Organic Chemistry Commons^™

Developing Covalent-Organic Frameworks For Protecting Against Radiation, Megan J. Francis

Senior Theses

This research focuses on the development of lightweight, thermostable dual-function materials for secondary radiation protection and sensing by the integration of hydrogen-rich aliphatic chains inside the porous matrix of covalent-organic frameworks (COFs). The main aims of this project are the synthesis of organic linkers for forming a robust porous COF, synthesizing the porous COF through a condensation reaction, the development of hydrogen-rich aliphatic chains, and integration of aliphatic chains into COFs through click chemistry. This manuscript outlines the methodology and development of a novel self-assembled crystalline, porous material engineered to combine the functions of a shield and sensitive dosimeter. The …

Synthesis And Complexation Of Monotosylated 4-Aminopyridine With Nickel (Ii) And Iron (Ii) Ions, Kingsley John Orie, Remy Ukachukwu Duru, Raphael I-Oro Ngochindo

Makara Journal of Science

Tosylated 4-aminopyridine and other sulfonylated compounds of amines comprise a substantial class of pharmaceutical drugs used as antibiotics in the field of medicine. This research aimed at the synthesis of tosylated 4-aminopyridine and the complexation of the tosyated 4-aminopyridine with Ni(II) and Fe(II) ions. The sulfonamide was prepared by the action of tosyl chloride on 4-aminopyridine in an aqueous alkaline medium. The complexes were synthesized by the reaction of Ni(NO₃)_2.6H₂O /Fe(NO₃)_2.6H₂O with sulfonamide derivative. These compounds were characterized through Ultraviolet Visible spectroscopy (UV–Vis), Fourier Transform Infer-Red (FTIR) spectroscopy, …

Oxidation Alters The Architecture Of The Phenylalanyl-Trna Synthetase Editing Domain To Confer Hyperaccuracy, Pooja Srinivas, Rebecca E. Steiner, Ian J. Pavelich, Ricardo Guerrera-Ferreira, Puneet Juneja, Michael Ibba, Christine M. Dunham

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

High fidelity during protein synthesis is accomplished by aminoacyl-tRNA synthetases (aaRSs). These enzymes ligate an amino acid to a cognate tRNA and have proofreading and editing capabilities that ensure high fidelity. Phenylalanyl-tRNA synthetase (PheRS) preferentially ligates a phenylalanine to a tRNA^Phe over the chemically similar tyrosine, which differs from phenylalanine by a single hydroxyl group. In bacteria that undergo exposure to oxidative stress such as Salmonella enterica serovar Typhimurium, tyrosine isomer levels increase due to phenylalanine oxidation. Several residues are oxidized in PheRS and contribute to hyperactive editing, including against mischarged Tyr-tRNA^Phe, despite these oxidized residues not …

Selenium Probes For The Detection Of Thioredoxin Reductase Activity, Tendai Joseph Mafireyi

Dissertations and Theses

The identification and quantification of proteins and enzymatic activity in living tissues frequently requires the use of invasive procedures such as biopsy. These techniques can inhibit measurements of protein levels in real-time, and the disruption of tissue can lead to the loss of important information concerning the spatial distribution and differential activities in various cell types. The use of small organic fluorescent probes that rely on activation or accumulation within a tissue embody robust methods of detection that address these issues. This dissertation describes the design, synthesis and evaluation of fluorescent probes that can detect the enzyme thioredoxin reductase (TrxR). …

Enhanced Platinum (Ii) Drug Delivery For Anti-Cancer Therapy, Marek T. Wlodarczyk

Dissertations, Theses, and Capstone Projects

Over the years, anti-cancer therapies have improved the overall survival rate of patients. Nevertheless, the traditional free drug therapies still suffer from side effects and systemic toxicity, resulting in low drug dosages in the clinic. This often leads to suboptimal drug concentrations reaching cancer cells, contributing to treatment failure and drug resistance. Among available anti-cancer therapies, metallodrugs are of great interest. Platinum (II)-based agents are highly potent and are used to treat many cancers, including ovarian cancer (OC). Cisplatin (cis-diaminedichloroplatinum (II)) is the first Food and Drug Administration (FDA)-approved metallodrug for treatment of solid tumors, and its mechanism …

Tools And Strategies For The Patterning Of Bioactive Molecules And Macromolecules, Daniel J. Valles

