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Investigating The In Vitro Antimicrobial Potential And Comprehensive Computational Studies Of New Schiff Base Derivatives, Abrar Hussain, Shahzaib Akhter, Hammad Nasir, Khurram Shahzad, Muhammad Arfan, Sand Hyun Park

Chemistry & Biochemistry Faculty Publications

Antimicrobial resistance (AMR) is a growing global health threat driven by multidrug-resistant bacteria (Staphylococcus aureus, Pseudomonas aeruginosa), and fungi (Candida albicans, and C. parapsilosis). This study evaluated six novel Schiff base derivatives (HSB-1 to HSB-6) through integrated in vitro antimicrobial activity and comprehensive computational studies. In vitro disk diffusion assay demonstrated the largest zones of inhibition against S. aureus for HSB-6 and HSB-1 (15–17 mm), activity against P. aeruginosa for HSB-5 and HSB-6 (12 mm), and moderate antifungal activity for HSB-4 (8–11 mm). Molecular docking results correlated with the in vitro findings with the binding energy ΔG = −12.3 kcal/mol …

Sulfhydryl-Functionalized Diarylethenes: Synthesis, Photoswitching, And Fluorescent Properties, Pramod Aryal, Jonathan Bietsch, Gowri Sankar Grandhi, Josh Choi, Guijun Wang

Chemistry & Biochemistry Faculty Publications

Sulfhydryl group (SH) plays important roles in reactions with various functional groups, especially in biologically active systems. Photoswitchable diarylethene (DAE) derivatives have demonstrated applications in many research fields. Among the many classes of diarylethene derivatives, thiol derivatives have not been extensively explored. In this study, we systematically synthesized and characterized a series of bis-thiol functionalized dithienylethene derivatives. The thiol groups in this series are attached directly to the thiophene, or through a phenyl or methylene linker. Each series incorporated both dithienyl cyclopentene and hexafluorocyclopentene bridges and total six thiol substituted diarylethenes were synthesized. Among the six sulfhydryl DAE derivatives, four …

Nonpyrogenic "Black" Nitrogen Likely Plays A Major Yet Underrecognized Role In The Global Nitrogen Cycle, João Vitor Dos Santos, Aleksandar I. Goranov, Kyle M. Lambert, Theodoro Da Rosa Salles, Susan J. Carter, Ann Pearson, Patrick G. Hatcher

Chemistry & Biochemistry Faculty Publications

Condensed aromatic nitrogen (ConAN) is commonly found in soil and aquatic environments. ConAN is broadly viewed by the biogeochemistry community as a combustion-derived product leading to its frequent designation as pyrogenic “black” nitrogen. Here, we provide evidence that ConAN can also form through nonpyrogenic pathways. In an experiment simulating biomass oxidation, pine wood boards assembled with iron nails were exposed to 12 years of natural environmental conditions. Nitrogen concentrations increased from 0.2 to 1.2 wt % with increasing proximity to the nail. Ultrahigh resolution mass spectrometry showed enrichment of nitrogen-containing compounds within the lignin and condensed aromatic domains. X-ray spectroscopic …

Land Use Influences Dissolved Organic Matter Composition In The U.S. Coastal Critical Zone Network, Aleksandar I. Goranov, Elizabeth V. Whitney, Brian R. Moyer, Katherine L. Tully, Patrick G. Hatcher, Yu-Ping Chhin

Chemistry & Biochemistry Faculty Publications

Coastal watersheds are highly productive biogeochemical systems supporting robust coastal fisheries and contributing significantly to the marine gross primary production flux. These ecosystems are comprised of civil infrastructure, farms, forests, and marshes, and their diversity is reflected in the quantity and quality of dissolved organic matter (DOM). Here, we assess the role of farming in influencing DOM from surface waters of six coastal tidal creeks adjacent to forest and farm sites in the US Critical Zone Network. Molecular fingerprinting using electrospray ionization - Fourier transform - ion cyclotron resonance - mass spectrometry revealed that farm-influenced DOM was enriched in nitrogen-, …

Multidentate Surfactant-Dependent Synthesis Of Giant Iridium Superstructures, Ramjee Balasubramanian, Maeren E. Hill

