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Non-Adjacent Anti Cyclobutane Pyrimidine Dimers As Intrinsic Probes Of Non-B Form Secondary Structures Of Dna, Natalia Eugenia Gutierrez Bayona

Arts & Sciences Electronic Theses and Dissertations

G-quadruplexes are four-stranded structures of DNA composed of G-quartets that have been proposed to play an extremely important role in replication, transcription, and translation. It has, however, been extremely difficult to unequivocally demonstrate that G-quadruplexes form in living cells due to the lack of probes that would allow for their unambiguous detection and location without disrupting the DNA or the cellular environment. To circumvent these problems, it was proposed that DNA itself could be used as an intrinsic photoprobe for certain classes of G-quadruplex structures and other non-B DNA conformations in vivo. Recently, we discovered that UVB irradiation of human …

Synthesis And Characterization Of Sodium Cathode Materials, He Zhou

McKelvey School of Engineering Theses & Dissertations

As sodium batteries hold great promise as a next-generation energy storage device to replace lithium batteries, the development of sodium battery materials has become increasingly urgent. The current study aims to investigate two potential sodium-ion battery cathode materials, Sodium Vanadium Phosphate, and Sodium Manganese Hexacyanoferrate, optimize the experimental procedures, conduct a systematic analysis of material properties and characterization, and ultimately determine the ideal synthesis conditions for these materials.

In the first part of the study, we focused on optimizing the synthesis of Sodium Vanadium Phosphate. By investigating various synthesis conditions, such as annealing temperature, pressure, ascorbic acid content, and material …

Synthesis, Radiolabeling And Evaluation Of A Suite Of Tracers With 44Sc For Detecting Extracellular Dna, Zhiyao Li

McKelvey School of Engineering Theses & Dissertations

Neutrophil extracellular traps involve the rapid translocation of DNA to the outside of the cell under certain stimuli. This structure forms a fibrous network that is able to limit the spread of pathogens and to kill microorganisms. It has also been shown to be present in various pathological processes such as inflammation, autoimmune diseases, and cancer metastasis. Currently, the formation process of NETs in vivo is being extensively studied. However noninvasive detection and quantitation has yet to be achieved. A class of PET tracers are described here that consists of a DNA dye as the backbone that is labeled with …

Effects Of Surface Ligation On Charge Extraction From Wurtzite Cadmium Selenide Quantum Platelets And Quantum Belts, Hailey Meyer

Arts & Sciences Electronic Theses and Dissertations

This dissertation presents the synthesis of flat, colloidal wurtzite CdSe quantum platelets and quantum belts for ligand exchange to novel and existing organic and inorganic L-, X-, and Z- type ligands. Use of these ligands in conjunction with the semiconductor nanocrystals allows for examination of their ligand exchange abilities, photoluminescence quenching efficiencies, and charge transfer properties.

First, zinc and cadmium dithiocarbamate compounds [M(S2CNR1R2)2] are used as ligands on wurtzite CdSe quantum belts. Complete ligand exchange is achieved when the belts are initially ligated with Cd(oleate)2, a Z-type ligand, prior to the exchange, as opposed to n-octylamine or ammonia, which are …

Local Spectroscopy Data Infrastructure: Solid State Nmr Crystallography With Experiment, First-Principal Analysis And Machine Learning, He Sun

Arts & Sciences Electronic Theses and Dissertations

Solid-state magnetic resonance (SSNMR) spectroscopy is a powerful tool for obtaining precise information about the local bonding and morphology of materials. The detailed local structure of crystalline materials cannot be easily solved by traditional experimental methods such as X-ray diffraction (XRD). SSNMR combined with first principal calculation methods such as density functional theory (DFT) can be of great use in this research area. The methodology that is called “NMR crystallography” today has been widely applied to the determination of a wide range of solid materials with an increasing amount of computationally simulated NMR spectra. The construction of a well-established computational …

Toward Enhancing The Synthesis Of Renewable Polymers: Feedstock Conversions And Functionalizable Copolymers, Tedd Casey Wiessner

