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Development of Improved Molecular Simulation Methodologies for Free Energy Calculations and Chemical Reaction Equilibria, and Application to CO2 Reactive Absorption

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Title: Development of Improved Molecular Simulation Methodologies for Free Energy Calculations and Chemical Reaction Equilibria, and Application to CO2 Reactive Absorption
Author: Kelly, Braden
Department: Department of Mathematics and Statistics
Program: Biophysics
Advisor: Smith, William
Abstract: This thesis explores and advances the methodology for in silico prediction of the composition of chemical systems at chemical reaction equilibrium (CRE), with the ultimate goal of their application to predictions of properties related to CO2 reactive absorption in appropriate solvents. Two major contributions are the application of a hybrid macroscopic/microscopic approach to solving the CRE problem, and incorporating polarization into alchemical free energy calculations. Computational methods for the CRE problem have been well established for calculation with macroscopic thermodynamic models, but are restricted in their usefulness due to their heavy reliance on parameters fitted to experimental data. On the other hand, at the microscopic level there exist well-established molecular simulation algorithms that use force-fields containing relatively few parameters for solving the CRE problem. Unfortunately they are system specific, and limited to either small molecules, or for larger molecules, very long simulation lengths, making them impractical for comparing a multitude of solvents for carbon capture applications. In this work we have developed a hybrid approach using molecular simulation free energy calculation techniques, paired with the macroscopic algorithm approach allowing the CRE problem to be rapidly solved. This avoids the major pitfalls of the individual microscopic/macroscopic approaches - relatively few parameters are required, and they have theoretical significance, allowing them to be used over a wide range of conditions. The CRE problem can be solved for large molecules, and without any system specific requirements. While using fewer parameters, classical FFs assume fixed partial charges located at atom centers. This is a serious limitation when the environment around a molecule changes, but its polarity stays constant. Free energy calculations are used to calculate the chemical potentials of species in solution, and the success of the CRE algorithm is dependent on the accuracy of the chemical potentials used in the calculation. We developed two methods, which, without using any additional parameters, account for the change in polarity experienced by a solute molecule during an alchemical free energy calculation. This results in more accurate free energy calculations than are possible using conventional FFs. We applied these methods to calculating protonation constants (pKa) for 26 amines relevant to carbon capture, and found improved results compared to conventional methods.
URI: http://hdl.handle.net/10214/17861
Date: 2020-04
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