Chemistry & Biochemistry Faculty Publications

Giant superstructures of iridium, comprised of smaller spherical and slightly larger anisotropic nanoparticles, were synthesized by reducing iridium chloride in the presence of resorcinarene, a class of tetrameric macrocyclic polyphenols, with sodium borohydride in ethanol in 30 min under mild conditions. These superstructures were characterized by a range of techniques including TEM, HRTEM, EDS and other spectroscopic methods. The impact of the macrocyclic surfactant, its features and reaction conditions in dictating the formation of giant iridium superstructures was evaluated. The packing density of nanoparticles in these giant iridium superstructures could be altered qualitatively by varying the duration of the reaction, …

Towards Novel Porphyrinoid Architectures: Synthesis Of Porphyrin Analogues With Two Six-Membered Exocyclic Rings, Amy L. Le, Timothy D. Lash

Faculty Publications – Chemistry

Tripyrranes with terminal ester protective groups were prepared by reacting 7-acetoxy-4,5,6,7-tetrahydroindoles with 3,4-diethylpyrrole in refluxing acetic acid-ethanol. Dibenzyl esters were deprotected by hydrogenolysis over 10% Pd/C and the resulting dicarboxylic acids were condensed with a series of dialdehydes in the presence of trifluoroacetic acid, followed by oxidation with FeCl₃ or DDQ, to give porphyrinoid products with two six-membered exocyclic rings. Reactions with a pyrrole dialdehyde gave porphyrins in 27-30% yield and good yields were also obtained using 2,5-furandicarbaldehyde and 4-hydroxy-2,6-pyridinedicarbaldehyde to prepare oxaporphyrins and oxypyriporphyrins. However, poorer results were noted for thiaporphyrins, benzocarbaporphyrins and oxybenziporphyrins due to their poor …

Exploring The Limitations Of Substrate Scope In Dimethylallyltryptophan Synthases, Evan T. Miller

Theses and Dissertations--Pharmacy

Natural products (NPs), are the largest source of bioactive compounds in Nature, and are essential to the treatment of human disease. Nearly 50% of drugs approved for use from 1981 to 2019 owe some aspect of their development to NPs, either in terms of their structure, pharmacophore, or mechanism of action. However, NPs are difficult to structurally optimize. Chemoenzymatic methods for NP derivatization have been increasingly seen as practical alternatives to traditional synthetic methods. Prenyltransferases (PTs) are involved in the primary and secondary metabolism of plants, bacteria, and fungi, and they are key enzymes in the biosynthesis of many clinically …

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 …

Basis Design For Electronic Structure And Beyond, Weishi Wang

Dartmouth College Ph.D Dissertations

At the intersection of quantum physics, quantum chemistry, and materials science, electronic structure is the study of electrons in solid-state and molecular systems. Electronic-structure computation relies on discretizing the many-electron Hamiltonian with a finite single-particle basis set. However, basis-set construction is conventionally treated as an ad hoc preprocessing step. This thesis develops an expressive and flexible framework for active, system-oriented basis-set design and numerical modeling strategies that treat basis functions as tunable representations to encode electronic ground-state information.

We first introduce a multi-layered, differentiable basis-construction framework that embeds a set of primitive parameters into mixed-contracted Gaussian-type orbitals. We then develop …

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 …

Modular Synthesis Of Conjugated Aromatic Systems Via Palladium-Catalyzed Cross-Coupling Reactions, Joden Russell Robinson

Dissertations, Master's Theses and Master's Reports

This thesis describes the development of a modular synthetic route to extended conjugated aromatic systems through iterative palladium-catalyzed Sonogashira crosscoupling reactions. The work was motivated by the challenge of preparing a discrete conjugated molecule in a controlled manner. The synthetic strategy used complementary protected alkyne functionalities that could be selectively activated. This enabled sequential deprotection and coupling reactions to predictably extend the molecular scaffold. Using this approach, a series of conjugated intermediates was prepared and exponentially extended. Spectroscopic characterization by NMR and mass spectrometry supported the structures of the isolated products and the success of the iterative elongation strategy. Overall, …

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 …

Development Of Novel Methods For Investigative Leads In Firearm And Explosive Related Incidents, Addio Joseph Fiordigigli Jr.