Arts & Sciences Electronic Theses and Dissertations

This thesis describes research under the rubric of the Center for Sustainable Polymers that is aimed at two separate goals. The goal of the first project (Chapters 1 and 2) was to develop a deeper mechanistic understanding of a method for the synthesis of linear α-olefins, while the second aimed at synthesizing statistical copolymers that incorporate olefin-containing monomers through ring-opening transesterification polymerization and showing that these copolymers could be functionalized. In Chapter 1, published methods for the conversion of fatty acids to linear α-olefins are reviewed to provide context for the mechanistic work we accomplished (Chapter 2). In Chapter 2 …

Functionalized Plasmonic Nanostructures For Ultrasensitive Single Cell Analysis, Priya Rathi

Arts & Sciences Electronic Theses and Dissertations

Ultrasensitive detection and quantification of soluble, secreted and cell surface-bound proteins is critical for advancing our understanding of cellular systems, enabling effective drug development, novel therapies, and bio-diagnostics. However, exiting technologies are largely limited by their sensitivity, making the detection and quantification of low-abundant proteins extremely challenging. This forms a major barrier in various fields of biology and biomedical sciences. In this work, we introduce novel cellular analysis methodologies based on plasmon-enhanced fluorescence for analyzing cell structure and probing surface and secreted proteins from cells. In the first part, we introduce plasmon-enhanced expansion microscopy and demonstrate the effectiveness of employing …

Development Of Redox-Responsive Phenazine-Based Foldamers. Acylative Kinetic Resolution Of Hydroxamic Acids, Jingwei Yin

Arts & Sciences Electronic Theses and Dissertations

Two different research directions have been presented in this thesis. The first project is about phenazine-based foldamers as molecular actuators. Researchers have been interested in the design and synthesis of foldamers and molecular actuators for years. We began our exploration by demonstrating that phenazine-1,6-dicarboxamides can function as redox-responsive molecular switches. We then designed and synthesized two generations of phenazine-based interleafed foldamers and studied their stability and redox behaviors under chemical and electrochemical conditions. In the second project, we have developed the first acylative kinetic resolution on hydroxamic acids. Although chiral hydroxamic acids have extensive applications, synthetic methods towards them are …

The Effect Of Ionization Density In Applications Of Radiation Detection, Dosimetry, And Therapy, Daniel Mulrow

Arts & Sciences Electronic Theses and Dissertations

This dissertation covers a wide range of topics but is linked by the common theme of radiation interacting with materials and studying the result of those interactions. The introduction describes the fundamentals of how radiation interacts with material and how we are able to detect that radiation and the application of how we use those interactions in radiation oncology. The thesis starts with a chapter detailing the temperature dependence of the photophysics in two organic scintillators. This chapter is the foundation for a future study that will look the degree to which these scintillators can distinguish between gammas and neutrons …

Design & Analysis Of Mixed-Mode Integrated Circuit For Pulse-Shape Discrimination, Bryan Orabutt

McKelvey School of Engineering Theses & Dissertations

In nuclear science experiments it is usually necessary to determine the type of radiation, its energy and direction with considerable accuracy. The detection of neutrons and discriminating them from gamma rays is particularly difficult. A popular method of doing so is to measure characteristics intrinsic to the pulse shape of each radiation type in order to perform pulse-shape discrimination (PSD).

Historically, PSD capable systems have been designed with two approaches in mind: specialized analog circuitry, or digital signal processing (DSP). In this work we propose a PSD capable circuit topology using techniques from both the analog and DSP domains. We …

Electrodeless Electrochemistry Enabled By Nonthermal Plasma, Harold Oldham

McKelvey School of Engineering Theses & Dissertations

The increasing availability and decreasing cost of electricity generated by renewable resources have motivated research into electrified chemical processing, whereby electrical energy is used to drive chemical transformations. Electricity-intensive processing techniques such as electrochemistry using solid electrodes has attracted attention in this context for the synthesis of organic compounds, such as high-value pharmaceuticals and renewable chemical production. Selective chemical transformations are achieved in conventional aqueous electrochemical systems by using external circuitry to bias solid electrodes, allowing for the preferential transfer of electrons between the electrode-liquid interface. Despite having the ability to promote controlled electrochemical reactions, configurations using solid electrodes are …

