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Joanne Stubbe And The Mechanistic Study Of Ribonucleotide Reductases, Madysen York

Natural Sciences Student Research Presentations

To catalyze the formation of deoxyribonucleotides from ribonucleotides, the enzyme has to remove an hydroxyl from the ribose sugar part of the molecule (circled in in green) (“Ribonucleotide Reductase”).

The problem is that hydroxyl doesn’t naturally want to break from the base it is attached to, leaving many researchers unable to discern the chemical process going on inside these enzymes that make the bond break possible (Strauss).

Mary Lowe Good And The Development Of Catalytic Solutions For Industrial Processes, Eleanor Heller-Walker

Natural Sciences Student Research Presentations

To study catalysts, Good used Mössbauer spectroscopy, a nuclear technique that measures how atoms absorb and emit gamma rays (“Mössbauer Spectroscopy”). This method helps scientists identify oxidation states, chemical environments, and structural changes in metal containing materials, especially iron.

This data revealed exactly how active metal sites in catalysts behave when exposed to exhaust gases, for example, when carbon monoxide (CO) or nitrogen oxides (NOₓ) contact the surface of the metal.

Transition Metal Alkoxide Complexes Synthesis Using Thallium Reagents And Design Of Iron(Ii)-Alkoxide Carbene Complexes And Their Reactivity, Lakshani Wathsala Kulathungage

Wayne State University Dissertations

ABSTRACTTRANSITION METAL ALKOXIDE COMPLEXES SYNTHESIS USING THALLIUM REAGENTS AND DESIGN OF IRON(II)-ALKOXIDE CARBENE COMPLEXES AND THEIR REACTIVITY by LAKSHANI WATHSALA KULATHUNGAGE May 2025 Advisor: Dr. Stanislav Groysman Major: Chemistry (Inorganic) Degree: Doctor of Philosophy

This dissertation focuses on the synthesis and reactivity of transition metal and main group metal alkoxide complexes. The dissertation began with exploring a novel, efficient synthetic route towards transition metal alkoxides involving thallium reagents. A novel dimeric Tl2(OCtBu2Ph)2 complex was synthesized in the reaction between a lithium alkoxide and thallium precursor TlPF6. Tl2(OCtBu2Ph)2 served as a convenient precursor to the formation of old and new transition …

Structural Impacts Of Canonical And Non-Canonical Oligonucleotide Modifications, Deepak Shrestha

Wayne State University Dissertations

Nucleic acids, including DNA (deoxyribonucleic acid) and RNA (ribonucleic acids), are the fundamental building blocks of living organisms. The events that cause modification of DNA/RNA are of interest because they impact the nucleic acid function. Targeting DNA is important for treating diseases such as cancer. Cisplatin (cisPt) is a well-studied drug that targets DNA and blocks replication, but its use is limited by adverse side effects and cellular resistance. Prevoius research addressed some of these challenges through development of platinum analogues such as carboplatin and oxaliplatin. Amino acid-linked platinum analogues (AAPt) are the focus of this thesis work. AAPt complexes …

Mass Spectrometry Combined With Chemical Biology To Study Human Ailments, Eric Thomas Jacquerio Davis

Wayne State University Dissertations

Post-translational modifications (PTMs) are essential as chemical changes that regulate protein function, activity, stability, interactions, and localization after protein synthesis. PTMs, such as phosphorylation, acetylation, and ubiquitination, can activate or deactivate proteins, influence their interactions with other molecules, and determine their cellular location. This regulation is vital for numerous biological processes, such as cell cycle control, signal transduction, and gene expression. Abnormal PTMs are linked to various diseases in humans, including parasitic infection, blood disorders, cancers, and neurodegenerative diseases, making their study crucial for understanding disease mechanisms and developing targeted therapies. In the Pflum lab, we are interested in the …

Dynamics Of Metal-Coordinated Coumarin Dyes For Photoswitching Applications, Danielle Jacoby

Open Access Dissertations

Optical transient absorption spectroscopy is a fundamental pump-probe technique that is used to analyze the photophysical and photochemical properties of molecules. Our research group specifically utilizes both a femtosecond and nanosecond set up to probe dynamics of molecules on time scales ranging from 100s of femtoseconds to approximately 50 microseconds. Chapter 2 is a standard operating procedure for the nanosecond transient absorption instrument.

