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Synthesis And Characterization Of Cu(Ii)-Cu(I) Mixed Valence Complexes, Hansani T. Lekam Wasam Liyanage

Masters Theses

Our study was focused on synthesis and characterization of new family of metal complexes that mimic the active site of copper containing enzymes. Our approach focused on preparing a series of metalloligands which vary systematically in structure and use them in combination with additional metallic centers to synthesize our desired complexes.

We synthesized a main ligand, which is named as HL^Q 2Pz, which contain a quinoline body, one amide bond and two pyrazolyl rings. We synthesized a copper complex by deprotonating HL^Q 2Pz using KOH. The ligand coordinated to the copper(II) center through its quinoline nitrogen, two of …

Application Of High-Resolution Accurate Mass (Hram) Mass Spectrometry For Analysis Of Lignin Model Compounds And The Post-Pretreatment Products, Fan Huang

Theses and Dissertations--Chemistry

Lignin, one of main components in the woody cell walls, is a complex heterogeneous biopolymer, which provides structural support and transportation of water in plants. It is highly recalcitrant to degradation (both chemically and environmentally) and protects cellulose from being degraded/hydrolyzed. Due to the structural complexity of native lignin, complete characterization and elucidation of lignin’s structure remains very challenging. The overarching goal of this work is to develop mass spectrometry based analytical methods to contribute to a better understanding of lignin structures.

This dissertation will focus on the development and application of High-Resolution Accurate-Mass (HRAM) Mass Spectrometry (MS) as main …

Towards The Total Synthesis Of 7-Epi-Clusianone, Shubhankar Dutta

Theses and Dissertations--Chemistry

Polycyclic polyprenylated acylphloroglucinols (PPAPs) are plant- (Guttiferae) derived natural products. They have fascinating bicyclo[3.3.1]nonane-2,4,9-trione or [3.2.1]nonane-2,4,8-trione cores decorated with prenyl or geranyl groups. More than 200 PPAPs have been isolated, but only a few of them have been synthesized, although most of the synthesized PPAPs are of type A and have an exo substituent at C (7). Here, we are trying to make a type B 7-endo PPAP, 7-epi-clusianone. The synthetic plan involves an alkynylation–aldol strategy to construct the bicyclic core. Having established the bicyclic core, the synthesis presents a new challenge: the oxidation of a very hindered …

Synthesis And Development Of Zwitterionic Pei (Zpei) For Optimized Delivery Of Nucleic Acids, Joseph Raleigh Duke Iii

Theses and Dissertations--Chemistry

Gene therapy holds promise for the treatment a wide range of diseases ranging from cystic fibrosis to cardiovascular disease to cancer. The need for safe and efficient gene delivery methods remains the primary barrier to human gene therapy. Non-viral vector materials, including polymers, can be designed to be biocompatible and non-immunogenic, but lack the efficiency to be clinically relevant. Gene therapy awaits the development of new materials that are both safe and efficient. Here, we have synthesized a series of modified zwitterionic polymers based on the common transfecting agent polyethylenimine (PEI). Using a variety of biochemical and biophysical methods we …

Fragment-Based Excitonic Coupled-Cluster Theory For Large Chemical Systems, Yuhong Liu

University of the Pacific Theses and Dissertations

Accurate energetic modeling of large molecular systems is always desired by chemists. For example, ligand-protein binding simulations and enzymatic catalysis studies all involve with a small energy difference. The energetic accuracy depends largely on a proper handling of electronic correlations. Molecular mechanics (MM) methods deliver a parameterized Newtonian treatment to these problems. They show great capability in handling large calculations but give only qualitatively good results. Quantum mechanics (QM) methods solve Schrödinger equations and exhibit much better energy accuracy, though the computational cost can be prohibitive if directly applied to very large systems.

Fragment-based methods have been developed to decompose …

Investigating Secondary Structure Features Of Yap1 Protein Fragments Using Molecular Dynamics (Md) And Steered Molecular Dynamics (Smd) Simulations, Ferdiemar Cardenas Guinto Jr.

University of the Pacific Theses and Dissertations

Molecular dynamics (MD) is a powerful tool that can be applied to protein folding and protein structure. MD allows for the calculation of movement, and final position, of atoms in a biomolecule. These movements can be used to investigate the pathways that allow proteins to fold into energetically favorable structures. While MD is very useful, it still has its limitations. Most notable, computing power and time are of constant concern.