Dissertations, Theses, and Capstone Projects

Hypersurface Photolithography (HP) is a printing method for fabricating structures and patterns composed of soft materials bound to solid surfaces and with ~1 micrometer resolution in the x, y, and z dimensions. This platform leverages benign, low intensity light to perform photochemical surface reactions with spatial and temporal control of irradiation, and, as a result, is particularly useful for patterning delicate organic and biological material. In particular, surface- initiated controlled radical polymerizations can be leveraged to create arbitrary polymer and block- copolymer brush patterns. Chapter 1 will review the advances in instrumentation architectures from our group that have made these …

Don't Sell Them Short, There's More To Bacterial Natural Products Than Antibiotics, Alison Clare Domzalski

Dissertations, Theses, and Capstone Projects

Recent genomic studies of microbiomes have revealed an overwhelming number of biosynthetic genes of unknown function. Most of these “cryptic” biosynthetic genes are not expressed in laboratory monocultures of individual microbes. Thus, there remains tremendous untapped potential for natural products discovery. Here we employ mixed microbial culture (MMC) as a simple yet powerful approach to awaken cryptic biosynthetic gene clusters. Our preliminary studies demonstrated that arrays of metabolites could be induced in MMCs upon environmental cues, such as surface adhesion. Using this system, we have screened, identified, and isolated bioactive bacterial metabolites, which were characterized structurally and biologically. Of the …

Immobilized-Enzyme Reactors Integrated Into Analytical Platforms: Recent Advances And Challenges, Bert Wouters Dr, Sinead Currivan, Noor Abdulhussain, T. Hankemeier, Peter J. Schoenmakers

Articles

Immobilized-enzyme reactors (IMERs) are flow-through devices containing enzymes that are physically confined or localized with retention of their catalytic activities. IMERs can be used repeatedly and continuously and have been applied for (bio)polymer degradation, proteomics, biomarker discovery, inhibitor screening, and detection. Online integration of IMERs with analytical instrumentation, such as high-performance liquid chromatography (HPLC) systems, reduces the time needed for multi-step workflows, reduces the need for sample handling, and enables automation. However, online integration can also be challenging, as reaching its full potential requires complex instrumental setups and experienced users. This review aims to provide an assessment of recent advances …

Automated Parsing Of Flexible Molecular Systems Using Principal Component Analysis And K-Means Clustering Techniques, Matthew J. Nwerem

Computational and Data Sciences (MS) Theses

Computational investigation of molecular structures and reactions of biological and pharmaceutical interests remains a grand scientific challenge due to the size and conformational flexibility of these systems. The work requires parsing and analyzing thousands of conformations in each molecular state for meaningful chemical information and subjecting the ensemble to costly quantum chemical calculations. The current status quo typically involves a manual process where the investigator must look at each conformation, separating each into structural families. This process is time-intensive and tedious, making this process infeasible in some cases, and limiting the ability of theoreticians to study these systems. However, the …

Synthesis Of Flagellin 22 As A Probe For Plant Signaling And Molecular Trafficking Towards Improved Crops, Edward Offei

Electronic Theses and Dissertations

Plant signaling involves the transport of information within and between plant cells from receptors to effectors. Plants are affected by biotic and abiotic stress conditions like insect attack and extreme temperatures, respectively, which cause disease, the induction of senescence and the reduction of crop yield. To improve plant traits for feed, fiber, and energy applications, it is critical to understand the short- and long-range signaling mechanisms plants use to control growth, biomass composition, senescence and responses to environmental stresses. It is known that many plant signaling molecules have profound effects on plants, through mechanisms that remain largely obscure. A key …

Micellar Nanocatalysis For Efficient Reactions., Uyen T Duong

Electronic Theses and Dissertations

Water is considered a green, sustainable, and inexpensive solvent for organic synthesis. However, performing organic reactions in water is especially challenging due to the inherent insolubility of substrates and catalysts. Inspired from Nature, where chemistry happens in water, micellar catalysis has recently gained much attention, especially for applications in pharmaceutical industry. Aqueous micelles are generally formed by amphiphile`s self-aggregation, a particular class of molecules possessing both hydrophobic and hydrophilic components. The aqueous micelle contains a hydrophobic cavity, which allows the lipophilic substrates and catalyst to go inside micelles, allowing their much higher localized concentration that enhances the reaction rates and …

Recent Studies On The Synthesis Of Medicinal Molecules., Paige Monsen

Electronic Theses and Dissertations

Medicinal chemistry interfaces synthetic organic chemistry, natural product chemistry and chemical biology, with a goal of yielding therapeutic agents. Natural products or compounds derived from natural sources such as plants, animals, and microorganisms, are often biologically active and render that compound a likely drug lead. For thousands of years humankind has utilized natural products for medicinal purposes and consequently scientists take advantage of both these compounds’ core structural characteristics and their modes of actions on selected targets as inspiration to develop therapeutics. Because the total synthesis of such complex molecules can be cumbersome and expensive, semi-synthetic methods on isolated natural …

