As countries pledge their commitment to a net-zero future, much of the previously forgotten climate change research were revitalized by efforts from both governmental and private sectors. In particular, the utilization of lignocellulosic materials saw a special spotlight in research interest for its abundance and its carbon removal capability during photosynthesis. The initial effort in mimicking enzymatic active sites of β-glucosidase will be explored. The crystalline covalent organic frameworks (COFs) allowed for the introduction of a variety of noncovalent interactions, which enhanced the adsorption and the catalytic activity against cellobiose and its glycosidic bonds. The physical processes associated with this reaction, such as the kinetics, equilibrium, and activation energies, will be closely examined and compared with existing standard materials and comparable advanced catalysts. In addition, several variants of COFs were synthesized to explore the effect of various noncovalent interactions with cellobiose. A radical-bearing COF was synthesized and characterized. The stability of this radical was examined by electron paramagnetic resonance spectroscopy (EPR) and its oxidative capability tested with model lignin and alcoholic compounds. The reaction products are monitored and identified using gas chromatography-mass spectroscopy (GC-MS). An oxidative coupling of phenol was explored, and its initial results are presented in chapter 5.

Transition metal oxynitrides are of growing interest for their use as electrocatalyst for nitrogen reduction reaction. The metals in the oxynitride used for catalytic process are stabilized in intermediate state for effective activation of nitrogen. Therefore, studying the interaction of metal oxynitrides films to ambient exposure is necessary. Here, sputter deposited vanadium oxynitride is compared to cobalt oxynitride using insitu Auger electron spectroscopy (AES), ex situ X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD) and scanning electron microscopy (SEM). After deposition in Ar/N2 environment, in situ AES spectra indicate that film is vanadium oxynitride despite oxygen is not the reactive gas. In contrast, in situ AES indicate film is pure cobalt nitride at the same base pressure and deposition condition (as vanadium). For ambient exposure, in situ AES indicate the incorporation of oxygen in the cobalt nitride film to form cobalt oxynitride. Ex situ XPS indicate both films get more oxidized but uniformly distributed as there is only slight difference in grazing and normal emission XPS. XRD and SEM also indicate how homogeneously distributed both films are. These finding confirms how important it is that transition metal centers are kept in intermediate oxidation state for the activation of nitrogen bond.

Design and development of novel one-step reactions that produce nitrogen-containing scaffolds is an invaluable area of chemistry due to the abundance of these moieties in natural products and biologically active molecules. Discovering novel methods using uncommon substrates and rare earth metals to access these significant scaffolds present a challenge. Over the course of my doctoral studies, I have designed, developed and optimized novel reactions by using rarely known substrates and rare earth metals that have afforded important nitrogen-containing scaffolds. The products obtained allow access to otherwise long-to-synthesize molecules and expeditious construction of biologically active molecules.

The recovery processes of critical metals from multiple sources have turned more and more attention due to the increasing demand and consumption of them in modern industry. Many metals are used as significant components in manufacturing of a variety of products and equipment, playing significant roles in the economic security and national security; those metals involve rare earth elements (REEs), precious metals which include gold, silver, and platinum group metals (PGMs), and other valuable metals such as lithium, uranium, nickel, et al. The traditional approach to obtaining the above metals is by hardrock mining of natural ores via chemical and physical processes. However, this method of mining and refining metals from minerals is usually energy-consuming, costly, and environmental-destructive. Thus, various approaches to extracting or recycling target metals from the seawater or the solution of secondary resources as an alternative to traditional hardrock mining have been developed, and thereinto, using functional porous adsorbents to selectively capture specific metal ions from the aqueous resources has attracted increasing attention due to its outstanding merits such as high efficiency, energy-saving process, low cost, and reduced environmental impacts

