Organic Chemistry Commons^™

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, …

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. …

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.

Corannulene: Optimized Synthesis And Four-Fold Reduction, Guy Rozenman

Electronic Theses & Dissertations (2024 - present)

Corannulene is a bowl-shaped π-conjugated fragment of the ball-shaped C₆₀-fullerene that undergoes stepwise multielectron reduction and can accept four electrons to form the aromatic tetraanion, C₂₀H₁₀⁴⁻. Prior literature has established this charge state in donor-solvated alkali-metal assemblies: early solution studies identified the formation of the tetraanion under lithium reduction in THF, and later X-ray diffraction crystallography demonstrated a triple-decker lithium sandwich in which two corannulene tetraanion decks encapsulate five Li⁺ ions. The central objective of this thesis is to determine whether the corannulene tetraanion can instead be isolated as a bulk solvent-free alkali-metal salt containing only corannulene and …

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 …

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 …

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, …

Utilizing Coal For Mesophase Pitch-Based Carbon Fiber Production: Precursors, Processes, And Progress, Christina M. Thompson

Theses and Dissertations--Chemistry

Graphitic materials possess unique properties due to the unique combination of layered crystalline structure and carbon’s low atomic weight. High performance carbon fiber is one such example, displaying exceptional strength-to-weight ratios, stiffness, and thermal and chemical resistance. These properties render high performance carbon fiber a critical structural reinforcement material in the manufacture of composites across various industries, such as for automotive and aerospace applications. However, balancing fiber performance with precursor and processing costs remains a challenge. As alternative carbonaceous feedstocks are explored, coal has gained interest for utilization in graphitic products as a relatively abundant and low-cost source of aromatic …

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 …

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 …

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 …

Salicylic Acid Heterocyclic Derivatives: Chemical Synthesis And Biological Activity, Rawaa Hefdi Zaooli, Marwa Abdulameer Mseer, Amneen Mohammed Alsayegh

Al-Bahir

Before a drug can be widely used, it must go through a long development process, starting from the discovery of the active ingredient and continuing with tests to confirm its safety and effectiveness. In this study, new olsalazine derivatives were synthesized, containing a fused morpholine-3-one ring and two five-membered heterocyclic rings (thiadiazole and oxadiazole). Common and readily available materials, such as salicylic acid (to prepare 2-hydroxy-5-nitrobenzoic acid) and inexpensive catalysts, were used to synthesize compounds from the first, 5,5'-(diazene-1,2-diyl)bis(2-hydroxy-3-nitrobenzoic acid) (A1), to the seventh, 6,6'-(diazene-1,2-diyl)bis(N-(4-(5-amino-1,3,4-oxadiazol-2-yl)phenyl)-3-oxo-3,4-dihydro-2H-benzo[b][1,4]oxazine-8-carboxamide) (A7).

Each compound was characterized by FT-IR and ¹H-NMR spectroscopy, along with physical properties such …

Discovery Of The Multi-Ion Bridge Intermediate: A Computational Exploration Of The Mechanism For Azomethine Ylide Formation From N-Oxides, Martin J. Neal

Electronic Theses and Dissertations

Density functional theory (DFT) provides a method for calculating the ground-state energies of complex molecular systems through evaluating the electron density instead of the full wave function. When results match either experimental outcomes, calculations with DFT offer a computationally efficient method to help explain chemical phenomena. The transformation of tertiary amine N-oxides to azomethine ylides, a simple route to the precursor for 1,3-dipolar cycloadditions that result in the pyrrolidine scaffolds found in natural products, has received only minimal attention due to concerns that its mechanism includes a highly electrophilic intermediate. Utilizing DFT to model the mechanism of the conversion …

Steam Distillation And Characterization Of Star Anise: Investigating Aroma And Aromaticity, Natalie Brattain

Discovery Day - Daytona Beach

"Steam distillation is a widely used technique for extracting essential oils from plant materials, allowing for the separation of volatile compounds while minimizing thermal degradation. In this study, steam distillation was used to extract the essential oil of Illicium verum (Star Anise) to investigate the relationship between aroma and aromaticity. While ""aroma"" refers to the sensory perception of a substance’s scent, ""aromaticity"" is a chemical property related to the stability of conjugated ring systems. This distinction for our compound was explored by using chemical characterization of the extracted oil. Following the steam distillation process, gas chromatography (GC) and mass spectrometry …

