Digital Commons Network^™

An Investigation Into The Potential Role Of Thioester Bonds In Prebiotic Atp Synthesis, Adam J. Ruf

Williams Honors College, Honors Research Projects

In this project I will attempt to show a potential prebiotic pathway for the synthesis of ATP. This pathway involves the use of thioester bond containing molecules, as derivatives of these bonds have been shown to exhibit enzyme-like catalytic properties. Nuclear magnetic resonance spectroscopy will be utilized to characterize each step of the pathway to ensure it is successful.

Pipeline Corrosion And Relevant Microbial Influence, Renee E. Bamberger

Williams Honors College, Honors Research Projects

This study investigated the role of microbial activity and oxygen availability in the corrosion of carbon steel pipelines with a focus on microbially influenced corrosion (MIC). Sediment collected from Old Woman Creek, Ohio, was used to simulate natural soil conditions, and carbon steel coupons were incubated under four treatments: nonsterile oxic, nonsterile anoxic, autoclaved oxic, and autoclaved anoxic over 85 days. Corrosion was assessed through mass loss measurements and the analysis of pH, sulfate, chloride, and dissolved iron concentrations. The greatest mass loss was observed in autoclaved oxic conditions, contrary to the initial hypothesis that microbial activity would greatly enhance …

Comparative Evaluation Of Hplc And Capillary Electrophoresis In Intestinal Permeability Of Oseltamivir Phosphate Via Single-Pass Intestinal Perfusion (Spip) Method, Senem Şanli, Gülpembe Halay, Mustafa Sinan Kaynak, Nurullah Şanlı

Arts & Sciences Faculty Publications

Introduction: Oseltamivir phosphate (OP), a widely used antiviral prodrug for influenza, requires accurate Biopharmaceutics Classification System (BCS) classification to inform formulation and bioequivalence decisions. Despite its high solubility, the permeability characteristics of OP remain inadequately defined. Methods: This study evaluated the intestinal permeability of OP using the in situ Single-Pass Intestinal Perfusion (SPIP) model in male Sprague Dawley rats. Two validated analytical methods - High-Performance Liquid Chromatography (HPLC) and Capillary Zone Electrophoresis (CZE) were developed and compared. Metoprolol tartrate served as the high-permeability reference standard, and phenol red was used to monitor water flux. Permeability coefficients (Peff) were calculated after …

Absolute Quantification And Identification Of Rna From Rna-Lipid Nanoparticles Using High Resolution Mass Spectrometry, Jason C. Funderburk

Theses and Dissertations

RNA therapeutics are a rising drug category with potential use for a range of conditions encompassing infectious diseases to therapies for cancer, diseases, and genetic disorders. RNA-lipid nanoparticles (RNA-LNPs) are the prominent delivery method for these therapeutics approved products include mRNA vaccines and polyneuropathy treatments. The emergency use authorizations and orphan drug status of current RNA-LNP drugs has allowed approval without finalization of the regulatory analytical procedures for quality monitoring. The objective of the study was to develop an LC-MS assay to simultaneously measure identity and concentration of two therapeutically relevant intact RNA constructs extracted from RNA-LNPs to enhance quality …

Design, Syntheses And Biological Applications Of Fluorescent Probes For Nad(P)H, Hsa And Cellular Microenvironment Sensing, Adenike M. Olowolagba

Dissertations, Master's Theses and Master's Reports

Fluorescent probes have emerged as powerful tools for investigating complex biological processes due to their high sensitivity, selectivity, and capability for real-time, non-invasive imaging. In particular, the detection of key biomolecules such as NAD(P)H, viscosity-related parameters, human serum albumin (HSA), and pH is essential for understanding cellular metabolism, redox homeostasis, and disease progression. In Chapter 2, three coumarin-based fluorescent probes (A–C) were designed, synthesized, and characterized for monitoring NAD(P)H levels in living cells. Probes A and B feature coumarin–cyanine hybrid structures linked via vinyl and thiophene bridges to 3-quinolinium acceptors, respectively, while probe C incorporates a dicyano moiety to replace …

