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Full-Text Articles in Organic Chemistry

Beyond Hydrophobicity: Aqueous Interfaces, Interactions And Reactions, Russell James Perkins Feb 2018

Beyond Hydrophobicity: Aqueous Interfaces, Interactions And Reactions, Russell James Perkins

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Many important chemical reactions from all branches of chemistry occur with water as a solvent. Furthermore, in environmental chemistry, biochemistry, and synthetic chemistry, key reactions occur in heterogeneous aqueous systems, where interfacial effects are particularly important. Despite the importance of aqueous environments and the tremendous amount of work done to study them, there are aspects that require further explanation and remain controversial. I have performed experimental studies to help elucidate the fundamental characteristics of aqueous systems, while examining specific phenomena across several fields.

The genetic disorder phenylketonuria (PKU) can result in increased levels of the aromatic amino acid phenylalanine in ...


Design And Synthesis Of Potential Tlr7 And Tlr8 Inhibitors, Patrick Nordeen Jan 2018

Design And Synthesis Of Potential Tlr7 And Tlr8 Inhibitors, Patrick Nordeen

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Toll-like receptors (TLRs) detect invading viral and bacterial pathogens and play a critical role in the initiation and regulation of the innate immune system. Over-active TLR signaling has been indicated in the disease pathology of numerous crippling inflammatory autoimmune disorders and inhibition of these receptors is of considerable interest for therapeutic intervention. TLR7 and TLR8 are the two TLRs that share the most similarity in both sequence and structure. Despite their similarity, selective inhibition represents a promising therapy for diseases such as systemic lupus erythematosus (lupus) and rheumatoid arthritis (RA). The goal of this master’s thesis is to identify ...


Development Of A Modular Synthesis Of Rigid Polyacene Dimers For Mechanistic Exploration Of Singlet Fission, Thomas James Carey Jan 2018

Development Of A Modular Synthesis Of Rigid Polyacene Dimers For Mechanistic Exploration Of Singlet Fission, Thomas James Carey

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Singlet Fission (SF) is a non-radiative, spin-allowed, photophysical process wherein a singlet excited state converts into a pair of spin-coupled triplet states. This process has implications for improving solar cell efficiency, as SF offers a way to process high energy photons by proportionating their energy into pairs of electronic excitations rather than wasting excess energy as heat. Of particular interest has been the study of molecular dimers, as these are the simplest systems capable of SF and offer a platform for understanding mechanistic details for the development of efficient SF systems.

This dissertation describes the development of a modular synthesis ...


Synthesis And Biochemical Evaluation Of Aminoboranephosphonate Phosphoramidimidate And Phosphoramidate Dna, Ayman Ghalib Alawneh Jan 2018

Synthesis And Biochemical Evaluation Of Aminoboranephosphonate Phosphoramidimidate And Phosphoramidate Dna, Ayman Ghalib Alawneh

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Antisense oligonucleotides are synthetic DNAs that bind to RNA and alter or reduce the biological activity of the target RNA. Studies performed in recent years have demonstrated that an antisense strategy can be utilized to address various issues in fundamental biomedical research and have additionally shown that this approach can be used to create novel therapeutic drugs. For example, IONIS Pharmaceuticals has so far commercialized three drugs using antisense oligonucleotides. These drugs target spinal muscular atrophy, homozygous familial hypercholesterolemia, and pouchitis. Antisense oligonucleotides targeting several other diseases are in various stages of clinical study at IONIS and elsewhere.

My research ...


Synthesis Of The Key Fragments Of Micrococcin P1 And Thiocillin I, Aaron Bret Hinds Jan 2018

Synthesis Of The Key Fragments Of Micrococcin P1 And Thiocillin I, Aaron Bret Hinds

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Thiopeptide antibiotics are members of the ribosomally synthesized and post-translationally modified peptide class of natural products. They contain a unique trisubstituted six-membered nitrogen ring decorated with azol(in)e heterocycles, dehydroamino acids, and a macrocyclic structure. Thiopeptides act by inhibiting the bacterial ribosome and have demonstrated potent activities against a wide range of Gram-positive pathogens.

This work describes the synthesis of the two key fragments used in our total syntheses of micrococcin P1 and thiocillin I. The “bottom” fragments were assembled through modification and coupling of amino acids as well as the use of a molybdenum catalyzed cyclodehydration of cysteine ...


