Organic Chemistry Commons^™

Why Are The Nitro And Sulfone Groups Poor Hydrogen Bonders?, Charles A. Kingsbury

Department of Chemistry: Faculty Publications

The interactions of water or methanol with nitromethane and dimethyl sulfone vs. comparison molecules, e.g. dimethylsulfoxide (DMSO), are reported. For nitromethane with water, the classical (edgewise) hydrogen bonded configuration is modestly stabilizing. However, the approach of water over the face of the nitro group is preferred in AM1 calculations. Generally, molecules such as sulfones and nitro compounds have lower energy bonding orbitals than sulfoxides. The energy of the n δ σ* interaction (e.g. nitro lone pair to O-H of water) thus is larger for the nitro and sulfone cases, and this interaction is less prevalent than other cases. Since …

Total Synthesis And Derivation Of Humulones And Lupulones As Possible Biologically Active Agents, Lucas R. Sass, Kristopher V. Waynant (Mentor)

Idaho Conference on Undergraduate Research

Humulones and lupulones have affirmed themselves as key ingredients in the multi-billion dollar brewing industry. Originally exploited for their bacteriostatic properties, these compounds also exhibit high levels of biological activity against a variety of diseases. Although quantifiable, the isolation and separation of specific humulones and lupulones has proven difficult, thus establishing efficient synthetic routes will be of value to those desiring exact bittering qualities and to the pharmaceutical community. Our investigations are towards developing a synthetic route to a library of humulones, lupulones, and their derivatives as possible biologically active agents against myriad diseases. The key step in our efficient …

Asymmetric Synthesis And Transition Metal-Catalyzed Cross-Coupling Arylations Of Selected Organolithiums, Barry Kyle Sharp

Graduate Theses and Dissertations

My former boss, Dr. Gawley, always loved to say, “The world is chiral” (à la Pasteur). From DNA and proteins to hands and feet, it is obviously true. Also, a wide variety of chemical products exist as single enantiomers. Advances in chemical technology have greatly accelerated asymmetric synthesis in the past quarter century, and namely, organolithiums, have been shown to provide a versatile route to chiral natural products and biologically active molecules. Versatility arises from the array of methods that produce a chiral organolithium. Dynamic thermodynamic resolution (DTR) is considered one of the most practical methods, but among the others …

Novel Azole-Based Rearrangements, Kolawole Folayele Ayinuola

Graduate Theses and Dissertations

This work describes efforts targeted at the development of novel reactivity modes for the Breslow intermediate, which was proposed by Breslow to explain the mechanism of action of thiamine-dependent enzymes. By employing this intermediate as a hydroxy-substituted N,S-ketene acetal, we successfully captured it via Claisen rearrangement towards the preparation of diaryl tertiary alcohol products that are isomers of the hitherto elusive intermediate. This strategy also constitutes an unusual disconnection for a Claisen rearrangement precursor.

We have also uncovered an unprecedented radical C-N bond scission of a Breslow intermediate when a fluorenyl group is installed on the azolium nitrogen atom. This …

Designing Fret Assays To Study Electrostatic Interactions Pertaining To The Binding Of Intrinsically Disordered Proteins, Ashley Ann Howard

Graduate Theses and Dissertations

Fibroblast growth factor receptor plays a major role in several biological processes. Without FGFR, a human cannot live. FGFR is involved in cell differentiation and wound healing. Of course, if FGFR signaling becomes unregulated, it causes severe distress in the body. Several cancers are contributed to high signaling levels, as well as developmental conditions like rickets and Kallmann’s syndrome. FGFR is thought to undergo an auto-inhibition (or self-regulatory) process in order to try to facilitate regulation. The exact method of this inhibition is currently unknown, but is proposed to involve the unstructured acid box region of FGFR. We developed a …

In Vitro Microdialysis Sampling Collection Of Volatile Organic Compounds (Voc's), Dodecafluoropentane (Ddfp) And Isoflurane, Valerie Shannon Mckinney

