Organic Chemistry Commons^™

The Role Of Catalytic Residue PKA On The Hydrolysis/Transglycosylation Partition In Family 3 Β-Glucosidases, Inacrist Geronimo, Christina M. Payne, Mats Sandgren

Chemical and Materials Engineering Faculty Publications

β-Glucosidases (βgls) primarily catalyze the hydrolysis of the terminal glycosidic bond at the non-reducing end of β-glucosides, although glycosidic bond synthesis (called transglycosylation) can also occur in the presence of another acceptor. In the final reaction step, the glucose product or another substrate competes with water for transfer to the glycosyl-enzyme intermediate. The factors governing the balance between the two pathways are not fully known; however, the involvement of ionizable residues in binding and catalysis suggests that their pK_a may play a role. Through constant pH molecular dynamics simulations of a glycoside hydrolase Family 3 (GH3) βgl, we …

Layer-By-Layer Assembled Membranes With Immobilized Porins, Sebastián Hernández, Cassandra Porter, Xinyi Zhang, Yinan Wei, Dibakar Bhattacharyya

Chemical and Materials Engineering Faculty Publications

New and advanced opportunities are arising for the synthesis and functionalization of membranes with selective separation, reactivity, and stimuli-responsive behavior. One such advancement is the integration of bio-based channels in membrane technologies. By a layer-by-layer (LbL) assembly of polyelectrolytes, outer membrane protein F trimers (OmpF) or “porins” from Escherichia coli with central pores ∼2 nm in diameter at their opening and ∼0.7 × 1.1 nm at their constricted region are immobilized within the pores of poly(vinylidene fluoride) microfiltration membranes, in contrast to traditional ruptured lipid bilayer or vesicle processes. These OmpF-membranes demonstrate selective rejection of non-charged organics over ionic solutes, …

Synthesis Of A Model Of The Bc Ring System Of Oxygenated Angucyclines, Xiaolan Wu, Abdullah Allaoa, Tony E. Nicolas

Publications and Research

Angucycline is a subclass of natural antibiotics, containing a characteristic tetracyclic ring structure, and featuring a wide range of biological functions, including antitumor, antiviral and antifungal properties. This extraordinarily therapeutic character has interested many chemists to develop efficient methodologies for synthesizing the tetracyclic ring system of angucycline. Construction of the BC ring configuration appears as a synthetic challenge. Successful installation of hydroxyl groups at the AB junction would pave the way for efficient syntheses. As a continuation of the previous work done on this system, our synthetic methodology focuses on the coupling of a suitably substituted Phthalide and an activated …

Developing Functionalized Peroxide Precursors For The Synthesis Of Cyclic And Spirocyclic Ethers, Anna J. Diepenbrock

Department of Chemistry: Dissertations, Theses, and Student Research

There is increasing interest in the development of methods for the synthesis of oxetanes and spirocyclic oxetanes, a class of molecules of interest to chemists as they synthesize libraries of possible drug target scaffolds with tunable physiochemical and biological properties.^1,2 Although most ethers are prepared through reaction of nucleophilic oxygen with electrophilic carbon, this work explores new reagents and routes for the synthesis of spirocyclic oxetanes based upon an application of "umpolung" or polarity reversal involving attack of nucleophilic carbon on the electrophilic oxygen of a peroxide (Scheme 1). In this work, a 2-carbon peroxide synthon for reverse etherification …

Development Of An Improved Synthesis Of S-D-Ribosyl-L-Homocysteine (Srh) And Progress Toward Srh Analogs Modified At The C3 Position, Emily Rouse

Master's Theses

Quorum sensing is a system that facilitates bacteria turning on and off gene expression depending on population density. System 2 quorum sensing is utilized by both Gram positive and Gram negative bacteria, and the quorum sensing molecule used in this system is AI-2. AI-2 is biosynthesized by the enzyme LuxS from the precursor SRH. This thesis describes an improved synthesis of SRH through the exploration of different protecting group strategies. The knowledge gained from the improved synthesis of SRH is then applied toward the synthesis of SRH analogues with increased steric bulk installed through use of a stereoselective anti-Mannich reaction. …

Tunable Copper Complexes For Sustainable Photocatalysis, David Kline

Posters-at-the-Capitol

Photoredox catalysis has direct applications in sustainable chemistry and thus an immense impact on our environment. With the ability to harness energy directly from the sun to catalyze useful chemical reactions, photocatalysts can help to eliminate the need for harsh reaction conditions and reduce generation of hazardous chemical waste. Photocatalysts based on Earth-abundant metals such as copper have recently emerged as sustainable alternatives to rare-earth metals including iridium and ruthenium, which are no longer required for many photocatalyzed chemical transformations.