Protein structure is inherently important due to the direct link between the structure of a protein and its function. One of the four levels of protein structure, the secondary structure, …

Solubility Enhancement Of Model Compounds, Lavanya Pitani

University of the Pacific Theses and Dissertations

Solubility is the amount of solute in the solvent system at phase equilibrium with certain temperature and pressure. Many of the new chemical entities are lipophilic molecules that require techniques to enhance solubility. Solubility enhancement can be achieved by either physical and/or chemical modification of the drug. Various techniques are available for solubility enhancement of poorly soluble drugs include particle size reduction, salt formation, solid dispersions, use of surfactants, prodrug, crystal modification, etc.

In this study, the three model drugs belong to BCS class II and IV having low solubility with a certain range of physicochemical properties were studies in …

Liposome-Coated Magnesium Phosphate Nanoparticle For Delivery Of Cytochrome C Into Lung Cancer Cells A549, Weizhou Yue

University of the Pacific Theses and Dissertations

Proteins are large biomolecules that have great therapeutic potential in treating many human diseases. However, chemical/enzymatic degradation, denaturation, and poor penetration into cells are some of the challenges for clinical use of intracellular proteins.

Previously, our group has developed cationic lipid-coated magnesium phosphate nanoparticle (LP MgP NP-CAT) formulations to enhance the intracellular delivery of the negatively charged protein catalase. The goal of the current research is to develop a formulation to deliver cytochrome c (CytC), a positively charged protein into lung cancer cells A549. Specifically, this thesis research prepares and tests liposome-coated magnesium phosphate nanoparticle for delivery of cytochrome c …

Preclinical Evaluation Of Ag10 For Therapeutic Use Against Familial Amyloid Cardiomyopathy And Its Application In Various Other Technologies, Mark Russell Miller

University of the Pacific Theses and Dissertations

Transthyretin (TTR) amyloidosis is a progressive, fatal disease in which deposition of amyloid derived from either mutant or wild-type TTR causes severe organ damage and dysfunction. TTR cardiomyopathy is an infiltrative, restrictive cardiomyopathy characterized by progressive left and right heart failure. Familial amyloid cardiomyopathy (FAC) is driven by pathogenic point mutations in the TTR gene that destabilize the TTR tetramer, prompting its dissociation into dimers and monomers, with subsequent misfolding, aggregation and deposition of toxic TTR amyloid aggregates in the myocardium. The most prevalent mutation that causes FAC is the V122I variant, carried by 3.4% of African Americans, that increases …

Synthetic Methods For Ester Bond Formation And Conformational Analysis Of Ester-Containing Carbohydrates, Sven Hackbusch

University of the Pacific Theses and Dissertations

This dissertation encompasses work related to synthetic methods for the formation of ester linkages in organic compounds, as well as the investigation of the conformational influence of the ester functional group on the flexibility of inter-saccharide linkages, specifically, and the solution phase structure of ester-containing carbohydrate derivatives, in general.

Stereoselective reactions are an important part of the field of asymmetric synthesis and an understanding of their underlying mechanistic principles is essential for rational method development. Here, the exploration of a diastereoselective O-acylation reaction on a trans-2-substituted cyclohexanol scaffold is presented, along with possible reasons for the observed reversal of stereoselectivity …

Platelet-Derived Microparticles And Their Role In Sepsis, Robert Tramel

Honors Theses

Causing at least 215,000 deaths in the U.S. annually- more than prostate cancer, breast cancer, and AIDS combined- and rising, sepsis is one of the most deadly medical conditions in America. Sepsis pathophysiology, however, is still incompletely understood, making it difficult for physicians to diagnosis and treat effectively. Given the time-sensitivity of treatment, researchers are now searching for new methods to identify sepsis early, developing more accurate prognostic markers, and developing new target therapeutic candidates. One biological component of interest in this research is the platelet-derived microparticle (PMP), a heterogeneous vesicle derived from the cell membrane of platelets found circulating …

An Integrative Synthetic, Spectroscopic, And Computational Study Of The Free Radical Chlorine Dioxide And Its Interactions With Hydrogen Bonded Networks, Sarah C. Sutton