Balancing Evidence Recovery: Hexane’S Effect On Biological And Non-Biological Traces In Sexual Assault Kits, Maya Richards

Honors Undergraduate Theses

This study investigated the effectiveness of solvent – based extraction methods for the recovery of lubricant residues from simulated sexual assault swabs, with emphasis on balancing chemical evidence recovery. Sequential extraction using ultra – pure water followed by organic solvents, hexane, dichloromethane (DCM), and ethyl acetate (EA), was evaluated across water – based, silicone – based, oil – based, and hygiene product matrices. Analysis was performed using Direct Analysis in Real Time – High Resolution Mass Spectrometry (DART – HRMS), and extraction efficiency was assessed through spectral correlation with neat reference samples. Results demonstrated that solvent performance was highly dependent …

Evaluating The Comparison Of Different Body Locations For Data Collection Using Galvanic Skin Response Of Forensic Chemistry Students When In Lecture And Laboratory Environments, Elisa Guerrero

Honors Undergraduate Theses

Anxiety is the response that humans can have when exposed to a stimulus. It can be caused by a multitude of factors, such as psychological, biological, or physiological stimuli. Anxiety can be presented as a state or as a trait in a person. Trait anxiety is typically seen as a more stable personality trait, whereas state anxiety is a more intense temporary emotional state. In our study, anxiety was regarded as a more state-like characteristic. A galvanic skin response (GSR) Shimmer3+ device can measure skin electro-conductance changes following stimulation. In a situation where a participant is experiencing anxiety, levels of …

Novel Chiral Interstellar Molecules: Quantum Anharmonic Ir And Vcd Predictions, Meredith Paik

Dissertations, Master's Theses and Master's Reports

The 2016 discovery of the chiral molecule propylene oxide (C₃H₆O) in the interstellar medium (ISM) has opened new avenues into explaining the origin of biomolecular homochirality on Earth. Thus, studies of chiral molecules in the ISM may be able to reveal more about the mechanism behind homochirality. However, while the search for chiral molecules in space has become an active field of study, astrochemical researchers have yet to detect other chiral molecules in the ISM. For this purpose, numerous characteristics for detectability have been outlined that may facilitate the discovery of other interstellar chiral molecules. With …

Connections Between Mathematics And Chemistry: An Interdisciplinary Undergraduate Curricular Initiative, George Ashline, Bret Findley

Journal of Mathematics and Science: Collaborative Explorations

In this article, we describe an undergraduate curricular initiative involving mathematics and chemistry faculty and students. Supported by a grant from the National Science Foundation Scholarships in Science, Technology, Engineering, and Mathematics Program, a program designed to encourage the study of and connections between quantitative fields and life sciences, this interdisciplinary collaboration features undergraduate student research and involves the development of curricular connections between mathematics and chemistry. Through this initiative, we have created activities for calculus courses featuring chemistry applications as well as activities for chemistry courses showcasing mathematical concepts. After the implementation of these curricular enhancements, we gathered student …

Crispr-Cas9 Unleashed: Gene-Slicing Adventures In The Cancer Battlefield, Shivakuma Sonnaila, Shilpi Agrawal

Chemistry & Biochemistry Faculty Publications and Presentations

Cancer, a global health menace, continues to pose significant challenges in terms of incidence and mortality, necessitating innovative therapeutic strategies. Despite existing treatments, the limitations persist, prompting a quest for novel approaches. The emergence of immunotherapy marked a transformative era in solid tumor treatments, yet its efficacy is constrained by adverse effects. Concurrently, the integration of advanced technologies into cancer treatment explores the vast potential residing at the molecular level through gene analysis and manipulation. This review articulates the role of state-of-the-art genome editing technology, notably clustered regularly interspaced short palindromic repeats (CRISPR-Cas9), in overcoming the constraints of immunotherapy for …

Nicotine, Bdnf, And Ꞵ-Adrenergic Ligand Receptors Regulate Soluble E-Cadherin Signaling In Non-Small Cell Long Cancer, Stuti Goel

