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Elucidating The Mechanisms Of Collagenase H From Hathewaya (Clostridium) Histolytica In Collagen Degradation And Developing A Cross-Linked Platform For Efficient Capture And Release Of Adeno-Associated Virus Serotype 2 (Aav2), Adjoa Otubea Bonsu

Graduate Theses and Dissertations

In biological systems, Hathewaya (Clostridium) histolytica secretes collagenases that degrade structural collagen in host tissues and cause tissue necrosis. Despite their detrimental effects, these enzymes have significant therapeutic potential by effectively digesting various collagen subtypes to treat connective tissue disorders. The bacterium produces two homologous collagenases, ColG and ColH, with a catalytic module crucial for hydrolyzing collagen and binding domains, including collagen-binding domains (CBDs) and polycystic kidney disease-like domains (PKDs), for substrate interaction.

Although the crystal structure of the catalytic module of collagenase G (ColG) has been determined, shedding light on its chew-and-digest mechanism, the structure of collagenase H (ColH) …

Synthesis And X-Ray Characterization Of Nickel Phosphide Nanostructures For Water Oxidation, David Thompson

Graduate Theses and Dissertations

The pursuit of earth-abundant 3d transition metal catalysts for alkaline water electrolysis remains an active area of research. While NiFe layered double hydroxides (LDH) are currently the most active catalysts for the oxygen evolution reaction (OER), doping Ni-based catalysts with phosphorus to form Ni metal phosphides has emerged as a promising alternative. However, the complex crystalline and amorphous phases of NiP_x have hindered their characterization, and the OER mechanism and origin of activity remain unclear. This dissertation aims to elucidate the synthesis, OER performance, and in situ reconstruction of amorphous NiP_x-based nanomaterials, with a focus on in …

Atomic Level Characterization For The Transport Cycle Conformational Pathways Of Multidrug Resistance Protein 1 (Mrp1), Samuel Wamwere Mwatha

Graduate Theses and Dissertations

The multidrug resistance-associated protein 1 (MRP1/ABCC1) is an ATP-binding cassette (ABC) transporter that mediates the cellular efflux of endogenous and xenobiotic substrates, including therapeutic drugs. Its overexpression is a major contributor to multidrug resistance in cancer, which tends to result in negative clinical results. Even with considerable progress made in structural biology, the intricate details of how membrane lipid composition affects the conformational changes and functional switches of MRP1 still lack explanation.

This thesis employs long-timescale, all-atom molecular dynamics (MD) simulations to study the influence of various lipids on MRP1 lipid bilayer environments. Both inward-facing and outward-facing conformations of MRP1 …

Synthetic Efforts Towards An Analog Of Ly426965, Macy Sproles

Honors Theses

The 5-hydroxytryptamine_1A (5-HT_1A) receptor is a key target in the treatment of various neuropsychiatric conditions, and the development of selective antagonists offers promising therapeutic potential.²⁴ This study aimed to develop a synthetic analog of LY426965, a selective 5-HT_1A receptor antagonist. The synthetic route was initiated from dimethyl-2-phenylmalonate, employing pig liver esterase (PLE) as an enantioselective biocatalyst to achieve regioselective hydrolysis of one ester moiety in the malonic diester intermediate.¹⁷ Through a series of stereochemically controlled transformations, a new intermediate was successfully synthesized. Although the target molecule was not obtained, a new compound was synthesized …

Novel Trimethoprim-Based Metal Complexes And Nanoparticle Functionalization: Synthesis, Structural Analysis, And Anticancer Properties, Abbas M. Abbas, Hossam H. Nasrallah, A. Aboelmagd, W. Christropher Boyd, Haitham F. Kalil, Adel S. Orabi