Previous work was successful at delineating reaction pathways for the photoactivated synthesis of an amine, [CztBu(PyriPr)(NH2−PyriPr)], by double intramolecular C−H activation and functionalization via irradiating a metal(II) azido complex, [CztBu(PyriPr)2NiN3. The present work seeks to expand upon earlier research, and to substitute the metal with iron or cobalt, and to expand the study to photocatalyzed intermolecular C−H activation and functionalization of organic substrates. Density functional theory (DFT) – B3LYP/6-31+G(d') and APFD/Def2TZVP – and time-dependent density functional theory (TDDFT) were used to propose a detailed pathway comprised of intermediates of low, intermediate, or high spin multiplicity and photo-generated excited states for the reaction of the azido complex, [CztBu(PyriPr)2MN3] to form the amine complex [CztBu(PyriPr)M(NH2−PyriPr)], M = Co, Ni or Fe, and the intermediates along the reaction pathway. For applications on quantum computing, the photophysical properties of photoactive d8 nickel(II) complexes are modeled. Such systems take advantage of a two-level system pathway between ground to excited state electronic transitions and could be useful for the discovery of successful candidates for a room temperature qubit, the analogue of a classical computational bit. A modified organometallic model, inspired by a nitrogen vacancy selective intersystem crossing model in diamond, was developed to take advantage of …

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 …

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 …

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 …

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.

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.

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 …

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 …

The Abraham solvation model (ABSM) is an experimentally derived predictive model used to help predict various solute properties. This work covers various uses for the ABSM including predicting molar enthalpies of vaporization, predicting solvent coefficients for two new solvents (2,2,5,5-tetramethyloxolane and diethyl carbonate), predicting values for multiple new ionic liquids (ILs). This work also introduces a novel method for updating IL ABSM parameters by updating cation- and anion-specific values using linear algebra and binary matrices.

Computational chemistry employs mathematical algorithms, statistics, and large databases to integrate chemical theory with experimental observations. Computational modeling allows us to make predictions concerning molecular properties and reactivity that ultimately lead to accurate assessment of the most important fundamental properties of chemical systems. Advances in theoretical techniques and computer power have dramatically increased the usefulness and importance of computational chemistry as a complement to experimental studies. This is especially relevant to catalytic reactions of industrial importance as well as the analysis of structural properties and the resulting spectroscopic phenomena in what are often otherwise counterintuitive models. This dissertation is a representation of the research I performed during my years as a graduate student in the Chemistry Department at the University of North Texas. My research has examined novel carbenes as efficient organocatalysts, structure-based design and optimization of small molecule drugs, and surveying methods to accurately describe structure and bonding and catalytic abilities of inorganic and organometallic systems. The works presented herein have been published or are awaiting submission to peer-reviewed scientific journals. A variety of computational techniques were employed in studying metal-mediated catalysis and organocatalysis as well as the structural and photophysical properties of systems containing closed-shell transition metal ions.

The first study project is based on modeling Earth abundant 3d transition-metal methoxide complexes with potentially redox-noninnocent ligands for methane C–H bond activation to form methanol (LnM-OMe + CH4 → LnM–Me + CH3OH). Three types of complex consisting of tridentate pincer terpyridine-like ligands, and different first-row transition metals (M = Ti, V, Cr, Mn, Fe, Co, Ni, and Cu) were modeled to elucidate the reaction mechanism as well as the effect of the metal identity on the thermodynamics and kinetics of a methane activation reaction. The calculations showed that the d electron count of the metal is a more significant factor than the metal's formal charge in controlling the thermodynamics and kinetics of C–H activation. These researches suggest that late 3d-metal methoxide complexes that favor σ-bond metathesis pathways for methane activation will yield lower barriers for C–H activation, and are more profitable catalyst for future studies. Second, subsequently, on the basis of the first project, density functional theory is used to analyze methane C−H activation by neutral and cationic nickel-methoxide complexes. This study identifies strategies to further lower the barriers for methane C−H activation through evaluation of supporting ligand modifications, solvent polarity, overall charge of complex, metal identity and counterion …

The direct epitaxial growth of multilayer BN by atomic layer deposition is of critical significance forfo two-dimensional device applications. X-ray photoelectron spectroscopy (XPS) and low energy electron diffraction (LEED) demonstrate layer-by-layer BN epitaxy on two different substrates. One substrate was a monolayer of RuO2(110) formed on a Ru(0001) substrate, the other was an atomically clean Ni(111) single crystal. Growth was accomplished atomic layer deposition (ALD) cycles of BCl3/NH3 at 600 K substrate temperature and subsequent annealing in ultrahigh vacuum (UHV). This yielded stoichiometric BN layers, and an average BN film thickness linearly proportional to the number of BCl3/NH3 cycles. The BN(0001)/RuO2(110) interface had negligible charge transfer or band bending as indicated by XPS and LEED data indicate a 30° rotation between the coincident BN and oxide lattices. The atomic layer epitaxy of BN on an oxide surface suggests new routes to the direct growth and integration of graphene and BN with industrially important substrates, including Si(100). XPS and LEED indicated epitaxial deposition of h-BN(0001) on the Ni(111) single crystal by ALD, and subsequent epitaxially aligned graphene was deposited by chemical vapor deposition (CVD) of ethylene at 1000 K. Direct multilayer, in situ growth of h-BN on magnetic substrates such as …