Senior Honors Theses and Projects

E-cadherin is a protein that normally helps cells adhere to each other. Sometimes, part of this protein is cleaved off and released outside the cell as soluble E-cadherin (sE-cad). When this happens, there is less E-cadherin left on the cell surface. Enzymes called matrix metalloproteases, especially MMP9, are responsible for this cleavage. In this study, we investigated E-cadherin in two non-small cell lung cancer cell lines, A549 and H1299. We found that treating these cells with brain-derived neurotrophic factor (BDNF), nicotine, or epinephrine increased the amount of MMP9 released into the surrounding media. When the cells were treated with propranolol, …

Development Of Photolabile Coumarin Linker For Rna Synthesis And Crisprcas9 Applications, Ian Mcclain

Electronic Theses & Dissertations (2024 - present)

The scope of RNA-based therapeutics continues to expand as more siRNA, mRNA, and CRISPR-based treatments are approved for various medical applications. Purification of synthetic RNA drugs is inherently challenging and requires considerable time and resources. New cost-effective and efficient purification strategies will expedite drug development process and will lower the drug costs. In this thesis I describe two generations of photolabile linkers for the non-chromatographic purification of therapeutic RNAs. In addition, the photolabile linker was utilized for regulation CRISPR-Cas9 gene editing. In the first part of the thesis, I describe the first generation of the photolabile coumarin-based linker for non-chromatographic …

Bio-Orthogonal Chemistry-Based Strategy To Turn-On And Turn-Off Crispr-Cas9 Gene Editing In Solution And In Live Cells, Bhoomika Pandit

Electronic Theses & Dissertations (2024 - present)

The CRISPR–Cas9 system is a widely popular tool for genome engineering. There is a strong interest in developing tools for temporal control of CRISPR-Cas9 activity to address some of the challenges and to broaden the scope of potential applications. In this thesis I describe two biorthogonal based approaches to either Turn-ON and Turn-OFF CRISPR-Cas9 gene editing.

In first project work I describe a bio-orthogonal chemistry-based approach to Turn-ON Cas9 nuclease activity with temporal precision. We report a TCO-acylimidazole reagent that acylates 2′-OH groups of RNA. Poly-acylation (“cloaking”) of RNA was optimized in vitro using a model 18-nt oligonucleotide, as well …

Analysis Of Δ¹¹B As A Seawater Ph Proxy: Comparing Ocean Circulation Inverse Model Output With Marine Calcifier Geochemistry, Jesse I. Dong

CMC Senior Theses

Increasing anthropogenic carbon flux into the oceans decreases seawater pH, alters dissolved inorganic carbon speciation, and reduces biogenic calcification. The marine calcifiers— specifically corals and coralline algae—incorporate elements from surrounding seawater into their carbonate structures, which preserve past records of ocean carbon chemistry. In particular, boron in biogenic carbonate is a potentially valuable proxy for historical ocean pH across human timescales. Within seawater, boron primarily exists as boric acid B(OH)3 and borate ions B(OH)4 - , where higher pH favors the formation of borate ions. Borate ions preferentially incorporate the heavier ¹¹B isotope over 10B. On the other hand, if …

31p Solution Nmr Investigation Of Abasic Dna, Clarissa R. Krimmel

Graduate Theses/Dissertations

Base excision repair (BER) mechanisms fix single base lesions in DNA, such as T:G mismatches. During the base excision repair mechanism, an abasic site (AP site) is formed as an intermediate. AP sites are unstable and highly mutagenic; they can stop DNA replication. This research investigates how the conformational properties of abasic sites in DNA affect the binding recognition of enzymes involved in DNA repair mechanisms, including BER. Three different abasic sequences are being analyzed for this research project. A second project looks at the effects of a naturally occurring purine derivative, hypoxanthine, on the DNA backbone. These hypoxanthine lesions …

A Dual-Emission Polymer-Dots/Gold-Nanoclusters Nanohybrid For Ratiometric Fluorescence Detection Of Hg²⁺, Sha Wu

