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Acenaphthene and 1,10-Phenanthroline-Fused Βeta-Functionalized Porphyrins
A series of acene-fused porphyrins and 1,10-phenanthroline-fused porphyrins were synthesized and characterized via NMR spectroscopy and mass spectrometry. The acene-fused porphyrins exhibit unique optoelectronic properties, most notably they exhibit highly red-shifted absorption bands. The 1,10-phenanthroline-fused porphyrins are of interest for their ability to bond to as variety of metals to form chelation complexes.
A Comprehensive Investigation of Photoinduced Electron Transfer and Charge Transfer Mechanisms in Push-Pull Donor-Acceptor Systems: Implications for Energy Harvesting Applications
Donor-acceptor systems exhibit distinctive attributes rendering them highly promising for the emulation of natural photosynthesis and the efficient capture of solar energy. This dissertation is primarily devoted to the investigation of these unique features within diverse donor-acceptor system typologies, encompassing categories such as closely covalently linked, push-pull, supramolecular, and multi-modular donor- acceptor conjugates. The research encompasses an examination of photosynthetic analogs involving compounds such as chelated azadipyromethene (AzaBODIPY), N,N-dimethylaminophenyl (NND), phenothiazine (PTZ), triphenylamine (TPA), phenothiazine sulfone (PTZSO2), tetracyanobutadiene (TCBD), and expanded tetracyanobutadiene (exTCBD). The strategic configuration of the donor (D), acceptor (A), and spacer elements within these constructs serves to promote intramolecular charge transfer (ICT), which are crucial for efficient charge and electron transfer. The employment of cutting-edge analytical techniques, such as ultrafast transient absorption spectroscopy, is integral to the study. Furthermore, a comprehensive suite of analytical methodologies including steady-state UV-visible absorption spectroscopy, fluorescence and phosphorescence spectroscopies, electrochemical techniques (including cyclic voltammetry and differential pulse voltammetry), spectroelectrochemistry, and density functional theory calculation (DFT), collectively contribute to the comprehensive characterization of push-pull donor-acceptor systems, with a particular emphasis on their potential as highly effective solar energy harvesting application.
Cross-Conjugation Effects on Fused β, β'–π–Extended Porphyrins
Cross-conjugation in molecules has been seen in nature for many years but was not pursued due to the difficulty of their synthesis and their lack of stability. Recently, it has become more interesting due to the rise of molecular electronics. Linear conjugation serves well as the wires to conduct electrons, but molecular electronics are made up of more than just wires. Molecules are needed that possess an on/off switch that can allow or deter conduction. Cross-conjugated systems show promise in their ability to be turned on or off from external stimuli. Pentacene quinone is a well-known cross-conjugated molecule that already shows promise in the field of molecular semiconductors. By synthetically fusing the pentacene quinone to the β, β' positions of a porphyrin, it has been shown that both the solubility and stability have been greatly improved. This has allowed us to pursue functionalization of the quinone moiety. Several new cross-conjugated pentacene quinone fused porphyrin systems were synthesized and studied. It was found that cross-conjugated platinum porphyrins show enhanced fluorescence, and phosphorescence that shifts toward the Near IR. Additionally, strong electron withdrawing groups show potential in charge transfer, and a lower HOMO to LUMO gap, while mildly withdrawing groups have a higher HOMO to LUMO gap. Furthermore, a new method to introduce halogenated methine bridges at the pentacene quinone core was developed, thus opening the doors to new polycyclic aromatic hydrocarbons to be synthesized and studied.
Design and Development of a Paper Spray Air Sampling Device for Use in Clinical, Defense, and Environmental Applications
Environmental monitoring is becoming increasingly important, primarily in urban areas due to the concentrated levels of human activities. The air sampling device presented is a novel method to sample air which harnesses the power of paper spray ionization paired with the intrinsic advantages of mass spectrometry such as high sensitivity, high selectivity, high throughput, and the ability to monitor multiple compounds at once.
Directing Transition Metal Catalysis of Second and Third Row Metals through Ligand Design
Ligand design is important due to a ligand's ability to tune properties of the transition metals, such as catalytic activity and selectivity. Gold(I) catalysts can be directly impacted by ligands electronically as well as with steric bulk when undergoing enantioselective and regioselective reactions. In the dissertation, a series of gold(I) acyclic diaminocarbenes were synthesized and used to explore the 1,6 enyne cyclization/hydroarylation. The use of metal templated synthesis of the gold(I) acyclic diaminocarbenes allowed for the gradual increase in steric bulk of the catalysts. In the end, it was shown that electronics play the major role in the regioselectivity for the 1,6 enyne cyclization/hydroarylation but localized steric bulk can control the catalytic reaction if placed strategically. Cross-coupling reactions used to form carbon-carbon or carbon-heteroatom bonds are important in the production of pharmaceutical chemicals on a large scale. Iron, an extremely cheap and earth abundant first row transition metal, has had some success in cross-coupling reactions. Iron does not go through the same catalytic cycle for cross-coupling as most transition metals, the most common of which is palladium. In the dissertation, a ligand was developed to induce Iron to undergo the same cycle as palladium. In addition, the same ligand was placed on palladium(II) and reduced to try to form and isolate a catalytically active palladium(0) complex.
Homoleptic and Heteroleptic Platinum(II) Complexes for Organic Light Emitting Diodes and Humidity Sensors: Synthesis, Characterization, and Applications
This dissertation focuses on the design, synthesis, characterization of platinum (II) pyridylazolate complexes and develop high performance organic light emitting diodes (OLEDs) and design and execute high-sensitivity humidity sensors based on the luminescent metal-organic complexes of platinum. A majority of existing platinum compounds do not dissolve in organic solvents, making it difficult to analyze the photophysical characteristics of complexes in solution, a key part of understanding chemical photophysical properties. Furthermore, due to the poor quantum yield, it is inefficient for use in devices such as OLEDs. Chapter 2 reports the synthesis and characterization of a novel heteroleptic platinum(II) pyridylazolate complex with high solubility and quantum yield. The photochemistry of the complex is studied, including efficiency, emission profiles, and lifetimes at different temperatures. Chapter 3 reports the power efficiency (lm/W), current efficiency (cd/A), external quantum efficiency (EQE), luminance and operating voltage (V) of OLED devices made with the heteroleptic platinum(II) pyridylazolate complex. The relation between thickness of hole transport layer and electron transport layer on performance of devices has been studied through building a variety of devices. Chapter 4 includes application of a homoleptic platinum(II) pyridylazolate complex in humidity sensor. In many environments, the relationship between moisture content and emissive wavelength has been investigated. This research reveals that regardless of the humidity level, there is a link between increasing the temperature and decreasing the moisture absorption capacity of the complex.