Electro-Organic Chemistry: An Alternative Pathway To Handle Redox Organic Reactions, Tiandi Wu

Arts & Sciences Electronic Theses and Dissertations

Electrochemistry provides an alternative pathway to handle redox organic reactions, especially for certain chemical process that can be only achieved through electrochemical process. Herein, there research projects are introduced to enrich the whole synthetic community, including an anodic oxidative cyclization studies to develop methodology on heterocyclic ring skeleton constructions, an electroreduction pathway exploration to more effectively obtain hydrazine from nitroso compounds, as well as a study in paired electrolysis process on which both anode and cathode are simultaneously employed to maximize overall atom and energy efficiency. Future directions on these projects are also demonstrated at the end of each chapters..

Interfacial Engineering And Photoelectrochemistry Of Patterned Metal/Semiconductor Heterostructures, Che Tan

McKelvey School of Engineering Theses & Dissertations

Photoelectrochemical (PEC) cells enable the conversion of solar energy into storable fuels, which is critical in overcoming the intermittent nature of this largest renewable source. However, the majority of semiconductors used as photoelectrodes in these cells have low conversion efficiencies and/or stabilities. Silicon (Si) is an attractive semiconductor material for photoelectrodes, but the development of efficient Si-based photoanodes is challenging due to their instability in alkaline solutions. Thus, one focus of this dissertation is the design and fabrication of highly stable nickel (Ni)-patterned Si photoanodes through interfacial engineering of the barrier heights. Recently, hot carriers in plasmonic metal nanostructures have …

Cyclodextrin-Based Supramolecular Drug-Delivery Nanomaterials And Shear-Thinning Hydrogels Using Ring-Opening Metathesis Polymerization, Ruihan Li

Arts & Sciences Electronic Theses and Dissertations

Cyclodextrins (CD) are a family of oligosaccharides that can non-covalently and precisely bind small hydrophobic drug molecules, such as antibiotics and anticancer drugs, through well-defined host-guest interactions inside the inner cavity of the macrocycle. Ring-opening metathesis polymerization (ROMP) is a versatile, functional group tolerant method of polymerization that is underexplored in biomedical applications relative to the more common controlled chain-growth polymerizations. In this dissertation, I describe my efforts to combine the supramolecular chemistry of CDs with that of ROMP using specialized functional monomers to synthesize several CD-based polymeric drug delivery nanomaterials. For example, in Chapter 2, a new type of …

Mass Spectrometry-Based Protein Footprinting: High-Throughput Maldi Platform And Large Protein Complexes Of Baf, Ruidong Jiang

Arts & Sciences Electronic Theses and Dissertations

Human’s advances in understanding biological processes rely heavily on the breakthroughs in biophysical tools. Mass spectrometry (MS)-based protein footprinting, which interrogates protein structures by measuring protein solvent assessable surface area (SASA), has grown rapidly in the last decade, successful in providing valuable data for numerous protein systems. This thesis focuses mainly on this technology.We set out to push the boundary of MS-based protein footprinting further into the new areas, preparing it for potential future applications including large-scale experiments that require high-throughput analysis the structure of large, complicated protein complexes. This thesis devotes five chapters to the method development of MS-based …

Using Single-Particle Fluorescence Microscopy To Elucidate The Role Of Structural Distortions And Defects In The Chemical Reactivity And Photophysics Of Cesium Lead Halide Perovskite Nanocrystals, Dong Wang

