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Raman Spectroscopic And Computational Study Of Hydrogen Bond Interactions Between Guanidine Hydrochloride, Trimethylamine N-Oxide (Tmao), Urea, And Water, Andrew Kamischke

Honors Theses

Proteins are broken down in the body and produce water, CO2, and ammonia as by-products. Ammonia is toxic to cells, making it a priority to be excreted. Urea is the key route for the transportation of ammonia out of the body and is the main component of urine. Guanidine is another important nitrogen-containing molecule that is structural like urea and plays important biological roles in the stabilization of proteins. Guanidine hydrochloride and Urea are known to denature proteins and this functionality continues to be a topic of great interest. Urea and guanidine contain many hydrogen bonding sites and interactions with …

Assembly Of A Protein-Based Hydrogel As A Vehicle For In Situ Drug Delivery, Austin Carroll

Honors Theses

The goal of this work is to develop a self-assembling, protein-based gel to deliver drugs at the site of chronic inflammation. There are two engineered protomers that comprise the gel; calmodulin- and M13- are their critical components. Numerous enzymes have been shown to undergo calcium-dependent regulation by calmodulin, an intracellular protein highly resilient to its chemical environment. One of these enzymes, myosin light chain kinase, contains a remarkable 26 residue portion known as the M13 peptide that has been demonstrated to bind to calmodulin in the presence of calcium through hydrophobic interactions. Because the extracellular space in vivo constitutes an …

Development Of A Gel Assay For Analysis Of Bovine Milk Casein, Masa Miscevic

Honors Theses

The main purpose of this research was to develop a gel assay for analysis of casein samples for ultimate application for studies of in vitro models for stomach and intestinal processing of dairy products in adults and infants. It is proposed that casein completely dissolves and is digestible in simulated gastric, and is somewhat soluble and digestible in simulated intestinal environments of adults and infants. The following experimental methods were devised to thoroughly examine behavior and properties of casein originating from different sources in range of solvents and varying pH values. First, casein was enriched in comparison to soluble materials …

Student Integration Into Stem Careers And Culture: A Longitudinal Examination Of Summer Faculty Mentors And Project Ownership, Michelle Richards-Babb

Faculty & Staff Scholarship

It is widely recognized that the United States needs to attract and retain more people in science, technology, engineering, and mathematics (STEM) careers. Intensive undergraduate research experiences (UREs) are one of the few strategies shown to improve longitudinal student interest and persistence in STEM-related career pathways; however, less is known about the underlying process linking activities to positive outcomes. The tripartite integration model of social influences (TIMSI) provides a framework for understanding the social influence processes by which students integrate into STEM careers and culture. The current study used a longitudinal design and latent growth curve modeling to examine and …

Purification Protocol Development And Analysis Of Binding Properties Of Calmodulin Collagen-Like Protein, Patrick P. Boddie

Honors Theses

Calmodulin is an intensely studied, intracellular, calcium-binding protein that is involved in diverse physiological processes. When bound to calcium, calmodulin undergoes a conformational change that allows it to bind specific target peptides with high affinity, one being the calmodulin binding region of myosin light chain kinase, herein called M13. This high affinity, calcium dependent association has made it a desirable choice for use in a biomaterial for drug delivery for non-steroidal anti- inflammatory drugs (NSAIDs). Two artificial genes have been designed by our lab for use in the proposed biomaterial: calmodulin collagen-like protein (CCLP), a construct composed of two calmodulin …

Studying The Effects Of Hydrogen Bonding In 1h-1,2,3-Triazole And Its Derivatives, Leah Alexandra Wallace

Honors Theses

1,2,3-triazole is used as a building block in many pharmaceutical drugs. The molecule has several derivatives that are useful in other areas including treating fungal infections and in dealing with some environmental issues. One of its derivatives, benzotriazole, is commonly used as an inhibitor of corrosion through the formation of a copper-benzotriazole complex. One area of particular interest in studying triazoles is the ability of these molecules to tautomerize. The hydrogen atom can move from the 1H position to the 2H position and this transfer is thought to be affected by solvent interactions. Here, we study the effects of hydrogen …

Harmful Algae, Algal Toxin, Taste And Odor Control And Mitigation In Public Water System, Haiting Zhang