Photoacids are molecules that undergo a change in the acidity of one of their protons when exposed to light. Utilizing this phenomenon, we have designed a series of dyes that, when bound to divalent first row transition …

Light, Symbiosis, And The Biology Of Corals, Taylor R. Lindsay

Open Access Dissertations

Light is critical for the survival of most shallow water scleractinian corals. Corals are mixotrophs, acquiring energy via both feeding on water column plankton and photosynthesis via a symbiotic relationship with dinoflagellates living within their tissues. Corals rely heavily on photosynthetically derived metabolites through this symbiotic relationship, intrinsically linking their biology to light availability. Corals are known to modulate their biology to maximize light capture. However, there is a limited understanding of the interaction between morphology, physiology, and energetic strategy, as well as how light may affect these relationships. In Chapter 1, we quantified the morphology, physiology and energetic …

Development And Characterization Of Polysaccharide-Based Controlled Drug Delivery Platforms, Amanda Pepler

Open Access Dissertations

Drug delivery research focuses on overcoming challenges in patient treatment. Most therapeutics are delivered systemically through oral or intravenous routes. However, these administration methods are often inefficient due to therapeutic hydrophobicity, poor bioavailability, and liver metabolic clearance, necessitating frequent dosing. When treatment plans require frequent dosing, patients experience significant fluctuations in therapeutic concentration in the bloodstream, which can increase adverse side effects. These factors contribute to low patient compliance. Therefore, the core focus of drug delivery research is to develop new administration routes for therapeutics. Drug delivery systems (DDS) that can target therapeutics to a localized region offer advantages over …

Beyond The Phonon Gas Model (Pgm): Unraveling The Unique Mechanistic Processes Dictating Thermal Transport In Highly Anharmonic And Disordered Materials, Sandip Thakur

Open Access Dissertations

Thermal transport in nonmetallic solids has traditionally been described by the phonon gas model (PGM), in which heat is carried by weakly interacting phonon quasiparticles in an ordered crystalline lattice. However, this model breaks down in materials characterized by strong anharmonicity, dynamic disorder, or structural complexity, features prevalent in many next-generation materials used in energy conversion, optoelectronics, and thermal management. This dissertation investigates thermal transport in such complex materials, including metal halide perovskites (MHPs), covalent organic frameworks (COFs), metal organic frameworks (MOFs), and 2D-3D heterostructures, through large-scale molecular dynamics (MD) simulations and frequency-resolved spectral analyses.

In MHPs, the work reveals …

Investigating The Photophysical Dynamics Of Anthracene And Acridine Derivatives Using Time-Resolved Spectroscopy, Sophia Tiano

Open Access Dissertations

Anthracenes and acridines are among the simplest visible light absorbing heterocyclic and polycyclic aromatic hydrocarbons and as such are extensively used in a variety of applications including photosensitizers and fluorescent sensors. Although the photophysics of some derivatives have been studied in the past, there is still a lot of unknown fundamental information that is vital in order to optimize these molecules for particular applications. Transient absorption spectroscopy was used to study the photophysics of the 9-substituted methyl, hydroxymethyl and formyl derivatives of acridine and anthracene. The growth and decay of the triplet-triplet absorption peak were quantified for each dye in …

Ultra-Rapid Electrophilic Cysteine Arylation Using Pyridinium Salts, Bradley M. Lipka

Open Access Dissertations

Small molecule-based bioconjugation enables in vitro and in vivo functionalization of proteins and peptides, significantly expanding the chemical space of biomacromolecules. Among these transformations, nucleophilic aromatic substitution (S_NAr) of cysteine residues is a widely employed strategy for protein bioconjugation.