Arts & Sciences Electronic Theses and Dissertations

Colloidal cesium lead halide perovskite nanocrystals (CsPbX3, X = Cl, Br or I) are attractive for optoelectronic applications due to their unique chemical and physical properties including high photoluminescence quantum yield, tunable bandgaps, high defect tolerance, and low-cost processibility. A facile method to tune the emission wavelength of perovskite nanocrystals is through anion exchange. For light emission applications, it is desirable to prepare CsPbX3 nanocrystals of uniform size and composition. However, the complex reaction kinetics of this chemical transformation may limit the compositional uniformity and color purity of the CsPbX3 nanocrystals produced by anion exchange when the transformation is scaled …

Method Development For Enhancing Sensitivity Of Dynamic Nuclear Polarization Nuclear Magnetic Resonance Spectroscopy For Structural Studies Of Pkc-Drug Interactions, Patrick Terrence Judge

Arts & Sciences Electronic Theses and Dissertations

To perform the most relevant structural studies on biological systems, experiments need to be carried out when the target proteins are in their endogenous cellular environment. Nuclear magnetic resonance (NMR) is well-suited to probe the structure and dynamics of a wide variety of systems, including biologically relevant proteins. However, NMR suffers from an inherent lack of sensitivity. Dynamic nuclear polarization (DNP) NMR is a powerful technique that is used to enhance NMR sensitivity by transferring the greater polarization of exogenously doped electron spins to nuclear spins of interest though the use of a high-power microwave source. Solid effect radicals offer …

Computational Approaches For Screening Drugs For Bioactivation, Reactive Metabolite Formation, And Toxicity, Noah Flynn

Arts & Sciences Electronic Theses and Dissertations

Cytochrome P450 enzymes aid in the elimination of a preponderance of small molecule drugs, but can generate reactive metabolites that may adversely conjugate to protein and DNA, in a process known as bioactivation, and prompt adverse reaction, drug candidate attrition, or market withdrawal. Experimental assays are low-throughput and expensive to perform, so they are often reserved until later stages of the drug development pipeline when the drug candidate pools are already significantly narrowed. Reactive metabolites also elude in vivo detection, as they are transitory and generally do not circulate. In contrast, computational methods are high-throughput and cheap to screen millions …

Enantioselective Synthesis Of Β-Amino Acid Derivatives Using Amidine-Based And Bifunctional Organocatalysts, Matthew Robert Straub

Arts & Sciences Electronic Theses and Dissertations

Two new enantioselective methodologies have been developed that have important implications for the asymmetric synthesis of β-amino acids and their derivatives. First, chiral amidine-based catalyst (ABC) HBTM-2 catalyzed an asymmetric cyclocondensation between in situ activated fluoroacetic acid and N-sulfonyl aldimines to give α-fluoro-β-lactams in highly enantioenriched form, achieving modest to excellent diastereoselectivities. These reactive lactams can then be quenched with various alcohols and amines to deliver the α-fluoro-β-amino acid derivatives in moderate isolated yields. Secondly, bifunctional double hydrogen bond donor-amine organocatalysts enable the catalytic alcoholysis of various racemic N-carbalkoxy-3-substituted isoxazolidin-5-ones, resulting in their kinetic resolution. The enantioenriched unreacted isoxazolidinone and …

Synthesis, Self-Assembly, And Material Applications Of Unimolecular Polyviologens, Abigail Delawder

Arts & Sciences Electronic Theses and Dissertations

Intellectual Gaps: Synthesis of high molecular weight, unimolecular, and sequence-defined polyviologens; spatiotemporal control over mechanical properties of materials using visible and near-IR light; on-demand, post hoc manipulation of materials

Intellectual Merit: Robust method for synthesizing higher-order polyviologens of distinct molecular weight; control the change in the mechanical properties of polymer-based, crosslinked materials using a wide range of wavelengths of light; degradation of viologen-crosslinked hydrogels

To understand fundamentally how viologens behave within a polymer chain, we needed a better and more efficient way of synthesizing these long chains of polyviologens. As simple as this process looks on paper, the synthesis is …

Modeling Small Molecule Metabolism In Human Liver Microsome To Better Predict Toxicity Risk, Na Le Dang