Doctoral Dissertations

“Recent years, harmful algal blooms occurrence has increased quickly in the surface water worldwide, which has become a concern for drinking water plants due to the ability of toxic algae (cyanobacteria) to produce cyanotoxins including microcystins (MCs), mainly MC-LR, cylindrospermopsin (CYN), and taste and odor (T&O) compounds. Various types of chemicals are widely used in drinking water treatment plants as oxidants for treating source water challenged with harmful algal blooms. In this study, the release and degradation of intracellular MC-LR due to oxidation of Microcystis aeruginosa (M. aeruginosa), most common specie of cyanobacteria, was examined kinetically. Effect of …

Synthesis Of Heterocycles Through Beta Lactams Ring Rupture, Bimal K. Banik

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Many Beta lactams are widely used as medicines. The 4-membered ring present in the beta lactams is under strain and therefore, it can undergo cleavage reactions to diverse compounds. Chemical manipulation of the resulting products affords numerous molecules of interest. In this perspective, some examples developed at our laboratory are discussed

Expeditious Green Synthesis Of Versatile Organic Compounds By Diverse Methods, Bimal K. Banik

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Synthesis of organic compounds requires organic solvents and reagents to promote them. Very often, toxic solvents are used for this purpose. Many organic reactions require molar proportion of reactants and reagents to accomplish the goal. Some reactions require longer reaction times and produce products without control of stereochemistry. Therefore, development of facile and effective organic reactions under environmentally friendly conditions is necessary. In this perspective, several reactions are discussed that are performed by microwave-induced reactions, catalytic procedures, in the absence of any solvents, one-pot method and in water. Important reactions are chosen to investigate the feasibility of conducting these reactions …

Versatile Catalytic Transfer Hydrogenations In Organic Synthesis, Bimal K. Banik, Khaled J. Barakat, Maghar S. Manhas

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Catalytic transfer hydrogenation reactions are extremely useful in organic synthesis. We have investigated numerous reactions with ammonium formate (and other hydrogen gas donor) and 10% Pd/C successfully without using hydrogen gas. The reactions are very fast and produced products with high yields. Reduction of unsaturated groups, hydrogenolysis, reductive bond cleavage, allylic deacetoxylation, and dehalogenation are conducted using this method. In some instances, useful selectivity of reactions is observed. Most of the reactions are investigated with β-lactams as the substrates.

Stereoselectivity Of Phthalimido Β-Lactams Formation: Synthesis Of 3-Amino Β-Lactams Through A Facile Deprotection Reaction, Armando Paniagua, Ram Naresh Yadav, Sunena Chandra, Bimal K. Banik

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Synthesis of amino β-lactams is a crucial objective because of the medicinal properties associated with them and the products derived from of them. Stereocontrolled synthesis of phthalimido β-lactams is performed and cis and trans-phthalimido β-lactams are deprotected with ethylene diamine (and other reagents) to amino β-lactams of diverse structures in excellent yield. This reaction is also conducted under solventless conditions to afford identical products.

Key Enzymes In Cancer: Mechanism Of Action And Inhibition With Anticancer Agents, Debasish Bandyopadhyay, Gabriel Lopez, Stephanie Cantu, Samantha Balboa, Annabel Garcia, Christina Silva, Diandra Valdes

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Several enzymes play significant role in different stages of cancer including proliferation, invasion, metastasis and angiogenesis. Mechanism of actions of a few key enzymes along with their inhibitors have been discussed with particular attentation to riboneucleotide reductase, thymidylate synthease, topoisomerase II, interleukins, cell survival proteins and aminopeptidase N.

Synthesis And Application Of Photoreactive Collagen Peptides, And Antiparasitic Agents, Alfredo Ornelas

Open Access Theses & Dissertations

Since the introduction of solid phase peptide synThesis in 1963, peptides and post-translationally modified peptides can be conveniently synthesized in the chemistry laboratory. In the past decade, there has been a remarkable increase in bioactive peptide research and the therapeutic peptide market value is expected to hit $25 billion this year. Peptides can also provide structural and biological functions and have emerged as promising novel biomaterials in tissue engineering. Here we will describe three different projects, which deal with different aspects of peptide chemistry, i.e. synthetic method development, exploration of new peptide biomaterials, and the use of cell penetrating peptides …

