Chemistry Commons^™

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 …

Explorations Of Dna-Single-Walled Carbon Nanotube Interactions To Develop Multiplexed Molecularly Specific Biosensors For Inflammation, Amelia K. Ryan

Dissertations and Theses

Inflammatory cytokines such as interleukin-6 (IL-6) and interleukin-12 (IL-12) are central regulators of immune signaling and key biomarkers of disease, yet existing assays for their detection remain slow, invasive, and lack multiplexing ability. This dissertation advances the development of single-walled carbon nanotube (SWCNT) optical nanosensors capable of real-time, multiplexed, and molecularly specific cytokine detection through innovative use of single-stranded DNA (ssDNA) interfaces.

First, an IL-6-specific DNA aptamer was employed as both a dispersing agent and recognition probe for SWCNT fluorescence sensing. Sequence modifications, including anchor domains, truncations, and thermally induced refolding, were systematically tested to optimize sensitivity and selectivity. The …

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 …

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 …

The Role Of Leptin In The Regulation Of The Soluble Amyloid Precursor Protein Alpha (Sappa) Levels In Non-Small Cell Lunch Cancer (Nsclc) Cell Media, Benjamin Haddad

Senior Honors Theses and Projects

We previously found that the levels of soluble amyloid precursor protein α (sAPPα) are partly regulated by acetylcholinesterase (AChE) in human non-small cell lung cancer cell lines A549 (p53 wild-type) and H1299 (p53-null). In this study, we hypothesize that sAPPα is partly regulated by leptin, a hormone classically recognized for its anorexigenic role in appetite regulation— yet recently shown to play a role in cancer cell signaling. It was observed that cells treated with leptin exhibited greater concentrations of sAPPα and lower concentrations of Aβ40/42 in the media compared to those of cells left untreated. An opposite effect was observed …

Identification Of Fentanyl And Fentanyl Analogs Found In Human Urine Using Gas Chromatography-Mass Spectrometry, Adam M. Fisher

Electronic Theses & Dissertations (2024 - present)

Identification of fentanyl and its analogs in unknown samples is a frequent practice completed in forensic crime labs, as the fentanyl epidemic continues. With the continued increase in illicit drug use, crime labs are not able to keep up with the flooding of new fentanyl analogs being developed, resulting in new analogs slipping past the crime labs’ authority. This research is to start to develop a database of commonly found fentanyl analogs in New York State. Gas Chromatography-Mass Spectrometry (GC-MS) is a widely used method for the detection and identification of illicit drugs in forensic crime labs. A database that …

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 …

Extreme Value Theory Analysis Of High Emitter Trends Across Four Us Cities From 1995 To 2021, M. Matti Maricq, Gary A. Bishop

Fuel Efficiency Automobile Test Publications

Extreme value theory provides a direct means to characterize the distribution of high emitters within a vehicle fleet and calculate statistical confidence intervals for comparisons. Defining a “high emitter” as the maximum emitter in a random sample of N vehicles implies in the limit of large N that high emitters follow an extreme value distribution, comprised of three distinct domains. The analysis of over twenty years of roadside remote sensing emissions measurements in Chicago, Denver, Los Angeles and Tulsa reveals clear differences between gasoline vehicle high emitter distributions across pollutants (hydrocarbons (HC), carbon monoxide (CO) and nitric oxide (NO)), but …

Epitaxial Growth Of Metal-Organic Framwork Thin Films By Electro-Conversion And Electrodeposition, Xiaoting Zhang

Doctoral Dissertations

Electrochemical epitaxy is a facile and inexpensive soft-solution process to fabricate highly ordered thin films. This research focuses on the epitaxial growth of metal-organic framework (MOF) thin films by electrochemical methods which include electro-conversion and electrodeposition.

First, an electrochemical conversion pathway was invented to achieve epitaxial MOF thin films. Epitaxial single-domain Cu-BTC(111) thin films were manufactured by electrochemical oxidation of Cu₂O(111) films electrodeposited on single-crystal Au(111). The single-crystal-like Cu-BTC(111) thin films with out-of-plane and in-plane order provide well-aligned 3.5 Å triangular windows along the [111] direction. Cu-BTC(111) foils were fabricated from the Cu-BTC/Cu₂O system by electrochemical …

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 …

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 …

Functionalized 2d Hexaazatriphenylene As Hydrogen Storage Platform: A Dft-Guided Design Approach, Islam Gomaa

Nanotechnology Research Centre

No abstract provided.