Arts & Sciences Electronic Theses and Dissertations

Adverse drug reactions (ADRs) are a serious problem with increasing morbidity, mortality, and health care costs worldwide. In the U.S., ADRs are responsible for more than 50% of acute liver failure cases and are the fourth most common cause of death, costing 100,000 lives annually.Idiosyncratic adverse drug reactions (IADRs) are immune-mediated hypersensitivity ADRs that are difficult to foresee during drug development. IADRs are often caused by reactive metabolites produced during drug metabolism. These reactive metabolites covalently attach to cellular components, and the resulting conjugates may provoke toxic immune response. Because reactive metabolites are short-lived, they can be difficult to detect. …

Computational Design Of Two-Dimensional Transition Metal Dichalcogenide Alloys And Their Applications, John Douglas Cavin

Arts & Sciences Electronic Theses and Dissertations

The discovery of bronze as an alloy of copper and tin is arguably the earliest form of material design, dating back thousands of years. In contrast, two-dimensional materials are new to the 21st century. The research presented in this dissertation is at the intersection of alloying and two-dimensional materials. I specifically study a class of two-dimensional materials known as transition metal dichalcogenides (TMDCs). Because of the large number of transition metals, there are many combinations of TMDCs that can be alloyed, making experimental exploration of the phase space of possible alloys unwieldly. Instead, I have applied first-principles methods to study …

In-Situ Imaging Of Surface Heterogeneity In Semiconductor Photocatalysts Using Singlemolecule Fluorescence Microscopy, Meikun Shen

Arts & Sciences Electronic Theses and Dissertations

Metal oxide semiconductors have been used as promising photocatalysts to convert solar energy into useful fuels, such as water splitting, carbon dioxide reduction, and nitrogen fixation reactions. However, the typical metal oxide photocatalysts' efficiency often suffers from their weak visible light absorption and low charge carrier mobilities. One common strategy to mitigate these limitations is to introduce oxygen vacancies into the lattice of the semiconductor photocatalysts. This strategy has been applied to many metal oxide photocatalysts, such as titanium oxide, tungsten oxide, and zinc oxide, and oxygen vacancies indeed enhance their catalytic activities. Various roles of oxygen vacancies have all …

Aerosol Vapor Synthesis Of Organic Processable Pedot Particles And Measuring Electric Conductivity Using A 3d Printed Probe Station, Yang Lu

McKelvey School of Engineering Theses & Dissertations

Conducting polymers are organic semiconductors characterized by conjugated backbones (alternating single-double bonds) that enable mixed ionic-electronic conductivity. Their polymeric nature, tunable band structure and reversible redox capability have demonstrated fundamental advances in the fields ranging from electrochemical energy storage, sensing, to electro/photo catalysis and neuromorphic engineering. Conjugated backbones, the origin of all the unique physical and chemical properties associated with conducting polymers, prevent their solubility due to high lattice energy which hinders processing. Current solution utilizes a long-chain polymer (PSS) as dopants to render conducting polymer water dispersible (PEDOT:PSS). Nonetheless, PSS is highly acidic and hydrophilic limiting applicability with acid-incompatible …

Integrated Mass Spectrometry-Based Method In Protein Chemistry: Metal-Binding Protein And Integral Membrane Protein, Chunyang Guo

Arts & Sciences Electronic Theses and Dissertations

Most biological processes are associated with protein catalysis. Characterizing protein structure, therefore, is crucial for understanding biological function. Mass spectrometry (MS)-based methods have emerged as a pivotal biophysical tool to interrogate protein structures; they can characterize protein-ligand/protein complexes that are refractory to conventional high-resolution means such as X-ray crystallography, Cryo-EM, and nuclear magnetic resonance (NMR) spectroscopy, in part owing to high molecular weight and significant flexibility. The integrated MS-based platform will provide topology and structural information of proteins from sketch to detail; native MS identifies protein complexes’ composition and stoichiometry; hydrogen-deuterium exchange MS (HDX-MS) detects the protein complexes’ dynamic change …

Synthesis And Characterization Of Putative Triplet Sensitizers In The Dark Pathway To Cyclobutane Pyrimidine Dimers Of Dna, Yanjing Wang