Although many reagents facilitate cysteine arylation, they are disadvantageous in two crucial aspects - limited synthetic modularity and undesired hydrophobicity. First, conventional cysteine arylating reagents are frequently activated by multiple electron-withdrawing groups (EWGs) on a single aromatic ring, leaving few synthetic handles to derivatize the reagents for advanced applications. Second, these labeling reagents are generally hydrophobic in nature and …

Identifying The Constituents Of Pyrolysis Oil Using Supercritical Fluid Chromatography- Fraction Collection (Sfc-Fc) And Gas Chromatography- Mass Spectrometry/Vacuum Ultraviolet Spectroscopy (Gc-Ms/Vuv), Sadid Morshed

2025 Fall Honors Capstones Projects - Archive

Plastic waste continues to accumulate as production increases and disposal methods remain insufficient. Even with recycling programs in place, much of the discarded plastic still ends up in landfills or waterways, eventually breaking down into harmful microplastics. One promising solution is the conversion of plastic waste into pyrolysis oil, which can also serve as an alternative feedstock for chemicals. Pyrolysis oil is produced by heating plastics to approximately 800 °C in the absence of oxygen, resulting in a complex mixture of hydrocarbons that includes paraffins, isoparaffins, olefins, naphthenes, and aromatics. Analyzing the amount of oxygen, nitrogen, and sulfur in these …

Direct Partial Oxidation Of Methane To Methanol Using Dioxygen Over Superhydrophobic Modified Catalysts, Oluchukwu V. Igboenyesi

Chemistry & Biochemistry Dissertations - Archive

Various methods for enhancing catalysts activity and productivity in gas to liquid synthesis like Direct Methane to Methanol Conversion and Fischer Tropsch Synthesis have been studied over the years. Some of these methods include the use of promoters, bifunctional catalysts, introducing steam, optimizing reaction conditions and catalyst modification. The choice of catalysts and their modification plays a critical role in improving the overall productivity in gas to liquid synthesis.

This research explored the superhydrophobic modification of heterogenous catalysts used in Direct Methane to Methanol Conversion (DMTM) and Fischer Tropsch Synthesis (FTS). The catalysts were modified with Perfluoro alkyls (PFSMA). The …

Copper-Based Oxide Semiconductors: Transparent Conductors And Ternary Alloys, Abhishek Rawat

Chemistry & Biochemistry Dissertations - Archive

This dissertation explores the strategic design and development of copper-based metal oxide semiconductors for photoelectrochemical (PEC) and optoelectronic applications, with a focus on advancing materials for sustainable energy technologies. Through a comprehensive investigation into copper vanadates and copper oxides, the work aims to understand and enhance charge transport, light-harvesting capabilities, and electronic structure modulation. The research integrates fundamental materials chemistry with applied photoelectrochemical studies to uncover the role of copper's d-electrons in mid-gap state formation, multifunctionality through electronic structure tuning, and the development of low-temperature transparent conductive oxides.

In chapter 2, we have discussed the attributes of copper metavanadate (CuV …

The Impact Of Inter-Subunit Communication On F420h2:Nadp+ Oxidioreductase: A Kinetic Approach, Jamariya A. Howard

Chemistry & Biochemistry Dissertations - Archive

F₄₂₀H₂:NADP⁺ Oxidoreductase (Fno) catalyzes the reversible reduction of NADP⁺ to NADPH using reduced F₄₂₀ as the hydride donor. Both NADPH and the F₄₂₀ cofactor play significant roles in various metabolic pathways, including glycolysis and methanogenesis, particularly in methanogenic and sulfate-reducing archaea. These organisms play an essential role in global carbon cycling by converting carbon dioxide to methane through the methanogenic pathway, which is directly tied to energy production. This thesis investigates the hydride transfer mechanism of Fno from the extreme thermophile Archaeoglobus fulgidus, using fluorescence binding, steady-state and pre steady-state kinetics.

Chapter 1 outlines the structural and spectral characteristics …

Investigating The Impact Of Pfas Contamination On Mental Health, Jihyun Kim

Open Educational Resources

To explore the intersection of environmental injustice, racial disparities, and public health through an examination of PFAS contamination in drinking water and its impact on communities of color. This study will address environmental, social, and health implications of PFAS exposure, with a specific emphasis on promoting equity and advocating for policy changes to rectify systemic inequalities.

