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).

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 …

Deposition of solid state materials span a wide variety of methods and often utilize high energy sources such as plasmas and ultra-violet light resulting in a wide variety of characteristics and applications. A fundamental understanding is essential for furthering the applications of these materials which include catalysis, molecular filtration, electronics, sensing devices, and energy storage among others. A combination of experimental and theoretical work is presented here on several materials including 2D silicates on Pd, boron oxide, and vanadium oxynitride. Silicate formation under low energy electron microscopy demonstrate film permeability to oxygen, while ab initio molecular dynamics simulations reveal the possible initial mechanisms associated with the formation of boron oxide films during atomic layer deposition. Lastly, vanadium oxynitrides have shown preferential sputtering of N over O sites and theoretical binding energies serve as a guide for assigning experimental x-ray photoelectron spectra.

With all the improvements in cancer treatments, multidrug resistance is still the major challenge in treating cancer. Cells can develop multidrug resistance (MDR) during or after treatment, which will render the cancer cells resistant not only to the chemotherapy drug being used but also to many other structurally- and mechanically-different chemotherapeutics. In the first project, the main focus was on development of drug resistant cell lines by selection with taxol. Gene changes in the L1T2 cell line after treatment with Taxol was studied. Treatment of L1T2 cells with taxol leads to changes in the expression of ABC transporter proteins, whereas the combination of Taxol with protease inhibitors leads to increased efficacy via inhibition of P-glycoprotein (P-gp). In the second project, we showed that our innovatively-designed Au-loaded poly(lactide-co-glycolic acid) nanoparticles (GPLGA NPs) are able to cross biological barriers and deliver inside the cells without being recognized by the ABC protein transporter. (We focus specifically on P-gp-mediated drug efflux in a model of HEK cell lines.) The concentration of gold was measured using inductively-coupled plasma/mass spectrometry (ICP-MS) after 6- and 24-hour treatment of GPLGA NPs, which did not show significant increase of gold inside the cells in presence of the P-gp inhibitor …

This study addressed five key applications of paper spray mass spectrometry (PS-MS): (i) comparative analysis of the microporous substrate with the cellulose-based substrate in drug detection; (ii) detection of more than 190 fentanyl analogs with their fragmentation pattern can be implemented in the future reference for quicker, accurate and sensitive determination; (iii) exploring sweat in a fingerprint to be considered an alternate method to recognize non-invasive markers of metabolites, lipids, narcotics, and explosive residues that can be used in forensic testing applications; (iv) extending and improving better, cost-effective and quick real-time monitoring of the diseased stage using biofluid samples to obtain vastly different lipid information in viral infection such as COVID-19; and (v) mass spectral detection in chemical warfare agent (CWA) stimulant gas exposure with microporous structure absorbency capabilities in air quality monitoring. This novel synthetic material is known as Teslin® (PPG Industries), consisting of a microporous polyolefin single-layered silica matrix, can be used for precise, sensitive, selective, and rapid sample analysis with PS-MS. The Teslin® substrate provided longer activation time for samples and an active signal with a higher concentration of ion formation and mobility compared to cellulose-based papers. Direct analysis of multiple samples showed that, besides being more …

The deposition of boron oxide (B₂O₃) films on silicon substrates is of significant interest in microelectronics for ultrashallow doping applications. However, thickness control and conformality of such films has been an issue in high aspect ratio 3D structures which have long replaced traditional planar transistor architectures. B₂O₃ films are also unstable in atmosphere, requiring a suitable capping barrier for passivation. The growth of continuous, stoichiometric B₂O₃ and boron nitride (BN) films has been demonstrated in this dissertation using Atomic Layer Deposition (ALD) and enhanced ALD methods for doping and capping applications. Low temperature ALD of B₂O₃ was achieved using BCl₃/H₂O precursors at 300 K. In situ x-ray photoelectron spectroscopy (XPS) was used to assess the purity and stoichiometry of deposited films with a high reported growth rate of ~2.5 Å/cycle. Free-radical assisted ALD of B₂O₃ was also demonstrated using non-corrosive trimethyl borate (TMB) precursor, in conjunction with mixed O₂/O-radical effluent, at 300 K. The influence of O₂/O flux on TMB-saturated Si surface was investigated using in situ XPS, residual gas analysis mass spectrometer (RGA-MS) and ab initio molecular dynamics simulations (AIMD). Both low and high flux regimes were studied in order to understand the trade-off between ligand removal and B₂O₃ …

