Electronic Theses and Dissertations

Date

2024

Document Type

Dissertation

Degree Name

Doctor of Philosophy

Department

Chemistry

Committee Chair

Nathan DeYonker

Committee Member

William A. Alexander

Committee Member

Yongmei Wang

Committee Member

Daniel R. Nascimento

Committee Member

Qianyi Cheng

Abstract

Magnesium tricarbide isomers are studied herein with coupled cluster theory and multireference configuration interaction to support their possible detection in astrochemical environments such as the circumstellar envelope surrounding the star IRC +10216 or in terrestrial laboratories. Overall, this work offers quantum chemical insight of rovibrational spectroscopic data for MgC3 using a quartic force field (QFF) based on CCSD(T) and CCSD(T)-F12 levels of theory at the complete basis set (CBS) limit. Additional corrections with small basis set CCSDT(Q) and scalar relativistic effects are also included in the analysis. Coupled cluster-based composite energies and multireference configuration interaction both predict that the 1A1 diamond isomer is 1.6 - 2.2kcal mol-1 lower in energy than the 3A1 diamond isomer. Most QM-cluster models of enzymes are constructed based on X-ray crystal structures, which limits comparison to in vivo structure and mechanism. The active site of chorismate mutase from Bacillus subtilis and the enzymatic transformation of chorismate to prephenate is used as a case study to guide construction of QM-cluster models built first from the X-ray crystal structure, then from molecular dynamics (MD) simulation snapshots. The Residue Interaction Network-based ResidUe Selector (RINRUS) software toolkit, developed by our group to simplify and automate the construction of QM-cluster models, is expanded to handle MD to QM-cluster model workflows. The 250 QM-cluster models sampled provide a mean ∆G ‡ of 10.3 ± 2.6 kcal mol-1 compared to the experimental value of 15.4 kcal mol-1 at 25 ◦C. Using 10 QM-cluster models of the Bacillus subtilis chorismate mutase active site, we seek to improve the accuracy of QM-cluster models of enzymes. Values of ∆G ‡ and ∆Grxn were calibrated with 31 types of density functional approximations (DFA), 5 semi-empirical methods, and 19 one-electron basis sets. This computational work examined three aspects of computational enzymology, 1) the convergence of kinetics and thermodynamics with respect to model size and composition, 2) the accuracy of predicted ∆G ‡ compared to experimental kinetics, and 3) finding a tractable level of electronic structure theory for computational enzymology workflows when models with over 200 atoms are necessary.

Comments

Data is provided by the student.

Library Comment

Dissertation or thesis originally submitted to ProQuest.

Notes

Embargoed until 10/5/2024

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Available for download on Saturday, October 05, 2024

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