Graduate Theses, Dissertations, and Problem Reports (ETD)

Criminal outbreaks and gun violence persist as a multifaceted global crisis, marked by escalating rates of homicide, suicide, and terrorism that destabilize communities and strain public resources. The proliferation of illicit firearms and homemade explosive devices, along with the complexity of modern criminal networks, necessitates innovative scientific tools to strengthen preventive intelligence operations and ensure that the legal process is grounded in physical evidence. More efficient detection of traces left behind at a crime scene can help prevent further harm or injury from follow-up attacks. This study aims to develop and evaluate new triage methods for characterizing gunshot residues (GSR) …

Net Carbonyl Ene Reactions Of Olefins With Aldehydes, Alexandra Mock

Honors Theses

Aldehydes and olefins react in the presence of base and TMSOTf to yield homoallylic alcohols. In this net ene reaction, TMSOTf acts as a Lewis acid to activate the aldehyde, leading to a strong oxygen-silicon bond that acts as a driving force in the reaction. In the proposed mechanism, the α-methylstyrene attacks the carbonyl carbon of the TMSOTf-activated aldehyde to produce a carbocationic intermediate. Elimination using a relatively bulky base (2,6-lutidine) provides the homoallylic alcohol. This reaction has proven robust in terms of the aldehyde and olefin scope.

Biochemical Investigations Of F420-Dependent Glucose-6-Phosphate Dehydrogenase From Cryptosporangium Arvum, Sarah T. Al-Noubani

2026 Spring Honors Capstones Projects

F₄₂₀-dependent glucose-6-phosphate dehydrogenase (FGD) catalyzes the conversion of glucose-6-phosphate to 6-phosphogluconolactone using the deazaflavin, Cofactor F₄₂₀. FGD from Mycobacterium tuberculosis has been investigated due to its health relevance to prodrug activation. More recently, FGD from Cryptosporangium arvum (Cryar- FGD) has been investigated due to its broader substrate specificity toward multiple sugar phosphates. Kinetic and NMR studies have shown that Cryar-FGD has dual catalytic activity as a dehydrogenase and isomerase. Further investigations are being conducted on Cryar-FGD to characterize key residues involved in catalysis.

To investigate the catalytically active residues of Cryar-FGD, …

Feasibility Of Upcycling Spent Lithium-Ion Battery To Carbon Dioxide Capture Adsorbent, Chimezie Frank Onwudinjo

Master’s Theses

This study investigates the feasibility of repurposing spent lithium-ion battery (SLIB) to lithium orthosilicate (Li₄SiO₄), a high temperature carbon dioxide sorbent. Two synthesis pathways including conventional acid-leaching method (Scenario 1) and a pyrolysis-based route (Scenario 2) were explored. Additionally, techno-economic analysis (TEA) and lifecycle assessment (LCA) of the two processes were also performed. Different analytical characterization techniques were performed to understand the material properties of Li₄SiO₄ including surface area, crystallinity, morphology and thermal stability. CO₂ capture performance of the synthesized Li₄SiO₄ was tested in a thermogravimetric analyzer (TGA) using …

Identification Of Modified Polymer End Groups For Correlations To Physical Properties, Tj Sacco

Williams Honors College, Honors Research Projects

Plastic has become the primary material for containers in both industrial and commercial fields. Plastics are the optimal choice since they have many physical properties that make them ideal candidates: durability, heat resistance, chemical stability, as well as their inexpensive production cost. Nowadays, the desire for more versatile plastics with strength, flexibility, hydrophobicity, and biodegradability has grown; however, concerns for plastic use have started to rise as well. The overuse of plastics poses a threat to the environment and people’s health: plastics are hard to break down completely which results in the formation of micro(nano)plastics (MNPs). In attempts to circumvent …

Comprehensive Analytical Investigation Of Tetrahydro-4h-Chromene And Dihydropyridine Derivatives, Ryan J. Burk

