This dissertation details the use of computational methods to understand the effect that cancer-related mutations have on proteins that complex with nucleic acids. Firstly, we perform molecular dynamics (MD) simulations of various mutations in DNA polymerase κ (pol κ). Through an experimental collaboration, we classify the mutations as more or less active than the wild type complex, depending upon the incoming nucleotide triphosphate. From these classifications we use quantum mechanics/molecular mechanics (QM/MM) to explore the reaction mechanism. Preliminary analysis points to a novel method for nucleotide addition in pol κ. Secondly, we study the ten-eleven translocation 2 (TET2) enzyme in various contexts. We find that the identities of both the substrate and complementary strands (or lack thereof) are crucial for maintaining the complex structure. Separately, we find that point mutations within the protein can affect structural features throughout the complex, only at distal sites, or only within the active site. The mutation's position within the complex alone is not indicative of its impact. Thirdly, we share a new method that combines direct coupling analysis and MD to predict potential rescue mutations using poly(ADP-ribose) polymerase 1 as a model enzyme. Fourthly, we perform MD simulations of mutations in the protection of …

Cobalt oxynitride films formed by magnetron sputter deposition of a Co target in N2 or NH3 plasma or, alternatively, by NH3 plasma nitridation of a Co film deposited on Si(100), show a divergence of properties arising from (a) N and O interactions for N and O atoms bonded to each other or through a common metal center and (b) the oxophilicity of the metal center itself. Core and valence band X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), and plane wave density functional theory (DFT) calculations have been used to probe chemical and electronic interactions of nitrogen-rich cobalt oxynitride CoO1-xNx (x > 0.7) films. DFT-based calculations supervised by the Cundari group show the zinc blende (ZB) structure is found to be energetically favored over the rocksalt (RS) structure for x > ~ 0.2, with an energy minimum observed in the ZB structure for x ~ 0.8 - 0.9. There is also agreement with experiment for core level binding energies obtained for DFT calculations based on the ZB structure and this forms the basis of a predictive model for understanding how N and O interactions impact the electronic and catalytic properties of these materials. Vanadium oxynitride films were deposited in a mixture …

Plasmonic photothermal therapy (PPTT) has a rising promise for treating different cancer cells such as lymphoma or stomach cancer. Technique development of PPTT using metallic nanoparticles is developed upon a modification of the irradiation therapy using two major changes: using a less harmful visible amber light (excluding blue light) and using gold-loaded biocompatible nanoparticles. Acrylate nanoparticles were loaded with desired types of gold nanoparticles at different sizes. The gold-loaded gold nanoparticles were conjugated to cancer cells. By selectively delivering the gold nanoparticles into cancer cells, irradiating a harmless amber visible light will achieve thermal ablation of the cancer cells. Based on imaging spectroscopy, flow cytometry, and cell viability assays, results showed reduction of gold-loaded viable cancer cells upon irradiating with amber visible light, no change in the number of cancer cells with irradiating with light only. On the other hand, DNA intercalation of a trinuclear gold(I), [Au(3-CH3,5-COOH)Pz]3 (Au3) is contrasted with the standard organic intercalators ethidium and ellipticine, as investigated computationally. Frontier molecular orbital energies of intercalators and DNA base pairs were determined and found that all intercalators are good electron acceptors with Au3 being the best electron acceptor having the lowest LUMO. DNA base pairs are better electron donors …

The rise of nutraceutical health formulations has increased the need for more stringent analytical testing methods. Complex matrices present a new problem when determining concentration of compounds of interest. The presented method uses LC-MS analysis with a novel sample preparation method in the determination of Beta-hydroxybutyric acid in health formulations. The use of an aqueous analytical column allows for separations of polar compounds after non-polar compounds are removed through C18 packed column filtration. The samples were analyzed through time-of-flight mass spectrometry and results show that this is an effective method for the presented samples with a range of expected concentrations of total BHB was from 11.80% to 38.92%. It was seen that all samples exhibited a less than 10% percent deviation from the expected concentrations of the nutraceutical health samples with the highest being 9.74 % for sample 9 and the lowest being sample 3 with a deviation of 0.08 % from expected values.