No Evidence For Trace Metal Limitation On Anaerobic Carbon Mineralization In Three Peatland Soils, Jason K. Keller, Jillian Wade

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Peatlands store roughly one-third of the terrestrial soil carbon and release the potent greenhouse gas methane (CH₄) to the atmosphere, making these wetlands among the most important ecosystems in the global carbon cycle. Despite their importance, the controls of anaerobic decomposition of organic matter to carbon dioxide (CO₂) and CH₄ within peatlands are not well understood. It is known, however, that the enzymes responsible for CH₄ production require cobalt, iron and nickel, and there is a growing appreciation for the potential role of trace metal limitation in anaerobic decomposition. To explore the possibility of …

Design And Synthesis Of Cpg-Lytic Peptide Conjugate, Brachytherapy Beads And A Combinatorial Library Of Primary Amines Used As Potential Therapeutics In The Treatment Of Cancers, Josanne-Dee Woodroffe

USF Tampa Graduate Theses and Dissertations

Cancer remains one of the most feared diseases affecting the modern world. Second to heart disease, it is the largest cause of deaths, affecting one in three persons. Cancer cells are formed when normal, healthy cells become damage, losing their normal regulatory mechanism that control cell growth. There are many different types and progression of these cancer cells that determine the type of treatment a patient receives. The primary focus of this dissertation is to propose three studies of anticancer agents. In Chapter one, a CpG-lytic peptide conjugate was designed to target receptors on the cell membrane to concentrate the …

Development Of Remote Hydroxylation Via Redox Catalysis And Mild Activation Of Thioglycosides For O-Glycosylation, Kristina Deveaux

LSU Doctoral Dissertations

The focus of this dissertation is the development of a C-H functionalization method using redox catalysis and the synthesis of saccharides using thioglycosides. Chapter 1 is a review of C-H functionalization and visible-light photoredox catalysis. Over the years there have been many significant contributions to the field of C-H functionalization. Select examples have been discussed and a foundation for the method developed in chapter 2 has been outlined. Chapter 2 discusses the development and optimization of a C-H functionalization method. This approach uses the Tz^o directing group and Ir(ppy)₃ to activate a remote C-H bond via 1,6- and …

Formation Of Highly Functionalized Indole Through Carbon-Carbon Bond Cleavage, Ryan A. S. Pike

Chemistry and Chemical Biology ETDs

Indoles are one of the most abundant heterocycles found in nature and have a wide range of functions. There are a wide variety of indole synthesis methods known both in synthetic chemistry and through biosynthesis. Many of the known indole synthesis routes use a benzene derivative or cyclized ring structure derivative as a starting material. Here, we describe a novel synthetic method utilizing 1, 3-diketones and fumaronitrile with a catalytic amount of base to form a highly functionalized indole as our product. We have isolated and characterized 12 functionalized indoles.

Progress Toward Phidianidine Analogues Containing A 1,2,3-Triazole Ring, David Laws Iii, Dillon King, Bryan H. Wakefield

Journal of the South Carolina Academy of Science

Phidianidines are a class of compound that has been extracted from the sea mollusk Phidianis militaris. These compounds have been shown to exhibit a variety of useful properties such as antihistamine effects, anti-cancer activity, agonism of the µ-opioid receptor and neuroprotection. The biological activities are thought to be caused by the 1,2,4- oxadiazole ring found within the molecule. The goal of this project is to synthesize analogues of phidianidine that contain a 1,2,3-triazole instead of the 1,2,4 oxadiazole ring using a method that will allow for other regions of the molecule to be changed. This will help to elucidate …

Ensemble-Based Modeling And Rigidity Decomposition Of Allosteric Interaction Networks And Communication Pathways In Cyclin-Dependent Kinases: Differentiating Kinase Clients Of The Hsp90-Cdc37 Chaperone, Gabrielle Stetz, Amanda Tse, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The overarching goal of delineating molecular principles underlying differentiation of protein kinase clients and chaperone-based modulation of kinase activity is fundamental to understanding activity of many oncogenic kinases that require chaperoning of Hsp70 and Hsp90 systems to attain a functionally competent active form. Despite structural similarities and common activation mechanisms shared by cyclin-dependent kinase (CDK) proteins, members of this family can exhibit vastly different chaperone preferences. The molecular determinants underlying chaperone dependencies of protein kinases are not fully understood as structurally similar kinases may often elicit distinct regulatory responses to the chaperone. The regulatory divergences observed for members of CDK …

A Colorimetric Competitive Displacement Assay For The Evaluation Of Catalytic Peptides, Anneliese Gest, Erika M. Aguiluz, Malik T. Mays, Xinyu Liu, Eliza K. Neidhart, Leah S. Witus

Faculty Publications

No abstract provided.