Dissertations and Theses

Heavy metals, such as Hg, Cd, Pb, and Cr, become a serious environmental problem because they are highly toxic, bioaccumulation, and long-term persistence, required a high sensitivity and selectivity detection method. Although laboratory testing instruments, such as inductively coupled plasma mass spectrometry, offer high sensitivity, their practical application is limited because they rely on large-scale equipment and complex sample pre-treatment processes. Single-emission fluorescence probes are simpler but can be affected by variations in probe concentration, excitation intensity, and measurement conditions. In this study, a dual-emission nanohybrid that consists of poly(9,9-di-n-hexylfluorenyl-2,7-diyl) (PDHF) and bovine serum albumin (BSA), termed as PDHF-Pdots/BSA-AuNCs nanohybrid, …

Superelectrophile Promoted Synthesis Of Heterospirocycles, Mariam A. Adegbenro

Graduate Research Theses & Dissertations

Spirocycles are important scaffolds with a wide range of applications in material science as well as in medicine. The introduction of a heteroatom into the spirocyclic framework can improve its electronic, photophysical, and structural properties. Various reports have been published on the incorporation of atoms other than carbon into the spirocycle. The work outlined in this dissertation involves the development of synthetic methodologies for the synthesis of hetero-spirocycles via superacid-promoted cyclization reactions. These concepts are summarized in Chapter 1.

Chapter 2: Aromatic imines were prepared from 9-fluorenone and azafluorenones, and these substrates were reacted in the Brønsted superacid, triflic acid, …

Supramolecular Self-Assemblies Of Ru( Ii ) Phototherapeutics: Biological Activity Of Micro- And Nano-Particles Acting As Reservoirs, Jérôme Laisney, Sarah M. Kriger, Dmytro Havrylyuk, Jason M. Unrine, David K. Heidary, Edith C. Glazer

Chemistry Faculty Publications

Ruthenium( II) coordination complexes have many appealing properties as prodrugs, but can suffer from poor aqueous solubility and short circulation times, drastically decreasing efficiency in vivo. Nanoformulations using a variety of carriers, such as inclusion in polymers/lipids or adsorption on inorganic nanoparticles have been applied to overcome this limitation, but unfortunately, these approaches raise additional concerns regarding the fate of the carriers, with potential long-term toxicity and accumulation in vital organs. Here, we present an alternative delivery strategy with formation of pure and polymer-supported supramolecular self-assemblies of Ru(II) complexes acting as ‘‘reservoirs’’. A facile preparation of size-controlled particles was achieved …

Characterization And Antimicrobial Activity Of Lignin-Derived Compounds In Ground Hurd Tissue Of Cannabis Sativa L. (Hemp) Cultivars, Jourdan E. Lakes, Anjam Sadik, Robert C. Pearce, Barbara L. Knutson, Stephen E. Rankin, Bert C. Lynn, Michael D. Flythe

Chemistry Faculty Publications

Objectives: Characterize lignin-derived compounds from the hurd of 10 fiber/grain Cannabis sativa L. cultivars and investigate the antimicrobial activity of select compounds on the wasteful ruminant bacterium, Acetoanaerobium sticklandii SR.   Methods: Hurd was processed using an aqueous ethanol solvent system and analyzed via GC-MS to identify and characterize lignin derivatives. Antimicrobial activity of the hurd and three monomers was assessed using solid (hurd) and liquid medium (monomers) bioassays against SR.   Results: 27 compounds were identified, most as monomers but a few were dimers, ethylated derivatives, and organic acids. There were approximately equal G- and S-units with substantially fewer H-units. Several …

Synthesis And Characterization Of Succinate Dehydrogenase Inhibitors H2/Z14 And C6/Z96 In Order To Combat Small Cell Lung Cancer, Lauren M. Graves

Honors Undergraduate Theses

The use of ubiquinone inhibitors to combat cancer is a recent development in medicinal science and procedures to efficiently synthesize these drugs remain limited. C6/Z96 and H2/Z14, two succinate dehydrogenase inhibitors, have been previously tested in vitro against NSCLC with positive results. Their similarity to ubiquinone is what makes them a strong candidate for a succinate dehydrogenase inhibitor at the ubiquinone binding site. The heterocyclic scaffolds and substituents are proposed to bind strongly through a combination of electronics, hydrogen-bonding, and fit, allowing them to bind well and prove to be more favorable than ubiquinone when competing for the Q-site. By …