Graduate Theses and Dissertations

Death by stroke occurs every four minutes to human beings. Strokes cause necrosis within the tissue of the brain due to deprivation of oxygen. Perfluorocarbons have the ability to transport oxygen to tissue and in return decrease cell death. Dodecafluoropentane (DDFP) is a volatile fluorocarbon and collection in vivo can be a challenge since this compound evaporates at room temperature. There is currently not an efficient collection method in vivo for compounds that are volatile. Without a method to collect DDFP it is impossible to be approved for clinical use since exact concentrations of the drug within the body will …

Diol-Mediated Versus Water-Mediated Proton Transfer Reactions, Angela Moses

DePaul Discoveries

The triple-proton-transfer reactions of 8H-1,8-naphthyridin-2-one (8H-naph) have been investigated by employing different ab initio quantum mechanical methods. The proton transfer reactions studied were facilitated through an adjacent 1,3-propanediol molecule or two adjacent water molecules. Identical proton transfer reactions were studied using a model system of 8H-naph to investigate the validity of computational approaches that use model systems to study more complex systems. The solvent effects on the structures were investigated for comparison to the initial gas phase calculations. The potential energy, reaction force, and work profiles were studied along the intrinsic reaction coordinate to monitor the developing proton transfer reactions.

Investigations Of Thioether Generation For S-D-Ribosyl-L-Homocysteine Synthesis, Brendan Corcoran

Master's Theses

Creation of the thioether linkage is a fundamental step for the chemical preparation of the bacterial quorum sensing molecule S-D-ribosyl-L-homocysteine (SRH). Although previous preparations of SRH and its analogues have been reported in the literature, they employ assorted methods with varied results. Therefore, a reassessment of the methodology used for synthetic preparation of the thioether bond in SRH-like molecules is here considered. This work examines four methods of thioether generation following two mechanisms, bimolecular nucleophilic substitution (S_N2) and radical-initiated thiol-ene coupling, in an attempt to generate SRH in a more efficient and reproducible manner. Both mechanisms address …

The Synthesis And Study Of The Biological And Colloidal Properties Of Bolaamphiphiles, Louis M. Damiano

Senior Honors Projects, 2010-2019

Over the past decade, antibiotic resistant bacteria have caused infections in patients throughout the world.^[1] The rise in antibiotic resistance is primarily due to the misuse and overuse of antibiotics. ^[1] To counter the increase in antibiotic resistance, infection control mechanisms have been aggressively researched in recent years. In particular, drug delivery has become a focal point to fight antibiotic resistant infections.^[2] Amphiphiles have a wide range of applications in the clinical setting, including the ability to inhibit bacterial transference because of their bactericidal activity. ^[3] Bolaamphiphiles are a subclass of amphiphiles that possess two or more hydrophilic …

Applications Of Organic Probes For Imaging And Analysis Of Different Cancer Cell Models, Hong Guan

Theses and Dissertations

Novel techniques for better studying cancer cell behavior and progression are extremely important. Our lab is interested in synthesizing specifically designed organic reagents and applying them in the studies of cancers. In this dissertation, we used organic probes to investigate cancer cells in the following topics: determination of amino acid concentration in different types of cancers, tumor toxicity of organic probes towards HER2 positive breast cancer cells, glycoproteins identification in breast cancer cells and development of enzyme activity assay for colon cancer cells.

The first chapter was focused on the determination of cysteine/homocysteine concentrations using turn-on sensors in cancer cells. …

Impact Of Ocean Acidification On Aphotic Biogeochemical Production Of Reactive Oxygen Species, Sarah Ann Murphy

Theses and Dissertations

Reactive oxygen species (ROS) are critical to global maintenance of the global organic carbon cycle, sulfur cycle, oxygen cycle, and transition metal cycles. The primary source of ROS is commonly considered to be photolysis or photochemically driven reactions, however ROS also exist in aphotic zones. A geochemical mechanism for the same in dark environments based on the tidally driven, episodic movement of anoxic groundwaters through oxidized, Fe(III) rich sediments is shown. Predictive models were developed based on in vitro experiments and tested using sediment samples collected from a saline tidal creek in the estuary at Murrell’s Inlet, South Carolina. These …

Facile Method For Large Scale Alignment Of One Dimensional Nanoparticles And Its Biomedical Application, Sheng Feng

Theses and Dissertations

Topographical cues can profoundly affect cellular behaviors. This thesis investigate how to utilize the topographical cues generated by two techniques, flow assembly and electrospinning, to regulate cellular behaviors.