Micelles And Lipid Nanoparticles: Catalysis And Biomedical Application., Faisal Ibrahim

Electronic Theses and Dissertations

RNA-based therapeutics is a rapidly expanding field due to its enormous potential for treatment of diseases through knockdown of genes or expression of therapeutic proteins. However, due to the overall negative-charge of an RNA molecule, RNA-based therapeutics must rely on delivery systems to overcome the various biological barriers for ultimate release of an RNA payload into the cytosol. Over the past three decades, the development of lipid-based RNA delivery systems, especially lipid nanoparticles (LNPs), have been comprehensively studied due to their unique properties. LNPs represent the most widely used delivery systems for RNA-based therapeutics, as evidenced by the clinical approvals …

Identification Of Chemical Structures And Substructures Via Deep Q-Learning And Supervised Learning Of Ftir Spectra, Joshua D. Ellis

Graduate Theses/Dissertations

Fourier-transform infrared (FTIR) spectra of organic compounds can be used to compare and identify compounds. A mid-FTIR spectrum gives absorbance values of a compound over the 400-4000 cm^-1 range. Spectral matching is the process of comparing the spectral signature of two or more compounds and returning a value for the similarity of the compounds based on how closely their spectra match. This process is commonly used to identify an unknown compound by searching for its spectrum’s closes match in a database of known spectra. A major limitation of this process is that it can only be used to identify …

Synthesis Of The Diazonium Zwitterionic Polymer/Monomer For Use As The Electrolyte In Polymer Electrolyte Membrane (Pem) Fuel Cells, Josiah Marshall

Electronic Theses and Dissertations

My research goals are to synthesize new zwitterionic perfluorosulfonimide (PFSI) monomer/polymers. They are expected to replace traditionally used perfluorosulfonic acid (PFSA) polymers as the electrolyte in PEM fuel cells. For the PFSI monomer preparation, we designed a nine-step synthesis route. Thus far, I have successfully completed the synthesis of 4- (2-bromotetrafluoroethoxy)-benzenesulfonyl amide, 4-acetoxybenzenesulfonic acid sodium salt, and 4-chlorosulfonyl phenyl acetate. The coupling reaction of 4-(2-bromotetrafluoroethoxy)- benzenesulfonyl amide with 4-chlorosulfonyl phenyl acetate, was troublesome due to slow reaction kinetics and byproducts. Additionally, I did a methodology study for the homopolymerziation of the perfluoro 3(oxapent-4-ene) sulfonyl fluoride monomer. We compared the weight …

Synthesis And Characterization Of Novel Organic Ligands With Their Complexes Of Platinum, Copper And Uranium, Mustafa Adnan Yasin Aldulaimi

Dissertations

Transition metal complexes of symmetrical and asymmetrical Schiff bases have played a significant role in the field of coordination, inorganic, and bioinorganic chemistry as models for biological, analytical, industrial, and pharmaceutical applications. Over recent years a great deal of interest has developed in new transition metal complexes of Schiff base ligand. The preparation of novel organic ligands is the most important step in the development of metal complexes that exhibit unique properties and novel reactivity. To highlight the presentation of this dissertation and to provide more detailed investigations, the dissertation was separated into six chapters according to the sequence of …

Functional Π-Organogelators: From Nanoribbons To Organic Phosphors, Sae Hui Lee

UNLV Theses, Dissertations, Professional Papers, and Capstones

π-Conjugated systems have been receiving notable attention in the field of organic material chemistry due to their interesting optical properties, assembling properties, and potential application in optoelectronics. Among various self-assembly methods, organogelation has been known to allow facile and easily reproducible molecular assembly. This work focuses on creating new π-organogelators with various side group modifications which in result allow proper tuning of the optical properties along with an effective self-assembly upon gelation. The research comprises of two chapters: 1) the first chapter focuses on N-heteroacenes (NHAs) with gelation property and 2) the second chapter investigates gelation induced phosphorescence (GIP) of …

The Phosphorescence Of Wind Cave Cavern, And The Level Of Organics Associated With It, Steven Gomez, Joshua Sebree

Summer Undergraduate Research Program (SURP) Symposium

An analysis of the level of organics in Wind Cave Cavern, South Dakota.

Analog Studies Of Organic Pathways In Wind Cave Through Cave Water And Crystals, Wilson Mcnaughton, Joshua Sebree Ph.D.

