Digital Commons Network^™

Mass Spectrometry-Based Rnomics : Global Surveys Of Ribonucleotide Modifications As Possible Indicators Of Cell Identity, Epigenetic, Metabolic And Pathological State, Rebecca Erin Rose

Legacy Theses & Dissertations (2009 - 2024)

Discovery of the regulatory roles of non-protein coding RNAs (ncRNAs), once considered “junk” or “transcriptional noise”, has prompted a reassessment of the significance of the multifaceted activities of RNA in cellular response, which can result in cell transformation and diseased states. This reassessment, however, can only be accomplished if techniques are developed to capture, characterize and quantify the more than 100 covalent post-transcriptional modifications (PTMs) that adorn natural RNAs. Undoubtedly, the creation of high-throughput platforms such as next-generation sequencing and RNA-seq have provided unparalleled accuracy and sensitivity, however, they rely on strand amplification procedures that are blind to the known …

Fluorinated Hypervalent Sulfur Compounds In Synthesis, Cortney Von Hahmann

Legacy Theses & Dissertations (2009 - 2024)

The polar and steric effects of pentafluorosulfanyl (SF5) substitution on selectivity and reactivity were investigated in the ketene imine [2+2] cycloaddition reaction. The kinetic resolution of racemic aldimines rely on the stereocontrol of cyclization by dipolar substituent effects. Functionalized SF5-bearing β-lactams are used in the preparation of conformationally constrained SF5-containing β-amino acids and peptides, in the study of novel antibacterial agents and in the design of new β-lactamase inhibitors.

Initiated Chemical Vapor Deposition (Icvd) Polymer Thin Films : Structure-Property Effects On Thermal Degradation And Adhesion, Vijay Jain Bharamaiah Jeevendrakumar

Legacy Theses & Dissertations (2009 - 2024)

Opportunities and challenges for chemical vapor deposition (CVD) of polymer thin films stems from their applications in electronics, sensors, and adhesives with demands for control over film composition, conformity and stability. Initiated chemical vapor deposition (iCVD) is a subset of the CVD technique that conjoins bulk free-radical polymerization chemistry with gas-phase processing. The novelty of iCVD technique stems from the use of an initiator that can be activated at low energies (150 – 300 °C) to react with surface adsorbed monomer to form a polymer film. This reduces risk for potential unwarranted side-reactions.

An Investigation Of Alkaline Earth And Rare Earth Elements In Human Bone Following Long-Term Parenteral Nutrition, Aubrey L. Galusha

Legacy Theses & Dissertations (2009 - 2024)

This investigation focused on a unique collection of archived human bones obtained post-mortem from 7 patients, who had received long-term parenteral nutrition (PN) for up to 21 years. Parenterals are administered intravenously as a nutritional supplement, and may be contaminated with metals, which are completely absorbed into the blood compartment. Some metal contaminants may be deposited in the body’s reservoir for inorganic elements – bone.

Distributions And Formations Of Hono In The Troposphere, Dennis Pu

Legacy Theses & Dissertations (2009 - 2024)

Nitrous acid (HONO) is an important reactive nitrogen species and a precursor to the hydroxyl radical. It plays important roles in reactive nitrogen recycling and in photo-oxidant formation in the troposphere. However, much is still unknown about its formation mechanisms and distributions in the troposphere. This research is part of NOMADSS (Nitrogen, Oxidants, Mercury, and Aerosol Distributions, Sources and Sinks) field study contributed by over 10 research groups in the United States to investigate the tropospheric chemistry of reactive nitrogen, mercury, oxidant and aerosols. One of the goals was to study the HONO distribution and formation mechanisms in the troposphere. …

Characterization Of Metallic And Semimetallic Oxide Nanoparticles In Industrial Wastewater And Associated Toxicity, Gary Roth

Legacy Theses & Dissertations (2009 - 2024)

Engineered nanomaterials (ENMs) play an increasing role in manufacturing and consumer products. Currently, there is no standard approach to studying ENM toxicity, and a growing body of literature suggests that ENMs may have toxicity differing from similar compounds in bulk or dissolved form. I examined ENMs used in the semiconductor manufacturing process called chemical-mechanical planarization (CMP) for their properties, removal in the wastewater treatment system (WWT), in-vitro toxicity, and location post-inhalation in-vivo. It was found that ENMs in CMP slurries have morphology determined by their elemental composition, but assessment of size and concentration can differ substantially between accepted techniques. Particles …