Chemistry & Biochemistry Dissertations

Novel calcium channel blockers (CCBs) with dihydropyridine (DHP) or tetrahydro-4H-chromene moieties are often chiral, so effective enantiomer separation methods are needed for continued drug development. The purpose of this dissertation is to outline a comprehensive method development model for the chiral separations of DHPs and tetrahydro-4H-chromene derivatives. The scope of this dissertation is to address analytical challenges during initial synthesis, chiral separations, and data analysis during post-processing for this class of chiral compounds. The first section focuses on the method development strategies for separations of DHPs in the sub/supercritical fluid (SFC) and normal phase modes with the 2-hydroxypropyl-β-cyclodextrin stationary phase. …

Novel Methods For Environmental Fluoride Measurement, Cable Warren

Chemistry & Biochemistry Dissertations

Fluoride analysis has been an important focus of analytical analysis for many years and will continue to be so going forward. Today, fluorinated compounds, specifically per/polyfluoroalkyl substances (PFAS), better known as “forever chemicals” have captured the moment and are the subject of vast research and regulation. Under this context, I have researched new methods of fluoride separation and concentration in complex media as well as a novel method of PFAS destruction and total organic fluorine analysis for screening of PFAS in aqueous samples. Through research and work on micro-scale detection methods, an understanding of the state of the art and …

The Forensic Implications Of Hydrochloric Acid (Hcl) Exposure On Dna Preservation In Human Teeth, Shaelyn Lee Zimmerman

Graduate Student Theses, Dissertations, & Professional Papers

Identity is a human right, and forensic anthropological methods are often aimed at returning identity to decedents. Three main pathways are used for the identification of human remains: fingerprints, dental records, and DNA analysis. Identification efforts may be hindered when perpetrators attempt to obscure the victim’s identity. In cases where corrosive substances, such as hydrochloric acid (HCl) are used, dental comparison and fingerprinting often fail and genetic analysis becomes the best chance of achieving personal identification.

Previous studies have shown teeth are an excellent source of DNA. Large, multi-rooted teeth, such as molars, are often preferred because they contain the …

Pullulan Production From Lignocellulosic Plant Biomass Or Starch-Containing Processing Coproduct Hydrolysates, Thomas P. West

Faculty Publications

The complex polysaccharide pullulan is characterized as a glucose-containing biopolymer that is both water-soluble and neutral in polarity. A variety of commercial applications exist for pullulan, including its utilization as a flocculant, a blood plasma substitute, a food additive, a dielectric material, an adhesive, or a packaging film. The fungus Aureobasidium pullulans has used several hydrolysates derived from plant biomass or starch-containing processing coproducts to support polysaccharide production. These include various plant biomass or processing coproduct streams such as lignocellulosic-containing peat, prairie grass, stalks, hulls, straw, shells, and pods or starch-containing coproducts from the processing of corn, rice, jackfruit seeds, …

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 …

Computer-Aided Molecular Design To Identify More Environmentally Friendly Pfas, Melvin M. Keita

Williams Honors College, Honors Research Projects

The goal of this project is to inversely design alternatives to per- and polyfluoroalkyl substances (PFAS) using Computer-Aided Molecular Design (CAMD). PFAS, also described as “forever chemicals”, have been used in industry and consumer products since the 1940s. PFAS can be found in drinking water, food, food packaging, waste sites, and other sources. Exposure to different PFAS can lead to increased risks of some cancers, immune effects, and reproductive effects. Pulling from existing data, this project will use quantitative structure-property relationships (QSPRs) to design PFAS alternatives that possess optimal properties to prevent adsorption into drinking water and other potential sources …

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 …

Green Modification Of A Coupling Reaction Between N-Acetylated Amino Acids And P-Nitrothiophenol, Kaitlyn S. Marley, Hannah M. Werle, John P. Morgan

SURF Posters 2026

Native Chemical Ligation (NCL) is a process by which smaller peptides can be linked together to form larger peptides and proteins, but the preparation of necessary thioester starting materials often relies on hazardous reagents. We report a greener synthesis of S-(4- nitrophenyl) N-acetylphenylalaninethioate, building upon the methodology reported by Raines et al.1 This literature synthesis uses N,N-dimethylformamide (DMF) as solvent in the final thioester coupling step to accommodate the limited solubility of N-acetylphenylalanine in less polar solvents. However, DMF is a known reproductive toxin and environmental hazard. Our research demonstrates that acidic water serves as a highly effective, benign alternative …

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 …

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 …