De Novo Protein Binding To Zinc Oxide Through Biomineralization Pathways, Jean-Mark A. Francis

Theses and Dissertations

De novo proteins are structurally distinct from proteins found in nature and thus capable of having their amino acid sequence modified to accomplish tasks such as increasing protein-nanoparticle binding without unfolding or decomposing. Zinc Oxide nanoparticles are functionally distinct from their bulk counterparts and are widely used as semiconductors in a variety of fields such as medicine and agriculture. With demand for these nanoparticles increasing, environmentally sustainable methods of Zinc Oxide nanoparticle synthesis are being investigated as an eco-friendly alternative to currently utilized but environmentally hazardous chemical and physical techniques. This research investigates the binding characteristics between Zinc Oxide nanoparticles …

Elucidating The Impacts Of Non-Covalent Interactions In Organic Materials Through A Multiscale Computational Approach, Sashen A. Ruhunage

Theses and Dissertations--Chemistry

Noncovalent interactions (NCIs) in π-conjugated organic materials serve as tunable levers that influence molecular structure and intermolecular interactions in the condensed phase and, in turn, impact the electronic, optical, and mechanical properties of these materials. NCIs include attractive dispersion, electrostatic, and induction interactions, as well as repulsive exchange interactions. However, how to design materials with NCI considerations remains an open question across many fields. Here, we seek to provide an electronic and atomistic perspective on these interactions through multiscale simulations to aid materials design, processing, and performance optimization. In this study, we investigate NCIs and their effects across various systems …

Student Familiarity With The Periodic Table Of The Elements: Results From Cued-Recall And Eye-Tracking Assessments On Memory, Victor A. Okuo

Theses and Dissertations--Chemistry

Learning element symbol–name associations and the spatial organization of elements on the periodic table is a foundational step in learning chemistry, supporting later understanding of chemical formulas, equations, bonding, and stoichiometry. Although students often rely on memorization strategies to learn periodic table content, this task is challenging due to the large number of elements and the apparent ambiguity in matching some element symbols to their names.

This study explores students’ recall of element names when given element symbols as cues and their knowledge of element locations on the periodic table when given element names as cues. The study also examines …

Application Of Paper Spray Mass Spectrometry For Screening Acetylcholinesterase Inhibitors, Diksha Gautam

Graduate Research Theses & Dissertations

Paper spray mass spectrometry (PS-MS) is a novel ambient ionization method that allows chemical and biological samples to be rapidly analyzed with little preparation being required. In this paper, PS-MS was set up and streamlined as an acetylcholinesterase (AChE)-monitoring platform in addition to screening an existing and newly produced AChE-inhibitors. The detection of the substrate, acetylcholine (m/z 146), and the AChE catalysis product, choline (m/z 104) was performed without applying chromatographic separation or derivatization to the dried paper substrates. Assay conditions were optimized in a systematic way, to develop a robust MS-compatible enzymatic workflow.

Calibration curves for both, acetylcholine and …

Swimming In Uncertainty: Filling Data Gaps And Providing An Educational Platform For Beach Water Quality At Tybee Island, Georgia, Lukas Roberson

College of Graduate Studies: Theses & Dissertations

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Swimming in beaches water contaminated with high levels of bacteria can make you sick. Current monitoring at the public beaches on Tybee Island consists of weekly monitoring and enumeration of fecal indicator bacteria that takes 24 hours for results. If the number of bacteria exceed regulatory limits, a public health advisory is issued, and affected waters are retested until …

Flexible Membrane Electrodes For Use In High-Capacity Lithium-Ion Batteries, David A. Denemark