Kinetics and Atmospheric Chemistry Studies of Halogenated Species
Quantitative information about halogenated hydrocarbons is important for understanding their impact on atmospheric ozone chemistry and climate change, their regulation, and the devising of improved substitutes. The Montreal Protocol aimed to regulate the utilization and manufacturing of hydrochlorofluorocarbon compounds (HCFCs), contributing to ozone layer depletion. The 2016 Kigali Amendment to the Montreal Protocol agreement, Annex C listed 274 HCFCs. Only 16 of them have been measured experimentally. The rest were set to zero by default. These reported global warming potentials (GWPs) play a crucial role in formulating policies for gradually reducing the usage and production of HCFCs to prevent atmospheric impact. Here we are studying 1-chloro-1-fluoro-ethane (CH3CHFCl) as a test of past theory. There are no prior experimental measurements of the reactivity of CH3CHFCl with hydroxyl (OH) radicals, which primarily determines its atmospheric lifetime, nor of its infrared (IR) spectrum. Saturated hydrofluorocarbons (HFCs) are non-ozone depleting substitutes for chlorofluorocarbons deprecated under the 1987 Montreal Protocol on Substances that Deplete the Ozone Layer, but they exhibit high global warming potentials (GWPs) and the Kigali Amendment adopted in 2016 outlines their phase down. Unsaturated HFCs offer more reactive alternatives, whose likely short atmospheric lifetimes would imply small GWPs. Because their GWPs are smaller than those for saturated HFCs by several orders of magnitude, and especially for fully fluorinated examples, several halogenated olefins are under consideration for practical application. We studied HCF2CF2CF=CF2, cis-HCF=HCF, trans HCF=HCF, CF2=CH2 unsaturated HFCs.
Kinetics and Thermochemistry of Halogen and Nitrogen Compounds
Halogen and nitrogen containing compounds play a key role in the atmospheric chemistry of the Earth. Through a mixed computational and experimental approach, the kinetics of these compounds with radicals common to the atmosphere have been explored. Using fundamental measurements such as the IR absorption cross-section, the rate constants of atmospheric reactions and the properties of product molecules have been derived. These results have been further extended to environmental applications such as the Global Warming Potential for a species. The present results can be used as a calibration for further experiments and as checks on computational predictions of environmental properties. Such modeling can aid in the development of future industrial reagents that are less hazardous to the atmosphere.
Metal Nitride Complexes as Potential Catalysts for C-H and N-H Bonds Activation
Recognizing the dual ability of the nitride ligand to react as a nucleophile or an electrophile – depending on the metal and other supporting ligands – is a key to their broad-range reactivity; thus, three DFT studies were initiated to investigate these two factors effects (the metal and supporting ligands) for tuning nitride ligand reactivity for C-H and N-H bond activation/functionalization. We focused on studying these factors effects from both a kinetic and thermodynamic perspective in order to delineate new principles that explain the outcomes of TMN reactions. Chapter 2 reports a kinetic study of C–H amination of toluene to produce a new Csp3–N (benzylamine) or Csp2–N (para-toluidine) bond activated by diruthenium nitride intermediate. Studying three different mechanisms highlighted the excellent ability of diruthenium nitride to transform a C-H bond to a new C-N bond. These results also revealed that nitride basicity played an important role in determining C–H bond activating ability. Chapter 3 thus reports a thermodynamic study to map basicity trends of more than a one hundred TMN complexes of the 3d and 4d metals. TMN pKb(N) values were calculated in acetonitrile. Basicity trends decreased from left to right across the 3d and 4d rows and increases from 3d metals to their 4d congeners. Metal and supporting ligands effects were evaluated to determine their impacts on TMNs basicity. In Chapter 4 we sought correlations among basicity, nucleophilicity and enhanced reactivity for N–H bond activation. Three different mechanisms for ammonia decomposition reaction (ADR) were tested: 1,2-addition, nitridyl insertion and hydrogen atom transfer (HAT). Evaluating nitride reactivity for the aforementioned mechanisms revealed factors related to the metal and its attached ligands on TMNs for tuning nitride basicity and ammonia N–H activation barriers.
Nitrogen Reduction Reaction: Deposition, Characterization and Selectivity of Transition Metal (V, Co and Ti) Oxynitrides as Electrocatalysts
The electrocatalytic nitrogen reduction reaction (NRR) is of considerable interest due to its potential for less energy intensive and environmentally friendly ammonia production which is critical for agricultural and clean energy applications. However, the selectivity of NRR compared to the hydrogen evolution reaction (HER) often poses challenges for various catalysts, including Earth-abundant transition metal oxynitrides like Ti, V, and Co. In this work, a comparative analysis of the selectivity of these three metal oxynitrides was conducted, each having different metal oxophilicities. A combination of electrochemical, surface characterizations and density functional theory (DFT) calculations were employed to directly assess NRR and HER activities under the same reaction conditions. Results show that cobalt oxynitrides exhibit NRR activity at pH 10, involving the electrochemical reduction of both lattice-bound nitrogen and dissolved N2, although more HER activity was observed. In contrast, vanadium oxynitride films displayed HER inactivity at pH 7 and 10 but demonstrated NRR activity at pH 7, while titanium oxynitrides were active at pH 3.2 but inactive under neutral and basic pH conditions. These comprehensive studies highlight substantial variations in HER and NRR selectivity based on transition metal oxophilicity/azaphilicity, indicating distinct mechanisms governing NRR and HER mechanisms.
