scholarly journals A Simple Method for Including Polarization Effects in Solvation Free Energy Calculations When Using Fixed-Charge Force Fields: Alchemically Polarized Charges

ACS Omega ◽  
2020 ◽  
Vol 5 (28) ◽  
pp. 17170-17181
Author(s):  
Braden D. Kelly ◽  
William R. Smith
Keyword(s):  
Free Energy ◽  
Force Fields ◽  
Solvation Free Energy ◽  
Free Energy Calculations ◽  
Fixed Charge ◽  
Simple Method ◽  
Energy Calculations ◽  
Polarization Effects

scholarly journals A Simple Method for Including Polarization Effects in Solvation Free Energy Calculations When Using Fixed-Charge Force Fields: Alchemically Polarized Charges.

2020 ◽  
Author(s):  
Braden Kelly ◽  
William Smith
Keyword(s):  
Free Energy ◽  
Electronic Structure ◽  
Force Fields ◽  
Free Energy Calculations ◽  
Fixed Charge ◽  
Basis Sets ◽  
Hydration Free Energy ◽  
Simple Method ◽  
Test Set ◽  
Partial Charges

<div><div>The incorporation of polarizability in classical force-field molecular simulations is an ongoing area of research. We focus here on its application to hydration free energy simulations of organic molecules. In contrast to computationally complex approaches involving the development of explicitly polarizable force fields, we present herein a simple methodology for incorporating polarization into such simulations using standard fixed-charge force-fields, which we call the Alchemically Polarized Charges (APolQ) method. APolQ employs a standard classical alchemical free energy change simulation to calculate the free energy difference between a fully polarized solute particle in a condensed phase and its unpolarized state in a vacuum. One electronic structure (ES) calculation to of the electron densities is required for each state: for the former, we use a Polarizable Continuum Model (PCM), and for the latter we use vacuum-phase electronic structure calculations.</div><div><br></div><div>We applied APolQ to hydration free energy data for a test set of 45 neutral solute molecules in the FreeSolv database, and compared results obtained using three different water models (SPC/E, TIP3P, OPC3) and using MBIS and RESP partial charge methodologies. ES calculations were carried out at the MP2 level of theory and with cc-pVTZ and aug-cc-pVTZ basis sets. In comparison with AM1-BCC, we found that APolQ outperforms it for the test set. Despite our method using default GAFF parameters, the MBIS partial charges yield Absolute Average Deviations (AAD) 1.5 to 1.9 kJ·mol<sup>−1</sup> lower than AM1-BCC.</div><div><br></div><div>We conjecture that this method can be further improved by fitting the Lennard-Jones and torsional parameters to partial charges derived using MBIS or RESP methodologies. </div></div>

scholarly journals A Simple Method for Including Polarization Effects in Solvation Free Energy Calculations When Using Fixed-Charge Force Fields: Alchemically Polarized Charges.

2020 ◽  
Author(s):  
Braden Kelly ◽  
William Smith
Keyword(s):  
Free Energy ◽  
Electronic Structure ◽  
Force Fields ◽  
Free Energy Calculations ◽  
Fixed Charge ◽  
Basis Sets ◽  
Hydration Free Energy ◽  
Simple Method ◽  
Test Set ◽  
Partial Charges