First of all, a facile and robust method to align one-dimensional (1D) nanoparticles (NPs) in large scale has been developed. Using flow assembly, representative rod-like nanoparticles, including tobacco mosaic virus (TMV), gold nanorods and bacteriophage M13, have been aligned inside capillaries by controlling flow rate and substrate surface properties. The properties of 1D NPs, such as stiffness and aspect ratio, play a critical role in the alignment. Furthermore, these hierarchically organized structures …

Tempo-Containing Romp Polymers As A Component For Treatment Of Traumatic Brain Injuries, Cameron H. Feriante

Honors College Theses

During a traumatic brain injury (TBI) sustained in combination with hemorrhagic shock the brain undergoes anoxic conditions resulting from swelling and blood loss. Traditional intravenous solutions are used to replace blood volume, but are unable to replace the blood’s oxygen carrying capacity. A proposed treatment based on isotonic solutions containing hemoglobin-based oxygen carriers (HBOC’s) which were intended to provide readily available oxygen was developed. However, cell-free hemoglobin was shown to have excessive oxidative potential. Polynitroxylated Pegylated Hemoglobin (PNPH) was developed to address this shortcoming. During PNPH synthesis a combination of polyethylene glycol (PEG) and (2,2,6,6-tetramethylpiperidin-1-yl)oxidanyl (TEMPO), is bound to the …

Fused Arene-Based Molecular Systems As Additives For Organic Photovoltaics, Rachana Neesu

Masters Theses & Specialist Projects

Organic photovoltaics (OPVs) are mainly based on organic semiconducting small molecules, macromolecules, and polymers, which form an active layer in photovoltaics. They act as an active material in absorbing light and causing charge mobility to generate electricity from sunlight. This thesis describes the molecular systems derived from fused arenes such as anthracene, pyrene, carbazole and thiophene for use as either a donor or an acceptor component of the active layer of OPVs. Two novel molecular systems (9- anthracenecarboxy-1-methylpyrene, (1) and Py-bi-TH-ANT, (2) were prepared using Steglich esterification and Grignard metathesis followed by Kumada coupling. The molecular structure of each was …

Methodology Development In Green Chemistry: Oxoammonium Salt Oxidations And Fluoroform Incorporation, Rebecca J. Wiles

University Scholar Projects

Central to the advancement of small molecule synthesis is the ability to develop methodologies that reimagine well known chemistry in a new, environmentally friendly manner. In this thesis two central themes emerge: oxoammonium salt oxidations and trifluoromethyl incorporation using fluoroform gas. Several projects have been developed surrounding oxoammonium salt chemistry, which are featured by their mild conditions, ease of use, and the metal-free, recyclable nature of the oxidant. Trifluoromethylation using fluoroform gas finds its utility in the use of a potent greenhouse gas waste product as a benchtop reagent.

Synthesis Of Diazonium Perfluoroalkyl(Aryl) Sufonimide (Pfsi) Zwitterions For Solid Acid Alkylation Catalysts, Husan Ahmad

Undergraduate Honors Theses

The final objective of this project is to create an environmentally friendly solid alkylation catalyst to replace the commercially available liquid acid catalysts, such as hydrofluoric acid and sulfuric acid, which are used in the petroleum industry. My research target is to synthesize the diazonium PFSI zwitterions, which can be chemically grafted on the silica as the solid alkylation catalyst. A 4-steps synthesis is designed to prepare the diazonium PFSI zwitterions. The first two steps were successfully completed in the lab. The first one is to prepare the starting material of 4-nitrobenzenesulfonamide from an ammonolysis reaction between 4-nitrobenzene sulfonyl chloride …

One-Step Synthesis Of Kanamycin Functionalized Gold Nanoparticles With Potent Antibacterial Activity Against Resistant Bacterial Strains, Hitesh Kumar Waghwani