Chemistry Faculty Publications

In this study, we synthesized a novel trimethoprim derivative, 4-(((2-amino-5-(3,4,5-trimethoxybenzyl) pyrimidine-4-yl)imino)methyl)benzene-1,3-diol (HD), by the reaction of trimethoprim with 2,4-dihydroxybenzaldehyde. We then prepared metal complexes of this derivative with Cu(II), Co(II), Ni(II), Ag(I), and Zn(II) and functionalized them with ZnO and Au nanoparticles. Their structures were confirmed through 1H NMR, mass spectrometry, FTIR, conductivity, thermal analysis, magnetic susceptibility, X-ray diffraction, UV-Vis spectroscopy, and TEM, revealing octahedral geometries for all complexes. Surface features were investigated using density functional theory (DFT) analysis. Pharmacokinetic parameters and target enzymes for HD and its complexes were computed using the SwissADME web tool, with the BOILED-Egg model …

A Study Of Ultrafast, Intense-Field Photodynamics In Carbon Dioxide, Carbon Disulfide, And Select Substituted Benzenes, Joshua Edwin Beck

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

The study of the photodynamics of molecules in ultrashort pulses of intense radiation continues to be of interest. Electric field strengths in such pulses can approach or exceed the typical electric field strengths binding the electrons to the nuclear framework (ke/a²₀ ≈ 5 × 10⁹ V/cm). The resulting excitation, ionization, and dissociation of molecular targets is of interest in many areas including attosecond science, femtochemistry, atmospheric science, high harmonic generation, and many other fields.

This dissertation investigates the photoionization and photofragmentation behavior of carbon dioxide, carbon disulfide, and the substituted benzenes nitrobenzene, aniline, as …

Development Of Mixed O/S-Donor Imidazole Thione Ligands For Trivalent Lanthanide/Actinide Separations, Rhianna Wolsleger

All Dissertations

Separation of lanthanides and actinides is difficult due to their very similar size and charge. Increasing selectivity for actinides over lanthanides is possible by incorporating a softer, more polarizable donor atom into a chelating ligand, since the softer donor atom is capable of greater orbital overlap with the 5f orbitals of the actinides vs the 4f orbitals of the lanthanides. Sulfur-containing imidazole thione chelating ligands have not been investigated for this purpose but possess a resonance structure that puts significant negative charge on the sulfur, enabling it to form strong metal-sulfur bonds compared to other sulfur-containing ligands such as thioethers …

Bpa Adsorption On Microplastics In Different Chemical Conditions, Addison Zehren

University Honors Program Senior Projects

Microplastics (plastic particles < 5 mm in size) are increasingly seen as a health and environmental issue, both for their direct effects when ingested by living organisms and for their ability to adsorb and concentrate other pollutants. Current water treatment processes do not adequately remove microplastics from municipal water supplies, so a thorough understanding of how microplastics affect water quality is needed. The objective of this study is to evaluate the effects of certain water quality parameters on the ability of polystyrene microplastics (PS MPs) to adsorb Bisphenol A (BPA). BPA is an endocrine disruptor (chemically like estrogen) used in plastics which can be released into the environment and act as a water pollutant. Water quality chemical parameters investigated were chloride, nitrate, phosphate, and copper ions. Concentrations of each solute were selected based upon Environmental Protection Agency (EPA) guidelines and previous results obtained from testing Chicago River water samples. A constant amount of PS MPs and BPA were added to each sample and the mixtures were shaken for 5 days to allow time for the BPA to adsorb. The samples were then filtered and the amount of BPA left in the water was determined by measuring its UV absorbance on a UV-vis spectrophotometer. BPA concentrations decreased in the water indicating that it had been adsorbed onto the microplastic surface, with the highest adsorption present with copper, which reduced BPA concentrations from 6.7 mg/L to 3.9 mg/L. Statistical analyses showed differences between copper, phosphate, nitrate, and chloride (df = 9, p = 0.002). Future work can apply these results to investigate the implications of pollutant transportation in urban waterways like the Chicago River.