Reducing Friction In Machine Oil Via Cesium-Hybridized Graphene Oxide Quantum Dot Additives, Islam Gomaa, Sherief Elsoudy, Maryam Galal, Ahmed Azim

Nanotechnology Research Centre

Friction and wear are among the most common causes of energy loss and component failure in mechanical systems, accounting for around 20–30% of total global energy consumption. Conventional lubricants fail to provide consistent performance in harsh conditions due to inadequate additive dispersion, agglomeration, and restricted surface reactivity. Recent advances in nanomaterial-based lubricants have shown promise, but it remains difficult to achieve significant friction and wear reduction at low additive concentrations while preserving stability. In this study, we synthesized and tested cesium-hybridized graphene oxide quantum dots (Cs-GOQDs) as novel lubricant additives. When incorporated into machine oil at 0.1 wt%, Cs-GOQDs reduced …

What Amino Acid Residue Is Responsible For The Interaction Of Atg11 With Its Autophagy Partner Atg9?, Patricia Omoyemwen Woghiren

Senior Honors Theses and Projects

Macroautophagy is a cellular function that involves the formation of a double membrane vesicle that isolates and transports cellular materials to the vacuole or lysosome for degradation and recycling. It is divided into selective and non-selective macroautophagy. Atg11 and Atg9 are two key proteins involved in selective macroautophagy, and their interaction is critical for selective macroautophagy. Specific residues on Atg9 critical for Atg11 binding have been identified, but similar residues on Atg11 have not been identified. The aim of my research was to identify a specific residue critical for Atg11’s interaction with Atg9. To this end, we carried out Yeast-twohybrid …

Ex Vivo Single-Molecule Analysis Of Ryanodine Receptor 2 Assembly In Cardiac And Neuronal Tissue, Qianye Yin, Christopher I. Richards

Chemistry Faculty Publications

Understanding receptor assembly is critical for elucidating the mechanisms underlying their function and regulation in physiological processes. While traditional in vitro single-molecule studies rely on isolating proteins from heterologous expression systems, they often fail to capture the in vivo physiological complexity involved in the organization and assembly of cell surface proteins. This protocol employs Total Internal Reflection Fluorescence Microscopy (TIRFM) to study GFP-tagged Ryanodine Receptor 2 (RyR2) molecules encapsulated within nanoscale vesicles. These vesicles, generated from organs rapidly extracted from the animal, effectively provide a snapshot of the receptor's assembly state at the time of extraction, enabling detailed analysis of …

Complexometric Titration Of Terbium(Iii) Compounds: An Analytical Blast From The Past Gives Purity Assurance When Modern Instruments Fail Us., Jake E. Timbes, Cameron Bateman, Justin Stace

Science University Research Symposium (SURS)

Lanthanide ions have attracted attention for applications in microwave electronics, memory devices, lighting applications, and chemical sensors. Terbium(III)-centered homoleptic complexes show promise as potential fluorescence-based chemical sensing agents. Tb(phen)2(NO3)3 (phen = 1,10-phenothroline) exhibits striking visible emission when excited by short-wave ultraviolet light; this emission is completely quenched by exposure to water or strong acid. However, the luminescence returns under relatively benign conditions. Unfortunately, our array of terbium(III) complexes are notoriously insoluble; rendering standard analytical techniques useless to assess purity, notably, 1H and 13C-NMR. Titration is a useful technique to give us, an assurance of purity—in conjunction with the ad-hoc purity …

Kinetic Analysis Of A Carbon-Rich Sico Model System, Takhya Holley

Chemistry & Biochemistry Theses - Archive

Kinetic Analysis of a Silicon Oxycarbide (polymethylhydrosiloxane/divinylbenzene) material was done for meaning of kinetic analysis methodology development. The material was synthesized using the standard procedure from, Blum 2005. A series of TGA’s was done using non-isothermal experiments. The analysis involved an initial isoconversional analysis using Friedman method, then decomposition of processes into individual processes using the Fraser-Suzuki function. The validation agreed within 1%, which is permissible by the ICTAC recommendations. The activation energies of the individual processes were determined using the Friedman method.The pre-dominant process #2 was found to have an activation energy of 220 +- 20 kj/mol and first-order …