Honors Theses

The free radical chlorine dioxide (ClO2) is a strong oxidizing agent that is used to purify drinking water and medical equipment. The existing literature shows discrepancies in the explanation of the solvent dependent properties of ClO2. The following thesis investigates these properties by integrating integrates inorganic synthesis, spectroscopic analyses, and computational methods. ClO2/water hydrogen-bonded networks were computed with the DFT method B3LYP with 6-31G(d,p) and 6-311++G(2df, 2pd) basis sets. Raman frequency computations were performed on local minima geometries. Experimental Raman spectra of chlorine dioxide solvated in water and methanol were obtained, and the fundamental symmetric stretch (nu1) of each spectrum …

Spectroscopic And Computational Studies Of The Hydrogen Bonding Interactions Of Hydroxyethyl Ethers, Ashley Elizabeth Williams

Honors Theses

The isoenzymatic form of microsomal cytochrome P450, CYP2E1, is involved in the formation of oxygen free radicals, specifically hydroxyethyl ether. Chronic alcohol abuse has been found to induce larger levels of CYP2E1 in the liver, thus increasing production of these harmful free radicals. Generation of the hydroxyethyl ether oxygen free radicals occurs during the metabolism of ethanol in microsomes. The hydrogen-bonding interactions of hydroxyethyl ethers with water have yet to be analyzed, and information regarding the interactions with water can be applied directly to biological systems. Here, we employ Raman spectroscopy and computational chemistry to study hydroxyethyl ether complexes in …

A Thermally Stabilized Fluorescent Organic Chromophore, Brendan P. Hughes

Graduate Dissertations and Theses

A fluorescent chromophore, hereby designated as cyanine dye, has been bound to generated zinc oxide nanoparticles. It has been shown that the material not only retains the characteristic absorption peak of the native chromophore, but it also continues to fluoresce with comparable intensity. The binding occurs through a Zn – O₂C bridge, which allows for vibrational relaxation as the dye heats up, yet also preserves the optical properties of the dye. This bond linkage can be observed from the comparison of FT-IR spectra of the nanoparticles and the native dye, designated by a shift in one of the …

Cytotoxicity Assay Of Self-Assembling Protein-Based Biomaterials, Peyton Vaughan

Honors Theses

Acute inflammation is a natural biological defensive response against infection,irritation, and injury. While inflammation is a natural process, chronic tissue inflammation has been implicated in the development of several different diseases. With the intent of minimizing collateral damage associated with long-term exposure of healthy tissues to anti-inflammatory drugs, the Pedigo laboratory has designed a system for the self-assembly of protein polymers as scaffolds for controlled-release of drugs to affected tissues. This protein polymer comprises two essential components, with the first component being the calcium-dependent protein, calmodulin, and the second being a corresponding binding peptide, M13. Because Calmodulin has a specific, …

Quercitrin And Afzelin Isolation: Chemical Synthesis Of A Novel Methicillin-Resistant Staphylococcus Aureus (Mrsa) Antibiotic Analogue, Taylor Ramsaroop

Honors Theses

The increasing prevalence of bacterial resistance to antibiotics is an epidemic where once easily treated infectious illnesses are becoming more difficult to treat, leading to prolonged suffering, exacerbated medical costs, and sometimes death. Methicillin-Resistant S. aureus (MRSA) is a strain of the Staph Infection causing bacteria that is resistant to penicillin-like beta lactam antibiotics and occurs at a high incidence in several countries in Europe, the Americas, and the Asia-Pacific region. In a routine screening of plant extracts, an extract of American Sycamore leaves (Plantus occidentalis) was noted to show promising activity against the experimental MRSA strain included in the …

Towards The Synthesis Of A Polyamine Perylenebisimide Derivative For Intercalation Into Quadruplex Dna, Bobby May

Honors Theses

Perylenebisimide intercalation in G-quadruplex DNA is an area of study that has increasing interest in cancer research. The ability of perylenebisimides to interrupt the structures of the G4 DNA on the end of telomeres has allowed for the observation of how the variable-regions of the perylenebisimide can have differing effects on anticancer properties. The purpose of this experiment was to synthesize a perylenebisimide with the intentions of observing its intercalating properties with G-quadruplex DNA. In order to accomplish this, dibenzylamine was substituted onto chloroacetonitrile through an SN2 reaction to produce 2-(dibenzylamino)acetonitrile. The 2-(dibenzylamino)acetonitrile was then reduced with LAH to yield …