Surface Engineering of Materials for Beyond-Microelectronics
All oxide heterostructure Cr2O3/TiO2-x was deposited on Al2O3(0001) single crystal via MBE. The analysis of interfacial interactions involving two metal oxides resulting in magnetic properties gave insights for using such heterostructures as potential spintronic device materials. The corundum phase epitaxial growth of TiO2-x on Al2O3 was characterized using XPS, AES, EELS, and LEED. The data obtained gives evidence of presence of two-dimensional electron gas at titania surface due to oxygen vacancies formation after deposition. On titania, the deposition of chrome in UHV results in the formation of oxidized chromia overlayer by abstraction of oxygen from the TiO2-x underlayer further increasing the number of vacancies present. In industrial R&D project, dry etching of multiple optical device components was performed using a novel angled etch prototype tool. The first set of experiments involved plasma etching of SiC thin films optimized for target application. The best-known method (BKM) worked from 300mm full wafer to 200mm product. In second experimentation, a variety of gray-tone photoresist received from customers were etched using BKM. Customer received etch rate on each gray-tone material. The third experiments compared recipe R1 to test recipe R2 on the test vehicle VDC. R2 showed faster etch rate but lower process repeatability (RMSE%). With continuous improvement of the tool and the process, two tools are operating products every day, a third prototype tool is about to be in pilot production.
Synthesis, Characterization, Standardization, and Validation of Luminescence Optical Chemosensors for the Detection of Carbon Dioxide, Aluminum Ions, and Silver Ions for Real-Life Applications
The presented dissertation encompasses three distinct investigations into novel complexes with diverse applications. Firstly, a Europium-based complex, K[Eu(hfa)4], exhibits remarkable potential for detecting dissolved CO2 in an ethylene glycol medium, offering a low limit of detection, rapid response times, and high signal-to-noise ratios. This complex demonstrates promise for quantifying CO2 concentrations and finds utility in sugar fermentation monitoring. Secondly, an innovative ratiometric optical sensor, Eu(tta)3([4,4'-(t-bu)2-2,2'-bpy)], showcases exceptional sensitivity and selectivity in detecting aluminum ions, making it suitable for environmental and biological applications. It exhibits reliable quantification in both methanol and aqueous samples, with remarkable accuracy validated by ICP-OES. Lastly, modifications to the Au3Pz3 complex synthesis enable the development of a silver ion sensor, paving the way for detecting silver ion leaching in real-life scenarios, such as silver nanoparticle-embedded bandages. The research extends to the synthesis of silver nanoparticles using various methods and foresees expanded in vitro and in vivo studies. These investigations collectively offer insights into the development of advanced sensing technologies with significant implications for a wide range of practical applications.
A Computational Study of Palladium (II) bis(NHC) Complexes and a Computational/Experimental Study of Gold (I) bisADC Complexes Utilizing Non-Covalent Interaction for Catalysis
Carbene ligands over these years have become a heavily utilizes and effective ligand for catalysis. The diamino carbene class of ligands are slightly less understood. The effects of bis(carbene) ligand structures of palladium (II) catalysts were investigated using the ETS-NOCV method. The results showed that the amount of π-backbonding played a major role in the rate of the reaction for these NHC complexes. The amount of pi acceptance from the ligand increased in correlation to the length of the methylene linkage in the ligand back bone resulting in increased catalytic activity. The ETS-NOCV method was used to determine the deformation densities that had a contribution to this interaction based on visual interpretation. The percent contribution of pi interactions provided a linear correlation to the natural log of the initial reaction rate, indicating that π-backbonding plays a crucial role in the overall catalytic activity of the palladium complexes. Gold (I) bis acyclic diamino carbenes (ADCs) were investigated for the possibility to be strong hydrogen bond catalysts. The ligand motif of the gold (I) bisADCs were found to be analogous thiourea compounds. Based on NBO analysis there were some improvements to hydrogen bond donicity in comparison to thioureas with the same functional group. The complexes were analyzed for hydrogen bond interactions and polarizations interactions between simple nitroolefin substrate and the catalyst using ETS-NOCV. Results showed that the compounds can form a stable hydrogen bonding system and activate the substrate. This capability is tunable by changing the electron withdrawing properties of the ligase motif, providing the idea that gold (I) bisADCs have potential to be good hydrogen bond catalysts. New thiourea-like gold (I) catalysts utilizing the acyclic diamino carbene motif that were hypothesized were synthesized using a one pot synthesis approach utilizing a metal templated synthesis method. The synthesis, characterization, and application prove …
Design and Synthesis of Gold (I) Acyclic Diamino Carbene Complexes as Metallodrugs for Cancer and for Asymmetric Catalysis
Many previous studies have demonstrated that gold compounds possess successful results in catalysis and in medicinal chemistry. The central aim of this dissertation is the design and synthesis of novel gold (I) acyclic diamino carbene complexes as a chemotherapeutic agent for triple-negative breast cancer (TNBC) and for catalysis. In this study, a series of chiral neutral and cationic gold (I) acyclic diamino carbene (ADC) complexes and neutral gold (I) bis- ADC complexes have been synthesized. As the chiral neutral gold (I) ADCs, four diastereomers of S binaphthyl L proline tertiary butyl ester gold (I) chloride, S binaphthyl D proline tertiary butyl ester gold (I) chloride, R binaphthyl L proline tertiary butyl ester gold (I) chloride, and R binaphthyl D proline tertiary butyl ester gold (I) chloride have been synthesized and characterized. Different chiral gold (I) ADC complexes with bulky chiral binaphthyl group and with different amine groups of morpholine, chiral proline methyl ester, and benzyl ester have been synthesized and characterized. After that four diastereomers of the nitrile adduct of cationic binaphthyl proline tertiary butyl ester nitrile and four diastereomers of the isonitrile versions of it have been synthesized and characterized. A series of gold (I) cationic bis ADC complexes have been synthesized and characterized. All these novel gold ADC complexes were tested for biological activity against TNBC cell line MDA-MB-231 and cationic S binaphthyl D proline ester isonitrile adduct, S binaphthyl D proline ester isonitrile adduct and R binaphthyl D proline ester isonitrile adduct gave promising inhibition rates. According to Lipinski's rule, lipophilicity determines the effectiveness of the drug absorption to the body through the lipid membrane. To determine the drug-likeness of the gold ADC complexes, log P values were calculated for some of the synthesized complexes using a modified shake flask method. Gold (I) ADC complexes have been …
β, β'-π-Extended Porphyrins: Exploration of Functionalization and Aromatic Character
Seventeen new dithiophenyl- and napthodithiophenyl- fused porphyrins were synthesized; from these an additional 7 porphyrin oligomers were also synthesized. Additionally freebase 2,7-dimethoxytriphenylene fused porphyrin was also synthesized from a freebase precursor. Aromatic indices NICS and AICD were used to evaluate these new molecules.