Molecular Dynamics Simulations Of Small Systems To Improve Base Pairing Parameters Of The Amber-99 Force Field, Angelo Christopher Setaro

Legacy Theses & Dissertations (2009 - 2024)

Simulations of biochemical systems are being increasingly used to further our understanding of those systems. In broad strokes, chemical simulations can be broken into two categories, those that are rooted in a quantum mechanical approach and those that are classically rooted. Molecular dynamics is one such classical method, which propagates motion of a chemical system via repeatedly solving Newton’s Laws of motion. This approach is less computationally intensive than the quantum mechanical methods and allows for the simulation of systems of tens of thousands of atoms, if not more.

Advanced Raman Spectroscopic Methods For Structural Characterization Of Amyloid Fibrils And Bionanotubes, Valentin Sereda

Legacy Theses & Dissertations (2009 - 2024)

Amyloid aggregation is a specific form of protein misfolding and self-assembly related to several degenerative pathologies like Alzheimer's and Parkinson's diseases, type-II diabetes, etc. This association with deadly diseases has made amyloid fibrils the focus of intensive research for many decades. Most recently, a significant interest to protein fibrils was also due to the application of the remarkable self-assembling capabilities to form well-structured nano-biomaterials. Self-assembly of short peptide sequences into well-organized structures is another important strategy for bottom-up fabrications of nano-biomaterials. One of the most commonly used building blocks is diphenylalanine, a short dipeptide that has been identified as playing …

The Genesis And Emergence Of Community-Associated Methicillin-Resistant Staphylococcus Aureus (Ca-Mrsa): An Example Of Evolution In Action?, Alan L. Gillen, Jason Conrad, Michael Cargill

Faculty Publications and Presentations

Staphylococcus aureus infections are a common cause of disease, particularly in colonized persons. Recently, a series of published articles have reported that community-acquired methicillin-resistant S. aureus (CA-MRSA) strains are evolving and increasingly becoming prevalent in households while health care acquired MRSA (HA-MRSA) is declining in the USA. The changing superbugs have often been used as an example of evolution in action. Although MRSA infections have become increasingly reported in the community, population-based studies of students preparing for the health professions having S. aureus and MRSA colonization are lacking. During the 2014–2015 school year 544 students were tested for MRSA carriage …

Pfam Catalyzed Enantioselective Diethylzinc Addition To Imines, Özdemi̇r Doğan, Eda Çağli

Turkish Journal of Chemistry

Chiral amines are important starting materials for the synthesis of biologically important compounds. Enantioselective addition of dialkylzinc reagents to imines is a reliable method for the synthesis of these compounds. Different chiral catalysts were developed and used for this method. Phosphorous based PFAM catalysts were tried for the first time in the enantioselective synthesis of amines by reacting diethylzinc with N-sulfonyl imines and N-diphenylphosphinoyl imines. Chiral amines were isolated with moderate to acceptable yields and enantioselectivities.

One-Pot And Solvent-Free Synthesis Of 3-(9-Hydroxy-3-Methoxy-7-Aryl-6,7,9,10-Tetrahydro-5$H$-Benzo[$H$]Thiazolo[2,3-$B$]Quinazolin-9-Yl)-2$H$-Chromen-2-Ones And Their Antibacterial Evaluation, Ravibabu Velpula, Janardhan Banothu, Rajitha Gali, Yakaiah Sargam, Rajitha Bavantula

Turkish Journal of Chemistry

A series of 3-(9-hydroxy-3-methoxy-7-aryl-6,7,9,10-tetrahydro-5$H$-benzo[$h$]thiazolo[2,3-$b$]quinazolin-9-yl)-2$H$-chromen-2-ones (5a-j) were synthesized by one-pot multicomponent reaction of 6-methoxy-1-tetralone, aryl aldehydes, and thiourea followed by cyclization with 3-(2-bromoacetyl)-2$H$-chromen-2-one in the presence of a Bronsted solid acid catalyst, poly(4-vinylpyridinium)hydrogen sulfate [P(4-VPH)HSO$_{4}$] (0.015 g), under solvent-free conditions at 120 $^{\circ}$C. All the synthesized compounds were characterized by spectral studies and screened for their in vitro antibacterial activity against S. aureus and B. thuringiensis (gram positive), and E. coli and K. pneumoniae (gram negative) bacterial strains. On comparing with the standard drug gentamicin, compounds derived from 4-methoxy and 3,4,5-trimethoxy benzaldehyde, i.e. 5g and 5h, showed broad spectrum antibacterial activity …

