off-center point-charges models and the lack of specific PB radii for halogens compatible with such implementations, in this work we assessed the performance of PBSA calculations for the estimation of ∆G solv values in water (∆G hyd ), also conducting an optimization of the halogen PB radii (Cl, Br, and I) for each EP model. We not only expand the usage of EP models in the scope of the General AMBER Force Field (GAFF) but also provide the first optimized halogen PB radii in the context of the CHARMM General Force Field (CGenFF), thus contributing to improving the description of halogenated compounds in PBSA calculations.</div>

scholarly journals Optimized Halogen Atomic Radii for PBSA Calculations Using Off-Center Point-Charges

2021 ◽  
Author(s):  
Andreia Fortuna ◽  
Paulo J. Costa
Keyword(s):  
Force Field ◽  
Free Energies ◽  
Field Methods ◽  
Amber Force Field ◽  
Center Point ◽  
Common Strategy ◽  
Poisson Boltzmann ◽  
General Force ◽  
Solvation Free Energies ◽  
Atomic Radii

<div>In force field methods, the usage of off-center point-charges, also called extra-points (EPs), is a common strategy to tackle the anisotropy of the electrostatic potential of covalently-bonded halogens (X), thus allowing the description of halogen bonds (XBs) at the molecular mechanics / molecular dynamics (MM/MD) level. Diverse EP implementations exist in the literature differing on the charge sets and/or the X–EP distances. Poisson–Boltzmann and surface area (PBSA) calculations can be used to obtain solvation free energies (∆G solv ) of small molecules, often to compute binding free energies (∆G bind ) at the MM PBSA level. This method depends, among other parameters, on the empirical assignment of atomic radii (PB radii). Given the multiplicity of off-center point-charges models and the lack of specific PB radii for halogens compatible with such implementations, in this work we assessed the performance of PBSA calculations for the estimation of ∆G solv values in water (∆G hyd ), also conducting an optimization of the halogen PB radii (Cl, Br, and I) for each EP model. We not only expand the usage of EP models in the scope of the General AMBER Force Field (GAFF) but also provide the first optimized halogen PB radii in the context of the CHARMM General Force Field (CGenFF), thus contributing to improving the description of halogenated compounds in PBSA calculations.</div>

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