First-Principles Modeling Of Nitazoxanide Analogues As Prospective Pfor-Targeted Antibacterials, Islam Gomaa

Nanotechnology Research Centre

Pyruvate:ferredoxin oxidoreductase (PFOR) is a key Achilles’ heel in anaerobic pathogens. We integrate electronic-structure calculations (DFT), cheminformatic QSAR metrics, and residue-resolved docking to distill a concise “recognition code” and translate it into practical design rules. Using nitazoxanide (Nita; ΔG(bind) ≈ −10.0 kcal·mol−1) as a well-established reference, productive binding requires a conserved triad: a hydrogen-bond donor addressing Thr-997 and Cys-840, a π–π stack with Phe-869, and a recurrent π–σ contact to Thr-997 that orients the scaffold. Deacetylation to tizoxanide unmasks the phenolic donor and raises local electrophilicity, yet it also slightly loosens pocket packing (−9.6 kcal·mol−1). Strategic halogenation introduces a σ-hole …

Rhenium Chalcogenide Clusters Containing Para-Substituted Phenylacetylide Ligands: Synthesis, Characterization, And Investigation Of Substituent Effects On Spectroscopic And Electrochemical Properties, Katherine L. Helmink, Cory A. Hicks, B. Sage Lauper-Cook, Steven J. Peters, Christopher J. A. Daley, Yann Molard, Lisa F. Szczepura

Faculty Publications – Chemistry

Four new organometallic [Re₆Se₈]²⁺-based cluster complexes containing para-substituted phenylacetylide ligands, [Re₆Se₈(PEt₃)₅(C≡C–C₆H₄–X)](SbF₆) where X = NO₂, CO₂Me, CH₃, and OMe, have been synthesized and fully characterized using ¹H, ¹³C{¹H} and ³¹P{¹H} NMR, IR, and UV–vis spectroscopy, HRMS, and elemental analysis. Three of these cluster complexes, [Re₆Se₈(PEt₃)₅(C≡C–C₆H₄–NO₂)]⁺, [Re₆Se₈(PEt …

Impact Of Y-Mixer Geometry And Flow Rate Modulation On Chemical Gradient Generators In Microfluidic Devices, Elizabeth Thurston Hutton

College of Graduate Studies: Theses & Dissertations

Various microfluidic structures are devised to generate tunable, stable spatiotemporal chemical gradients for single-cell studies. This work addresses the role of Y-mixer junctions in generating nonlinear gradients by increasing the width of one arm (bias), which is suspected to cause premature diffusion within the mixer. This study introduced a cinching feature to narrow the wider arm locally and redefine the junctions of these biased Y-mixers using four novel geometries defined by a 5-micrometer drawing rule. Furthermore, three flow rate factors allowed us to explore the impact on the generated gradient landscapes. The results showed that the four novel designs similarly …

Quantifying Inositol Phosphate Dephosphorylation To Understand The Role Of Recalcitrant Organic Phosphorus Forms On Harmful Algal Blooms In Freshwater Systems, Iffat Tasnim

College of Graduate Studies: Theses & Dissertations

Organophosphorus such as phytic acid, a surrogate species of inositol phosphate (IP), may serve as a source for orthophosphate (OP) in freshwater. In absence of OP, competent aquatic microorganisms upregulate the production of specialized enzymes to obtain growth-sustaining OP from organic phosphorus (org-P) forms. The contribution of recalcitrant org-P to the OP pool has been overlooked due to the lack of capable tools to measure OP production from org-P accurately. The objective of this study was to quantify OP production from phytic acid (a surrogate form of recalcitrant org-P) to assess the contribution of recalcitrant org-P forms to the total …

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, …

Synthesis Of Novel Schiff Bases And Their Metal Complexes, Ryan J. Lukkarinen

Theses and Dissertations

Presented in this thesis is the synthesis and characterization of multiple thiosemicarbazones and dithiocarbazates, as well as their corresponding metal complexes. Chapter 1 is an introductory chapter exploring the significance and potential applications of this work. Chapter 2 focuses on thiosemicarbazone synthesis and characterization. Chapter 3 describes the synthesis and characterization of dithiocarbazates. Chapter 4 details metal complex synthesis using the previously described ligands. Chapter 5 summarizes the conclusions of the research and future work that may stem from it.

New Psychoactive Substances Detected In Wastewater Samples Collected Along The Interstate Highway Rest Areas In Kentucky, Durga Prasad Kodati

Murray State Theses and Dissertations

The rapid emergence and proliferation of new psychoactive substances (NPS) pose significant challenges to public health and law enforcement. The potential for abuse and toxicity of these substances, which are intended to mimic the effects of controlled drugs, has been raising concerns as these compounds are designed to evade being regulated. There are traditional methods of tracking NPS, such as seizures and forensic toxicology, but they are delayed and seldom effective because these substances continue to evolve rapidly. Wastewater-based epidemiology (WBE) has emerged as a promising tool for real-time surveillance of drug consumption. The primary objective of this research was …

Effect Of Single Screw Extrusion Process Parameters On Gel Formation And Properties In Polycaprolactone Films, Kitthanya Ritthichai

Chulalongkorn University Theses and Dissertations (Chula ETD)

This research focuses on the production of polycaprolactone (PCL) films using the commercial grade CAPA 6800 through a continuous single-screw extrusion process. This method serves as an alternative to conventional solution-based film fabrication that requires solvents and chemical reagents. The effects of processing temperature (80–120 °C), screw design (mixing screw and plain screw), and extruder-barrel cooling system (water-cooled and air-cooled) on film quality, gel formation, thermal properties, and mechanical properties of PCL films were investigated. Based on the processing of high-purity PCL pellets, the results indicate that the processing temperature, screw design, and barrel-cooling system did not affect the chemical …