Spectral, Electrochemical, and Photochemical Characterization of Donor-Acceptor Supramolecular Systems
This dissertation research work focuses on the investigation of novel donor-acceptor systems elucidating their photochemical properties, anion binding, and their potential application in the development of artificial photosynthetic systems. The explored systems are based on oxoporphyrinogen (OxPs), porphyrins, fullerene, and boron dipyrromethene (BODIPY) based donor-acceptor systems. The photochemical properties of novel molecular systems were elucidated using UV-vis spectroscopy, fluorescence spectroscopy, electrochemical methods, computational calculations, and ultrafast transient absorption spectroscopy. A novel BODIPY-oxoporphyrinogen dyad which is able to bind with fluoride anion promoting the excited state ultrafast electron and energy transfer events mimicking the primary events in natural photosynthesis was introduced. Further, self-assembly of supramolecular complexes based on oxoporphyrinogens, fullerene, and different zinc porphyrin dimers was explored. The formed self-assembled complexes have shown photoinduced electron transfer. A novel push-pull supramolecular construct based on the spiro-locked N-heterocycle-fused zinc porphyrin was studied. The excited state charge separation and stabilization of this push-pull system was enhanced by the complexation with fluoride anion. Also, the effect of BODIPY functionalization and linkers on the electron transfer properties of a series of carbazole–BODIPY and phenothiazine-BODIPY dyads were investigated. These findings are important to develop advanced and efficient BODIPY-based donor-acceptor systems for efficient light harvesting applications. The entire study aims to expand our understanding of these systems and contribute towards the advancement of sustainable energy technologies.
Synthesis and Studies of Platinum- and Palladium-Based Porphyrin-Fullerene Conjugates to Study the Long-Lived Charge-Separated States
The research presented in the dissertation deals with the synthesis, characterization, photophysical, electrochemical, and pump probe studies of porphyrin-fullerene based donor-acceptor conjugates. The first chapter provides insights into the introduction of the thesis, which explains the events that occur in natural photosynthesis and the mimicking process of an artificial photosynthesis based on natural photosynthesis, works done in covalently and non-covalently linked donor acceptor systems, and the penetration of the literature related to the long-lived charge-separated states donor-acceptor conjugates. The second chapter details the physical methods employed to monitor the various photochemical processes in the donor-acceptor moiety. The third chapter focusses on designing and synthesizing a platinum porphyrin-fullerene dyad used for long-lived charged-separated state. The formation of a high-energy, long-lived radical ion pair by electron transfer from the triplet excited state is orchestrated in the dyad. The porphyrin ring is modified with three triphenylamine which act as secondary electron donors. The spin state of the electrons leading to the formation of long-lived charge-separated state is demonstrated by time-resolved optical and EPR spectroscopy. The fourth chapter studies metal ligand axial coordination. Two porphyrins were self-assembled via metal-ligand axial coordination of phenyl imidazole functionalized fulleropyrrolidine. A 1:2 complex formation with ImC60 was observed in the case of (TTP)Co, while for (TPA)4PCo only a 1:1 complex was possible. Spectroelectrochemistry revealed the formation of Co (III) porphyrin cation instead of Co (II) porphyrin radical cation during the oxidation of phenyl imidazole coordinated cobalt porphyrin. Using computational and electrochemical results, an energy level diagram was constructed to visualize the various photochemical events. Using femtosecond transient absorption spectroscopy, it was possible to observe the energy transfer and charge-separation process. The fifth chapter deals with the singlet oxygen generation of platinum and palladium porphyrins. In this chapter, a series of meso-substituted porphyrins are synthesized and metalated by platinum …
Synthesis, Kinetic Studies, and Structural Investigations of Osmium and Ruthenium Clusters
Addition reactions of ten neutral nucleophiles and seven anionic nucleophiles with the pentaosmium pentadecacarbonyl carbido cluster Os5C(CO)15 have been kinetically studied and several important reactivity trends have been established. The calculated activation parameters support an associative mechanism involving the attack of nucleophiles on the parent cluster in the rate-limiting step. Decarbonylation reactions of neutral arachno clusters Os5C(CO)15L have also been kinetically studied and different reactivity trends have been observed. Reactions of Os5C(CO)15 with both neutral and anionic nucleophiles produce corresponding arachno clusters in good yield. Neutral arachno clusters decarbonylate when heated to yield corresponding nido clusters. All studied anionic arachno clusters are resistant to decarbonylation, but most of them readily react with organic acids to form corresponding hydrido clusters. Reactions of anionic arachno clusters with methyl triflate yielded several new clusters. Exploration of metal-ligand bond lengths in the respective pairs of arachno and nido clusters yielded a valuable conclusion with regard to steric effects prevalent in these molecules. The mechanisms for polyhedral structural rearrangements between arachno and nido derivatives of the pentaosmium carbido cluster have been proposed. Thermolysis of cluster Ru3[Ph2PCH(Me)PPh2](CO)10 in the presence of diphenylacetylene yields alkyne-substituted clusters Ru3(PhCCPh)[Ph2PCH(Me)PPh2](CO)8 and Ru3(PhCCPh)[Ph2PCH(Me)PPh2](CO)7 as the major products. The backbone-modified diphosphine in both clusters has facilitated the growth of single crystals suitable for X-ray crystallography. The kinetics for the conversion between two clusters have been investigated and the calculated activation parameters were found to be inconsistent with a rate-limiting step involving a dissociative loss of CO.
Cleaner Futures: Covalent Organic Frameworks for Sustainable Degradation of Lignocellulosic Materials
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.
Magnetron Sputtering of Transition Metal Oxynitrides and Their Characterization with Auger Electron Spectroscopy and X-ray Photoelectron Spectroscopy
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.
One-Step Synthesis of 1,3,4-Oxadiazines, 4,5,6,7-Tetrahydro-1h-Indoles, and Functionalized Benzo[B]Carbazoles Catalyzed by Rare Earth Metal Triflates and Cooperative Enamine-Bronsted Acid
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.