New Synthetic Reactions Towards Global Chlorination And Enamides Functionalization, Mirza Ardella Saputra

LSU Doctoral Dissertations

This dissertation focuses on two main projects, global chlorination and enamide functionalization, which both encompass in cationic intermediates. Inspired by the desires to find a new chlorination method, global chlorination project is emphasized in chapter one and chapter two, in which chapter one details various known chlorine-containing natural products, including alkyl chlorides and vinyl chlorides. This chapter also describes the previously known protocols to synthesize alkyl chlorides in the attempts of chlorosulfolipids total syntheses, as well as several known reactions to synthesize vinyl chlorides that are both important functional groups in organic synthesis. Chapter two depicts our novel synthetic reaction …

Formation Of Carbon-Carbon And Carbon-Hetero Bonds Through Gold Catalysis, Boliang Dong

USF Tampa Graduate Theses and Dissertations

This dissertation mainly contains two parts: one is C-X (C, O, S) bond formation through gold(I) catalysis, one is new applications via gold(I/III) redox catalysis.

In first part, gold(I) catalysts would be introduced and their general applications, then the TA-Au species will be emphasized including the design, synthesis, characters and their application in catalysis. The applications are well developed during the past decade in our group, but here only involves three examples regarding C-C, C-O and C-S bond formations. From these effective applications, the unique stability and reactivity of TA-Au will be studied and explained, which is the reason and …

Synthesis, In Vitro Characterization And Applications Of Novel 8-Aminoquinoline Fluorescent Probes, Adonis Mcqueen

USF Tampa Graduate Theses and Dissertations

Malaria is a parasitic disease that is caused by the plasmodium parasite. Plasmodium infection has affected man for thousands of years. With advances in drug discovery over the past century, malaria has evolved to possess resistance to most mainline therapeutics. This war of drug discovery vs plasmodium evolution continues to be fought to this very day, with attempts to eradicate malaria worldwide. Frontline treatments such as chloroquine, artemisinin, and atovaquone/proguanil have all seen parasitic resistance in strains of P. vivax as well as P. falciparum. While plasmodium possesses resistance to most classes of anti-malarials, the 8-aminoquinoline (8-AQ) class has …

Synthesis, Characterization And Application Of Sugar-Based Low Molecular Weight Gelators, Ifeanyi Simeon Okafor

Chemistry & Biochemistry Theses & Dissertations

Low molecular weight gelators (LMWGs) are an interesting class of compound that have gained considerable attention especially because of their potential applications for soft biomaterials. Carbohydrate based low molecular weight hydrogelators and organogelators are able to selfassemble and form ordered supramolecular structures, which are useful for exploring biomedical applications. The resulting gelators are responsive to external stimuli because of the weak noncovalent intermolecular forces and interaction that influences self-assembly. Stimuli-responsive supramolecular organogels with interesting properties in response to external environmental stimuli have gained considerable attention due to their applications in biomaterials, sensors and for drug delivery.

One of the major …

Synthesis Of Small Molecule Heterocycles As Antimicrobial And Anticancer Agents, Zakeyah Ali Alsharif

Student Theses and Dissertations

This thesis contains three chapters. In chapter one, the synthesis of dihydropyrido-pyrimidones derivatives by using hexafluoroisopropanol (HFIP) as a solvent was reported and the synthesized compounds were tested against different bacteria but no activity was observed. In the second chapter, the syntheses of thiazoline and thiazole derivatives were reported. In this methodology, HFIP was used to promote for the reaction and sixty new molecules were synthesized. Two of these compounds showed promising activity as a potent anti-cancer agent against several cell lines. In the third chapter, pyrazole derivatives were synthesized and tested against different types of bacteria. Among these compounds, …

Fatty Acid Concentration And Phase Transitions Modulate Aβ Aggregation Pathways, Pratip Rana, Dexter Dean, Edward Steen, Ashwin Vaidya, Vijayaraghavan Rangachari, Preetam Ghosh

