Physical Sciences and Mathematics Commons^™

Development Of Novel Protein Digestion And Quantitation Methods For Mass Spectrometic Analysis, Yongling Ai

Dissertations

Proteins are the workhorses of biology, playing multifaceted roles in maintaining cellular function, signaling, and response to environmental cues. Understanding their abundance and dynamics is pivotal for unraveling the complexities of biological processes, which underpins the foundations of molecular and cellular biology. Accurate measurement of protein quantities provides insights into cellular homeostasis, facilitates the discovery of biomarkers, and sheds light on the molecular mechanisms of diseases, bridging the gap between the molecular intricacies of proteins and their functional consequences in health and disease. The evolution of protein quantitation methodologies, from classical colorimetric assays to sophisticated mass spectrometry-based approaches, has expanded …

New Methods For Stereoselective Glycosylation In Application To Significant Biomedical Targets, Melanie L. Shadrick

Dissertations

Glycosyl halides have been utilized for glycosylation reactions since the early studies by Arthur Michael, nearing the end of the 19^th century. Koenigs and Knorr then utilized silver salts to activate glycosyl bromides and chlorides to create synthetic glycosides. Many efforts to improve the outcome of reactions with glycosyl halides have emerged. The key emphasis has traditionally been placed on reaction rates, product yields, and stereocontrol. Recently, our lab reported that silver(I) oxide-mediated Koenigs-Knorr glycosylation reaction can be dramatically accelerated in the presence of catalytic acid additives. Methods to improve glycosylation was explored using mannosyl and glucosyl bromides. However, …

Binding Interactions Of Biologically Relevant Molecules Studied Using Surface-Modified And Nanostructured Surfaces, Palak Sondhi

Dissertations

This research focuses on the field of surface nanobioscience, wherein different nanosurfaces that will be used as working electrodes in the electrochemical cell are manufactured and surface modified to understand the critical binding interactions between biologically significant molecules like proteins, carbohydrates, small drug molecules, and glycoproteins. This research is essential if we are to determine whether a synthetic molecule can serve as a therapeutic candidate or diagnose a disease in its early stages. In order to fully understand the binding interactions, the study begins with defining some of the fundamental concepts, principles, and analytical tools for biosensing.

Afterwards, we addressed …

Data-Driven 2d Materials Discovery For Next-Generation Electronics, Zeyu Zhang

Dissertations

The development of material discovery and design has lasted centuries in human history. After the concept of modern chemistry and material science was established, the strategy of material discovery relies on the experiments. Such a strategy becomes expensive and time-consuming with the increasing number of materials nowadays. Therefore, a novel strategy that is faster and more comprehensive is urgently needed. In this dissertation, an experiment-guided material discovery strategy is developed and explained using metal-organic frameworks (MOFs) as instances. The advent of 7r-stacked layered MOFs, which offer electrical conductivity on top of permanent porosity and high surface area, opened up new …

Computational And Experimental Investigation Of Elemental Sulfur And Polysulfide, Jyoti Sharma

Dissertations

Petroleum processing results in the generation of significant quantities of elemental sulfur (S₈), leading to a surplus of sulfur worldwide. Despite its abundance and low cost, the use of sulfur in value-added organic compound synthesis is limited due to its unpredictable and misunderstood reactivity. This dissertation aims to address this issue by tackling it from two angles. Firstly, by utilizing Density Functional Theory (DFT) calculations, the reactivity of sulfur in the presence of nucleophiles is studied. This facilitates the identification of organic polysulfide intermediates that can be generated under different conditions, as well as the corresponding reactivity for …

High Resolution Intracavity Laser Absorption Spectroscopy Of Transition Metal-Containing Diatomic Molecules, Kristin Bales

Dissertations

Three transition metal-containing diatomic molecules have been studied using intracavity laser spectroscopy. Many of the transitions were recorded using a Fourier-transform spectrometer for detection, allowing collection at Doppler-limited resolution for the gas phase molecules. Several vibrational bands in two electronic transition systems of tantalum fluoride (TaF) have been analyzed, and new molecular constants provided. Transitions involving six electronic states of tungsten sulfide (WS) have been analyzed, with new and updated constants provided, including a deperturbation analysis of three vibrational bands in two of the states. Finally, a fresh perspective on two electronic states of tungsten oxide (WO) included a deperturbation …

V-Shaped Temperature Dependences And Pressure Dependence Of Elementary Reactions Of Hydroxyl Radicals With Several Organophosphorus Compounds, Xiaokai Zhang

Dissertations

Organophosphorus compounds have brought increasing attention since they are widely used as flame-retardants, which can take effect in combustion via reactions with reactive radicals. These reactions are influenced by variables such as temperature and pressure, resulting in a temperature and pressure dependent rate constant. Studying this reaction kinetics has great importance in both combustion reaction and atmospheric environment.