Design And Synthesis Of Immune Signaling Modulators, Adam Joseph Csakai Jan 2017

Design And Synthesis Of Immune Signaling Modulators, Adam Joseph Csakai

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

The immune system is comprised of tissue, cells, and chemicals that have been evolutionarily developed to protect ourselves from simple pathogenic components such as viruses and allergens, and more complex invading organisms such as bacteria, fungi, and parasites. This network of tissue, cells, and chemicals can even identify and remove compromised host cells, such as cancer cells. The components of the immune system can be organized into two categories: the innate immune system and adaptive immune system. Components of the innate immune system can be further organized into two categories: physical barriers and leukocytes. Physical barriers, such as skin, hair ...


Development And Evaluation Of Novel Triazospirocycles As Histone Demethylase Inhibitors, Shane M. Walls Jan 2017

Development And Evaluation Of Novel Triazospirocycles As Histone Demethylase Inhibitors, Shane M. Walls

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Gene expression is guided by epigenetic regulation, which can turn genes on and off, allowing for varied cellular phenotypes. This is accomplished by adding or subtracting functional groups on the tails of proteins around which DNA coils. These changes are made by enzymes such as histone methyltransferases (HMTs) that add methyl groups to specific lysine residues found on histone tails or histone demethylases (HDMs) that remove them. The process of histone modification is necessary for cellular growth and differentiation, but irregular activity is associated with mental disabilities and diseases such as cancer. These ideas will be briefly discussed in a ...


The Design, Synthesis, And Testing For Inhibition Of Polymyxins Resistance Protein, Arna, And The Conversion Of Esters To Acid Chlorides Using Thionyl Chloride, Jacob Arthur Greenberg Jan 2017

The Design, Synthesis, And Testing For Inhibition Of Polymyxins Resistance Protein, Arna, And The Conversion Of Esters To Acid Chlorides Using Thionyl Chloride, Jacob Arthur Greenberg

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

One of the most commonly found drug resistant Gram-negative bacteria is Pseudomonas aeruginosa, and more than 80% of CF patients die of progressive lung disease caused by P. aeruginosa. It has been found that 44% of isolates express a resistance mechanism for the innate immune system’s Cationic Antimicrobial Peptides (CAMPs) from as early as 3 months old. This resistance is accomplished through the addition of positively charged moiety 4-aminoarabinose to the lipid-A portion of lipopolysaccharide, which is ordinarily negatively charged. The addition of this moiety decreases the overall negative charge associated with the cell, therefore the effectiveness of CAMPs ...


Starting Materials For The Synthesis Of Biradicaloid Heterocycles As Small Chromophores For Singlet Fission, Sachin Nedungadi Jan 2016

Starting Materials For The Synthesis Of Biradicaloid Heterocycles As Small Chromophores For Singlet Fission, Sachin Nedungadi

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

The present work is directed toward the synthesis of small chromophores capable of exhibiting singlet fission which can be utilized for application in solar cells to increase efficiency. Singlet fission is a process by which an excited chromophore shares its excitation energy with a neighboring ground state chromophore and they both are converted into triplet excited states.1,2 The chromophores under investigation are based on the structure of 2,5- diketopiperazines and their derivatives. The synthesis of 3,6-dibromo-1,4-dimethyl-2,5- diketopiperazine, which is the precursor to the desired biradicaloid species, was achieved successfully. The final reduction to give ...


Molecular Architectures Constructed Through Dynamic Covalent Chemistry: A Voyage From Phenylene Vinylene Macrocycles And Porphyrin Cages To Their Self-Assembled Complexes, Chao Yu Jan 2016

Molecular Architectures Constructed Through Dynamic Covalent Chemistry: A Voyage From Phenylene Vinylene Macrocycles And Porphyrin Cages To Their Self-Assembled Complexes, Chao Yu

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

The objectives of this thesis are to utilize dynamic covalent chemistry (DCvC) to prepare organic macrocycles and cages, construct subsequent complex architectures through self-assembly, and investigate the properties and applications of these compounds for supramolecular chemistry, transmembrane channels, gas adsorption, etc. Traditionally, organic macrocycles and cages are prepared via irreversible bond formation reactions, which usually require multi-step syntheses and tremendous synthetic efforts, result in low overall yields. DCvC, which enables reversible bond breaking/forming, and allows the most thermodynamically stable product to form predominantly at equilibrium, has largely facilitated the preparation of organic macrocycles and cages.

