Organic Chemistry Commons^™

Methodology Studies For Dearomatized Dimer And Beta-Lactone-Mediated Native Chemical Ligation In Organic Synthesis, Xinhao Fan

Legacy Theses & Dissertations (2009 - 2024)

Chapter 1: Dimers of naphthalenol derivatives were synthesized by photocatalysis, cobalt(II) acetylacetonate. Several functional groups were tolerant of its skeleton. This novel dimer was connected through a reversible sigma bond. Its reversibility was confirmed by chiral HPLC and 1H-NMR experiments. Through EPR and Stern-Volmer quenching experiments, we proposed the reaction mechanism. The reversibility property can be potentially beneficial in polymers, self-healing, and memory materials.Chapter 2: We report an epimerization-free native chemical ligation reaction by β-lactone-mediated peptides. This approach can achieve Thr-Xaa efficiently and rapidly. Besides, it has a broad side-chain tolerance. Through the competition reaction experiment, it was demonstrated that …

A Local Mode Study Of Ring Puckering Effects In The Infrared Spectra Of Cyclopentane, Edwin L. Sibert Iii, Peter F. Bernath

Chemistry & Biochemistry Faculty Publications

We report and interpret recently recorded high-resolution infrared spectra for the fundamentals of the CH₂ scissors and CH stretches of gas phase cyclopentane at −26.1 and −50 ^○C, respectively. We extend previous theoretical studies of this molecule, which is known to undergo barrierless pseudorotation due to ring puckering, by constructing local mode Hamiltonians of the stretching and scissor vibrations for which the frequencies, couplings, and linear dipoles are calculated as functions of the pseudorotation angle using B3LYP/6-311++(d,p) and MP2/cc-pVTZ levels of theory. Symmetrization (D_5h) of the vibrational basis sets leads to simple vibration/pseudorotation Hamiltonians whose solutions …

The Acute Physiological Response Of Polar Bears To Helicopter Capture, John P. Whiteman, Henry J. Harlow, George M. Durner, Eric V. Regehr, Steven C. Amstrup, Anthony M. Pagano, Merav Ben-David

Biological Sciences Faculty Publications

Many wildlife species are live captured, sampled, and released; for polar bears (Ursus maritimus) capture often requires chemical immobilization via helicopter darting. Polar bears reduce their activity for approximately 4 days after capture, likely reflecting stress recovery. To better understand this stress, we quantified polar bear activity (via collar‐mounted accelerometers) and body temperature (via loggers in the body core [T_abd] and periphery [T_per]) during 2–6 months of natural behavior, and during helicopter recapture and immobilization. Recapture induced bouts of peak activity higher than those that occurred during natural behavior for 2 of 5 bears, …

On The Stratospheric Chemistry Of Midlatitude Wildfire Smoke, Susan Soloman, Kimberlee Dube, Kane Stone, Pengfei Yu, Doug Kinnison, Owen B. Toon, Susan E. Strahan, Karen H. Rosenlof, Robert Portmann, Sean Davis, William Randel, Peter Bernath, Chris Boone, Charles G. Bardeen, Adam Bourassa, Daniel Zawada, Doug Degenstein

Chemistry & Biochemistry Faculty Publications

Massive Australian wildfires lofted smoke directly into the stratosphere in the austral summer of 2019/20. The smoke led to increases in optical extinction throughout the midlatitudes of the southern hemisphere that rivalled substantial volcanic perturbations. Previous studies have assumed that the smoke became coated with sulfuric acid and water and would deplete the ozone layer through heterogeneous chemistry on those surfaces, as is routinely observed following volcanic enhancements of the stratospheric sulfate layer. Here, observations of extinction and reactive nitrogen species from multiple independent satellites that sampled the smoke region are compared to one another and to model calculations. The …

Ozonized Biochar Filtrate Effects On The Growth Of Pseudomonas Putida And Cyanobacteria Synechococcus Elongatus Pcc 7942, Oumar Sacko, Nancy L. Engle, Timothy J. Tschaplinski, Sandeep Kumar, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

Background

Biochar ozonization was previously shown to dramatically increase its cation exchange capacity, thus improving its nutrient retention capacity. The potential soil application of ozonized biochar warrants the need for a toxicity study that investigates its effects on microorganisms.