Tunable Surface Interactions In Adsorbing Polymer Solutions, Sorour Hosseini

Open Access Theses & Dissertations

A simple formalism is suggested, to calculate the most likely configuration of a finite polymer, between two surfaces on which the monomers can adsorb. Grafted polymers typically enhance the stability of colloidal dispersions, via the long ranged steric repulsion due to the overlap of their polymer brushes, which can be thicker that the typical range of the DLVO interactions. However, if the polymers are adsorbing on the colloidal surfaces, there is the possibility of bridge formation between particles and therefore long-range attractions are induced (a procedure commonly used for the flocculation of colloidal suspensions). The two effects are competing and …

Development Of A Dna Aptamer That Specifically Inhibits Human Carbonic Anhydrase Ii, Afroz Karim

Open Access Theses & Dissertations

Carbonic anhydrases (CA) are a family of enzymes that catalyze the rapid interconversion of carbon dioxide and water to bicarbonate. Carbonic anhydrase II is the most abundant protein in the cytosol. CA II inhibitors are emergent therapeutic targets for the development of antiglaucoma agents. Glaucoma is a disease affecting large number of people and characterized by an elevated intraocular pressure due to excessive secretion of aqueous humor. The enzyme CA II is responsible for the secretion of aqueous humor. Isoforms of CA II such as CA IV and CA I are present in many tissues and organs other than the …

Variety-Dependent Physiologic And Biochemical Effects Of Copper Nano Particles On Rosie And Green Bok Choy (Brassica Rapa) Phenotypes, Chaoyi Deng

Open Access Theses & Dissertations

The effects of Cu-based nanoparticles (NPs) in bok choy (Brassica rapa subsp. chinensis) are unknown. In this study, Rosie and Green, two varieties of bok choy, with different anthocyanin content, were cultivated for 70 days in soil amended with copper oxide nanoparticles (nano CuO), bulk copper oxide (bulk CuO) and copper chloride (CuCl2) at 75, 150, 300 and 600 mg Cu/kg soil. Cu and essential elements in tissues, and relative chlorophyll content, were determined. In both varieties, nano CuO treatments caused significantly more Cu uptake in roots and shoots, compared with bulk CuO and ion CuCl2 (p ≤ 0.05). Additionally, …

Solvent And Concentration Effects Governing The Hierarchical Organization Of Asphaltenes: A Small-Angle X-Ray Scattering Study, Hasan Rejoanur Rahman

Open Access Theses & Dissertations

Asphaltenes are a group of planar molecules found in crude oil and are prone to aggregation which often causes blockage of pipes along the oil production stream resulting a huge economic downside. In an effort to understand the hierarchical organization of asphaltene in different solvents and concentrations, the solution structure of various asphaltene solutions were studied using small-angle x-ray scattering (SAXS). Solvents were chosen based on miscibility maps. Such maps are generated on the critical value of the solubility parameter difference between asphaltenes or asphaltene components, and a range of solvents. The critical factors that affect asphaltene and asphaltene component …

Geostatistical And Geospatial Distribution Of Multiple Metallic Elements In Agricultural Regions Of The Mid-Continental Usa, Najwah Alssaeidi Ahmed Almesleh

Open Access Theses & Dissertations

Regional geochemical mapping constitute the chemistry of the surface of the earth in a large scale and relatively low sample density. It is widely accepted scientific activity and man uses some cases to identify contamination. In the present study, data present in national geochemical survey database was used to investigate the chemical loading loading of the agricultural soil. In the mid-continent region of the United States. Several traditional parameters were used mainly the enrichment factor (EF), and geoaccumulation index (I geo). Total chemical influence (TCI) maps were used to guide sampling. In addition, regional trace element chemistry of bedrock was …

Insights Into The Interaction Of Copper Oxide Nanopar-Ticles With Sweetpotato (Ipomoea Batatas (L.) Lam.): The Role Of Lignin On Copper Uptake And Translocation, Nestor Javier Bonilla Bird

Open Access Theses & Dissertations

Sweetpotato [Ipomoea batatas (L.) Lam.] is widely cultivated in many countries worldwide. The world production of sweetpotato is around 127 billion tons and it is ranked seventh in the world as a staple food. After harvesting, sweetpotato storage roots are treated with fungicides to prolong shelf life. Lignin plays an important role in the conservation of the storage roots. One of the practices to activate the lignification pathway is called “curing process.” The roots are placed under 80% relative humidity at a temperature of 29 ºC for a period of 7 to 15 days, followed by a cooling period at …

Electrocatalysts Based On Organic Macrocycles For Electrochemical Water Splitting, Yanyu Wu

Open Access Theses & Dissertations

Water splitting, which is the dissociation of water into hydrogen and oxygen gases, can be separated into two half reactions corresponding to the hydrogen evolution reaction and oxygen evolution reaction (HER and OER, respectively). Both reactions offer a promising way for storing energy into the form of chemical bonds, which is an important strategy for the development of clean-energy technologies. A main area of interest while studying HER and OER is to design effective and robust electrocatalysts made from earth-abundant materials. This dissertation describes several homogeneous and heterogeneous systems for the electrocatalytic generation of hydrogen and oxygen gases.

