Graduation Year

2020

Document Type

Dissertation

Degree

Ph.D.

Degree Name

Doctor of Philosophy (Ph.D.)

Degree Granting Department

Chemistry

Major Professor

H. Lee Woodcock, Ph.D.

Committee Member

Arjan van der Vaart, Ph.D.

Committee Member

Wayne Guida, Ph.D.

Committee Member

David Merkler, Ph.D.

Committee Member

Joseph D. Larkin, Ph.D.

Keywords

Computational Chemistry, Statistical Mechanics, Computational Biochemistry, Free Energy Simulations, Docking Simulations, QM/MM, Molecular Dynamics Simulations

Abstract

Chemistry is the study of matter and its transformations. Computational chemistry uses computer models to study chemistry in all its intricate complexity. In this thesis I hope to accessibly introduce fundamental concepts central for computational chemistry including quantum mechanics, molecular mechanics, and multiscale modeling. I then present several works which I have conducted throughout my graduate career employing many different computational methods. The investigations described here can be summarized as follows. Chapter 2.1 modeling proteins involved in crustacean molting, and identifying possible inhibitors to this molting. Chapter 2.2 modeling d-fructose bound to synthetic saccharide receptors with hopes of improving saccharide binding and chemosensing. Finally, Chapter 2.3 modeling PET plastic oligomers and how they bind to two newly identified enzymes: PETase, and the more efficient double mutant PETase. I also discuss how computational models can and are being actively improved within the discipline. Those works include chapter 3.1 describing in depth, state of the art techniques for calculating free energy from molecular dynamics simulations. Chapter 3.2 illustrating particular challenge cases for free energy simulations. Chapter 3.3 highlights the need for benchmarked free energy simulation data sets, we provide one such data set to the computational chemistry community. And finally Chapter 3.4 applies free energy simulation methodology to the calculation of pKas of small molecules in solution. I found the field of computational chemistry serendipitously, but as I prepare to take my first steps into an independent career as a computational chemist I believe strongly my passions thrive in this field. This field which uses physics and mathematics to model chemical phenomena and apply those models to biochemical questions. I hope the reader may draw some inspiration from this fascinating subject matter as it has fueled me for years.

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