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Computational Studies on the Non-Covalent Interactions of Asphaltene Model Compounds and Related Systems
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- Author / Creator
- King, Nathanael
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In this thesis, the non-covalent interactions of asphaltene model compounds are explored computationally using a combination of semi-empirical methods and density functional theory. New methods and workflows are developed with which to make more accurate predictions for reduced computational expense. In Chapter 2, a new synthetic procedure for pyrene-4,5-dione is disclosed. In developing this procedure, unusual purification difficulties were encountered, which led to the computational study in Chapter 3. Here, we used the Grimme group’s conformer-rotamer ensemble sampling tool (CREST) to generate ensembles of the low-energy homodimers of pyrene, pyrene-4,5-dione, and pyrene-4,5,9,10-tetraone, and of the heterodimer of pyrene with pyrene-4,5,9,10-tetraone. These ensembles were then further refined using density functional theory (DFT) to give high-quality geometries and energies. We found that the difficulty in purification in Chapter 2 likely originated in the relatively strong interactions between pyrene and pyrene-4,5,9,10-tetraone, which could cause the formation of a cocrystal and interfere with the purification of pyrene-4,5-dione. When the same computational methodology was extended to realistic model asphaltene systems, it became apparent that CREST was providing insufficient sampling of conformational space for those systems, so Chapter 4 details the development and implementation of a new algorithm for non-covalent complexes of flexible monomers, including those involving microhydration. This new algorithm is still based on GFN2-xTB metadynamics, like CREST, but it uses modified settings, with a somewhat weaker biasing, intended to preserve important directed non-covalent interactions for longer, and starts each cycle from a diversity of structures found in the previous cycle, rather than just from the single lowest-energy structure that CREST uses. Thus, we have termed the new algorithm a Low-Energy Diversity-Enhanced variant on CREST (LEDE-CREST). Chapter 5 applies LEDE-CREST to a realistic system of asphaltene model compounds for which there is experimental data available (Org. Biomol. Chem., 2015, 13, 6984-6991). Various different stoichiometries of clusters of model compounds were tested. LEDE-CREST was used to explore the possible geometries for each stoichiometry, and the lowest-energy structure found by LEDE-CREST was then reoptimized using DFT. Unfortunately, due to computational cost of using DFT for systems of this size, we were unable to reoptimize even a portion of the ensembles. The results give insight into motifs in model compound aggregation, the relative importance of different interaction modes (π-π stacking, hydrogen bonding), and shed some doubt on the importance of microhydration. Chapter 6 discusses the results of the entire thesis, and presents directions for future work.
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- Graduation date
- Fall 2023
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- Type of Item
- Thesis
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- Degree
- Doctor of Philosophy
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- License
- This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.