Arts & Sciences Electronic Theses and Dissertations

The cyclobutane pyrimidine dimer (CPD) is the major photoproduct resulting from direct absorption of UVB radiation in sunlight by DNA that results in C to T mutations found in human skin leading to skin cancer. CPDs can also be produced through the action of photosensitizers that can absorb longer wavelength UVA that is not absorbed efficiently by DNA and transfer triplet energy to the DNA. Most recently, CPDs was discovered to be formed in the dark following UV irradiation of melanocytes. This dark pathway was proposed to result from an indirect pathway to CPDs that involves triplet energy transfer from …

Metal Salt Hydrolysis For Electrochemically Active Conducting Polymer Nanocomposites, Hongmin Wang

Arts & Sciences Electronic Theses and Dissertations

The diversity of nanostructures obtained from organic polymerization is limited when compared to the vast amount of inorganic nanostructures. This dissertation will focus on a synergistic mechanism between organic polymerization and in situ inorganic salt hydrolysis for developing electrochemically active organic-inorganic hybrid nanostructures. The degree of polymerization, crystallinity and doping level of the conjugated polymer backbone is controlled using oxidative radical vapor-phase polymerization resulting in organic semiconductors featuring high crystallinity and superior electrical conductivity. An aqueous metal salt solution of iron (III) chloride serves as an oxidant for initiating the polymerization and interestingly, this inorganic salt hydrolyzes in situ producing …

Light-Directed Growth Of Semiconductor Nanomaterials By Photoelectrodeposition, Chu Qin

Arts & Sciences Electronic Theses and Dissertations

In this work, the chemical and physical properties of semiconductor microcrystals and metastable polymorphs were transformed through photoexcitation during electrochemical synthesis. Interfacial charge transfer using photogenerated carriers were used to successfully control the growth of metal oxide semiconductors and change their morphology, composition improve their catalytic activity. The main material systems studied in this thesis are electrodeposited copper oxide (Cu2O) and manganese oxide (MnOx) semiconductor films. Illumination can direct the shape transformation of Cu2O crystals at the nanoscale by facet-selective charge transfer. During photoelectrodeposition on Cu2O microcrystals with well-developed facets, light mediates the deposition of copper metal selectively on the …

Synthesis, Core-Shell Growth, And Surface Chemistry Of 2-Dimensional Cadmium Telluride And Cadmium Selenide Nanocrystals, Haochen Sun

Arts & Sciences Electronic Theses and Dissertations

This dissertation presents the synthesis, shell deposition, and surface ligand-exchange chemistry of 2-dimensional cadmium telluride and cadmium selenide nanocrystals. Flat, colloidal 2-dimensional CdTe and CdSe nanoplatelets are promising materials for optical and electronic applications. The research presented here will enable better understanding of their properties and facilitate further applications.First, a new tellurium precursor, tris(dimethylamino)phosphine telluride is readily prepared and is found to have superior reactivity than the trialkylphosphine tellurides that are commonly used for nanocrystal synthesis. Wurtzite CdTe nanoplatelets, (CdTe)13 magic-size nanoclusters, and CdTe quantum wires are synthesized with this precursor, and are fully characterized. It is demonstrated that in …

Surface Modification Of Ii-Vi Semiconducting Nanocrystals, Calynn Morrison

Arts & Sciences Electronic Theses and Dissertations

This dissertation presents the compositional analysis of semiconductor materials by inductively coupled plasma optical emission spectroscopy (ICP-OES), a novel low-temperature shell growth precursor and installation pathway, and L-type for Z-type ligand exchange experiments conducted with four metal dithiocarbamate ligands. The techniques employed in the compositional analysis of semiconductor materials by inductively coupled plasma optical emission spectroscopy (ICP-OES) have a profound influence on the accuracy and reproducibility of the results. In Chapter 3, we describe methods for sample preparation, calibration, standard selection, and data collection. Specific protocols are suggested for the analysis of II-VI compounds and nanocrystals containing the elements Zn, …