Masters Theses & Specialist Projects

On the verge of entering the post-antibiotic era, numerous efforts are in place to regain the losing potential of antibiotics which are proving ineffective against common bacterial infections. Engineered nanomaterials, especially gold nanoparticles (GNPs) capped with antibacterial agents are proving to be an effective and novel strategy against multi-drug resistant (MDR) bacteria. In this study, we report a one-step synthesis of kanamycin-capped GNPs (20 ± 5 nm) utilizing the combined reducing and capping ability of the aminoglycoside antibiotic, kanamycin. Antibacterial assays showed dosedependent broad spectrum activity of Kan-GNPs against Gram-positive (Staphylococcus epidermidis and Enterococcus durans), Gram-negative (Escherichia coli and Enterobacter …

Thiophene And Derivatives For Use In Pyridazines And Thiapentalenes, Benjamin Tyree Cannon

Masters Theses & Specialist Projects

This thesis introduces the idea of Band Theory and how it can be used to describe a solid-state materials ability to carry an electrical charge. Next, this thesis defines what makes a material a conductor, semiconductor, or insulator. Semiconductors are attracting interest in chemistry, as well as in the manufacturing of consumer electronics, because of their ability to carry a charge, without the risk of short-circuiting like traditional conductors.1,4 Organic semiconductors, which behave differently than traditional semiconductors, are of particular interest because they offer mechanical flexibility, lowcost, simplicity, and the ability to be manufactures at low temperatures.6 Nonorganic and organic …

Green Chemistry As A Tool For Understanding The Toxic Substances Control Act: A Lecture Module For Undergraduate Students, Molly R. Blessing

Honors Scholar Theses

The Toxic Substances Control Act (TSCA) is the central form of chemical regulation existent in the United States today, yet scientists are often unaware or uncertain of its provisions. Violations of TSCA by unknowing chemists set industry and government unnecessarily at odds. A lecture on TSCA was developed for undergraduate students that uses the concept of green chemistry to promote interest and incentivize learning. Green chemistry methods are cleaner and less wasteful than traditional chemical ones, and many companies using them are at the forefront of technological innovation. The lecture explains both green chemistry and TSCA, includes company case studies, …

Novel [3,3]- And [1,3]- Rearrangements Of Azole-Derived N,X-Ketene Acetals, Sefat A. Alwarsh

Graduate Theses and Dissertations

The formation of carbon-carbon bonds in organic chemistry is fundamentally important. One of the major reactions that chemists have widely investigated is the Claisen rearrangement. Based on the fundamental features of this rearrangement, chemists exploited the capability of the transformation and invented their own variations of Claisen-type rearrangements. Our goal in this project is to develop a novel variation of the Claisen rearrangement using azole compounds, which are common heteroaromatic ring systems that are present extensively in the biomedically important natural products. We propose here novel methodologies of preparing 2-substitution azole derivatives using aza-based Claisen rearrangement, N,X-ketene acetals that requires …

Methodology Development In Green Chemistry: Oxoammonium Salt Oxidations And Fluoroform Incorporation, Rebecca J. Wiles

Honors Scholar Theses

Central to the advancement of small molecule synthesis is the ability to develop methodologies that reimagine well known chemistry in a new, environmentally friendly manner. In this thesis two central themes emerge: oxoammonium salt oxidations and trifluoromethyl incorporation using fluoroform gas. Several projects have been developed surrounding oxoammonium salt chemistry, which are featured by their mild conditions, ease of use, and the metal-free, recyclable nature of the oxidant. Trifluoromethylation using fluoroform gas finds its utility in the use of a potent greenhouse gas waste product as a benchtop reagent.