In this thesis, Chapter ...


Organic Molecular Cages As Templates For The Synthesis Of Metallic Nanoparticles: From Stabilization To Application And Assembly, Ryan Mccaffrey Jan 2016

Organic Molecular Cages As Templates For The Synthesis Of Metallic Nanoparticles: From Stabilization To Application And Assembly, Ryan Mccaffrey

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Shape-persistent 3-D covalent organic polyhedrons (COPs) with well-defined intrinsic cavities have been well studied in materials chemistry due to their applications in host-guest chemistry, chemical sensing and gas adsorption and separation. However, the use of 3-D COPs as endo-templates for the synthesis of metallic nanoparticles has not been intensely explored. The purpose of the work described within this thesis is to answer the following questions: Can discrete, purely organic hollow molecular structures be designed in such a way as to facilitate the size-controlled synthesis of metallic nanoparticles? What are the applications of such organic-inorganic hybrid structures? Is it feasible for ...


New Methods In Carbohydrate Chemistry: Dehydrative Glycosylation With Cyclic Phosphonium Anhydrides And Α-Selective Glycosylation Of Glycosyl Phosphinites, Lance Taylor Dockery Jan 2016

New Methods In Carbohydrate Chemistry: Dehydrative Glycosylation With Cyclic Phosphonium Anhydrides And Α-Selective Glycosylation Of Glycosyl Phosphinites, Lance Taylor Dockery

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Achieving a high level of efficiency in carbohydrate synthesis is dependent upon reactions that can provide high yields and stereoselectivity at the anomeric position. The nature of the glycosidic bond as either α or β configuration poses the greatest obstacle. The development of methods to control this inherent feature while also giving high yields is a primary goal for the field of carbohydrate chemistry. This thesis examines the potential for two new methods to overcome these challenges: dehydrative glycosylation with cyclic phosphonium anhydrides and glycosylation of glycosyl phosphinites. A collection of cyclic phosphonium anhydrides were prepared and tested with a ...


Property-Guided Synthesis Of Tricyclic Indolines To Confront Antibiotic Resistance In Methicillin Resistant Staphylococcus Aureus, Patrick Michael Barbour Jan 2016

Property-Guided Synthesis Of Tricyclic Indolines To Confront Antibiotic Resistance In Methicillin Resistant Staphylococcus Aureus, Patrick Michael Barbour

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Antibiotics are essential to modern medicine. They have enabled surgery to become routine and allowed for the development of advanced treatments for cancer and burn patients. However, a reservoir of genes that confer resistance and aid in host colonization is distributed across the microbial world and decreases the ability of modern medicine to control infection. We have not been able to sustainably counteract this with new drugs and resistance has been observed for all antibiotics that have been employed in the clinic. New classes of antibiotics are needed, but we also need to explore ways to restore the efficacy of ...


Development Of Polyimine-Based Dynamic Covalent Networks: From Malleable Polymers To High-Performance Composites, Philip John Taynton Jan 2015

Development Of Polyimine-Based Dynamic Covalent Networks: From Malleable Polymers To High-Performance Composites, Philip John Taynton

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Since the advent of synthetic polymers over a century ago, polymer science and technology development has transformed and enhanced our way of life from clothing to food storage to electronics and automobiles. To suit different applications, two broad categories of synthetic polymers have been developed: linear polymers, or thermoplastics, which can be melted, or solubilized, and reprocessed into a new shape or form; and network polymers, or thermosets, which are usually unable to be melted or reshaped once cured. The irreversible and permanent nature of thermosets was initially desirable for enabling high strength and long service lifetimes, but also makes ...


Development And Evaluation Of Chemical Probes For The Study Of Histone Demethylases, Laura Marholz Jan 2015

Development And Evaluation Of Chemical Probes For The Study Of Histone Demethylases, Laura Marholz

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

The expression of only certain particular genes out of a complete genome is what allows a cell to have a unique phenotype. Epigenetic control of gene regulation is exerted through a variety of mechanisms including DNA methylation, chromatin remodeling, and covalent histone modifications. One such modification, the methylation of histone lysine residues, is able to be ‘erased’ by several families of proteins termed histone lysine demethylases (HDMs). These proteins have been shown to be vital in many natural cellular processes, and their aberrant activity has been associated with certain disease states. A summary of these topics will be introduced along ...