Synthesis And Characterization Of New Inorganic Materials In Different Length Scales; From Nanometer To Micrometer, Kirkland Sheriff

All Dissertations

In this dissertation there are a new series of Preyssler polyoxometalate (POM) crystalline solids created using electrochemical potential. It was found that using electrochemical potential, where nucleation and reduction occur simultaneously, was a convenient method for exploratory synthesis creating new crystalline solids in aqueous solution and at room temperature. The general structure feature reveals that Preyssler POM was covalently linked by various metals from the d and f block including Co²⁺, Ni²⁺, La³⁺, Nd³⁺, Gd³⁺ and Ho³⁺ where the POM was reduced by 2 to 4 electrons. The resulting solids …

Composition And Rich/Lean Loading-Dependent Density Measurements Of A Series Of Aqueous Ionic Amines For Co2 Capture, Claudia Nguyen

Honors Theses

As climate change worsens worldwide, there is a drive to develop more efficient and sustainable methods to mitigate its impact through carbon capture methods like carbon dioxide scrubbing. Carbon scrubbing directly captures carbon dioxide (CO2) emissions from industries or power plants before they are released into the environment. The CO2 captured can be utilized for various applications or can be stored underground. However, this method faces numerous challenges, such as the degradation of the solvent or corrosion of equipment. As a result, research has expanded to find a better medium to overcome these issues. In particular, aqueous ionic amines (AIA) …

Toxicity And Biodegradability Of Novel Boronium Vs Conventional Ammonium-Based Antimicrobial Compounds In Wastewater Treatment Systems, Noor Shalan

Honors Theses

Quaternary ammonium compounds (QACs) are highly effective as disinfectants, herbicides, and pesticides; thus, overuse causes elevated levels of residual toxicity in domestic and industrial wastewater. QACs can be toxic to essential bacteria breaking down pollutants in wastewater treatment plants (WWTPs) and can remain untreated in effluent, harming the environment, and contributing to antibiotic resistance, posing risks to human health. Novel boronium-based antimicrobial compounds have demonstrated efficacy in eliminating bacteria, fungi, and viruses. If the boronium compounds exhibit lower residual toxicity, they could offer a promising alternative to QACs. Because these compounds are still in development, their potential toxicity to the …

Organocatalyst Frameworks For Co2 Reduction To Methanol: Selectivity Control And Mild-Condition Activation, Nehal Asif

Honors Theses

This study investigates the development and application of organocatalysts for the reduction of CO₂ under mild and sustainable conditions. A key focus is the synthesis of an organo-boronic acid–amine catalyst system (derived from thianthren-1-ylboronic acid and diethanolamine) and its subsequent evaluation in reactions with labeled CO₂. Through NMR analyses, including time-resolved monitoring of isotopically labeled substrates, the formation of formyl intermediates and downstream products such as formate and methoxy species was confirmed, demonstrating active CO₂ transformation. Multiple catalyst variants (NA1 series) were screened to assess activity and selectivity, with experimental conditions optimized in terms of temperature, solvent selection, and the …

Biomimetic Design Of Mechanochromic Single-Chain Nanoparticle Polymer Networks, Samuel Robinson

Honors Theses

Hydrogels are a class of polymer networks that show promise in many biomedical applications but are typically limited in use due to their brittle nature. Synthesizing hydrogel networks that are comparable to biological materials has long been an area of interest. In this study, we are working to create a polymer network inspired by the muscular protein, titin. Titin can unfold under mechanical tension, releasing stored length, making the muscle material extensible and durable. To mimic this behavior, we propose creating a polymer network with similar stored length using single chain nanoparticles (SCNPs) cross-linked with phenolphthalein (PP) and β-cyclodextrin (β-CD). …

Modeling Degradation In Li-Ion Batteries: Analyzing Single-Cell Degradation And Applying It To Customized Pack-Level, Mohannad Y. Alkhalil

Durham School of Architectural Engineering and Construction: Dissertations, Theses, and Student Research

The rapid expansion of lithium-ion (Li-ion) battery applications in areas such as electric vehicles (EVs), renewable energy storage, and portable electronics has drawn attention to the need for improving their performance, safety, and longevity. As Li-ion batteries become essential across technologies, understanding degradation mechanisms is critical for optimizing design and ensuring reliable operation. This work provides a detailed overview of modeling degradation in Li-ion batteries, focusing on single-cell behavior and its implications for pack-level performance.