This work discusses applications of computational simulations to a wide variety of chemical systems, to investigate intermolecular interactions to develop force field parameters and gain new insights into chemical reactivity and structure stability. First, we cover the characterization of hydrogen-bonding interactions in pyrazine tetracarboxamide complexes employing quantum topological analyses. Second we describe the use of quantum mechanical energy decomposition analysis (EDA) and non-covalent interactions (NCIs) analysis to investigate hydrogen-bonding and intermolecular interactions in a series of representative 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([bmim][Tf2N]) ion pairs extracted from classical equilibrium and non-equilibrium molecular dynamics simulations. Thirdly, we describe the use of multipolar/polarizable AMOEBA force field to study the extraction of benzene from a gasoline model employing 1,3-dimethylimidazolium tetrafluorobrorate, [DMIM][BF4], and ethylmethylimidazolium tetrafluorobrorate, [EMIM][BF4]. Fourthly, we cover the recent improvements and new capabilities of the QM/MM code "LICHEM". Finally, we describe the use of polarizable ab initio QM/MM calculations and study the reaction mechanism of N-tert-butyloxycarbonylation of aniline in [EMIm][BF4], and ground state destabilization in uracil DNA glycosylase (UDG).

With the reliability requirements of automobile microelectronics pushing towards near 0 ppb levels of failure control, halide induced corrosion issues in wire bonded devices have to be tightly controlled to achieve such a high reliability goal. With real-time corrosion monitoring, for the first time we demonstrated that the explosive H2 evolution coupled with the oxygen reduction reaction, occurring at the critical Al/Cu interfaces, is the key driving force for the observed aggressive corrosion. Several types of passivation coating on Cu wire surfaces to effectively block the cathodic H2 evolution were explored with an aim to disrupt this explosive corrosion cycle. The properties of the protective coating were evaluated using various analytical techniques. The surface coating exhibited high thermal stability up to 260 °C (evaluated using TGA analysis). A uniform, highly hydrophobic coating (surface contact angle of >130° with water), was achieved by carefully controlling CVD parameters such as time of deposition, surface control of Cu metal, amount of inhibitor compound loading, temperature of coating process etc. FTIR spectroscopy combined with corrosion screening was used to optimize the CVD passivated coating with strong chemisorption. SEM and EDX, XPS were carried out on various coated surfaces to understand the composition and selectivity …

Donor-acceptor systems have unique properties that make them ideal candidates for solar energy harvesting through mimicry of natural photosynthesis. This dissertation is focused on unraveling those unique properties in various types of donor-acceptor systems. The systems investigated are categorized as closely linked, push-pull, supramolecular, and multi-unit. As part of the study, photosynthetic analogues based on BF2-chelated dipyrromethene (BODIPY), porphyrin, phthalocyanine, truxene, ferrocene, quinone, phenothiazine (PTZ), perylenediimide (PDI), fullerene (C60), dicyanoquinodimethane (DCNQ), tetracyanobutadiene (TCBD), and triphenylamine (TPA) are investigated. The effects of proximity between donor-acceptor entities, their geometrical orientation relative to each other, push-pull character of substituents, and competitive energy and electron transfer are examined. In all systems, primary events of photosynthesis are observed, that is absorption and energy transfer and/or electron transfer is witnessed. Ultrafast transient absorption spectroscopy is utilized to characterize the photo-induced events, while other methods such as steady-state luminescence, cyclic voltammetry, differential pulse voltammetry, chronoamperometry, and computational calculations are used to aid in the characterization of the donor-acceptor systems, in particular their applicability as solar energy harvesters.

