Organic Chemistry Commons^™

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.

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 …

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 …

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, …

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 …

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 …

Design, Synthesis, And Characterization Of Phosphonate-Functionalized Diimide Ligands For Metal-Organic Framework Construction, Kenya Rosas, Jonathan Uribe

Posters - 2026

• Metal–organic frameworks (MOFs) are solid, porous materials composed of metalions reacted with organic linkers

• MOFs are customizable through variations in their metal ions, organic linkers, and the functional groups of the organic linker all yielding a structure with different properties

• MOFs have a variety of applications, ranging from storage and catalysis to drug delivery

• The synthesis and characterization of four phosphonate-based diimide ligands:
  • N,N´-bis(phosphonomethyl)-pyromellitimide (PPMI).
  • N,N´-bis(phosphonobenzyl)-pyromellitimide (PPMI-Ph).
  • N,N´-bis(phosphonomethyl)-3,3′,4,4′-biphenylenediimide (PBDI).
  • N,N´-bis(phosphonobenzyl)-3,3′,4,4′-biphenylenediimide (PBDI-Ph).

• These ligands were then coordinated with zinc or copper metal ions to make MOFs.

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

Electronic Theses & Dissertations (2024 - present)

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

The first part of this dissertation focuses on establishing …

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

Electronic Theses & Dissertations (2024 - present)

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

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 …

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, …