A Symmetry Exploration Into Covalent Tetracene Dimers With Tunable Electronic Coupling For Singlet Fission, Jamie Lynn Snyder Jan 2015

A Symmetry Exploration Into Covalent Tetracene Dimers With Tunable Electronic Coupling For Singlet Fission, Jamie Lynn Snyder

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

One process that has the potential of efficiently harvesting solar energy is singlet fission (SF), a process by which one photon of light can produce two excited states. Investigations of three different series of bistetracene (BT) were used to explore the effect of symmetry on the rate and driving force of SF, as well as the electronic coupling. A dimer and the corresponding monomer were used to build a synthetic infrastructure and explore preliminary photophysics. All of the dimers were connected by one to three norbornyl bridges and exhibit various amounts of electronic coupling.

The first section of this dissertation ...


Structure-Property Relationships In De Vries Smectic A Liquid Crystals, Mark James Conroy Moran Jan 2015

Structure-Property Relationships In De Vries Smectic A Liquid Crystals, Mark James Conroy Moran

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Liquid crystals (LCs) have become inextricably linked with the display industry in recent years. As screen sizes increase the response time of the LC must decrease to maintain picture quality. A rare subset of the chiral smectic A (SmA*) , known as the de Vries SmA* phase, shows fast switching times, large electroclinic tilts, native gray-scale and small layer shrinkage when driven by an electric field, making it an attractive alternative to SmC* materials for next-generation displays. The de Vries SmA* phase is typically formed by molecules with one or more tails that strongly suppress out-of-layer fluctuations.

The first part of ...


Design, Synthesis, And Thermotropic Liquid Crystal Behavior Of Novel Tris(Imidazolium) Ionic Organic Compounds, Magdalene Reynolds Schenkel Jan 2014

Design, Synthesis, And Thermotropic Liquid Crystal Behavior Of Novel Tris(Imidazolium) Ionic Organic Compounds, Magdalene Reynolds Schenkel

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Thermotropic ionic liquid crystals (TILCs) are a relatively new field of liquid crystals (LCs) research. TILCs have the internal organization of traditionally uncharged LCs as well as many of the unique characteristics of organic molten salts known as room-temperature ionic liquids (RTILs). Within the latter's family of `designer solvents', which include many ionic moieties with varying advantages, imidazolium salts offer a cheap and modular ionic moiety to build ionic organic compounds with characteristics tailored to specific needs. The advances in these ionic liquid crystals (ILCs) have led to research in soft materials with improved gas separation, electrolytic, and reactive ...


Expanding The Chemistry Of In Vitro Selections Against Extracellular Mycobacterial Glycolipids, Lia Germaine Rebits Jan 2014

Expanding The Chemistry Of In Vitro Selections Against Extracellular Mycobacterial Glycolipids, Lia Germaine Rebits

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Despite the drastic decline in tuberculosis-related mortality due to the development of a vaccine and the discovery of effective anti-mycobacterial antibiotics during the middle part of the twentieth century, there has been a resurgence of the disease since the 1980's primarily caused by the emergence of HIV/AIDS and drug-resistant Mycobacterium tuberculosis strains. The need for improved diagnostic tests that are capable of greater specificity, sensitivity, and rapidity than the current tests is apparent and such tests would contribute significantly to the number of lives saved annually. A DNA aptamer-based biosensor has the potential to meet these challenges; aptamers ...


Asymmetric Recognition Of Nucleobase Features By Dna Polymerases, Travis John Lund Jan 2013

Asymmetric Recognition Of Nucleobase Features By Dna Polymerases, Travis John Lund

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

This work describes an investigation into the recognition of nucleobase features by several DNA polymerases. I used of a series of pyrimidine analogues modified at O2, N-3, and N4/O4 to determine how the Klenow fragment of DNA polymerase I, an A family polymerase, and two B family DNA polymerases, human DNA polymerase α and herpes simplex virus I DNA polymerase, choose whether or not to polymerize pyrimidine dNTPs. Removal of these heteroatoms generally impaired polymerization, with the effects varying from mild to severe. Removing O2 of a pyrimidine dNTP vastly decreased incorporation by these enzymes ...