Isolation And Identification Of Bioactive Constituents Of Plant Pathogenic Fungi And Targeted Synthesis Of Isochromanone Analogs, Brandon Clausen

Honors Theses

An unknown fungal species was cultured from necrotic Brachiaria eruciformis leaves found in Oxford, Mississippi. The fungus was identified via molecular techniques as Pyricularia grisea. This fungus was grown on Czapek Dox broth culture medium for 21 days under continuous light at 24 0C. The culture filtrate was extracted with ethyl acetate and concentrated. The major bioactive compound, namely pyrichalasin H, was isolated using TLC-guided fractionation and identified via spectroscopic techniques. The compound was then tested for bioactivity on monocotyledons, dicotyledons and agriculturally important fungal species. Cellular leakage, chlorophyll content and root/shoot length bioassays were also performed to probe the …

Cadmium Disruption Of Calcium-Dependent Dimerization Of Neural Cadherin, Dylan Ritter

Honors Theses

Cadherins are a family of transmembrane proteins that dimerize to form junctions between cells in the presence of calcium. Due to the necessity for proper cell adhesion during cell differentiation in development, we are examining whether binding of other metallic divalent cations would disrupt calcium-sensitive dimerization of neural cadherin in vitro. Specifically, we are studying the effect of cadmium(II) on the linkage between calcium binding, dimerization, and dimer disassembly. Cadmium toxicity became recognized during the Industrial Revolution, with particular attention gained during the Itai-Itai disease outbreak in China during the 1910s. This toxicity, partnered with the role of cadherin in …

Non-Traditional Examination: A Study To Improve Academic And Research Performance Of Undergraduate Organic Chemistry Students#, Bimal K. Banik, Ram Naresh Yadav, Sunena Chandra

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

An investigation of conducting a presentation examination instead of a classical written examination method on academic and research performance of undergraduate chemistry students was performed at the University of Texas-Pan American. The results suggest that chemistry students do much better in the presentation examination compared to the written examination at the advanced organic chemistry course. But, the performances of the students in the lower level courses are mixed. However, students do much better in research work when presentation examination was conducted.

Carbon Dioxide-Mediated Preparation Of Pyrroles In Water Following Paal Knorr Method, Ram Naresh Yadav, Bimal K. Banik

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

Carbon dioxide-mediated new reaction of 2,5-hexanedione and primary amino compounds in water-THF produced N-substituted pyrroles in excellent yield. This method for the preparation of pyrroles is novel, simple, and efficient.

Ammonium Chloride-Induced Synthesis Of Pyrroles Via Paalknorr Reaction, Debasish Bandyopadhyay, Bimal K. Banik

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

Reaction of commercially available 2,5-hexanedione and primary amino compounds in the presence of ammonium chloride produced N-substituted pyrroles in excellent yield. In contrast to other available methods, this current procedure for the preparation of pyrroles is exceedingly simple, efficient, and eco-friendly and therefore, may find numerous applications in this field.

Dihydropyridines As Calcium Channel Blockers: An Overview, Thelma Salazar, Andres Gonzalez, Debasish Bandyopadhyay

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

Cardiovascular disease remains one of the leading causes of death in the United States. It is estimated that 1 in every 3 American adults suffer from high blood pressure. Hypertension, a precursor to most cardiovascular diseases, continues to grow at an alarming rate and is seldom managed carefully. Attempts have been made to manage hypertension and reduce the morbidity and mortality of the cardiovascular organ through methods including diets, increased amount of exercise, and medications. Many commercial drugs have been derived from dihydropyridine due to its antihypertensive property. Dihydropyridine derivatives work by acting as calcium channel blockers blocking the intake …

Identification And Characterization Of A Chemical Compound That Inhibits Methionyl-Trna Synthetase From Pseudomonas Aeruginosa, Sara Robles, Yanmei Hu, Tahyra Resto, Frank Dean, James M. Bullard

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

Background: Pseudomonas aeruginosa is an opportunistic pathogen problematic in causing nosocomial infections and is highly susceptible to development of resistance to multiple antibiotics. The gene encoding methionyl-tRNA synthetase (MetRS) from P. aeruginosa was cloned and the resulting protein characterized.