The first study investigated the deposition and characterization of the CoO and Co3O4 phases of cobalt oxide. It was determined that both phases can be easily distinguishable by XPS, LEED and EELS and grown by only altering the oxygen partial pressure during MBE deposition. This fundamental knowledge gives a foundation for further experiments involving graphene growth on cobalt oxides. The second study focused on the layer-by-layer growth of graphene on another metal oxide, MgO. Past research gives promise of favorable interfacial interactions at the graphene/MgO interface though the exact growth mechanism is unknown. Layer by layer growth by MBE resulted in the characterization of a complex graphene oxide/buckled graphene/ graphene heterostructure confirmed by XPS, AES, LEED and EELS and supported by DFT calculations performed by the project's collaborators at the California Institute of Technology. This detailed look into graphene growth give valuable information that can be allied to graphene growth on similar oxide surfaces. The last project deviates from graphene-based studies and instead focused on interfacial interactions between two metal oxides, chrome oxide and titanium oxide. A corundum phase TiO2-x film was grown on Al2O3 via MBE and characterized using XPS, AES, LEED, and EELS. Data taken gives evidence of …

Machine learning and artificial intelligence are increasingly becoming mainstream in our daily lives, from smart algorithms that recognize us online to cars that can drive themselves. In this defense, the intersection of machine learning and computational chemistry are applied to the generation of new PFAS molecules that are less toxic than those currently used today without sacrificing the unique properties that make them desirable for industrial use. Additionally, machine learning is used to complete the SAMPL6 logP challenge and to correlate molecules to best DFT functionals for enthalpies of formation.

The present thesis mainly proposes to explore the potential of aza-macrocycles in metal-organic frameworks (MOFs) for applications related to unprecedented open macrocycle cavities. Strategies such as direct arylation of secondary amines as well as multidentate coordination were applied to constrain the intramolecular flexibility of as-obtained macrocyclic compounds. Several desired materials, i.e. MMCF-4, MMCF-5/MMCF-5t/MMCF-5t-aa, MMCF-5, HMMCF-1, were obtained. They are proved superior to traditional materials in the field of "turn-on" lanthanide luminescence, deep desulfurization of flue gas, recovery of Platinum-group metals, etc. Powder/single-crystal X-ray diffraction (PXRD/SCXRD), synchrotron-based X-ray and extended X-ray absorption fine structure (EXAFS), density functional theory (DFT) theoretical calculations, etc., were employed for deep-understanding the mechanisms. These studies shed light on the construction of hierarchically porous materials with two levels of porosity, i.e., one from the frameworks and the other one from the aza-macrocycles. Incorporation of aza-macrocycles into the MOF architectures not only leads to fundamental significance in bridging the chemistry of MOFs with supramolecular chemistry but also elicits unique properties from the hybrid materials obtained. As a paradigm for constructing frameworks with accessible macrocyclic cavities based on "constrained" aza-macrocycle ligands, this thesis paves the way for the further development of this framework family in the future.

This dissertation demonstrates that it is possible to create a donor-acceptor system that can transform sunlight into electrons. By using site-directed synthesis, it was possible to create a novel trans-A2B2 porphyrin. In the pursuit of creating a supramolecular system, both the novel (TPA-BT)2ZnP and C60imidazole combined in solution such that the nitrogenous lone pair of C60 imidazole would coordinate axially to the zinc atom in the porphyrin. The conjugates' characterization utilized spectral, electrochemical, and computational techniques. Computational studies revealed in the optimized structure that the HOMO localized on the porphyrin and LUMO centered over the C60imidazole entity. Rehm-Weller calculations showed feasibility of singlet-electron transfer. Femtosecond transient absorption studies documented an efficient photoinduced charge separation in the conjugate. The subsequent work through steady-state and time-resolved transient absorption techniques that photoinduced electron transfer takes place between the synthesized phenylimidazole functionalized bisstyrylBODIPY (BDP(Im)2) and three selected zinc tetrapyrroles. This dyad consisted of BDP(Im)2 and either zinc tetratolylporphyrin (ZnP), zinc-tetra-t-butyl phthalocyanine (ZnPc), or zinc tetra-t-butyl naphthalocyanine (ZnNc) in a solution solvated by σ-dichlorobenzene (DCB). The three dyads (BDP(Im)2:ZnP, BDP(Im)2:ZnPc, and BDP(Im)2:ZnNc) were investigated by spectroscopic, computational, and electrochemical methods. The 1:1 complex of the dyads in optical absorption studies were approximately ~104 M-1 suggesting …