Results

In the study presented here, we found that the filtrates collected from ozonized pine 400 biochar and ozonized rogue biochar did not have any inhibitory effects on the soil environmental bacteria Pseudomonas putida, even at high dissolved organic carbon (DOC) concentrations of 300 ppm. However, the growth of Synechococcus elongatus PCC 7942 was inhibited by the ozonized biochar filtrates at …

Development Of Accurate And Efficient Computational Methodologies For Predicting Protein-Ligand And Protein-Protein Binding Free Energies, Alexander Hamilton Williams

Theses and Dissertations--Pharmacy

Computational modeling is an invaluable tool in the drug discovery process either for small ligand or protein therapeutics. The widespread availability of protein X-Ray Crystal and Cryo-Electron Microscopy (Cryo-EM) structures has allowed for more accurate molecular dynamics (MD) simulations that are not reliant on methods such as homology modeling, which may produce structures that require significant computational time to demonstrate their stability. In this thesis we describe several novel methodologies for the computationally efficient modeling of protein/ligand and protein/protein complexes that may be employed within both large-scale virtual screenings and lead compound optimization. These methodologies may also be utilized in …

Non-Chromatographic Oligonucleotide Purification And Automated Polyethyleneglycol Synthesis, Dhananjani N. A. M. Eriyagama

Dissertations, Master's Theses and Master's Reports

Synthetic oligodeoxynucleotides (ODN) have various applications in many areas such as, synthetic biology, chemical biology, antisense drug development, and data storage. As a result, there is a high demand for synthetic ODNs. Many advances have been made with ODN synthesis the purification still remains a bottleneck. The non-chromatographic purification method is developed to address this problem. Similarly, polyethylene glycols (PEGs) have been used in many areas including pharmaceutical applications, surface science, and nanomedicine due to its unique properties. However, monodispersed PEG synthesis is expensive with existing methods. A novel automated solid phase synthesis method is developed to obtain monodispersed PEGs. …

Chromatography-Mass Spectroscopy Analysis Of Native American Pottery For Maple Syrup Residues, Alexis Wirtz

Honors Program Theses

The research conducted regards whether or not Native Americans understood how to create maple syrup before the influence of Europeans. The analytical technique that was used is gas chromatography-mass spectrometry (GC-MS). This technique assisted in understanding what organic residues resided within the pottery and what those organic residues tell us about Native American history. An analysis of organic residues was performed on the following types of pottery: proof of concept pottery, weathered pottery (an analog of the proof of concept), and Native American pottery. The residues used in analysis were obtained through the usage of different solvent systems - Acetone: …

Establishing The Relative Composition Of Functionalized Thiols In Mixed Ligand Gold Nanoparticles By 1h-Nmr Spectroscopy, Matthias Carroll

All Master's Theses

Functionalized gold nanoparticles (AuNPs) are of interest for their optical and electrical properties, specifically the surface plasmon resonance phenomenon and potential applications for medicine and nano-circuitry. In this study, the ligand composition of small (~5 nm diameter) thiol functionalized AuNPs with mixed ligand monolayers was investigated to better understand how the molar feed ratio of ligands used during their synthesis influences the composition of ligands on the particle’s surface. The system under study was a combination of two ω-functionalized thiols, mercapto ethoxy ethoxy ethanol (MEEE) and mercapto pentyl trimethyl ammonium chloride (MPTMA). UV/Visible spectrophotometry, dynamic light scattering, and electron …

Tandem Addition/Fragmentation Reactions Of Vinylogous Acyl Sulfonates, Kristen S. Nerbecki

Graduate Theses, Dissertations, and Problem Reports (ETD)

Fragmentation methodology has been used in organic synthesis to produce complex organic compounds. This work is focused on fragmentation reactions leading to the subsequent construction of neopentylene-fused carbocycles, which are found in several important natural products and are difficult to prepare. These are produced by utilizing an optimized fragmentation methodology from the Dudley group. The methodologies build starting materials called nonaflates and triflates with a gem-dimethyl substituent that is seen in many natural products. Nonaflates and triflates are similar in structure, but nonaflates pose benefits that are an advantage over triflates, like cost effective synthesis and more stable compounds. A …