Summer Undergraduate Research Program (SURP) Symposium

In Wind Cave, organic molecules from the surface dissolved in water will slowly filter down into the cave through the porous limestone. While the water slowly proceeds down through the limestone, the water dissolves the limestone along the way. This dissolving of the limestone causes a quasi-equilibrium that deposits the organic molecules into the calcite structures found in Wind Cave. These large trapped organic molecules, mainly humic and fulvic acid, can be tracked by using UV light. The UV light causes these molecules to fluoresce blue, while the calcite structures generally do not have a strong blue fluorescence. The water …

Synthesis Of Small Molecules For The Treatment Of Infectious Diseases, Elena Bray

USF Tampa Graduate Theses and Dissertations

Drug discovery’s impact on modern healthcare cannot be measured. In the past year, the world has watched scientists all around the globe work together to help protect the public from the novel coronavirus pandemic. Although sometimes slow and costly, drug discovery is important for advancing modern society. Drug discovery is at the core of treating diseases and in particular, infectious diseases. In the first chapter an overview of drug discovery will be discussed in a brief manner.

The second chapter will introduce infectious diseases. In modern society, the development of small molecule treatments for treating bacteria, viruses, and fungi has …

Pt-Containing Conjugated Polymers And Small Molecules For Bhj Photovoltaic Devices, Yunjeong Kwon

Chemistry and Chemical Biology ETDs

The current state of organic photovoltaic (OPV) devices involve series of small molecular or polymeric systems that can absorb light from the solar spectrum in concert with another material that acts as an acceptor material. Together these materials serve to generate and split bound excitation species then transport the separate charges to their respected electrode. Several limitations have restricted the widescale use of these materials. Since these devices have their genesis in organic materials the OPV devices inherit short exitonic lifetimes, narrow absorption window and a lack of precise control over the morphology. To overcome these limitations, additional molecular engineering …

Mechanistic Insights Into Iron-Catalyzed C–H Bond Activation And C–C Coupling, Samantha M. Brewer, Timothy M. Schwartz, Magy A. Mekhail, Lara S. Turan, Timothy J. Prior, Timothy J. Hubin, Benjamin G. Janesko, Kayla N. Green

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Iron-catalyzed C–C coupling reactions of pyrrole provide a unique alternative to the traditional Pd-catalyzed counterpart. However, many details regarding the actual mechanism remain unknown. A series of macrocyclic iron(III) complexes were used to evaluate specifics related to the role of O₂, radicals, and μ-oxodiiron-complex participation in the catalytic cycle. It was determined that the mononuclear tetra-azamacrocyclic complex is a true catalyst and not a stoichiometric reagent, while more than one equivalent of a sacrificial oxidant is needed. Furthermore, the reaction does not proceed through an organic radical pathway. μ-Oxodiiron complexes are not involved in the main catalytic pathway, …

Stereocontrolled Mannosylation By Hydrogen-Bond-Mediated Aglycone Delivery, Catherine Alex

Dissertations

Stereocontrolled Mannosylation by Hydrogen-Bond-Mediated Aglycone Delivery

Carbohydrates are the essential bio-molecules of life as they form the forefront of interactions with receptors, proteins, pathogens, or neighboring cells. On cell-surfaces, carbohydrates are mostly found as linear or branched glycoconjugates, and a majority of them are linked via either 1,2-cis or 1,2-trans O-glycosidic linkages. There is no template-driven pathway for achieving the synthesis of glycans unlike other biomolecules like proteins and nucleic acids. The synthesis of 1,2-trans glycosides can be reliably achieved via the neighboring group assistance. The synthesis of 1,2-cis glycosides is difficult because, beyond weak anomeric effects, there are …

Functionalized Ionic Liquids For Improved Co2 Hydrogenation Catalysts, Amol Nanduji Jaybhaye

Masters Theses & Specialist Projects

Climate change is one of the biggest problems we are facing today, and anthropogenic greenhouse gases contribute significantly to it. Among greenhouse gasses, carbon dioxide emission is increased drastically and affecting majorly for increasing global temperature, and anything we can do to mitigate carbon dioxide emission will be helpful. A carbon dioxide hydrogenation reaction is a promising technique that can convert carbon dioxide into value-added chemicals, but the reaction rate is slow, and for that, we can use catalysts that will accelerate the reaction rate. Platinum-based nanoparticles have sparked research related to energy and environmental catalysts. Catalytic properties are depending …