Porous Organic Polymer-based Nanotraps for Metal Resource Recovery/Extraction from Water
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
Theoretical Studies of Photoactive Metal Complexes with Applications in C-H Functionalization and Quantum Computing
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 the formation of excited states. Tanabe-Sugano diagrams predict areas where these excited states may relax via phosphorescent emission. Under Zeeman splitting, these transitions create the conditions required for a two-level system needed to design a functional organometallic qubit.
Aromaticity, Supramolecular Stacks, and Luminescence Properties of Cyclic Trinuclear Complexes
The dissertation covers three major topics: metal-assisted aromaticity, synthetic approaches to tailor donor-acceptor supramolecular stacks, and photoluminescence properties of cyclic trinuclear complexes (CTCs) of d10 metals. First, multiple theoretical approaches are adapted to discuss in detail the origin of aromaticity of CTCs, putting forward a metal-assisted aromaticity model. Next are the discoveries of donor-acceptor stacked CTC–CTC' complexes from both experimental and computational perspectives, reporting multiple novel crystallography-determined structures and revealing their pertinent intermolecular ground-state charge transfer. The spontaneous binding behavior is also determined by UV-vis and NMR titrations and rationalized as the cooperation of multiple supramolecular interactions, including metallophilicity, electrostatic attraction, and dispersion. The last part includes systematic investigations of photoluminescence properties of halogen-metal-bonded CTCs and sandwich-like cation–π-bonded heptanuclear clusters based on CTCs. The cooperative effects of metal-centered conformation, the heavy-atom and relativistic effects from both the halogen and metal atoms play complementary roles in the phosphorescence process to promote the inter-system crossing and radiative transitions.
An Investigation into the Micromechanical and Corrosion Properties of Additively Manufactured Stainless Steel 316L
In this thesis, micro-mechanical properties and corrosion resistance of laser powder bed fusion (L-PBF) processed additive manufactured (AM) 316L stainless steel parts were investigated for different combinations of processing parameters. Various laser powers were employed for the fabrication of all AM 316L stainless steel parts. Nanoindentation, areal roughness, and electron backscattered diffraction (EBSD) characterization were used to characterize the surface of the AM samples prior to corrosion testing. Open circuit potential (OCP), linear polarization resistance (LPR), electrochemical impedance spectroscopy (EIS), and potentiodynamic polarization tests were done to compare AM L-PBF 316L stainless steels with different processing parameters. Overall, it was observed that the AM part having a 56.67 J/mm3 volumetric energy density (VED) exhibits the best micro-mechanical characteristics. This sample also had the lowest areal surface roughness and smallest grain size. Consequently, this parameter combination had better corrosion resistance compared to the other AM processed 316L parts. The results are useful in process calibration when fabricating for corrosion resistance applications and provide insights into the relationship among nano-mechanical, crystallography, and long-term corrosion performance.
Investigation of Ionic Liquid Phases for Chromatographic Separation of Fentanyl Analogues
Opioid abuse and in particular fentanyl, a synthetic opioid, has been of concern in the last decade. Fentanyl is an illicit drug of concern to due to its prevalence and potency. Research to date has focused on supporting law enforcement by developing methods suitable for chemical profiling and identifying fentanyl from various matrices. However, methods geared towards analysis of fentanyl isomeric analogues are rare. Analysis of isomers is challenging due to similar mass spectral fragmentation patterns and exhibiting co-elution using common gas chromatographic columns. Developing methods to use in forensic labs utilizing already available equipment will advance current capabilities in the detection of fentanyl compounds. Thus, investigation into alternative stationary phases and development of special gas-liquid chromatographic (GLC) based methods for isomeric fentanyl analogues has been done. Several studies were done to investigate the use of ionic liquid chromatographic phases in analyzing fentanyl analogues. The first study focused on investigating the thermal stability of ionic liquids to identify those suitable to withstand the high oven temperatures that was needed to elute fentanyl analogues in gas chromatography. Total synchronous fluorescence spectroscopy and differential scanning calorimetry were demonstrated to be sensitive enough to detect the decomposition products of ionic liquids. In the second study, gas chromatographic analysis was done on fentanyl analogues using an ionic liquid stationary phase as well as two commonly used stationary phases for comparison purposes. The applicability of the developed methods was tested using standard fentanyl analogue samples as well as in-house synthesized samples on all three columns. In the third study, quantitative structure property relationship equations were developed to predict the retention time of fentanyl analogues on two of the gas chromatographic stationary phases used in the second study.
Nanofluidic Membrane Based on Covalent Organic Framework: Design Strategies and Applications
Nanofluidic is an emerging field of applying fluid properties in nanochannels or nanostructures. The nanoporous channel with a pore size of less than 100 nm will strongly affect the motion of the fluid. Meanwhile, the pore environment, such as hydrophilic and hydrophobic properties, charge density, and host-guest recognition would be crucial for the transportation of molecules and ions in the pore. This thesis is focused on the synthesis, characterization of nanofluidic membranes and their applications to reverse electrodialysis. Chapter 1 focuses on the importance and objective of this work. Chapter 2 gives an overview of nanofluidic and classical nanofluidic structure–covalent organic frameworks (COFs). In Chapter 3, a series of COFs membranes with different surface charge densities were designed by employing a multivariate (MTV) strategy. A volcano-like relationship between the surface charge density and output power density was observed when the membranes were applied for osmotic energy harvesting. Chapter 4 integrates the temperature gradient to the covalent organic frameworks nanofluidic system to further explain the thermophoretic mobility of ions. The recorded osmotic energy production density was obtained while ion concentration polarization was alleviated with increasing hydrodynamic convection effects. In Chapter 5, a coupled photon-electron-ion transport behavior across ionic covalent organic framework membranes with chromophoric porphyrin struts was demonstrated. Photoexcitation-induced ion transmission was developed by converting external light into electric signals. Chapter 6 includes the summary of this thesis.
