Ab Initio Free Energy Perturbation Calculations of Solvation Free Energy Using the Frozen Density Functional Approach

1994 ◽  
Vol 98 (20) ◽  
pp. 5183-5187 ◽  
Author(s):  
T. Wesolowski ◽  
A. Warshel
Keyword(s):  
Free Energy ◽  
Ab Initio ◽  
Density Functional ◽  
Solvation Free Energy ◽  
Functional Approach ◽  
Free Energy Perturbation ◽  
Energy Perturbation

scholarly journals Solvation Free Energy of Protonated Lysine: Molecular Dynamics Study

2021 ◽  
Vol 7 (2) ◽  
pp. 69-75
Author(s):  
S. P. Khanal ◽  
B. Poudel ◽  
R. P. Koirala ◽  
N. P. Adhikari
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Energy Difference ◽  
Solvation Free Energy ◽  
Free Energy Perturbation ◽  
Free Energy Difference ◽  
Free Energy Of Solvation ◽  
Acceptance Ratio ◽  
Energy Perturbation ◽  
Dynamics Simulations

In the present work, we have used an alchemical approach for calculating solvation free energy of protonated lysine in water from molecular dynamics simulations. These approaches use a non-physical pathway between two end states in order to compute free energy difference from the set of simulations. The solute is modeled using bonded and non-bonded interactions described by OPLS-AA potential, while four different water models: TIP3P, SPC, SPC/E and TIP4P are used. The free energy of solvation of protonated lysine in water has been estimated using thermodynamic integration, free energy perturbation, and Bennett acceptance ratio methods at 310 K temperature. The contributions to the free energy due to van der Waals and electrostatics parameters are also separately computed. The estimated values of free energy of solvation using different methods are in well agreement with previously reported experimental value within 14 %.

scholarly journals Solvation free energy of light alkanes in polar and amphiphilic environments

BIBECHANA ◽  
2018 ◽  
Vol 16 ◽  
pp. 92-105
Author(s):  
Sunil Pokharel ◽  
Shyam Prakash Khanal ◽  
N P Adhikari
Keyword(s):  
Free Energy ◽  
Solvation Free Energy ◽  
Intermolecular Potential ◽  
Free Energy Perturbation ◽  
Biological Macromolecules ◽  
Molecular Models ◽  
Acceptance Ratio ◽  
Energy Perturbation ◽  
Dynamics Simulations ◽  
Atom Potential

Computer simulations of molecular models are powerful technique that have improved the under- standing of many biochemical phenomena. The method is frequently applied to study the motions of biological macromolecules such as protein and nucleic acids, which can be useful for interpreting the results of certain biophysical experiments. In this work, we have estimated the solvation free energy for light alkane (methane, ethane, propane and n-butane) dissolved in water and methanol respectively over a broad range of temperatures, from 275 K to 375 K, using molecular dynamics simulations. The alkane (methane, ethane, propane and n-butane), and methanol molecules are described by the OPLS-AA (Optimized Potentials for Liquid Simulations-All Atom) potential, while water is modeled by TIP3P (Transferable Intermolecular Potential with 3-Points) model. We have used the free energy perturbation method (Bennett Acceptance Ratio (BAR) method) for the calculation of free energy of solvation. The estimated values of solvation free energy of alkane in the corresponding solvents agree well with the available experimental data.BIBECHANA 16 (2019) 91-104

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