College of Graduate Studies: Theses & Dissertations

Wearable electronic devices require high-capacity flexible batteries to improve user comfort and increase usage time per charge. In this thesis, flexible lithium-ion battery (LIB) electrodes are prepared using a novel and scalable phase inversion method, embedding one-dimensional SnO₂ nanowires and double-walled carbon nanotubes within a porous polyacrylonitrile asymmetric membrane. The optimized electrode delivered an initial specific discharge capacity of 915.93 mAh g⁻¹, approximately 2.5 times greater than conventional graphite anodes, with 61.99% capacity retention after 45 cycles. The incorporation of a carbon mesh substrate further enhanced both electrochemical and mechanical performance, achieving 89.46% capacity retention after 45 cycles and a …

Fumigant Toxicity Of Essential Oils From Chemotypes Of Curry Tree (Murraya Koenigii) Against Adult African Malaria Mosquito (Anopheles Gambiae Sensu Stricto), Clarence M. Mang’Era, Fathiya M. Khamis, Ahmed Hassanali, Paul O. Mireji

All Peer-Reviewed Publications

The toxicity of fumigant formulations of essential oils (EOs) from curry tree (Murraya koenigii (L.) Spreng (Rutaceae)) against African malaria adult mosquito (Anopheles gambiae sensu stricto (Giles, 1902) (Diptera: Culicidae: Culicini)) was evaluated to identify most effective chemotype of the curry tree against the mosquitoes. Ninety-two compounds (91.78%–96.47% coverage) in the EO profiles were identified, among which EO isolated from curry tree chemotype from Kibwezi was most toxic. This chemotype had a median lethal dose (LD50) of 3.6 × 10⁻³ mg/cm³ (95% CI: 2.70–4.58) and a lethal time (Ti50) of 1.91 ± 0.086 h (p < 0.001). The equivalent LD50 of EOs of chemotypes from Mombasa, Makindu, and Malindi in Kenya was 4.9 × 10⁻³, 6.6 …

Investigation Of Fine-Grain Cu And Cu Alloys For Low-Temperature Hybrid Bonding Applications, Sarabjot Singh

Electronic Theses & Dissertations (2024 - present)

Hybrid bonding has emerged as a key enabler for next-generation three-dimensional (3D) integration, offering fine-pitch interconnects and improved electrical performance. However, conventional Cu–Cu hybrid bonding typically requires elevated temperatures to achieve sufficient diffusion and interface quality, posing challenges for temperature-sensitive device integration and process compatibility. This work investigates materials engineering approaches to enable low-temperature Cu–Cu bonding through both microstructure design and alloying strategies.

This work begins by examining grain refinement in Cu as a pathway to enhance diffusion through increased grain boundary density, providing efficient atomic transport without introducing additional elements. Three Cu-based systems Cu–Co, Cu–Ag, and Cu–Al were systematically …

Photo And Spatial Control Of Rna Structures And Functions: Exploring Positional Effects And Photo-Responsiveness Of Azobenzene Modified Nucleotides, Jinxi Du

Electronic Theses & Dissertations (2024 - present)

RNA molecules perform many important biological functions by forming complex three-dimensional structures stabilized by base pairing, tertiary interactions, and metal ion coordination. Because RNA function depends strongly on its structure, methods that allow reversible control of RNA conformation and activity are important for understanding RNA behavior and for potential therapeutic applications. However, achieving reversible and site-specific control of RNA structure, especially at the single-nucleotide level, remains challenging. In this dissertation, I developed and applied azobenzene-modified nucleotides as a chemical tool to enable optical and spatial control of RNA structure and function.

The first part of this dissertation focuses on establishing …

The Chemistry Of Red Lipstick: The Impact Red Lipstick Has On Society, Lilliana Weldeslassie

Electronic Theses & Dissertations (2024 - present)

Cosmetic chemistry is deeply embedded in everyday life, shaping the products people use from morning to night. Among these, red lipstick stands out as a formulation that blends complex chemistry with a cultural meaning. This thesis examines the scientific foundations of red lipstick through its chemical composition, pigment structure, toxicological history, analytical methods, and evolving sustainability practices. Historically, red lipsticks relied on high-risk ingredients such as lead, mercury, and other toxic metals, reflecting an era before chemical safety and regulatory oversight were incorporated.²¹ Modern formulations have established safer synthetic dyes, natural waxes, plant-based oils, and stabilizers created to optimize …