Design And Synthesis Of New Type I Bicontinuous Cubic Lyotropic Liquid Crystal Monomers Based On The Gemini Framework For Molecular-Size Separation Applications, Brian R. Wiesenauer Jan 2013

Design And Synthesis Of New Type I Bicontinuous Cubic Lyotropic Liquid Crystal Monomers Based On The Gemini Framework For Molecular-Size Separation Applications, Brian R. Wiesenauer

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

The overall objective of this thesis research was the design and synthesis of new type I bicontinuous cubic (QI) phase-forming, gemini-shaped lyotropic liquid crystal (LLC) monomers for the preparation of nanoporous polymer membrane materials. These new QI -phase LLC monomers were designed to overcome several shortcomings of previously developed QI -phase LLC monomers in the Gin research group that include expensive and difficult synthesis, poor film processibility, and limited blendability with additives. The first method for obtaining this objective was the synthesis of six homologues of a new gemini ammonium LLC monomer, two of which exhibit a ...


Development Of A Novel Lewis Acid For Intramolecular Vinylogous Aldol Reactions, Its Application To The Synthesis Of (+)-Peloruside A, And Design And Synthesis Of Lanthanide-Binding Nucleosides For Solution Phase Characterization Of Rna By Nmr, Jeffrey Allyn Gazaille Jan 2012

Development Of A Novel Lewis Acid For Intramolecular Vinylogous Aldol Reactions, Its Application To The Synthesis Of (+)-Peloruside A, And Design And Synthesis Of Lanthanide-Binding Nucleosides For Solution Phase Characterization Of Rna By Nmr, Jeffrey Allyn Gazaille

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

While in the Sammakia Lab, I have focused broadly on developing and applying new approaches to organic synthesis that increase the cache of methods for the synthesis and use of complex organic molecules. My research efforts can be classified into (i) the development and application of new methods for the synthesis of complex natural products, and (ii) the use of organic molecules as probes for problems in chemical biology. The application of the intramolecular vinylogous aldol reaction with ATPH toward the synthesis of (+)-peloruside A, the development of the novel Lewis acid, ATNP, which promotes the vinylogous aldol reaction of ...


Formal Total Synthesis Of Diazonamide A, Cheng-Kang Mai Jan 2011

Formal Total Synthesis Of Diazonamide A, Cheng-Kang Mai

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

This dissertation describes efforts toward the total synthesis of diazonamide A, a complex marine natural product. First, efficient methods to prepare 3,3-diaryloxindoles from 3-aryloxindoles were developed via either Pd-catalyzed alpha-arylations or nucleophilic aromatic substitutions using the oxindole enolate as the nucleophile. Second, this method has been successfully applied to a formal synthesis of diazonamide A via the highly diastereoselective construction of the C10 quaternary center. Third, a cyclization precursor for a cascade alpha-arylation/direct arylation approach to the total synthesis was synthesized and tested, and this substrate was found to be failed to cyclize. Finally, two approaches to the ...


Ion-Neutral Chemistry Of Importance To Astrophysical And Cosmological Environments, Oscar Martinez Jr. Apr 2010

Ion-Neutral Chemistry Of Importance To Astrophysical And Cosmological Environments, Oscar Martinez Jr.

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Scientific studies have led to a more thorough understanding of processes directing the evolution of the Universe. In addition to observational studies with telescopes, terrestrial laboratory studies now contribute to the knowledge encompassed by astronomy and astrophysics. The laboratory-astrophysics experiments performed for this thesis focused on topics ranging from the birth of the first stars and galaxies to chemical processes important to the interstellar medium (ISM).

Models attempt to derive a better understanding of certain cosmological and astrophysical environments. Their reliability, however, depends heavily on the accuracy of data employed. Our contributions to laboratory astrophysics are based on the use ...


The Synthesis Of Unnatural Morphine Derivatives As Glial Activation Inhibitors And The Synthesis Of Corticosterone-Glucuronide, Morin Mae Frick Jan 2010

The Synthesis Of Unnatural Morphine Derivatives As Glial Activation Inhibitors And The Synthesis Of Corticosterone-Glucuronide, Morin Mae Frick

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

A novel, non-neuronal mechanism to explain the development of opioid tolerance and dependance has been described. This mechanism involves the activation of spinal cord glia. Glia are important contributors to the creation of enhanced pain states via the release of neuroexcitatory and proinflammatory substances. Data suggest that glia also release neuroexcitatory substances in response to morphine, thereby opposing its effects. Inhibiting glial activation could therefore increase the clinical utility of analgesic drugs. The synthesis of advanced intermediates for the development of a series of novel morphinan-like structures that are potential glial activation inhibitors will be discussed.

Corticosterone displays an intense ...