Estimating Vapor Pressures Of Pheromone Compounds Using Gas Chromatographic Retention, Bipasha Sarker

Chemistry & Biochemistry Theses - Archive

Accurate determination of the vapor pressures of organic materials is important for predicting the sample’s environmental impact. It is difficult to directly measure accurate and precise vapor pressures of chemical compounds with direct experimental methods. Thus, indirect or predictive models for estimating vapor pressures are used. In this study, we follow a gas−liquid chromatography (GLC)-based approach, where retention data is correlated with vapor pressure using multiple reference standards. The method (GLC-RTyS) requires temperature-dependent retention factors (k-values) for test compounds and reference standards with known vapor pressures at matching temperatures. It has been observed that reference standards selected according to functional …

Supporting Information For: "Synthesis And Characterization Of Γ-Acyloxyl-Ε-Caprolactones”, Greyson Greischar, Tapiwa Gono Phiri, Ellie Haljun, Jenna Ray, Meheret Ourgessa, Garrett Thesing, Lila Lofving, Aidan Clark, Suzanna Bator, Durwynn Jno Baptise, Wyatt Cole, Michael Itschner, Yutan D.Y.L. Getzler

Data Sets

This dataset contains the raw, unprocessed NMR data for the title compounds of the paper "Synthesis and characterization of γ-acyloxyl-ε-caprolactones” published in iScience (DOI: 10.1016/j.isci.2026.115190. NMR spectra were acquired on a JEOL-ECZS 400 MHz spectrometer in CDCl3 (Cambridge Isotope Labs, 99.8% D) and are saved in the .jdf format. Chemical structures in this document will be represented in the SMILES format. The paper details the synthesis of eight lactones, with variation of the exocyclic ester. Within this set, we consider CC(OC(CC1)CCOC1=O)=O (7-oxooxepan-4-yl acetate or γ-acetyl-ε-caprolactone) to be the parent compound. The R group pendant from the exocylic carbonyl in this …

Progress Toward The Synthesis Of Pyridine-Containing Macrocycles Using Dynamic Alkyne And Olefin Metathesis, Stephen Kwas , '25

Senior Theses, Projects, and Awards

Tubular structures are ubiquitous in nature and possess functions ranging from the structural ones played by microtubules to transporting necessary ions across cell membranes by membrane proteins. In addition, the excellent electronic and structural properties of carbon nanotubes have made them of great interest to chemists. Yet, the functionalization of these nanotubes is hindered by unselective post-modification, often requiring harsh reaction conditions. As such, the assembly of macrocycles into nanotubular structures has been widely studied by chemists. One such way to make these materials is by using dynamic, reversible reactions to synthesize pyridine-containing macrocycles in high yields. Due to inherent …

Hydrogen Peroxide Production From Light-Driven Water Oxidation Via Nickel Oxide-Titanium Dioxide Heteronanocrystals, Mahfuz Ahammed Swadhen

Dissertations and Theses

High dependence on fossil fuels for energy carries risks for the environment, health, energy, and geopolitical stability. One of the solutions to address this is solar energy utilization, and the use of semiconductors for photocatalytic water splitting is a tantalizing prospect. An n-type semiconductor TiO2 combined with p-type NiO producing a heteronanojunction shows effective light-driven oxidation of H2O into H2O2. We developed a synthetic method to attach NiO nanoparticles on the surface of anatase TiO2 nanorods. We characterized the materials with UV-visible spectroscopy, powder X-ray diffraction, and electron microscopy. We immobilized the HNCs on fumed silica and removed organic surfactants …

Verification Of Real-Time Smoke Simulations: A Case Study On Early Summer North American Wildfire Events, Daniel Bonilla