This study is focused on kinetics of several elementary reactions of combustion importance. The kinetics of hydroxyl radicals were studied using pulsed laser photolysis coupled to transient UV-vis absorption spectroscopy over the 295 - 837 K temperature range and the 1 - …

Development Of Innovative Multi-Drug Approaches To Counteract Illicit Drug Abuse In The Uae Population, Manal Ali Alhefeiti

Dissertations

The abuse of addictive substances is on the rise in the United Arab Emirates (UAE) population. Consequently, the UAE government spends about Dhs 5.5 billion annually on the rehabilitation of drug addicts. Blood, urine, and hair tests can reveal signs of sporadic or chronic drug use. Given the list of banned chemicals in the UAE, our main objective in this work was to develop a novel analytical method to identify and measure banned substances, especially prescription and over-the-counter drugs in the UAE. We developed and validated a rapid, sensitive and reliable liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) approach for the targeted …

Combustion Soot Nanoparticles: Mechanism Of Restructuring And Mechanical Properties, Ali Hasani

Dissertations

Soot, a product of incomplete combustion of fossil fuels, is a global warming agent. The effect of soot particles on climate depends on their morphology. Freshly released soot particles are fractal lacey aggregates, but they often appear collapsed in atmospheric samples collected away from emission sources. A body of work has concluded that the collapse is caused by liquid shells when they form by vapor condensation around soot aggregates. However, some recent studies argue that soot remains fractal even when engulfed by the shells, collapsing only when the shells evaporate. To reconcile this disagreement, the effects of the condensation and …

Synthetic Amphiphiles As Antibiotic Potentiators, Helena Spikes

Dissertations

Antibiotic resistance has become a massive threat to modern medicine. Bacteria acquire resistance either through genetic mutations or mobile genetic elements, such as plasmids. The growing resistance crisis is exacerbated by over-prescription of antibiotics and improper use. As antimicrobial resistance becomes more widespread, superbugs (bacteria resistant to more than one class of drug) have evolved. Since few new drugs reach clinical trials and even fewer are approved by the FDA, we must find a way to make existing drugs more potent. One technique to accomplish this is by using combination therapy. By administering two or more drugs at a time, …

Ferrocenium Salt Aided Substitution Reactions And Synthesis Of Glycosylated Curcumin Derivatives, Deva Saroja Talasila

Dissertations

Organic synthesis has been significantly advanced with the employment of transition metal complexes. The discovery of transition metal catalysts provided the synthetic community with powerful tools for accelerating reactions and making them more selective and efficient. Many chemical reactions do not happen without a catalyst.

Iron-based catalysts have several advantages for the chemical industry because it is a non-toxic and ecologically friendly metal. Our group previously found that ferrocenium cations with a 3+ oxidation state of iron-catalyzed propargylic substitution reactions at low temperatures. The sandwich structure of ferrocenes allows substituents to be introduced on the cyclopentadienyl rings, which allows for …

Novel Thioglycosides As Versatile Glycosyl Donors For Oligosaccharide Synthesis, Ganesh Shrestha

Dissertations

This thesis is dedicated to the development of new methodologies for efficient synthesis of carbohydrate building blocks and their application to chemical glycosylation. S-Indolyl (SIn) anomeric moiety was investigated as a new leaving group. Understanding of the reaction pathways for the SIn moiety activation was achieved via the extended mechanistic study. The activation profile of indolylthio glycosides required large excess of activators. This drawback was partially addressed by the development of N-alkylated SInR derivatives. The activation process was studied by NMR and the increased understanding of the mechanism led to a discovery of different activation pathways taking place with …