The PyBaMM (Python Battery Mathematical Modeling) package, an open-source battery simulation tool written in Python, is used for single-cell simulations. Liionpack, another Python-based library, is …

From Molecular Crystals To Catalytic Surfaces: Computational Approaches To Complex Systems, Thiago Henrique Da Silva

Boise State University Theses and Dissertations

Understanding and modeling complex systems is one of the core challenges in modern science. Whether it be the intricate interactions within molecular crystals, the evolving mechanisms of bacterial resistance, or the dynamics of catalytic surfaces, accurately representing these systems is essential for scientific progress. This dissertation addresses these challenges by focusing on advances in computational modeling, demonstrating how various methods such as Density Functional Theory (DFT), machine learning, and custom-developed methods can simplify and help predict complex behaviors across multiple domains. By applying and understanding the scope of these methods to each field, this work underscores how computational modeling bridges …

Development And Characterization Of Aso-Based Ribonuclease Targeting Chimera For The Degradation Of Cug Rna Repeat Expansion In Myotonic Dystrophy Type, Audrey Coons

Chemistry

Myotonic Dystrophy Type 1 is a multisystemic genetic disorder that primarily affects the muscles in the body leading to such pathologies as myotonia, muscle atrophy, insulin resistance and even neurological deficits. This disorder is caused by a series of CUG repeats in the 3’ untranslated region of the DMPK gene; symptoms appear after around 34 repeats. These repeats form foci when MBNL1 protein that deals with alternative splicing of many events in the body, forms aggregations around these repeats. These foci render the MBNL 1 proteins useless. There is no FDA approved therapeutic, but many RNA targeting therapeutics have been …

Mechanistic Investigation Of Ring-Opening Polymerization Of Polycaprolactone Using Tin(Ii) Catalysts: Ligand Effects And Biomedical Applications, Eva-Larue M. Barber

Honors Scholar Theses

This research explores the mechanistic aspects of ring-opening polymerization (ROP) of ε-caprolactone (CL) to produce polycaprolactone (PCL), a biodegradable polymer widely used in biomedical applications. The study investigates how light exposure and catalyst concentration influence polymerization efficiency, using tin(II) 2-ethylhexanoate [Sn(Oct)₂] as the catalyst in a non-polar toluene solvent at 90 °C. Reactions were conducted under either ambient light or black light bulb (BLB) illumination, with monomer-to-catalyst ratios of 1:1 and 200:1.

Proton nuclear magnetic resonance (¹H NMR) spectroscopy was used to analyze conversion efficiency by tracking the disappearance of monomer signals and appearance of characteristic PCL peaks. Results revealed …

Effects Of Ph On Product Yield Of One-Electron Oxidation To Guanine Derivatives, Abdul-Kadir Ibrahim

Electronic Theses and Dissertations

One-electron oxidation plays a major role in oxidative DNA damage in biological cells. Guanine, the most oxidizable DNA base, has been the major focus of studies on oxidative damage to DNA initiated by one-electron oxidation (OEO). The current study aims at understanding the mechanisms of photooxidation of guanine derivatives with OEO in acidic medium. D1A* and D1B*, which are the products of dGuo in acidic medium, were obtained from dGuo upon photolysis at 485 nm of the reaction mixture in the presence of S₂O₈^2- as the oxidant and Ru(II)(bpy)₃²⁺ as a photosensitizer. D1A* and …

Kinetic Analysis Of Hydrolysis And Hydrothermal Conversion Of Methyl Cellulose To Dodecane, Joseph Olembo Were

Electronic Theses and Dissertations

Environmental pollution due to emission of greenhouse gases and increasing global energy demand are some of the concerns associated Analysis with the use of fossil fuels. These concerns have triggered the exploration of sustainable and efficient methods for renewable energy production. One such method is the conversion of cellulosic biomass to hydrocarbon fuels using hydrogen bronze metals. Cellulose is the most abundant biomass globally, and thus its utilization can lead to more sustainable energy production. Previous studies have reported the conversion of cellulose to hydrocarbons at high temperatures and hydrogen pressure. This work focuses on the conversion of methyl cellulose …

A Kinetic Analysis On Hydrolysis And Hydrothermal Conversion Of Cellulose To Dodecane, Joel Nyangoka Onyancha