Pitzer Senior Theses

As wildfire intensity and frequency escalate in times of unprecedented climate change and severe droughts, it is important to enhance forecasting models that accurately and efficiently predict wildfire smoke movement. NOAA’s experimental Rapid-Refresh Forecasting System with Smoke and Dust (RRFS-SD) aims to improve upon the High-Resolution Rapid Refresh- Smoke (HRRR-Smoke), by extending the domain to include all of North America and incorporating new developments in physics and wildfire parameterizations. Our work explores the process of adding satellite Aerosol Optical Depth (AOD) data, through AERONET, as an additional method of verification of the RRFS-SD experimental model. Using a case study on …

Transient Transmembrane-Electrostatically Localized Protons And Transmembrane Potential In A Laser Flashed Bacteriorhodopsin Purple Membrane Open Flat Sheet - Summary, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

The transmembrane-electrostatically localized protons/cations charges (TELCs, also known as TELPs) model may serve as a unified framework to explain a wide range of bioenergetic phenomena. Transient transmembrane-electrostatically localized protons (TELPs) and transmembrane potential in a laser flash-energized bacteriorhodopsin (bR) purple membrane (PM) open flat sheet are now better analyzed. Under the Heberle et al. (1994) experimental conditions, the number of bR molecules is now calculated to be 8200 per PM open flat sheet with a diameter of 600 nm. With a single-turnover laser flash intensity of 3 mJ/cm² to photoexcite 10% of the bR molecules, the laser flash-induced peak TELCs …

Experimental Absorption Cross Sections For Zro, Léo Lavy, Peter F. Bernath, Manish Bhusal, Jacques Liévin

Chemistry & Biochemistry Faculty Publications

Absorption cross sections for ZrO are provided and can be used as a template to interpret spectra of S-type stars. The ZrO spectrum was measured in emission from a carbon furnace at 2700 K and calibrated using synthetic spectra of ⁹⁰Zr¹⁶O. A set of nearly isolated molecular lines has been used for the calibration. We also thoroughly review the literature on the spectroscopy of ZrO. Comparison of the experimental spectrum with currently available line lists revealed issues in ZrO spectral simulation. (a) Within band systems, the relative intensities are not always well reproduced. (b) We identify yet unreported band systems, …

Chemoproteomic Profiling Of A Carbon-Stabilized Gold(Iii) Macrocycle Reveals Cellular Engagement With Hmox2, Sailajah Gukathasan, Chibuzor Ngozi Olelewe, Libby Ratliff, Jong H. Kim, Alyson M. Ackerman, J. Robert Mccorkle, Sean Parkin, Gunnar F. Kwakye, Jill M. Kolesar, Samuel G. Awuah

Chemistry Faculty Publications

In this work, we discovered a novel organometallic gold(III) macrocycle, Au-Mac1, that demonstrates anticancer potency in a panel of triple-negative breast cancer cells (TNBC), and based on this complex, a biotinylated-Au-Mac1 probe was designed for target identification via chemoproteomics, which uncovered the engagement of HMOX2 of the heme-energy metabolism pathway. Using orthogonal chemical biology and molecular biology approaches, including immunoblotting, flow cytometry, and cellular thermal shift assays, it was confirmed that Au-Mac1 engages HMOX2 in cells. Downstream effects of Au-Mac1 on the depletion of mitochondrial membrane proteins and bioenergetics point to the potential role of HMOX2 in cancer. Importantly, Au-Mac1 …

Electrochemical Observation And Ph Dependence Of All Three Expected Redox Couples In An Extremophilic Bifurcating Electron Transfer Flavoprotein With Fused Subunits, Debarati Das, Wassim El Housseini, Monica Brachi, Shelley D. Minteer, Anne-Frances Miller

Chemistry Faculty Publications

Bifurcating enzymes employ energy from a favorable electron transfer to drive unfavorable transfer of a second electron, thereby generating a more reactive product. They are therefore highly desirable in catalytic systems, for example, to drive challenging reactions such as nitrogen fixation. While most bifurcating enzymes contain air-sensitive metal centers, bifurcating electron transfer flavoproteins (bETFs) employ flavins. However, they have not been successfully deployed on electrodes. Herein, we demonstrate immobilization and expected thermodynamic reactivity of a bETF from a hyperthermophilic archaeon, Sulfolobus acidocaldarius (SaETF). SaETF differs from previously biochemically characterized bETFs in being a single protein, representing a …