Methods: MetRS was kinetically evaluated and the KM for its three substrates, methionine, ATP and tRNAMet were determined to be 35, 515, and 29 μM, respectively. P. aeruginosaMetRS was used to screen two chemical compound libraries containing 1690 individual compounds.

Results: A natural product compound (BM01C11) was identified that inhibited the aminoacylation function. The compound inhibited P. aeruginosa MetRS with an …

Methods For Producing Graphene From Petroleum By-Products, Eva M. Deemer

Open Access Theses & Dissertations

N/A

Complementary Charged Molecular Imprints Of West Nile Virus Antibodies, Julio Rincon

Open Access Theses & Dissertations

There is a significant demand for robust and stable receptor molecules that can mimic biological molecules, such as antibodies. Relying only on natural recognition molecules have greatly limited the uses and capabilities of many aspects of health sciences due to product expense and stability. This is especially important in medically underserved areas where the lack of resources and faulty or limited cold-chain makes antibody based diagnostics very difficult to implement.

With molecular imprinting, it is possible to recognize diseases with the added advantage of product stability, long term use, fast preparation and ease of scalability, all while being cost effective. …

Design And Regioselective Synthesis Of Fullerene Derivatives For Metal-Organic Hybrid Architectures, Catalina Suarez

Open Access Theses & Dissertations

In the last years different fullerene derivatives and endohedral fullerenes have been reported and their potential applications as electronic, magnetic, catalytic, biological and optical materials have been explored. In this work we describe the characterization of new endohedral fullerenes; the exohedral functionalization of fullerenes with organic addends or metal clusters and their application in metal-organic hybrid architectures.

We synthesized fullerene polymers with a variety of staircase linear architectures, zigzag polymers and a perfectly linear polymer using an hexakis-fullerene adduct with two 4,5-diazafluorene groups located at trans-1 positions, using Hg, Cd, Zn and33 Cu as the metal centers. Our results showed …

Synthesis Of New Fullerene Derivatives For Photovoltaic And Biological Applications, Edison Castro

Open Access Theses & Dissertations

Functionalized fullerenes exhibit improved solubility and different chemical and physical properties that allow applications in multiple fields such as photovoltaic and biological applications. Currently, perovskite solar cells (PSCs) are the most rapidly developing type of solar cells with certified efficiencies rising from 3.8% in 2009 to 22.1% in 2016. The good electron transporting and solution processable properties of most fullerene derivatives make them the most popular electron transporting materials (ETMs) in inverted perovskite solar cells (PSCs).

The work is reported in 11 chapters. We start with a fullerene overview followed by cleaver and elegant methodologies that allow the synThesis of …

Biofunctionalized Capillary Flow Channel Platform Integrated With 3d Nanostructured Matrix To Capture Circulating Tumor Cells, Shashwat Banerjee, Ganesh Khutale, Vrushali Khobragade, Narendra Kale, Milind Pore, Govind Chate, Archana Jalota-Badhwar, Manoj Dongare, Jayant Khandare

Articles

Circulating tumor cells (CTCs) from peripheral blood account genetic information for cancer diagnosis and overall disease monitoring. Analysis of “liquid biopsy” holds immense promise as it may lead to new approaches for cancer treatment. The study reports effective and continuous flow microchannel system for isolating CTCs using transferrin conjugated 3D matrix synthesized by crosslinking polyethylene glycol-Fe3O4 nanostructures for rapid and efficient capturing of CTCs. The platform provides option of using multiple microchannel units in series that can influence higher cell-capture efficiency due to increasing cell-substrate contact frequency. CTCs are captured with high efficiency even at low concentration of target cells …

Polymer Grafted Nanoparticles For Designed Interfaces In Polymer Nanocomposites, Mohammad Mohammadkhani

Theses and Dissertations

This dissertation presents the design, synthesis, and characterization of polymer nanocomposite interfaces and the property enhancement from this interface design. Through the use of reversible addition fragmentation chain transfer (RAFT) polymerization for the grafting of polymer chains to silica nanoparticles, the surface of silica nanoparticles can be manipulated to tune the properties of nanocomposites by controlling the interface between the particles and the polymer matrix.

In the first part of this work, compatibility of 15 nm silica nanoparticles grafted with different alkyl methacrylates with linear low density polyethylene was investigated. SI-RAFT polymerization of hexyl, lauryl, and stearyl methacrylate on silica …