Electronic Theses and Dissertations

Cellulose, the most abundant biomass on Earth, offers a promising pathway for alternative energy through conversion into alkane hydrocarbons. Traditional methods rely on high temperatures and high-pressure hydrogen, often derived from petroleum. In this study, we investigated the conversion of Microcrystalline Cellulose using hydrogen metal oxides (bronzes) under milder conditions. Following ASTM E3417-24 hydrolysis protocols, we employed hydrogen bronzes with toluene for product extraction. This approach enabled conversion at lower temperatures without pressurized hydrogen. Products were analyzed using Gas Chromatography Mass Spectrometer for identification and Gas Chromatography Flame Ionization Detector for quantification. Our findings revealed the formation of a possible …

Investigation Into The Effectiveness Of G-C3n4 For The Degradation Of Indigo Dye In Aqueous Solution Via Electrocatalysis, Rolando R. Barron Jr

Theses and Dissertations

Indigo dye (IUPAC 2-(3-hydroxy-1H-indol-2-yl)indol-3-one) is one of the most used dyes in the textile industry worldwide with more than 40,000 tons produced each year. It can elicit adverse physiological responses in humans including vomiting, diarrhea, and other gastrointestinal conditions, and it is toxic in large amounts. There is also evidence to suggest that indigo is a teratogen and genotoxic in aquatic life. Environmentally, the enormous amount of indigo used in the textile industry has caused rivers and waterways to run blue as well as severely impacting aquatic and plant ecosystems. The chemicals used in its synthesis are also …

Comparison And Evaluation Of Overlay And Leveling Binder In Traffic Circle Construction, Pratik Neupane

Graduate Theses and Dissertations (2019 - present)

Traffic circles play a vital role in managing traffic flow and ensuring safety, yet their unique traffic conditions make them prone to early cracking and deformation. This study evaluated the performance of overlay and leveling binder asphalt mixtures for a reconstructed traffic circle at the University of South Alabama, using plant-mixed laboratory-compacted (PMLC) specimens. Volumetric analyses were performed to determine maximum specific gravity (Gmm), bulk specific gravity (Gmb), and air voids content. Laboratory tests were conducted on both the overlay and leveling binder layers using indirect tensile cracking test (IDEAL-CT) and indirect tensile rutting test (IDEAL-RT) to assess cracking tolerance …

Protein Structural Changes Of Envelope Glycoprotein In Human Immunodeficiency Virus Type 1, Abigail S. Bridges

Chemistry & Biochemistry Undergraduate Honors Theses

The envelope glycoprotein (Env), present on the viral surface of human immunodeficiency virus type 1 (HIV-1) facilitates host cell infection, making it a critical target for immune responses and vaccine development. Env is able to transition through three prevalent prefusion conformational states, state-1 (pre-triggered), state-2 (closed), and state-3 (open). By transitioning through these conformation states, Env can successfully evade immune responses and initiate viral entry into the host cell. This study uses molecular dynamics (MD) simulations to analyze the conformational dynamics of the mature, cleaved Env glycoprotein in the state-2 conformation (PDB ID: 4ZMJ). Simulations were conducted with five replicates, …

Molecular Insights: Advances In Single Molecule And Single Particle Detection For Analysis Of Chemical, Physical, And Biological Phenomena, James Ethan Batey

Chemistry & Biochemistry Undergraduate Honors Theses

This thesis is focused on recent advancements made in the field of chemical imaging, optical microscopy, and recent developments that have improved spatial, temporal, or spectral resolution or have made certain techniques more accessible and cost effective for their wider adoption. This thesis is organized based on the systems of interest we studied with each new technique. Although, it is important to note that many of the methods here can be used with a multitude of systems even if not explicitly mentioned. The first chapter of this thesis will discuss the current state of chemical imaging, common terminology, and important …

Using Gaussian Process Regression To Learn Thermodynamic Equations Of State With Uncertainty Quantification, Austen T. Lee