Cultivating Teacher Expertise In The Landscape Of Green Chemistry: The Development Of Pedagogical Content Knowledge In Beyond Benign’S Lead Teacher Program, Philip Charles Nahlik

Dissertations

Chemistry Education, Green Chemistry, Pedagogical Content Knowledge, Professional Learning Communities, Sustainability, Teacher Training

Investigation Of Carbon Dioxide Oxidation Reaction Pathways On Rh(111) Via Reflection Absorption Infrared Spectroscopy (Rairs), Elizabeth A. Jamka

Dissertations

CO oxidation, RAIRS, Rh(111), Surface Science, UHV

Evaluating The Impact Of Submarine Groundwater Discharge On Nutrients And Trace Elements In Coastal Systems: The Examples Of The Tuckean Swamp (Australia) And The Mississippi Sound (Usa), Amy Moody

Dissertations

Submarine groundwater discharge (SGD) is the advective flow of both fresh terrestrial groundwater and recirculating seawater through aquifer sediments, which is released into the coastal ocean. In this dissertation, I evaluated the impact of SGD on the distributions and input of trace metals and nutrients. In the Tuckean Swamp, an estuary in Australia dominated by coastal acid sulfate soils, I determined the impact of groundwater on Ba and U during the flood season, when the local aquifer is flushed out after a rapid increase in water table elevation. For Ba and U, groundwater contributed up to 18 and 66 % …

A Study Of Red Snapper (Lutjanus Campechanus) Ecology In The Northern Gulf Of Mexico And The Effect Of Variable River Outflow Using Stable Isotope Analysis Of The Food Web And Eye Lenses, Caitlin C. Slife

Dissertations

In the Mississippi Bight and surrounding waters, river outflow impacts the basal resources of the Red Snapper food web, altering carbon sources and impacting prey and predator isotopes. In this study, the impact of riverine outflow on nutrients, particulate organic matter (POM), and physical water parameters on Red Snapper and their food web was analyzed using stable isotope and stomach content analysis over 5 years. The Mississippi, Pearl, Pascagoula, and Mobile rivers were included in the analysis of river impact. The Mississippi and Mobile rivers were found to significantly impact nutrients and POM in the region. River outflow was also …

Designing Dynamic And Degradable Polymeric Materials With Thiol-X Chemistries, Reese Sloan

Dissertations

With plastic production poised to increase in coming years, there arises a need to develop new polymeric materials designed to combat the global pollution crisis. A commonly utilized approach in addressing this challenge is to employ a responsive functional moiety into the polymer architecture. Thiol-X reactions, a commonly utilized class of “click” reactions, have garnered broad implementation in new stimuli-responsive materials. This work specifically focuses on utilizing radical-mediated thiol-ene coupling and base-catalyzed thiol-isocyanate reactions to develop a library of ternary thiol-ene/thiourethane covalent adaptable networks (CANs) and hydrolytically labile poly(thioether ketal) thermoplastics. CANs are a class of network materials capable of …

Mechanism Of Sila- And Germafluorenes For Biological Applications, Shelby Jarrett

Dissertations

2,7-disubstituted silafluorenes and germafluorenes, originally designed for OLED applications, are a class of fluorescent dyes that have gained recent interest as probes for bioimaging and as biosensors to monitor cellular dynamics and interactions. Desirable biological probes absorb in the visible region, have high extinction coefficients, high quantum yield and excellent photostability. Here, their spectral properties are investigated under aqueous conditions for relevant biological applications. These molecules display intense blue fluorescence in the solid state and in solution, have high extinction coefficients, and exhibit appreciable solubility in aqueous solution. To better understand potential applications, the mechanism of fluorescence was investigated. It …

Analysis Of The Zebrafish Olfactory System Using Immunohistochemistry And Enhanced Techniques Of Desorption Electrospray Ionization Mass Spectrometry (Desi-Ms), Tara Lynn Maser

Dissertations

Desorption electrospray ionization (DESI-MS) is an ambient ionization technique where the sample is analyzed directly from a surface with very minimal sample preparation under ambient conditions and follows ESI-like ionization mechanisms. DESI-MS has proven powerful in analyzing or imaging lipids and other small molecules directly from biological samples and even allows for subsequent histological staining and analyses. However, DESI-MS is less widely used for protein analysis due to a lack of sensitivity and the complex diversity of proteins in biological samples.