Parameterization of Ionic Liquids and Applications in Various Chemical Systems
In this work, the development of parameters for a series of imidazolium-based ionic liquids molecules, now included in the AMOEBA force field, is discussed. The quality of obtained parameters is tested in a variety of calculations to reproduce structural, thermodynamic, and transport properties. First, it is proposed a novel method to parameterize in a faster, and more efficient way parameters for the AMOEBA force field that can be applied to any imidazolim-based cation. Second, AMOEBA-IL polarizable force field is applied to study the N-tert-butyloxycarbonylation of aniline reaction mechanism in water/[EMIM][BF4] solvent via QM/MM approach and compared with the reaction carried out in gas-phase and implicit solvent media. Third, AMOEBA-IL force field is applied in alchemical calculations. Free energies of solvation for selected solutes solvated in [EMIm][OTf] are calculated via BAR method implemented in TINKER considering the effect of polarization as well as the methodology to perform the sampling of the alchemical process. Finally, QM/MM calculations using AMOEBA to get more insights into the catalytic reaction mechanism of horseradish peroxidase enzyme, particularly the structures involved in the transition from Cp I to Cp II.
Porous Materials as Drug Delivery Systems
The porous materials discussed in this dissertation are metal-organic frameworks (MOFs) and porous liquids. Due to their high surface areas, tunable structures, and controllable porosities, MOFs have been explored for a wide variety of drug delivery applications. In chapter 2, MOFs have been used as magnetothermal-triggered release carriers through spatially distributed iron oxide nanoparticles within MOF matrix as a magnetic heating mediator and surface-grafted thermal-responsive nanocap as an alternating magnetic field (AMF)-responsive gatekeepers, achieving monitoring of drug release via external AMF by a conformational change of nanocap. In chapter 3, MOF, as a non-toxic loading carrier, encapsulate naringin, a natural product to serve as a multifunctional bio-platform capable of treating Gram-positive bacteria and certain cancers by slowly and progressively releasing the encapsulated naringin as well as improving and modulating immune system functions through the synergies between naringin and MOF. In chapter 4, porous liquid with unique solvent-free fluidity properties as a drug delivery platform for the first time. The interaction between hollow silica nanoparticle and polymerized ionic liquid, followed by ionic grafting brush of poly (ethylene glycol) telomer, makes this designed porous liquid responsible for high drug-loading and pH-responsive drug-releasing abilities along with slow degradation behavior. In addition to their high loading and controlled release, In vitro cell viability and cell uptake are also studied, thus opening up new opportunities for long-term chemotherapy.
Ranaspumin Protein Characterization and Applications for Both Environmental and Medical Purposes
The Túngara frog (Engystomops pustulosus) from Central America creates a bio-foam that protects their young from dehydration, microbial degradation, and even predators during early development. The foam is composed of unique proteins known as Ranaspumin 1-6 (RSN 1-6). These RSN proteins have been synthetically synthesized and verified with Circular Dichroism (CD) to determine their critical micelle concentration, antimicrobial properties, and stability at varying temperatures and pH ranges. Throughout these characterizations, RSN 2 was determined to establish/produce antimicrobial properties, express stability at temperatures between 20 – 60oC, and express stability at a pH range of 5-8. Therefore, RSN 2 was isolated and utilized for medical and environmental applications. With the addition of RSN 2, the separation of aromatics was achieved in tar-sands with the assistance of a Tangential Flow Filtration (TFF) system. With only three passes through the TFF system, the RSN 2 solution isolated approximately 35% of the aliphatic region, and approximately 70% of the aromatic region. Finally, RSN 2 was implemented into an organ preservation solution for organ transplant surgery. By observing two different biomarkers, including Cardiolipin (CL) and alkali metals/alkaline earth metals for a change in concentration to verify organ viability. Resulting in the RSN 2 solution as well as a 50:50 solution composed of RSN 2 and a ‘gold standard' solution, has the potential to replace the on the market preservation solutions. Therefore, a simple bio-foam such as RSN 2 has the potential to advance both the medical and environmental fields.
Sulfur-Based Organic Compounds as Novel Corrosion Inhibitors for Brass and Aluminum Alloy Protection in Acid Cleaning Solutions
In this study, thiol and two disulfide compounds have been tested as new corrosion inhibitors for brass and aluminum alloys. Pyridine-2-thiol and 2,2'-dipyridyl disulfide were tested for brass alloys in 0.5 M H2SO4 solution and both inhibitors showed excellent corrosion protection against the aggressive corrosive ion attack. Both inhibitors adsorbed to brass surface forming a protective film via a chemisorption process. XPS studies showed formation of Cu-S bond which allows these molecules to chemisorb on to brass surfaces. Pyridine-2-thiol, 2,2'-dipyridyl disulfide and 4'4-diaminodiphenyl disulfide were tested as corrosion inhibitors for AA6061-T6 alloy in 1 M HCl solution and all inhibitors showed excellent corrosion protection over wide range of temperatures. To evaluate the corrosion inhibition efficiencies many different instruments and electrochemical techniques were used. Overall results from this study showed sulfur-based corrosion inhibitors can be used effectively to mitigate the corrosion process of brass and aluminum alloys in acidic solutions.
Bifunctional Enamine‐Metal Lewis Acid Catalysis and α-Enaminones for Cyclization Reactions
The use of enamines continues to be an important tool in organic syntheses as both a catalyst and reactant. The addition of metal catalysts coupled with enamine catalysis has generated many reactions that normally would not occur separately. However, catalysts' incompatibility is an issue that we wish to solve allowing new chemistry to occur without hindrance. The use of enamines has continued to be a well-studied area of organic chemistry, but the field is ripe for different types of enamines to gain the spotlight. Enaminones are enamines with both nucleophilic and electrophilic properties. They allow reactions that are normally not possible with enamines to become obtainable. Chapter 1 is a brief introduction on enamines and the reason they gained so much attention. Then ends with enaminones and what makes them interesting reactants. Chapter 2 described a new synthesis for the tricyclic synthesis of chromanes using a novel bifunctional catalyst system of enamine-metal Lewis acid giving great yields (up to 87 %yield) and excellent stereoselectivity (up to 99 % ee). Chapter 3 covered new reactions for ring-open cyclopropane (up to 94% yield), tetrahydroquinolinones (up to 84% yield) and enantiospecific tetrahydroquinolinones (up to 84% yield and 97% ee) using α-enaminone and donor-acceptor cyclopropanes. Finally, Chapter 4 focused a new method for synthesizing benzobicyclo[3.2.1]octanes with an added sterically bulky quaternary center and imine functionalization giving yields between 36-73% yield using α-enaminone with alkylidene malonates.