Characterization Of Cellulase Enzyme Inhibitors Formed During The Chemical Pretreatments Of Rice Straw, Kalavathy Rajan

Graduate Theses and Dissertations

Production of fuels and chemicals from a renewable and inexpensive resource such as lignocellulosic biomass is a lucrative and sustainable option for the advanced biofuel and bio-based chemical platform. Agricultural residues constitute the bulk of potential feedstock available for cellulosic fuel production. On a global scale, rice straw is the largest source of agricultural residues and is therefore an ideal crop model for biomass deconstruction studies. Lignocellulosic biofuel production involves the processes of biomass conditioning, enzymatic saccharification, microbial fermentation and ethanol distillation, and one of the major factors affecting its techno-economic feasibility is the biomass recalcitrance to enzymatic saccharification. Preconditioning …

The 8-Silyloxyquinoline Scaffold As A Versatile Platform For The Sensitive Detection Of Aqueous Fluoride, Xinqi Zhou

Department of Chemistry: Dissertations, Theses, and Student Research

As one of the most essential elements in nature, fluoride has been well known and extensively studied since the 16^th century. Since then the two-edged nature of fluoride in biological systems has been well described. Specifically, moderate fluoride exposure can aid in tooth and bone development, while fluoride overexposure results in the depilating disease known as fluorosis. Because of the side effects upon overexposure of fluoride, there is a need to develop fast and straight forward methods to sensitively and selectively detect and quantify fluoride concentration in drinking water. With this goal in mind and by taking advantage of …

Synthesis Of Β-Triphosphotriester Pronucleotides, Yousef Beni, Chandravanu Dash, Keykavous Parang

Chemistry Faculty Research

Dinucleoside phosphorochloridite was synthesized from phosphorus trichloride and three nucleoside analogs, 3′-fluoro-2′,3′-dideoxythymidine (FLT), 2′,3′-dideoxy-5-fluoro-3′-thiacytidine (FTC), and 2′,3′-dideoxy-3′-thiacytidine (3TC), in a multistep synthesis. Polymer-bound N-Boc p-acetoxybenzyl 5′-O-2′-deoxythymidine was reacted with dinucleoside phosphorochloridite in the presence of 2,6-lutidine, followed by the reaction with dodecyl alcohol and 5-(ethylthio)-1H-tetrazole, oxidation with tert-butyl hydroperoxide, and acidic cleavage, respectively, to afford the β-triphosphotriester derivatives containing three different nucleosides.

Novel Photodynamic Therapy Agents: Biochemical Analysis, Eboni D. Pullen

Honors College Theses

Bioinorganic photochemistry is a rapidly advancing research area in the field of bioinorganic chemistry. This project seeks to build upon the growing field by synthesizing and analyzing new photodynamic therapy (PDT) agents. There are three major generations of PDT agents. The first generation consists of chemically modified natural hematoporphyrins, which are not of great interest in the phototherapeutic field due to their low distinguishability between tumor cells and healthy cells, and extended skin photosensitivity in patients. The second generation consists of organic dyes, aromatic hydrocarbons, polypyrolics complexes, and semi-conductors, but is also not of much interest due to the same …

The Phytotoxic Virulence Factor Bcsnod 1 From Botrytis Cinerea, Gnana Sreekar Nidadavolu, Hana Mcfeeters

Research Horizons Day Posters

No abstract provided.

Synthesis And Characterization Study Of Biomimetic Tetradentate Ni Complexes, Nirupama Singh

Research Horizons Day Posters

No abstract provided.

Active Site Mimics Of Nickel Superoxide Dismutase, Victoria Grace Snider

Research Horizons Day Posters

No abstract provided.

High Mannose Binding Lectins - A New Class Of Attractive Antifungals, Tyler Hays Jones

Research Horizons Day Posters

No abstract provided.

Non-Covalent Affinity Materials For Protein Structure Determination Via Single Particle Reconstruction Analysis Cryo-Electron Microscopy, Minji Ha

Open Access Theses

Single particle analysis (SPA) by cryogenic electron microscopy (Cryo-EM) is one of the powerful tools for determining biological macromolecule structure, particularly when combined with computational methods or X-ray crystallography. However, the SPA is challenged by sample processing efficiency. In this work, polyrotaxane (PRTx) was designed and synthesized such that laterally and rotationally mobile lysine nitrolicacetic acid (Lys-NTA) modified α-cyclodextrins (α-CD) were threaded onto a polyethylene glycol (PEG) core. Polyrotaxanes threaded with amine modified α-CD were also designed and synthesized for stoichiometric control of His-tagged protein capture by PRTx. For higher efficiency of single particle analysis along a single strand of …