Monovalent coinage metal complexes have been of significant interest due to their rich photophysical properties. This dissertation focuses on the design, synthesis, and characterization of gold, silver, and copper phosphors. Chapter 2 investigates new physical and photophysical properties of a gold diphosphine dimer in the solid state. Thermally activated luminescence switching between two structural states is discussed. Chapter 3 includes the photochemistry of closed shell group 11 transition metals with dithiophosphonate and diphosphine ligands as heteroleptic, homoleptic and heterometallic systems. Chapter 4 reports the synthesis and characterization of a cyclic trinuclear gold imidazolate complex with high electron dentistry and π- base properties. The trinuclear gold (I) complexes reactivity with silver(I) and sodium cations is explored. The photochemistry of all complexes are screened for efficiency, emission profiles and lifetimes as potential materials to be used in OLEDs and other molecular devices.

Computational techniques, mostly density functional theory (DFT), were applied to study metal-based catalytic processes for energy conversion reactions. In the first and second projects, the main focus was on activation of the light alkanes such as methane, which have thermodynamically strong and kinetically inert C–H bonds plus very low acidity/basicity. Two Mo-oxo complexes with the different redox non-innocent supporting ligands, diamide-diimine and ethylene-dithiolate, were modeled. These Mo-oxo complexes are modeled inspired by active species of a metalloenzyme, ethylbenzene dehydrogenase (EBDH). The results for the activation of the benzylic C–H bond of a series of substituted toluenes by modeled Mo-oxo complexes show there is a substantial protic character in the transition state which was further supported by the preference for [2+2] addition over HAA for most complexes. Hence, it was hypothesized that C–H activation by these EBDH mimics is controlled more by the pKa than by the bond dissociation free energy of the C–H bond being activated. The results suggest, therefore, promising pathways for designing more efficient and selective catalysts for hydrocarbon oxidation based on EBDH active site mimics. Also, it is found that the impact of supporting ligand and Brønsted/Lowry acid/base conjugate is significant on the free energy barrier of …

Artificial photosynthesis is the process, which mimics the natural photosynthesis process in order to convert solar energy to chemical energy. This process can be separated into four parts, which are antenna system, reaction center, water oxidation center, and proton reduction center. If we only focus on the ‘antenna system and reaction center' modules, expanding the absorption band in antenna system and generating long-lived charge separated state in reaction center are two fantastic strategies to design the molecules in order to improve the efficiency of the artificial photosynthesis process. In the first work of this dissertation, mono-18-crown-6 and mono-ammonium binding strategy was used to connect BODIPY- C60 supramolecular based donor–acceptor conjugates. The meso- position of BODIPY was modified by benzo-18-crown-6, and the 3, 5 methyl positions were replaced by two styryl groups, which covered additional donor (triphenylamine or 10-methylphenothiazine). The acceptor is a fulleropyrrolidine derivative, which included an ethyl ammonium cation. The absorbance wavelengths of the donor covered 300-850 nm, which is the visible/near IR region (wide band capturing). The ultrafast charge separation and relatively slow charge recombination was found from femtosecond transient absorption study. Next, a ‘two point' bis-18-crown-6 and bis-ammonium binding strategy was utilized to link BODIPY- C60 supramolecular …

Computational chemistry has gained interest as a characterization tool to predict photoluminescence, reactivity and structural properties of organic and transition metal complexes. With the rise of methods including relativity, these studies have been expanded to the accurate modeling of luminescence spectra of complexes with considerable spin-orbit splitting due to heavy metal centers as well as the reaction pathways for these complexes to produce natural products such as hydrogen gas. These advances have led to the synthesis and utility of more effective catalysis as well as the development of more effective organic light emitting diodes (OLEDs) through the incorporation of organometallic complexes as emitters instead of typical organic emitters. In terms of significant scientific advancement presented in this work is in relation to the discovery of significant spin-orbit splitting in a gold(I) alkylphosphine complex, where the splitting results in the states that emit in different colors of the visible region of the electromagnetic spectrum. This work also reveals the discovery both computationally and experimentally, of a genuine polar-covalent bond between two-closed shell metals. This work highlights a complex with an incredibly short gold(I) – copper(I) intermetallic distance leading to a vibrational frequency and dissociation energy that is on par with those …