This dissertation involves inorganic/organometallic catalysis models, in particular the functionalization of carbon-hydrogen and carbon-carbon bonds. Computational methods have been utilized to better understand the factors affecting the kinetics and thermodynamics of C−H and C−C bond activation/functionalization in this dissertation. Chapter 2 investigates methane C−H activation with a diiminopyridine nitride/nitridyl complex of 3d transition metals and main group elements via three competing pathways: 1,2-addition/[2 + 2] addition, insertion and H-atom abstraction/proton coupled electron transfer. Chapter 3 investigates a transition metal catalyzed C=C bond functionalization involving C−N bond formations to synthesize aziridines from aromatic and aliphatic alkenes. The study focuses on anionic 3d transition metal (M = Mn, Fe, Co and Ni) triphenylamide-amine complexes with nitrene active intermediates for the aziridination reactions. Chapter 4 investigates a disphenoidal Ni(II) azido complex participating in intramolecular C−H functionalization and amination via a putative Ni nitridyl intermediate and a 1,2-addition/[2 + 2] addition pathway. In Chapter 5, methane oxidative addition to the Cp*ML (Cp* = η5-C5Me5; M = Co, Rh, Ir , L = CO, PMe3) motif is compared and contrasted when the classic CO and PMe3 ligands are replaced with the cyclic alkyl(amino) carbene (CAAC) as ancillary ligands.

Poor medical adherence attributed to patient compliance has impacted the medical community, at times, in a deleterious fashion. To combat this, the medical community has attempted to provide therapeutics in the form of absorption enhancing techniques. To improve the absorption rate techniques such as drug encapsulation using proteins, liposomes, or nanotransfersomes have been developed using mass spectrometry. These techniques, have aided in the enhanced absorption of analytes with low bioavailability, including curcumin, simvastatin, and lysozyme. Specifically, mass spectrometry allows for the development and monitoring of nanotransfersome encapsulated analytes and the permeation across the dermal membrane. This transdermal delivery would eliminate the problems encountered during first pass metabolism, while allowing for higher concentrations of analyte to be maintained in the blood serum. This can be coupled to a thermosensitive gelatin that provides for a dose control mechanism to be accomplished, allowing multiple doses to be delivered using one transdermal patch system. The novel delivery system developed using mass spectrometry, allows the analyte to be delivered into the circulatory system at a controlled dosage, via transdermal absorption. This system will aid in eliminating problems associated with patient compliance, as the patient is no longer reliant on memory to self-dose. Further, this system …

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.

Computational chemistry examination of the bond dissociation enthalpies of tungsten and main group elements. Includes quantification and calibration of theoretical methods to address the question of bond strengths including component σ and π molecular bonds.

In the first part of this dissertation work, Al bond pad corrosion behavior was investigated in the presence of common industrial contaminants such as chloride (Cl-) and fluoride (F-). Al corrosion while in direct contact with Cu displayed rapid hydrogen (H2) gas evolution and dendrite propagation. In contrast, Al without bimetallic contact showed only minor surface roughening. This observed difference in the corrosion mechanism between Cl- and F- is attributed to the solubility of the corrosion products (AlCl3 vs. AlF3) formed on the Al surface. Our subsequent work explored corrosion prevention inhibition of wire-bonded devices (WBD) in the Cl- environment. Our research shows that the Al bond pad was protected against corrosion by chemically modifying the surface of the Cu wires, thereby preventing the H2 evolution. The inhibitor was observed to be highly selective, thermally stable, hydrophobic, and cost-effective, making it viable for industrial application of this coating for Al bond pad corrosion prevention. In the second part of the dissertation work, we utilized a novel approach of using ultraviolet-visible spectroscopy (UV-Vis) as a chemical-sensitive monitoring tool of the chemical environment in Cu etch bath. The UV-Vis technique illuminates the roles of H+, Cl-, Cu+, and Cu2+ to the etch …