Effective Recognition Of Multiple Anions By An Azobenzene--Al$^{\Mathbf{3+}}$ System, Ye Zhang, Ping Jia, Zhangfa Tong, Hai-Bo Liu, Jing Wang

Turkish Journal of Chemistry

A ready-to-use multifunctional coordinative system, 2,2'-dihydroxyazobenzene --aluminum (III) (DHAB--Al$^{3+})$, was created to recognize several anions effectively through three channels, namely colorimetric detection, UV-Vis spectroscopy, and fluorescence spectroscopy. Under naked eye visualization, the H$_{2}$PO$_{4}^{-}$ can be readily distinguished from the other anions by the DHAB--Al$^{3+}$ system through a change in color from reddish-orange to light yellow. H$_{2}$PO$_{4}^{-}$ was qualitatively detected by using UV-Vis and fluorescence spectra. Differentiating SO$_{3}^{2-}$, HPO$_{4}^{2-}$, and HCO$_{3}^{-}$ anions colorimetrically is difficult; thus, CO$_{3}^{2-}$, SO$_{3}^{2-}$, HPO$_{4}^{2-}$, and HCO$_{3}^{-}$ were discriminated by adopting distinct changes in the UV-Vis spectra. CO$_{3}^{2-}$, HPO$_{4}^{2-}$, and HCO$_{3}^{-}$ were accurately quantified using fluorescence spectra. …

Boron Nitride Colloidal Solutions, Ultralight Aerogels And Freestanding Membranes Through One-Step Exfoliation And Functionalization, Weiwei Lei, Vadym Mochalin, Dan Liu, Si Qin, Yury G. Gogotsi, Ying Chen

Chemistry Faculty Research & Creative Works

Manufacturing of aerogels and membranes from hexagonal boron nitride (h-BN) is much more difficult than from graphene or graphene oxides because of the poor dispersibility of h-BN in water, which limits its exfoliation and preparation of colloidal solutions. Here, a simple, one-step mechano-chemical process to exfoliate and functionalize h-BN into highly water-dispersible, few-layer h-BN containing amino groups is presented. The colloidal solutions of few-layer h-BN can have unprecedentedly high concentrations, up to 30 mg ml^-1, and are stable for up to several months. They can be used to produce ultralight aerogels with a density of 1.4 mg cm …

Occurrence, Monitoring And Removal Of Drinking Water Contaminants By Advanced Technologies, Danielle Marie West

Doctoral Dissertations

"In order to maintain drinking water primary standards compliance under the USEPA Stage 2 Disinfectant Disinfection Byproducts Rule, drinking water treatment plants (DWTPs) are switching from free chlorine (FC) to chloramines (MCA). Concerns are raised as MCA disinfection has been linked N-nitrosamine formation. N-nitrosamines are a group of nitrogenous DBPs (N-DBPs) which are highly carcinogenic in comparison to regulated DBPs (THMs and HAAs, generated by FC disinfection). Also in the forefront of drinking water concerns are other emerging drinking water contaminants such as perchlorate. Perchlorate is a contaminant which can enter drinking water from natural deposits or through introduction by …

Detection And Removal Of Emerging Environmental Contaminants, Ruipu Mu

Doctoral Dissertations

"Water is a very crucial natural resource for human. The increasing number of contaminants detected in water bodies has drawn considerable increasing attention over the last decade. There are numerous emerging environmental contaminants which may cause serious health issues. The recent occurrence studies of these contaminants show both industrial and household activity introduction of chemicals into water resources. These various sources result in a large variety of chemicals such as explosives, pharmaceutical and personal care products (PPCPs) and disinfection byproducts detected in water worldwide. Due to the relatively low contaminant concentrations, development of new and improved detection methods along with …