Faculty Publications

Aggregation of amyloid β (Aβ) peptides is a significant event that underpins Alzheimer disease (AD) pathology. Aβ aggregates, especially the low-molecular weight oligomers, are the primary toxic agents in AD and hence, there is increasing interest in understanding their formation and behavior. Aggregation is a nucleation-dependent process in which the pre-nucleation events are dominated by Aβ homotypic interactions. Dynamic flux and stochasticity during pre-nucleation renders the reactions susceptible to perturbations by other molecules. In this context, we investigate the heterotypic interactions between Aβ and fatty acids (FAs) by two independent tool-sets such as …

How To Be A Successful Organic Chemist, Alexander H. Sandtorv

PDXOpen: Open Educational Resources

How to be a successful organic chemist is meant as an introductory text for undergraduates taking organic chemistry teaching labs. The text is a clear and practical introduction to safety, chemical handling, organic chemistry techniques, and lab reports.

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Synthesis And Evaluation Of Tetrahydroprotoberberines As Dopamine Receptor Ligands, Satishkumar V. Gadhiya

Dissertations, Theses, and Capstone Projects

Dopamine (DA) receptors belong to the G-protein coupled receptors (GPCRs) family, divided in to two groups based on their high homology transmembrane domains; D1-like DA receptors (D1, D5) and D2-like DA receptors (D2-D4). DA receptor specific ligands have been exploited as a means for studying the prognosis and curing several CNS disorders. Though several efforts have been devoted to discover selective and potent DA receptor ligands, complete selectivity within the DA receptor subtypes remains a challenge.

Tetrahydroprotoberberines (THPBs) are a group of naturally occurring tetracyclic alkaloids that belong to the tetrahydroisoquinoline family. A wide range of biological activities are associated …

Stereospecific Electrophilic Fluorination Of Alkylcarbastannatrane Reagents, Xinghua Ma

Dissertations, Theses, and Capstone Projects

The introduction of fluorine atoms into organic molecules significantly changes their physical, chemical, and biological properties. Fluorinated organic compounds are used as pharmaceuticals, agrochemicals, materials, and tracers for positron emission tomography (PET). For example, the site-specific fluorination of drugs can block sites of phase I metabolism by cytochrome P450 enzymes as well as improve target-binding affinities. In view of the unique features of fluorine-containing compounds, there has been increasing interest in the development of novel methods for the synthesis of fluorinated molecules, especially the site-specific monofluorination of complex molecules. Herein, we present the enantiospecific conversion of chiral secondary alkylcarbastannatranes into …

Identification Of Hydrated And Dehydrated Lipids And Protein Secondary Structures In Seeds Of Cotton (Gossypium Hirsutum) Line, Diwas Kumar Silwal, Nsoki Phambu, Bharat Pokharel, Ahmad Naseer Aziz

Chemistry Faculty Research

Cottonseeds from two parents (TM-1 and 3-79) and their 17 progeny (chromosomal substitution) lines were analyzed for various secondary structures of proteins and moisture content of lipids, separately in hulls and kernels. Fourier transform infrared spectroscopy (FTIR) was used on mature seeds from Upland cotton (G. hirsutum) progeny lines and parents. Based on secondary structures of proteins and hydration levels of lipids, differences were observed among the cottonseeds. The two progeny lines – CS-B12sh and CS-B22sh retained lipid moisture content and protein secondary structures similar to both parents, while CS-B06, CS-B15sh and CS-B16 remained distinct from either parent. On the …

The Discovery And Development Of Metal-Free Arylation Reactions With Unsymmetrical Diaryliodonium Salts, Sunil Kumar Sundalam

Dissertations and Theses

Functionalizing arenes and heteroarenes has been an active area of research since the 19th century, due to the presence of these molecular structures in many industrially important sectors. A tremendous amount of research has been published in achieving these chemical transformations using stoichiometric reagents and transition metal-catalyzed reactions. However, challenges still remain. An alternative and comparable methodology to metal-catalyzed reactions to overcome the drawbacks will advance this particular area of research is desirable.