Mother nature has laid out a beautiful blueprint to capture sunlight and convert to usable form of energy. Inspired by nature, donor-acceptor systems are predominantly studied for their light harvesting applications. This dissertation explores new donor-acceptor systems by studying their photochemical properties useful in building artificial photosynthetic systems. The systems studied are divided into phthalocyanine-porphyrin-fullerene-based, perylenediimide-based, and aluminum porphyrin-based donor-acceptor systems. Further effect of solvents in determining the energy or electron transfer was studied in chapter 6. Such complex photosynthetic analogues are designed and characterized using UV-vis, fluorescence spectroscopy, differential pulse voltammetry and cyclic voltammetry. Using ultrafast transient absorption spectroscopy, the excited state properties are explored. The information obtained from the current study is critical in getting one step closer to building affordable and sustainable solar energy harvesting devices which could easily unravel the current energy demands.

A rapidly growing topic of great interest is the adaptation of benchtop analytical instrumentation for use in outdoor harsh environments. Some of the areas that stand to benefit from field instrumentation development include government agencies involved with the preservation of the environment and institutions responsible for the safety of the general public. Detection systems are at the forefront of the miniaturization movement as the interest in analyte identification and quantitation appears to only be accessible through the use of analytical instrumentation. Mass spectrometry is a distinguished analytical technique known for its ability to detect the mass-to-charge (m/z) ratios of gas-phase ions of interest. Although these systems have been routinely limited to research lab-based analysis, there has been considerable development of miniaturized and portable mass spectrometry systems. Membrane Inlet Mass Spectrometry (MIMS) is becoming a common method of sample introduction that is subject to significant development. MIMS allows for minimal sample preparation, continuous sampling, and excludes complicated analyte introduction techniques. Sampling is accomplished using a semipermeable membrane that allows selective analyte passage into the vacuum of the mass spectrometer. MIMS is becoming the preeminent choice of homeland security and environmental monitoring applications with increasing opportunities for the future development of specialized …

Benzannulation to porphyrin 2,3 positions has previously been accomplished using various methodologies in the past century, yet there remain limited methodologies to both annulate to the porphyrin periphery and add functional moieties that can then be derivatized for diverse applications. This dissertation describes the development of synthetic routes and characterization of a variety of linearly-annulated, functionalized, β,β'-π-extended porphyrins. There are five chapters in this dissertation, the first of which introduces synthesis and properties of porphyrins and π-extended porphyrins. Chapter 2 describes synthesis of pentacenequinone-fused and pentacene-fused poprhyrins with distinct and new optical absorbance properties. In chapter 3, synthesis and characterization of benzimidazole-fused porphyrins displaying external metal binding capability is described. The synthetic method developed in chapter 3 is extended in chapter 4 to synthesis of bisbenzimidazole-fused porphyrin dimers that show split Soret character, likely due to excitonic coupling between porphyrins of the dimer. Chapter 5 summarizes this dissertation and describes future directions that this dissertation provides foundation for.

Molecular dynamics simulations and QM/MM calculations can provide insights into the structure and function of enzymes as well as changes due to mutations of the protein sequence.

Mechanical pressure offers unique control over the energy landscape of chemical reactions, opening up pathways that are inaccessible through conventional thermochemistry. We hypothesize that the reduced dimensionality defines the conformational space of the high-pressure reaction, giving rise to new selectivity that is unavailable in 3D systems. Here, we demonstrate this concept through the pressure-controlled topochemical polymerization of the diacetylene molecule deca‐3,5‐diyn‐1‐amine (DDA) incorporated in the two-dimensional (2D) perovskite [DDA]2PbBr4. Compression at 3 GPa drives the first topochemical polymerization through 1,2 addition, forming a polyene product at room temperature. The reaction is initiated by the mechanical bending of the linear DDA molecule, a mechanism fundamentally different from the 1,4-addition in 3D solids. Importantly, pressure hinders the second 1,2-addition by disfavoring the gauche conformation between the remaining acetylene groups, allowing for the selective formation of polyene versus polyacene products. We characterize the reaction mechanisms and products using spectroscopies (Raman, X-ray photoelectron, ultraviolet-visible), X-ray diffraction and density-functional theory simulations. These results highlight the important role of dimensionality in high-pressure chemistry, and offers a new paradigm for creating low-dimensional functional materials.

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 …