Chemical Engineering Undergraduate Honors Theses

This study investigates the use of derivative-informed Gaussian Process (GP) models to estimate thermodynamic behavior across temperature and density by building a Helmholtz-based equation of state. Argon, a stable monatomic gas, was chosen as a case study within the vapor region. The GP model was trained using values of experimentally measurable properties found by taking first and second derivatives of the original potential function. Results show that while the GP model offered uncertainty quantification and informed thermodynamic behavior, it predicted values that deviated from the ground truth depending on the property. The model exhibited high confidence in regions with substantial …

Silver Nanoparticles In Ammonia Sensing And Photovoltaics, Madhuka Liyanage

All Dissertations

Nanocomposite films (NCF) containing silver nanoparticles (AgNPs), separated by thin layers of silica/poly-4-vinylpyridine/polyvinylpyrrolidone, were fabricated via drop casting, spin coating, dip coating on glass substrate and drop casting on nylon filter membranes. The more uniform films were produced by drop casting on nylon filter membranes due to their solvent wicking properties. The films demonstrate electrical conductivity that varies in response to moist ammonia and water vapors. The changes in conductivity are attributed to hydrogen bonding between ammonia and water molecules with the silica/polymer layers, as well as the direct adsorption of ammonia onto the silver surface. Notably, NCFs with polyvinylpyrrolidone …

Qualitative And Quantitative Analysis Of New Psychoactive Substances And Related Metabolites Using Liquid Chromatography-Ion Mobility-Mass Spectrometry (Lc-Im-Ms), Ralph Aderorho

All Dissertations

The increasing prevalence of novel psychoactive substances (NPS) in illicit drug markets has posed significant challenges for forensic and clinical toxicology, primarily due to the structural similarity and diversity among these compounds. This dissertation investigates the application of advanced liquid chromatography-ion mobility-mass spectrometry (LC-IM-MS/MS) techniques, using the high-resolution Structures for Lossless Ion Manipulations (SLIM) platform and the drift tube ion mobility spectrometry (DT-IMS), for the qualitative and quantitative analysis of various types of synthetic opioids, synthetic cannabinoids, psychedelics and xylazine. By combining IMS separations with mass spectrometry and targeted chemical derivatization, this work enhances the ability to distinguish and characterize …

The Evolution Of Nanoparticles In Nanoparticle Doped Optical Fibers, Mary Cahoon

All Dissertations

Optical fiber and fiber laser technologies based on silica glass are critical to many technologies today. One method to improve the optical performance of laser fibers is engineer the local environment around the active elements in the glass. To that end, this Dissertation focused on the fabrication and characterization of fibers made with nanoparticles incorporated into the glass to control the local composition. First, the nanoparticle composition and structure was analyzed as it evolved from from the initially-synthesized form to incorporation into the dense aluminum-silicate glass. The aluminum oxide in the glass was found to be important not only to …

To Bee Or Not To Bee: Investigating Pesticide Behavior Inside And Outside Of Semi-Field Cages, Mallory Bingham

Undergraduate Honors Capstone Projects

Bees play an important role in ecosystems and food production through pollination. One such bee, the alfalfa leaf cutting bee (ALCB) is a very efficient pollinator and is essential in alfalfa seed production. However, bees face increasing harm, most notably due to the deleterious effect of pesticides used in agriculture, and much research is dedicated to investigating the extent of effects that pesticides have on different bee populations. One common tool used to study the effects of pesticide exposure on bees is semi-field cages. These cages have some key advantages, such as restricting bee foraging to plots sprayed with pesticides …

Synthesis, Characterization, And Redox Properties Of Select 1,4-Diazocine-6,11-Diones Towards An Electrochromic Dye-Set, Jeffrey Scott Richards

Open Access Theses & Dissertations

The daily consumption of personalized digital visual information depends on the current purview of electronic-based displays. Present manufacturers utilize modern technologies, such as LCD, OLED, QLED, and electronic ink, or "E Ink," in their devices to display text, pictures, and other forms of media to individual users. However, as modern society continues to rely on the use of digital displays, the demand for low-power alternatives will continue to rise as their application in varying scenarios is realized. Currently, "E Ink" technology continues to grow as the dominant solution in the e-readers and digital signage marketplace, and can even be seen …