A major goal of this research has been to obtain new neurobiological knowledge by combining histology and mass spectrometry …

The Design, Synthesis, And Characterization Of Copper-Based Metal-Organic Frameworks For Their Investigation Against Cancer And Their Effect As Anti-Microbial Agents, Sandy Elmehrath

Dissertations

A wide range of nanomaterials have been developed for biomedical applications, such as drug delivery, biomedical imaging, and sensors. Nanomaterials can include nanoparticles (NPs) and nanofibers with various dimensions that are both natural and synthetic. A successful nanomaterial, for use in biological applications, is characterized by its biocompatibility, biodegradability, intrinsic high surfaces area, high interconnected porosity, and functionality. These features were achieved with the development of metal-organic framework (MOF) nanostructures. MOFs are assemblies of metal ions and organic linkers that are built into different geometries and can exist in all dimensions (up to 3-D). The choice of linkers with well-defined …

Atmospheric Mercury Chemistry: Detection, Kinetics, And Mechanism, Na Mao

Dissertations

The presence of mercury in the environment is of global concern due to its toxicity. The atmosphere is an important transient reservoir for mercury released by human activities and natural sources. The knowledge of atmospheric mercury chemistry is critical for understanding the global biogeochemical cycle. In the atmosphere, mercury primarily exists in three forms: gaseous elemental mercury (GEM), gaseous oxidized mercury (GOM), and particulate-bound mercury (PBM). Over the last decade, the existing knowledge of mercury cycle has dramatically changed: (1) There has been increasing evidence that current detection methods do not accurately quantify gaseous oxidized mercury and a technique which …

Development Of Novel Mass Spectrometric Methods For Reaction Screening, Oligosaccharide Detection, And Nitrosamine Quantitation, Qi Wang

Dissertations

Benefitting from its high detection sensitivity and specificity, mass spectrometry (MS) has become a powerful technique in academia and industry. The aim of this dissertation study is to develop new mass spectrometric methods for organic reaction screening, detection of oligosaccharide/glycan in complex matrices, and nitrosamine absolute quantitation.

First, an electrochemistry/mass spectrometry (EC/MS) platform is built to generate an N-cyclopropylaniline radical cation electrochemically and to monitor its reactivity toward alkenes, which leads to the discovery of a new redox neutral reaction of intermolecular [3 + 2] annulation of N-cyclopropylanilines and alkenes. Net redox neutral electrosynthesis is quite rare in synthetic organic …

Bis(Tryptophan) Amphiphiles: Design, Synthesis And Efficacy As Antimicrobial Agents, Michael Mckeever

Dissertations

Amphiphiles play important roles in nature. These molecules contain both hydrophilic and hydrophobic regions, leading to some astonishing properties. The lipid bilayer of the cell membrane is a fascinating organization of amphiphilic phospholipids. Natural and synthetic amphiphiles, such as antimicrobial peptides, interact with the cell membrane. Such interactions can impact transport of molecules across the cell membrane, disrupting cell functions. In this work, a library of tryptophan-containing amphiphiles was synthesized and their antimicrobial properties were explored.

First, a library of bis(tryptophan) amphiphiles was synthesized. Preparation included a coupling reaction of a diamine with tryptophan residues, via their carboxy-termini, at …

Hydrolytically Degradable Thermosets With Tunable Degradation Profiles Via Ketal-Based Crosslinks, Benjamin Alameda

Dissertations

Thermoset polymer networks are ubiquitous in the construction of high-performance materials due to their excellent mechanical properties, solvent resistance, and thermomechanical performance. However, the crosslinked structure that instills these materials with favorable performance also makes them incredibly resistant to degradation and are nearly impossible to recycle – adding to the ever-growing problem of plastic pollution. Hydrolytically degradable thermosets have emerged as a potentially sustainable alternative to traditional thermosets by affording networks that are inherently degradable in aqueous environments. This dissertation focuses on the development of hydrolytically degradable thermoset networks with tunable degradation behavior through the implementation of ketal-based crosslinks. Given …