Fermented Foul Play: A Real-World Forensic Scenario To Enhance Student Engagement And Understanding Of Instrumentation And Analytical Data Analysis, Abigail Hoermann, Laci Joy Walmer, Matthew J. Goss

Student Scholar Symposium

A forensic-style investigation was introduced in an upper-level instrumental analysis course to foster collaboration and application of theoretical concepts in a laboratory setting. Students were provided with kombucha samples collected from a simulated crime scene and tasked with determining ethanol concentrations using Gas Chromatography–Mass Spectrometry (GC-MS). By independently preparing serial dilutions, establishing calibration curves, and interpreting mass spectra, they practiced quantitative analytical techniques and engaged in evidence-based problem solving. Notably, Sample C demonstrated elevated ethanol levels (6.4% v/v), suggesting possible adulteration and deepening the forensic narrative. Through this scenario-driven format, students strengthened both their technical competencies and their ability to …

Photoflow Synthesis And Characterization Of Cis- And Trans-N-Isohumulone, Gregory M. Giovine, Bradley Gallow, Trevor Smith, Bruce Hamper

Undergraduate Research Symposium

Previously published efforts by the Hamper group demonstrated the viability of photochemistry in the isomerization of n-humulone to n-isohumulone. Photochemical isomerization reactions of n-humulone performed under 400nm light over 8 hours resulted in high yields (84% reported) of largely trans-n-isohumulone (>95%). These promising results invited further examination of the photochemical process and the application of photoflow procedure. Herein we report the beginnings of a comprehensive slate of n-humulone isomerization reactions performed under iterative photoflow conditions.

The Chemistry Of Color: A Comparative Analysis Of Natural And Synthetic Dyes In Textile Application, Caitlyn Pinaga Cpht

Honors Program Theses and Research Projects

The Chemistry of Color: A Comparative Analysis of Natural and Synthetic Dyes in Textile Application examines how color functions at the intersection of chemistry, culture, and environmental responsibility. This project traces the evolution of dyeing from ancient natural pigment traditions, rooted in ecological knowledge, agricultural practices, and cultural identity, to the industrial rise of synthetic dyes, whose laboratory precision enabled unprecedented consistency, brightness, and global textile expansion. Through experimental swatch analysis, the study compares the behavior of natural dyes derived from plants and food sources with modern fiber-reactive and synthetic dye classes on a range of fibers including cotton, bamboo …

The Malonate Template: The Key To Unlocking Novel Amino Acids, Thomas Owens

Dissertations

The “Malonate Template” provides access to various amino acids, all from a common intermediate. Herein, demonstrates the use of the malonate template to establish a synthetic route to both 2-thiohistidine and 2-thio-3-N-methyl-histidine from a benzyl methyl malonate derived intermediate. Furthermore, efforts exploiting the applicability of the malonate template for the of both 2-thiohistidine and 2-thio-3-N-methyl-histidine as a suitable alternative to methods previously described by Erdelmeier are described.

The method presented incorporates modifications to the biomimetic pathway described by Erdelmeier for the synthesis of 2-thiohisidine. By exploiting the biomimetic formation of 2-thiohisitidne’s mechanism via mass spectrometry, we …

Geochemical Analysis Of The Eagle Ford Shale In Webb And Dimmit Counties, Tx, Natalie G. Girlinghouse

Electronic Theses and Dissertations

The Late Cretaceous Eagle Ford Shale of South Texas is a mixed carbonate–siliciclastic succession that serves as both a prolific hydrocarbon source and reservoir. This study integrates chemostratigraphy, mineralogical analysis, and elemental ratio proxies to reconstruct depositional environments and assess controls on detrital influx, paleoproductivity, and redox conditions across multiple cores in Webb and Dimmit counties. Major, trace, and redox-sensitive elements were evaluated alongside Total Organic Content (TOC) and carbonate content to identify stratigraphic trends and environmental shifts.

Results reveal distinct geochemical signatures between the Upper and Lower Eagle Ford Shale, with the Lower Eagle Ford characterized by elevated Al-rich …