Synthesis And Cyclotrimerization Of Sulfonyl Enynes, Alexa C. Martin

Graduate Theses, Dissertations, and Problem Reports (ETD)

The synthesis of complex, polysubstituted aromatic rings from simple, non-aromatic building blocks is a consistent challenge to the synthetic community. Neopentylene ring fusions are found in several natural products but are largely absent from synthetic compound libraries. This discrepancy reflects the limitations in modern chemical synthesis. Utilizing, in part, a thoroughly developed fragmentation/olefination methodology from the Dudley Lab, a library of novel 1-sulfonyl-1,6-enynes have been developed. In this methodology, they are prepared in three steps from dimedone (5,5-dimethyl-1,3-cyclohexanedione), an inexpensive starting material. A total of 14 novel 1-sulfonyl-1,6-enynes were synthesized. These substrates were subjected to a novel benzannulation reaction based …

Utilization Of The Yamamoto Cyclotrimerization Reaction Towards The Synthesis Of Polycyclic Aromatic Compounds, Josh Ledrew

Theses and Dissertations (Comprehensive)

The overall theme of this research was to synthesize and study the structure-property relationships of novel polycyclic aromatic compounds capable of self-assembling to form liquid crystalline, and microporous structures, as well as molecules capable of molecular recognition. The unifying theme that connects this research is the utilization of the Yamamoto coupling reaction to access the desired polycyclic aromatic hydrocarbon targets. More specifically, the scope of the Yamamoto coupling reaction was explored for the synthesis of electron-deficient triphenylene derivatives that are otherwise difficult to prepare. The molecules prepared via the Yamamoto coupling reaction are expected to be further utilized as intermediates …

Poly(Β-Gal-Thr): A New Scalable Synthetic Mucin, Manuel A. Lema

Dissertations and Theses

A method for the preparation of glycosylated polypeptides via the nucleophilic ring-opening polymerization of a glycosylated N-carboxyanhydride (NCA) monomer is reported. The synthesis of 2,3,4,6-tetraacetyl-β-galactose-threonine N-carboxyanhydride (β-AcO-Gal-Thr-NCA) monomer in 5 steps with an 8 % overall yield is described, and the single-crystal X-ray structure is provided. The effect of a series of Ni⁰-based organometallic initiators, nucleophilic amine initiators, co-catalysts, and solvents on the polymerization were explored. The kinetics of the three most promising conditions were studied in greater detail. The conditions that provided the highest yield, low polydispersity (Ð), and …

Photocatalytic Degradation Of Lignin By Supported Silver Nanoparticles, Ning Wei

Theses and Dissertations--Chemical and Materials Engineering

Lignin is the second most abundant form of biomass on earth. The phenolic structure and high carbon to oxygen ratio make lignin an attractive renewable source of fuel and chemicals. However, its recalcitrance and heterogeneous nature prove difficult for decomposing lignin’s polymer structure and separation of the products. This work has focused on the use of low-energy catalytic approaches to overcome these barriers. A mimic of the lignin degrading enzyme laccase, consisting of a copper cluster Cu4Py4I4 modified with AgNO3, was developed to function similarly to the laccase active site. The prepared copper complex solution was found to be active …

Synthesis Of 6,6- And 7,7-Difluoro-1-Acetamidopyrrolizidines And Their Oxidation Catalyzed By The Nonheme Fe Oxygenase Lolo, Nabin Panth

Theses and Dissertations--Chemistry

One of the remarkable steps in loline alkaloid biosynthesis is the installation of an ether bridge between two unactivated C atoms in 1-exo-acetamidopyrrolizidine (AcAP). LolO, a 2-oxoglutarate-dependent nonheme Fe oxygenase, catalyzes both the hydroxylation of AcAP and the resulting alcohol's cycloetherification to give N-acetylnornoline (NANL). The mechanism of hydroxylation is well understood, but the mechanism of the oxacyclization is not. I synthesized difluorinated analogs of AcAP in an attempt to further understand the mechanism of the unusual cycloetherification step.