Rhodium-Catalyzed Decarbonylation Of Aroyl Chlorides, Wiktoria M. Koza

Dissertations

The development of efficient strategies for the synthesis of aryl–halogen bonds is highly desirable due to the prevalence of these moieties in pharmaceuticals, agrochemicals, and organic synthesis. Although there are numerous applications of aryl chlorides in chemistry, an efficient strategy for the preparation of these molecules is underdeveloped. Transition metal-catalyzed decarbonylation provides an efficient and selective approach for aryl–halogen bond formation. There has been significant progress in the development of new decarbonylation strategies, particularly involving aldehydes for the synthesis of new carbon–hydrogen (C–H) bonds or for cross-coupling reactions. However, transition metal-catalyzed decarbonylation methods for carbon–halogen (C–X) bond formation have been …

Hydrophobically Modified Isosorbide Dimethacrylates As Biomaterials For Bisphenol A Free Dental Fillings, Bilal Marie

Dissertations

Amalgam and Bisphenol A glycerolate dimethacrylate (BisGMA) are the main dental filling materials in use today. Because of the negative perception of amalgam and its lower esthetic appeal, as well as the desire to replace the endocrine disruptor Bisphenol A, which is the building block of BisGMA, there has been a critical need to search for safer alternatives to these dental filling materials.

Isosorbide is a sugar-based molecule generally recognized as safe. It has been extensively studied as a replacement to the Bisphenol A core in various materials. However, isosorbide is extremely hygroscopic, and water uptake in dental fillings causes …

Synthesis Of Molecular Probes For The Detection Of Toxic Analytes, Rashid Mia

Dissertations

Two different types of molecular probes have been synthesized. The first family of probes is the coumarin class of compounds. These chemodosimters are referred to as Low Molecular Weight Fluorescent probes (LMFP). The other type of molecular probe is a macrocycle known as a pillar[5]arene receptor.

The chemodosimters (2.12a-c and 3.12a) were synthesized in four to five steps. The photophysical properties were extensively studied in various solvent systems (DMSO, CH₃CN, DMF, MeOH, EtOH, Me₂CO, MeCO₂Et, CHCl₃, C₆H₅Me, and C₆H₆). Dimethyl sulfoxide (DMSO) …

Lxr Acts As A Differentiator In The Regulation Of Fas And G6pdh Gene Expression Under Insulin Resistant Conditions, Jaafar Hachem

Dissertations

Diabetes is a chronic disease that effects 10 percent of the world’s population and causes more than 1.5 million deaths a year and billions of dollars in associated health care cost. It can lead to very serious complications such as renal failure, liver cirrhosis, heart attack, and vision loss. The most common type of diabetes is type 2 diabetes. Type 2 diabetes arises when blood glucose levels remain chronically high due to insulin resistance. The reason for this elevation is due to the failure of insulin to allow tissues to uptake glucose causing problems in subsequent metabolic pathways. Over the …

Mechanisms And Applications Of Improved Protein Analysis By Desorption Electrospray Ionization Mass Spectrometry (Desi-Ms), Roshan Javanshad

Dissertations

Electrospray ionization mass spectrometry (ESI-MS) is a soft ionization technique that allows detection of macromolecules, such as intact proteins, by the formation of multiply charged ions from solutions. Desorption electrospray ionization mass spectrometry (DESI-MS) is an ambient ionization technique that directly samples analyte from a surface during ESI-MS analysis. Although DESI-MS is highly accomplished at the analyses of metabolites, lipids, and other small molecules, it is far more limited when it comes to protein analysis. While most of the field in ambient ionization MS has moved towards primarily applications, our approach has been to explore the use of DESI-MS and …

New Methods For The Synthesis, Activation, And Application Of Thioglycosides, Samira Escopy

Dissertations

From their ubiquitous presence in Nature to their vital roles in biology and medicine, carbohydrates (sugars or glycans) are essential molecules of life, which are made and/or utilized by every living organism. Our cells are coated with sugars that are involved in almost every biological process and defensive mechanism in our body. To mention some of their crucial biological functions, carbohydrates are essential source of energy, they participate in blood coagulation, immune defense, cell growth, cell-cell interaction, and anti-inflammatory processes. Understanding of glycan functions and structure is crucial for the development of vaccines and therapeutics. Producing complex carbohydrates in sufficient …