<div><div>The incorporation of polarizability in classical force-field molecular simulations is an ongoing area of research. We focus here on its application to hydration free energy simulations of organic molecules. In contrast to computationally complex approaches involving the development of explicitly polarizable force fields, we present herein a simple methodology for incorporating polarization into such simulations using standard fixed-charge force-fields, which we call the Alchemically Polarized Charges (APolQ) method. APolQ employs a standard classical alchemical free energy change simulation to calculate the free energy difference between a fully polarized solute particle in a condensed phase and its unpolarized state in a vacuum. One electronic structure (ES) calculation to of the electron densities is required for each state: for the former, we use a Polarizable Continuum Model (PCM), and for the latter we use vacuum-phase electronic structure calculations.</div><div><br></div><div>We applied APolQ to hydration free energy data for a test set of 45 neutral solute molecules in the FreeSolv database, and compared results obtained using three different water models (SPC/E, TIP3P, OPC3) and using MBIS and RESP partial charge methodologies. ES calculations were carried out at the MP2 level of theory and with cc-pVTZ and aug-cc-pVTZ basis sets. In comparison with AM1-BCC, we found that APolQ outperforms it for the test set. Despite our method using default GAFF parameters, the MBIS partial charges yield Absolute Average Deviations (AAD) 1.5 to 1.9 kJ·mol<sup>−1</sup> lower than AM1-BCC.</div><div><br></div><div>We conjecture that this method can be further improved by fitting the Lennard-Jones and torsional parameters to partial charges derived using MBIS or RESP methodologies. </div></div>

A Simple Method to Predict and Interpret the Formation of Azeotropes in Binary Systems Using Conventional Solvation Free Energy Calculations

2019 ◽  
Vol 58 (50) ◽  
pp. 22626-22632 ◽  
Author(s):  
Sydnee N. Roese ◽  
Griffin V. Margulis ◽  
Alexa J. Schmidt ◽  
Cole B. Uzat ◽  
Justin D. Heintz ◽  
...  
Keyword(s):  
Free Energy ◽  
Binary Systems ◽  
Solvation Free Energy ◽  
Free Energy Calculations ◽  
Simple Method ◽  
Energy Calculations

A Simple Method for Incorporating Polarization Effects in Solvation Free Energy Calculations Using Fixed-Charge Force Fields

2020 ◽  
Author(s):  
Braden Kelly ◽  
William Smith
Keyword(s):  
Free Energy ◽  
Electronic Structure ◽  
Force Fields ◽  
Free Energy Calculations ◽  
Fixed Charge ◽  
Basis Sets ◽  
Hydration Free Energy ◽  
Simple Method ◽  
Test Set ◽  
Partial Charges

<div><div>The incorporation of polarizability in classical force-field molecular simulations is an ongoing area of research. We focus here on its application to hydration free energy simulations of organic molecules. In contrast to computationally complex approaches involving the development of explicitly polarizable force fields, we present herein a simple methodology for incorporating polarization into such simulations using standard fixed--charge force-fields, which we call the Alchemically Polarized Charges (APolQ) method. APolQ employs a standard classical alchemical free energy change simulation to calculate the free energy difference between a fully polarized solute particle in a condensed phase and its unpolarized state in a vacuum. One electronic structure (ES) calculation to of the electron densities is required for each state: for the former, we use a Polarizable Continuum Model (PCM), and for the latter we use vacuum-phase electronic structure calculations.</div><div><br></div><div>We applied APolQ to hydration free energy data for a test set of 45 neutral solute molecules in the FreeSolv database, and compared results obtained using three different water models (SPC/E, TIP3P, OPC3) and using MBIS and RESP partial charge methodologies. ES calculations were carried out at the MP2 level of theory and with cc-pVTZ and aug-cc-pVTZ basis sets. In comparison with AM1-BCC, we found that APolQ outperforms it for the test set. Despite our method using default GAFF parameters, the MBIS partial charges yield Absolute Average Deviations (AAD) 1.5 to 1.9 kJ·mol<sup>−1</sup> lower than AM1-BCC.</div><div><br></div><div>We conjecture that this method can be further improved by fitting the Lennard-Jones and torsional parameters to partial charges derived using MBIS or RESP methodologies. We note that APolQ can in principle be applied to any pure or mixed solvent.</div></div>

Performing solvation free energy calculations in LAMMPS using the decoupling approach

2020 ◽  
Vol 34 (6) ◽  
pp. 641-646
Author(s):  
Vikram Khanna ◽  
Jacob I. Monroe ◽  
Michael F. Doherty ◽  
Baron Peters
Keyword(s):  
Free Energy ◽  
Solvation Free Energy ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Decoupling Approach
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