Hypervalent iodine compounds offer a promising approach to metal-free arylation reactions. These mild, air and moisture stable compounds have showed significant success as non-toxic and metal-free reagents …

Synthesis Of Healable Organic Semiconductor Through Dioxaborolane Bond, Junchen Liu, William W. Mcnutt, Jianguo Mei

The Summer Undergraduate Research Fellowship (SURF) Symposium

The field of organic semiconductors have gained enormous attention the past few decades. Organic materials offer numerous advantages over their inorganic counterparts. Recently a number of works have demonstrated organic semiconductors with healable properties. We aim to investigate the healable ability of an organic semiconductor by mimicking a vitrimer system through the reversible dioxaborolane bond. Vitrimers are polymers with reversible crosslink system. It has been reported that the use of the borane-oxygen bond as the crosslink showed good mechanical performance. The electrical properties will be inspected for the vitrimer-like polymer. In this report we describe a Diketopyrrolopyrrole base polymer incorporating …

Enantioselective Γ- And Δ -Borylation Of Unsaturated Carbonyl Derivatives: Synthesis, Mechanistic Insights, And Applications, Gia L. Hoang

Department of Chemistry: Dissertations, Theses, and Student Research

Chiral boronic esters are valuable synthetic intermediates widely used in a variety of stereospecific transformations. Transition metal-catalyzed asymmetric hydroboration (CAHB) of alkenes is among the most popular methods for their preparation. Enantioselective hydroboration of activated alkenes (i.e., vinyl arene derivatives or conjugated carbonyl compounds) have been extensively studied by many research groups. We, on the other hand, are interested in enantioselective hydroboration of unactivated alkenes utilizing coordinating functional groups (e.g., carbonyl derivatives) to give functionalized, chiral boronic esters. While conjugate addition and C–H activation methodologies provide efficient alternatives to CAHB for enantioselective beta-borylation of carbonyl compounds, direct gamma- and delta-borylations …

Synthesis And Catalytic Evaluation Of Novel C-Alpha-Methyl-Beta-Proline Analogues, And Concise Synthetic Approach To Nh-Fmoc-S-Trityl-C-Alpha-Methyl Cysteine, Hari Kiran Kotapati

Dissertations

In the field of chemistry there is a growing demand for small molecule organocatalysts such as amino acids, more specifically proline and its analogues, which could catalyze various key chemical reactions in the synthesis of several biologically important molecules. Even though natural proline is reported to catalyze various chemical reactions, its use as organocatalyst is limited mainly due to the solubility issues in the reaction media and high catalyst loadings, which is not very ideal for bulk scale manufacturing. To address these limitations we planned to develop unnatural analogues of proline that could catalyze the reactions with lower catalyst loadings …

A Novel Method For Synthesis Of Hydroxytyrosol, Emmanuel Onobun

Electronic Theses and Dissertations

Hydroxytyrosol, 3,4-dihydroxyphenolethanol, a naturally occurring polyphenol most common in olive tree (Olea europaea), is one of the most effective member of the polyphenols family, because of its remarkable antioxidant activity, its ability to inhibit oxidation of low density lipids (LDL), and its protection against DNA oxidative damage. Hydroxytyrosol, which is widely used in cosmetics and food supplements industries, can be purchased as an olive oil extract that contains low concentration of hydroxytyrosol besides other polyphenols. The price and low natural abundance of hydroxytyrosol make alternative synthetic sources very attractive. In this research, a novel method for the synthesis of pure …

Ab Initio Methyl Linoleate Bond Dissociation Energies: First Principles Fishing For Wise Crack Products, Zachary Ryan Wilson

Graduate Theses/Dissertations

With the prices of petroleum reflecting demand for this finite resource, attention has been turned to alternative sources of energy. Biodiesel, defined as fatty acid methyl esters (FAMEs), exhibits many of the same properties as conventional diesel but is derived from biological sources. FAMEs are subsequently thermally cracked to form more light-weight petrochemical products. I aim to further understand the thermal cracking procedure, at an atomic-level, in hopes that this may aid in future engineering of viable fuels. I studied the effective computational modeling of bond disassociations in the FAME methyl linoleate. Bond dissociation in a 44-reaction database with known …

Electronic Structure Evaluation Of Competing Pathways In The Gold(Iii)-Catalyzed Ohloff-Rautenstrauch Cyclosimerization Converting Propargylic Acetates To Carene-Like Natural Products, Jeremy M. Hines

Graduate Theses/Dissertations

Propargylic acetates can lead to complex transformations upon exposure to a gold catalyst. Gold catalyzed transformations also allow for simple synthesis of a number of natural products. Gold (III)-cycloisomerization of a 5-acetoxy-1,6-enyne is reported to proceed through two pathways that differ in the order of major events: cyclization followed by ester migration (“cyclization first”) or the reverse (“migration first”). Both pathways could theoretically proceed in either order. This rearrangement is called the Ohloff-Rautenstrauch rearrangement and has high regio- and stereocontrol affording a bicylo[4.1.0]heptane carbon substructure. This rearrangement allows for the synthesis of the carene class of natural products. Computational modeling …