Chemically Optimized Cu Etch Bath Systems for High-Density Interconnects and the FTIR Operando Exploration of the Nitrogen Reduction Reaction on a Vanadium Oxynitride Electrocatalyst
Printed circuit board manufacturing involves subtractive copper (Cu) etching where fine features are developed with a specific spatial resolution and etch profile of the Cu interconnects. A UV-Vis ATR metrology, to characterize the chemical transitions, has been developed to monitor the state of the bath by an in-situ measurement. This method provides a direct correlation of the Cu etch bath and was able to predict a 35% lower etch rate that was not predicted by the three current monitoring methods (ORP, specific gravity, and conductivity). Application of this UV-Vis ATR probe confirmed that two industrial etch baths, in identical working conditions, confirmed a difference in Cu2+ concentration by the difference of the near IR 860nm peak. The scope of this probe allowed chemically specific monitoring of the Cu etch bath to achieve a successful regeneration for repeated use. Interlayer dielectrics (ILDs) provide mechanical and electrical stability to the 3D electrical interconnects found in IC devices. It is particularly important that the structural support is created properly in the multilayered architecture to prevent the electrical cross signaling in short range distances. A combined multiple internal reflection and transmission FTIR has been employed for the characterization of silicon oxycarbonitride (SiOCN) films. These dielectric low-k films incorporate various functional groups bonded to silicon and require chemical bonding insight in the transformation and curing process. Distinct SiOx bonding patterns were differentiated, and the structure of the films can be predicted based on the amount of Si network and caged species. Further optimization of the FTIR analysis must minimize interference from moisture that can impact the judgement of peak heights. To accommodate this, a high-quality glove box was designed for dry air feedthrough to achieve a 95% moisture reduction during analysis, where less than 0.1 mAbs of moisture is detected in the spectra (without additional …
Computational Investigations of Catalytic Activity by Metal-Containing Complexes
This dissertation delves into the catalytic activity of multiple metal-containing complexes with an emphasis on the activation of C–H bonds in small molecules and olefin oligomerization. The research contained in these works employs computational methodologies to better understand the thermodynamics and kinetics of the reactions. Computations can be used to quickly identify novel models and find ideal substitutions for improved catalyst design. Within this dissertation, multiple molecules of divalent and trivalent main group element-containing complexes as well as Group 13 dimetallene complexes were investigated with density functional theory (DFT) to identify their ability to activate C–H of hydrocarbons, including methane, by quantifying their thermodynamics and kinetics of reaction. With several substitutions to the base complex, improved catalysts were designed to decrease the energy barriers of the activations. Multiconfiguration self-consistent field methods were also employed to characterize the biradical character of these Group 13 compounds. Olefin oligomerization by zirconium boratabenzenes with various ancillary pendant groups was also investigated via DFT to identify the most ideal variations as well as the most likely reaction pathway.
The Development of the Attitudes Towards Organic Chemistry Instrument
In this study, undergraduate student attitudes towards organic chemistry and the influences that shape those attitudes were explored using the Attitudes Towards Organic Chemistry Instrument (ATOC) to collect both qualitative and quantitative data. The findings from the qualitative ATOC items provide evidence that students displayed a wide range of attitudes towards organic chemistry, including positive, negative, neutral, and blended attitudes. Five major influences were shown to have shaped these attitudes including the reputation of the course, students' educators, experiences with organic chemistry, experiences with introductory chemistry, and individual experiences. Students responses longitudinally provide evidence that their influences and attitudes change over time in the course. The findings from the quantitative ATOC items provided evidence that the data generated was valid and reliable, and a relationship was found to exist between what students think and what they had heard about the course. Limitations of this investigation, as well as implications for research and practitioners, are discussed.
Earth Abundant Transition Metal Catalysts for Activation and Functionalization of Light Hydrocarbons
Light hydrocarbons activations, functionalization, and reactions have been a subjects of catalysis research for decades but dominated by the rarer and more expensive noble metals. Switching over to using the more earth abundant third row transition metals could be more economical and less toxic but come with their own challenges. Their use as catalysts with light hydrocarbons could be employed better utilize and more efficiently use our hydrocarbon resources that the world still depends on.
Ultrafast Charge Transfer in Donor-Acceptor Push-Pull Constructs
Ultrafast charge and electron transfer, primary events in artificial photosynthesis, are key in solar energy harvesting. This dissertation provides insight into photo-induced charge and electron transfer in the donor and acceptor constructs built using a range of donor and acceptor entities, including transition metal dichalcogenides (TMDs, molybdenum disulfide (MoS2), and tungsten disulfide (WS2)), N-doped graphene, diketopyrrolopyrrol (DPP), boron-dipyrromethene (BODIPY), benzothiadiazole (BTD), free base and metal porphyrins, zinc phthalocyanine (ZnPc), phenothiazine (PTZ), triphenylamine (TPA), ferrocene (Fc), fullerene (C60), tetracyanobutadiene (TCBD), and dicyanoquinodimethane (DCNQ). The carefully built geometries and configurations of the donor and (D), acceptor (A), with a spacer in these constructs promote intramolecular charge transfer, and intervalence charge transfer to enhance charge and electron transfer efficiencies. Steady-state UV-visible absorption spectroscopy, fluorescence and phosphorescence spectroscopies, electrochemistry (cyclic voltammetry (CV) and differential pulse voltammetry (DPV)), spectroelectrochemistry (absorption spectroscopy under controlled potential electrolysis), transient absorption spectroscopy, and quantum mechanical calculations (density functional theory, DFT) are used to probe ground and the excited state events as well as excited state charge separation resulting in cation and anion species. The current findings are useful for the increased reliance on renewable energy resources, especially solar energy.