Design Of Antioxidant Monomer, Augustine Osilamah Yusuf

Masters Theses & Specialist Projects

Reactive oxygen species such as hydrogen peroxide are present at the sites of inflammation in the body. Degradable polymeric nanoparticles have shown great promise in a range of biomedical applications which include preferential delivery of therapeutics to such inflamed sites. We are working towards a new class of materials expected to have tunable degradation rates in the presence of hydrogen peroxide. These new materials consist of three parts: degradable linkages, antioxidant groups, and unreactive filler monomers such as methylmethacrylate. We have synthesized a polymerization initiator with a degradable linkage, and we have shown that using this initiator to synthesize another …

Investigation Of Factors Influencing Recombination Versus Disproportionation Of Complex Radicals Formed By C-N Homolysis Of Breslow Type Intermediates And Related Compounds, Taylor Burnett

Graduate Theses and Dissertations

Electron rich enamines are capable of C-N bond homolysis and subsequent recombination and/or disproportionation. It is unclear what causes these radicals to undergo recombination or disproportionation. Density Functional Theory (DFT) calculations do not provide a transition state for the recombination and disproportionation processes and therefore they cannot be used to predict the favorable reaction. Breslow intermediates formed by deprotonation of thiazolium salts and reaction with aromatic aldehydes are examples of electron rich enamines. These breslow intermediates can undergo C-N bond homolysis to form a radical pair the either recombine or disproportionate. Upon investigation of the factors influencing recombination and disproportionation, …

An Experimental Study Of Evaporites On Titan: Implications For Lake Composition And Future Missions, Ellen Czaplinski

Graduate Theses and Dissertations

Titan is the only other planetary body in the solar system with liquid on the surface. With a surface temperature and pressure of 89 – 94 K and 1.5 bar (N2), respectively, Titan’s lakes are comprised of liquid hydrocarbons, predominantly methane and ethane. Over time, Titan’s lakes may evaporate, leaving behind residual deposits (evaporites). The evaporation processes and composition of the evaporites is poorly understood. I address these outstanding questions by experimentally investigating the physical and spectral properties of evaporites at Titan surface conditions using an experimental chamber.

Chapter 1 addresses the formation of ethylene evaporites. Ethylene evaporites form more …

Microfabrication And Electrochemical Characterization Of A Novel Su-8 Probe With An Array Of Individually Addressable Electrodes Suitable For Redox Cycling Experiments In Ultra-Small Volumes, Mahsa Lotfi Marchoubeh

Graduate Theses and Dissertations

Redox cycling is an electrochemical technique that utilizes closely spaced generator and collector electrodes to cycle reversible redox species between their oxidative states. With advantages in signal amplification, selectivity of species based on their electrochemical reaction mechanism, and limited or no background subtraction, this technique is well suited for selective detection of important electrochemically active molecules such as dopamine at basal or slowly changing levels.

Miniaturized medical devices have become an area of great interest for measurement of chemicals in limited volumes with low concentrations or in sensitive tissues. A probe on a polymeric SU-8 substrate with suitable dimensions and …

The Development Of Novel Carbohydrate-Based Gelators And Their Applications As Advanced Soft Materials, Joedian Morris

Chemistry & Biochemistry Theses & Dissertations

Low molecular weight gelators (LMWGs) are attractive molecules that have been explored extensively due to their practical applications in many disciplines. These small molecules self-assemble forming solid-like gels via three-dimensional cross-linked networks with the solvent as the key component within the matrix. Carbohydrate-based LMWGs are small molecules that can form solid-like gels in water, organic solvents, and aqueous solutions. They have great potential to be utilized in different applications because carbohydrates are biocompatible and can be made from easily accessible and renewable resources. Designing gelators is still a challenge within the field, even though researchers have developed tools to predict …

Assessing Competitive Reaction Rates In The Nitration Of 2-Methylbiphenyl, Biphenyl, And Toluene To Determine Steric Restriction In Resonance-Stabilized Planarization Of The Carbocation Intermediates, Victor A. Hanson, Tristan Wine, Kevin Bartlett, Joshua Padilla, Alessandro Rizzi

Honors Projects

Electrophilic aromatic substitution (EAS) reactions have long been a fundamental addition to sophomore-level organic chemistry classes, allowing students the opportunity to explore the electron donating and withdrawing effects of electrons contained in the substituents of the aromatic reactant. In this paper we present preliminary findings on the nitration of methylated biphenyls using kinetic and regioselective assessments to analyze steric influences on the planarization of 2-methylbiphenyl after EAS nitration. Our preliminary findings show that nitration favors the methylated phenyl ring of 2-methylbiphenyl, indicating that the steric influence of the methyl group restricts planarization of the carbocation intermediate. Furthermore, a competition nitration …