Purdue University Graduate School
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QM/MM Applications and Corrections for Chemical Reactions

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posted on 2023-05-18, 12:46 authored by Bryant J KimBryant J Kim

In this thesis, we present novel computational methods and frameworks to address the challenges associated with the determination of free energy profiles for condensed-phase chemical reactions using combined quantum mechanical and molecular mechanical (QM/MM) approaches. We focus on overcoming issues related to force matching, molecular polarizability, and convergence of free energy profiles. First, we introduce a method called Reaction Path-Force Matching in Collective Variables (RP-FM-CV) that efficiently carries out ab initio QM/MM free energy simulations through mean force fitting. This method provides accurate and robust simulations of solution-phase chemical reactions by significantly reducing deviations on the collective variables forces, thereby bringing simulated free energy profiles closer to experimental and benchmark AI/MM results. Second, we explore the role of pairwise repulsive correcting potentials in generating converged free energy profiles for chemical reactions using QM/MM simulations. We develop a free energy correcting model that sheds light on the behavior of repulsive pairwise potentials with large force deviations in collective variables. Our findings contribute to a deeper understanding of force matching models, paving the way for more accurate predictions of free energy profiles in chemical reactions. Next, we address the underpolarization problem in semiempirical (SE) molecular orbital methods by introducing a hybrid framework called doubly polarized QM/MM (dp-QM/MM). This framework improves the response property of SE/MM methods through high-level molecular polarizability fitting using machine learning (ML)-derived corrective polarizabilities, referred to as chaperone polarizabilities. We demonstrate the effectiveness of the dp-QM/MM method in simulating the Menshutkin reaction in water, showing that ML chaperones significantly reduce the error in solute molecular polarizability, bringing simulated free energy profiles closer to experimental results. In summary, this thesis presents a series of novel methods and frameworks that improve the accuracy and reliability of free energy profile estimations in condensed-phase chemical reactions using QM/MM simulations. By addressing the challenges of force matching, molecular polarizability, and convergence, these advancements have the potential to impact various fields, including computational chemistry, materials science, and drug design.


Degree Type

  • Doctor of Philosophy


  • Chemistry

Campus location

  • Indianapolis

Advisor/Supervisor/Committee Chair

Jingzhi Pu

Additional Committee Member 2

Christoph A. Naumann

Additional Committee Member 3

Ian K. Webb

Additional Committee Member 4

Jonah Z. Vilseck