"You get what you pay for" vs "You can alchemize": Investigating Discovery Research Experiences in Inorganic Chemistry/Chemistry Education via an Undergraduate Instructional Laboratory
Synthesis of d10 complexes of monovalent coinage metals, copper(I) and gold(I), with dithiophosphinate/diphosphine ligands -- along with their targeted characterization and screening for inorganic or organic light emitting diodes (LEDs or OLEDs, respectively) -- represents the main scope of this dissertation's scientific contribution in inorganic and materials chemistry. Photophysical studies were undertaken to quantify the phosphorescence properties of the materials in the functional forms required for LEDs or OLEDs. Computational studies were done to gain insights into the assignment of the phosphorescent emission peaks observed. The gold(I) dinuclear complexes studied would be candidates of OLED/LED devices due to room temperature phosphorescence, visible absorption/excitation bands, and low single-digit lifetimes -- which would promote higher quantum yield at higher voltages in devices with concomitant lower roll-off efficiency. The copper(I) complexes were not suited to the OLED/LED applications but can be used for thermosensing materials. Crystallographic studies were carried to elucidate coefficients of thermal expansion of the crystal unit cell for additional usage in materials applications besides optoelectronic devices. This has uncovered yet another unplanned potential application for both copper(I) and gold(I) complexes herein, as both types have been found to surpass the literature's threshold for "colossal" thermal expansion coefficients. Two other investigations represent contribution to the field of chemistry education have also been accounted for in this dissertation. First, a 12-week advanced research discovery experiment for inorganic chemistry has been designed to help students develop application-based content expertise, as well as to introduce students to research experiences that are similar to those found in academia, industry, and government research laboratories. Students are expected to develop a novel research project through conducting a literature search to find suitable reaction protocols, incorporating synthetic techniques, collecting data, characterizing products and applications of those products, and presenting their results. This multi-week research discovery experiment is centered …
Computational Modeling of Cancer-Related Mutations in DNA Repair Enzymes Using Molecular Dynamics and Quantum Mechanics/Molecular Mechanics
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 telomeres 1 (POT1) enzyme. The investigated variants modify the POT1-ssDNA complex dynamics and protein—DNA interactions. Fifthly, we investigate the incorporation of remdesivir and other nucleotide analogue prodrugs into the protein-RNA complex of severe acute respiratory syndrome-coronavirus 2 RNA-dependent RNA polymerase. We find evidence for destabilization throughout the complex and differences in inter-subunit communication for most of the incorporation patterns studied. Finally, we share a method for determining a minimum active region for QM/MM simulations. The method is validated using 4-oxalocrotonate, TET2, and DNA polymerase λ as test cases.
Deposition and Characterization of Thin Metal Oxide Heterostructures for Electronic and Magnetic Device Applications
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 the presence of a two-dimensional election gas at the TiO2-x surface because of oxygen vacancies present after deposition. Deposition of chrome in UHV results in the formation of an oxidized chrome overlayer by abstraction of oxygen from the TiO2-x underlayer increasing the number of vacancies present. MOKE measurements taken by the project's collaborators at the University of Nebraska-Lincoln indicate that there is an interfacial exchange bias at the interface of the two oxides, a favorable property for magnetic device applications.
In vitro Biomedical Application and Photothermal Therapy Evaluation of Gold Complexes and Gold Nanoparticles
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 having the lowest HOMO values, and from the intercalators and base pairs' HOMO/LUMO energies, it is evident the intercalators will overlap with the HOMO of DNA stabilizing the intercalators. Interaction energies (kcal/mol) were obtained as a function of distance, r (angstroms). Results show that the theoretical treatment SDD-WB97XD outperforms SDD-LSDA in both adenine-thymine (AT) systems with ethidium and Au3 intercalators. In both guanine-cytosine (GC) and AT pairs, the Au3 has the lowest interaction energies among these common intercalators, suggesting a potential intercalating drug. Experimental DNA intercalation studies were attempted and methods of finding intercalation binding constants were established, showing gold …
Machine Learning in Computational Chemistry
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.
Metal-Macrocyclic Frameworks based on Aza-Macrocycles: Design Strategies and Applications
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.
Novel LC-MS Method for the Analysis of Beta-Hydroxybutyric Acid (BHB) in Health Formulations
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.
Porphyrin and BODIPY Derived Donor-Acceptor Multi-Modular Systems: Synthesis, and Excited State Energy and Electron Transfer Studies
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 moderately stable binding. Spectral and electrochemical studies of the dyads used to generate energy level diagrams indicated that PET was thermodynamically unfavorable in BDP(Im)2:ZnP but favorable when the zinc tetrapyrrole is selectively excited dyads—as confirmed in femtosecond transient absorption studies. In the third work, two novel tetrads, consisting of charge stabilizing triphenylamine (TPA) to either bithiophene (BT) or terthiophene (TT) via a covalent linker that is attached to the meso-position of a BODIPY. This BODIPY was further extended by linking it to fulleropyrrolidine via a catechol linker to a modified BODIPY. Computational studies revealed the electronic structures of the tetrads, …
Synthesis and Characterization of Vanadium and Cobalt Oxynitride Surface Chemical and Electronic Structure for Electrochemical Reduction of N2 to NH3
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 of O2/Ar/N2 environments on α-Al2O3(0001) or SiO2/Si(100) substrates to obtain films with varied N/O stoichiometries via magnetron sputter deposition using a vanadium target. Films deposited on the Al2O3(0001) substrates generally, though not always, exhibited a (111) orientation, which is consistent with a rock salt structure. The enhancement of the surface properties of vanadium oxynitride was explored to improve its catalytic properties.
Corrosion Mechanism and Prevention of Wire Bonded Device in Microelectronic Manufacturing and Spectroscopic Investigation of Copper Etch Chemical Equilibria for High Density Interconnect Application
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 bath while also providing a means to monitor the Cl- in the broad UV peak at 250 nm. The UV-Vis probe successfully demonstrated the etch rate difference between the two etch bath solutions and help in the restoration of the etching bath. Additionally, the proof-of-concept experiments (POC) to investigate UV enhanced etching for achieving anisotropic etching in PCB fabrication showed promising preliminary results with the need to develop additional etching techniques.
Donor-Acceptor Artificial Photosynthetic Systems: Ultrafast Energy and Electron Transfer
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.
Instrumental Development and Implementation of Portable Membrane Inlet Mass Spectrometry for Homeland Security and Environmental Applications
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 systems. The steadfast development of miniaturized mass spectrometry systems with efficient operation capabilities for a variety of applications gives promise to the further development of MIMS technology as well as other analytical instrumentation.
Linearly-Annulated, Functionalized, β,β'-π-Extended Porphyrins
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.
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