In Chapter …

Fabrication And Application Of Functional Polymer-Protein Coreshell Nanoparticles, Lin Lu

Theses and Dissertations

The study of polymer-protein nanoparticles is of increasing interest due to their various potential applications in biosensing, imaging, bioseparations, gene and drug delivery, etc. Synthetic polymers can be tailored with different functional groups and properties, therefore, they can serve as platforms to impart proteins with additional features and assist proteins to better perform biological functions. In this dissertation work, we were mainly focusing on the preparation of polymer-protein core-shell nanoparticles by synthesizing new functional polymers and assembling them with proteins for different applications. In chapter 1, a pyridine grafted diblock copolymer P(CL-g-Py)-b-PCL was prepared through ROP and CuAAC reactions. …

Probing Solvent Effects In Aromatic Interactions Using Molecular Balances, Josef M. Maier

Theses and Dissertations

Aromatic interactions play a key role in many important processes, such as the formation and stability of biological and synthetic assemblies, facilitation of molecular recognition processes, and catalysis of chemical reactions. One of the key factors determining the strength of aromatic interaction is the solvent environment. Therefore, developing model systems that can accurately measure the influence or effects of solvents on non-polar interaction strengths is a task of great importance. Over the years, we have been approaching this challenge via designing and analyzing molecular devices that can quantitatively report aromatic interaction energies under various solvent and chemical environments. With this …

Mechanisms Of Decarboxylation In The Cyp152 Family Of Cytochrome P450s, José Armando Amaya

Theses and Dissertations

Intense interest has focused on the development of enzymes as next-generation catalysts for the production of molecules with biotechnological potential. OleTJE, a member of the cytochrome P450 CYP152 family is an excellent candidate for the generation of advanced biofuels. OleTJE catalyzes the hydrogen peroxide-dependent decarboxylation of Cn fatty acids to produce Cn-1 terminal alkenes. Despite the ability of this enzyme to yield long chain alkenes with nearly exclusive chemoselectivity, its reactivity towards shorter chain length substrates results in undesired levels of hydroxylated side-products, limiting its industrial potential. Previous transient kinetic studies have demonstrated that, despite its unusual chemistry, the reaction …

Understanding The Adsorption And Nucleation Of Transition Metals On A Model Carbon Support, Grant S. Seuser

Theses and Dissertations

Heterogeneous catalysis plays a vital role in the commercial production of chemicals. However, much is still unknown about the fundamental surface chemistry involved in catalyst preparation and the surface chemistry of the catalysts themselves. In the first part of this work, a surface science approach was employed to develop a fundamental understanding of the surface chemistry of strong electrostatic adsorption (SEA) of metal precursors on a model carbon support, highly oriented pyrolytic graphite (HOPG). SEA is a wet impregnation method in which anionic/cationic metal precursors are adsorbed onto positively/negatively charged functional groups by adjusting the pH of the solution above …

Crystal Structure Of (2-{[(8-Aminona­Phthalen-1-Yl)Imino]­Meth­Yl}-4,6-Di-Tert-Butyl­Phenolato-Κ3n,N′,O)Bromido­Nickel(Ii), Patrick O’Brien, Matthias Zeller, Wei-Tsung Less

Chemistry: Faculty Publications and Other Works

The title compound, [NiBr(C25H29N2O)], contains an NiII atom with a slightly distorted square-planar coordination environment defined by one O and two N atoms from the 2-{[(8-aminonaphthalen-1-yl)imino]methyl}-4,6-di-tert-butylphenolate ligand and a bromide anion. The Ni—O and Ni—N bond lengths are slightly longer than those observed in the phenyl backbone counterpart, which can be attributed to the larger steric hindrance of the naphthyl group in the structure of the title compound. The molecule as a whole is substantially distorted, with both the planar naphthalene-1,8-diamine and imino–methyl– phenolate substitutents rotated against the NiN2OBr plane by 38.92 (7) and 37.22 (8), respectively, giving the molecule …