I prepared 6,6-F₂-AcAP in eight steps from N,O-protected 4-oxoproline. The key step was a Dieckmann …

Crystal Engineering Of Asymmetric And Pyrene Fused Annulenes For Use In Organic Electronic Materials, Garrett Fregoso

Theses and Dissertations--Chemistry

Since the development of TiPS Pentacene, the use of trialkylsilylethynyl groups has become a commonly utilized moiety for stabilizing, solubilizing, and directing crystal packing of acenes and acene-like compounds, leading to the development of a well-defined series of trends that aid in the prediction of crystal packing for the development of organic semiconducting materials. While these trends have been extensively studied in mainly symmetric linear systems, it is important to determine how, if at all, asymmetry of the aromatic core affects these well-defined trends. This constitutes the basis of Chapter 2, which explores the crystal engineering and physical properties of …

Application Of Mass Spectrometry For Characterization Of Plant-Based Phenolics And Alkaloids, Masoumeh Dorrani

Theses and Dissertations--Chemistry

Plant-derived compounds have the potential to produce value-added compounds with a variety of applications. For example, the lignin part of the lignocellulosic biomass, produced in large quantities as waste from the paper and pulp industries, is a rich source of phenolics with potential applications in the renewable energy sector, pharmaceutical, and chemical industries. On the other hand, plant alkaloids are the primary source for developing plant-derived therapeutics. Unfortunately, the recalcitrant nature of plant cell walls, low extraction yields of small secondary metabolites, and the lack of effective analytical methods for a rapid and accurate identification of plant-based compounds and plant’s …

1,2-Diamination Of Alkenes Via Reduction Of 1,2,3-Triazolinium Ions, Setareh Saryazdi

Theses and Dissertations--Chemistry

1,2-Diamine substructures are prevalent functional motifs in natural products, pharmaceutical compounds, and ligands. The interesting functionalities of 1,2-diamines have inspired many synthetic chemists to design various methodologies for preparing these structures from simple precursors such as alkenes. In this work, we described two different but related methods using simple and easily accessible reagents for 1,2-diamination of alkenes. In the first method, an alkene undergoes 1,3-dipolar cycloaddition with an organic azide to form a 1,2,3-triazoline. Subsequent N-alkylation of the generated 1,2,3-triazoline gives the 1,2,3-triazolinium ion, which is then hydrogenated over Raney Ni with a balloon of H₂ to produce …

Asymmetric Cuh-Catalyzed Reductive Coupling Of Alleneamides With Carbonyl Electrophiles And The Mechanistic Investigation Into The Suzuki-Miyaura Cross-Couplings Of Electron-Deficient Systems, Samantha L. Gargaro

Theses and Dissertations

Most natural products and other biologically active small molecules contain multiple stereogenic heteroatoms throughout their carbon scaffold. As a result, methods to install these multi-heteroatom functionalities efficiently are highly desirable. Reductive coupling reactions have been studied extensively, and reductive allylation has been a key method for generating chiral secondary and tertiary allylic alcohols. This work focuses on utilizing naturally abundant and inexpensive Cu for the asymmetric reductive coupling of alleneamides with carbonyl electrophiles to access highly functionalized multi-heteroatom scaffolds that are difficult to produce via traditional methods. Described herein are methods for these asymmetric reductive coupling reactions. Chapter 1 describes …

The Synthesis And Biocatalytic Reduction Of Beta-Keto Alkynes, Rhema M. Francis

College of Graduate Studies: Theses & Dissertations

The preparation of enantiopure homopropargyl alcohols (but-3-yn-ols) is of high importance to the scientific community. They are employed as valuable pharmaceutical intermediates and are opportune to generate antiviral nucleoside analogues. Chiral inducement of these molecules thus far has been poor (low ee) and has constituted a key challenge for asymmetric synthesis in the last few decades. Enzyme-catalyzed enantioselective reductions of ketones have become popular to produce thus-prepared synthons on an industrial scale. Among them, biocatalysts (dehydrogenases, reductases) emerge as a biodegradable option for chemical transformations, in comparison to chiral catalysts that employ highly toxic metals. This research investigates the catalytic …