Dna Lesions Produced From The Reaction Of Diols And 5-Formylcytosine And Their Effects On Dna Replication, Brock Allen

University of the Pacific Theses and Dissertations

Nucleic acids are complex macromolecules that are susceptible to both endogenous and exogenous damage. This study explored damage resulting from interactions with environmental nucleophilic toxins, such as a variety of diols and amines found in industry. These nucleophiles can react with electrophilic groups, such as 5-formylcytosine. 5-formylcytosine is an oxidation product of the epigenetic base 5-methylcytosine. It is typically removed by thymine DNA glycosylase (TDG) but is known to accumulate in the genome, making the formyl group susceptible to attack. In this study we used GC/MS and ESI-MS to show that DNA lesions from the nucleophilic addition reaction of toxins …

Construction Of Supramolecular And Coordination Compounds From Pyridyl Bis-Urea Macrocycles, Bozumeh Som

Theses and Dissertations

The self-assembly of macrocyclic molecules in solution and in the solid state modulates and in many cases enhances their properties for applications in sensing, catalysis and optoelectronics. The self-assembled structures are typically organized by non-covalent interactions such as hydrogen bonding, π-π stacking and dipole-dipole interactions. Our group has focused on the design and synthesis of bis-urea macrocycles that can self-assemble into solid cylinders or tubular structures affording crystalline materials. These macrocycles consist of two urea groups and two rigid C-shaped spacers. Easy functionalization of this system enables access to bis-urea macrocycle structures that could serve as molecular reactors, coordinating ligands …

Mechanistic Investigations Of The Iron(Iii)-Catalyzed Carbonyl-Olefin Metathesis Reaction, Susan Phan

Master's Theses

Iron(III)-catalyzed carbonyl-olefin ring-closing metathesis represents a new approach toward the assembly of molecules traditionally generated by olefinˆ’olefin metathesis or olefination. Herein, we report detailed synthetic, spectroscopic, kinetic, and computational studies to determine the mechanistic features imparted by iron(III), substrate, and temperature to the catalytic cycle. These data are consistent with an iron(III)-mediated asynchronous, concerted [2+2]-cycloaddition to form an intermediate oxetane as the turnover-limiting step. Fragmentation of the oxetane via Lewis acid-activation results in the formation of five- and six-membered unsaturated carbocycles.

Reduced Graphene Oxide-Modified Screen-Printed Carbon Electrode For Determination Of Homocysteine Using Catechol, Suchapa Naranaruemol

Chulalongkorn University Theses and Dissertations (Chula ETD)

Homocysteine (Hcy), also known as 2-amino-4-mercaptobutyric acid, is a biomarker that is directly associated with an increased risk of cardiovascular diseases (CVDs). In this work, catechol (CA), which is redox active, had been used as an electron transfer mediator to facilitate the oxidation of Hcy. Typically, CA was first electrochemically immobilized onto the surface of screen-printed carbon electrode; however, the obtained CA-functionalized electrode did not show the electrocatalytic activity towards the detection of Hcy. Therefore, the deter– mination of Hcy was investigated in the solution containing CA using differential pulse voltammetry (DPV) at the reduced graphene oxide-modified screen-printed carbon electrode …

Modification Of Screen-Printed Carbon Electrode With Mxene/Conductive Polymer Composites For Hydrogen Peroxide Detection, Supawat Neampet

Chulalongkorn University Theses and Dissertations (Chula ETD)

MXene (Ti3C2), a two-dimensional material consisting of transition metal carbides, nitrides or carbonitrides was prepared by etching method for modification electrode of a novel nanocomposites consisting of platinum nanoparticles (PtNPs) and polyaniline (PANI) via electrodeposition and electropolymerization, respectively. The fabricated MXene/PANI/PtNPs nanocomposite modified on surface screen-printed carbon electrode (SPCE) were characterized by scanning electron microscopy SEM) with energy dispersive X-rays spectroscopy (EDX), X-ray powder diffraction (XRD), and transmission electron microscopy (TEM) to verify the presence of nanocomposite materials and indicate their morphologies. This electrode was applied for the detection of hydrogen peroxide (H2O2), which is a common electroactive product from …