Illuminating The Interactions And Functions Of Glutaredoxins, Bola Proteins, And Erv1 In Iron Homeostasis, Adrian Colleen Dlouhy

Theses and Dissertations

Iron is a redox-active protein cofactor required for essential cellular functions such as respiration, however excess intracellular iron can generate damaging reactive oxygen species. Understanding how cells regulate iron levels is critical for treatment of human diseases that span from anemia to iron overload disorders. Glutaredoxins (Grxs) with a CGFS active site are highly conserved proteins shown to have roles in iron homeostasis and iron-sulfur cluster assembly, thus earning them the title “the Iron Whores”. They can exist either as a [2Fe-2S] cluster-bound dimer or an apo monomer, suggesting conservation of structure and function. In addition, Grxs interact with the …

In Vitro Study Of Wound-Healing Capabilities Of Bioactive Glass Fibers Under Various Culture Conditions, Sisi Chen

Masters Theses

"Bioactive borate glass has been recognized to have both hard and soft tissue repair and regeneration capabilities through stimulating both osteogenesis and angiogenesis. However, the underlying physiological and cellular mechanism behind this function remains unclear. In this study, in vitro dynamic flow modules were designed to mimic the micro-environment near the vascular depletion and hyperplasia area in wound-healing regions, and were used to investigate the biocompatibility and functionality of borate glass nano-/micro-fibers. Glass-cell interactions were investigated either by dosing fibers to the upstream of or co-cultured with cells, and two types of borate glasses (with or without CuO/ZnO doped were …

Redox Active Lipophilic Ruthenium Complexes As Potential Anti-Cancer Drugs, Nagham Alatrash

Chemistry & Biochemistry Dissertations - Archive

The dinuclear ruthenium(II) polypyridyl complexes (RPCs) [(phen)2Ru(tatpp)Ru(phen)2][PF6]4 (P4+) and the monomeric [(phen)2Ru(tatpp)]Cl2 (MP2+) are promising candidates for anti-cancer drug development in terms of the observed anti-tumor activity in vivo and in vitro. These complexes contain the redox-active tatpp (9,11,20,22-tetraazatetrapyrido[3,2-a:2'3'-c:3'',2''-1:2''',3''']-pentacene) ligand which seems to be the critical component for biological activity. These complexes cleave DNA when reduced in situ to a radical species. Both complexes exhibit selective cytotoxicity toward cultured malignant cell lines and showed inhibition of tumor growth in vivo. This work expands on this platform by preparing and examining more lipophilic analogues of P4+ and MP2+. Specifically, four lipophilic …

Chemistry 106 Chemistry For Health Professions Fall 2015, Sheryl Drake

Chemistry Courses

No abstract provided.

Biginelli Synthesis And Characterization Of Potentially Anti-Proliferative Dihydropyrimidinone Thione Analogs, Timothy K. Summers

Theses and Dissertations

No abstract provided.

Chemoselective Formation Of Unsymmetrically Substituted Ethers From Catalytic Reductive Coupling Of Aldehydes And Ketones With Alcohols In Aqueous Solution, Nishantha Kumara Kalutharage, Chae S. Yi

Chemistry Faculty Research and Publications

A well-defined cationic Ru–H complex catalyzes reductive etherification of aldehydes and ketones with alcohols. The catalytic method employs environmentally benign water as the solvent and cheaply available molecular hydrogen as the reducing agent to afford unsymmetrical ethers in a highly chemoselective manner.

Genetic Algorithm Optimization Of Point Charges In Force Field Development: Challenges And Insights, Maxim Vadimovich Ivanov, Marat R. Talipov, Qadir K. Timerghazin

Chemistry Faculty Research and Publications

Evolutionary methods, such as genetic algorithms (GAs), provide powerful tools for optimization of the force field parameters, especially in the case of simultaneous fitting of the force field terms against extensive reference data. However, GA fitting of the nonbonded interaction parameters that includes point charges has not been explored in the literature, likely due to numerous difficulties with even a simpler problem of the least-squares fitting of the atomic point charges against a reference molecular electrostatic potential (MEP), which often demonstrates an unusually high variation of the fitted charges on buried atoms. Here, we examine the performance of the GA …

Characterization Of Terrestrial Dissolved Organic Matter Fractionated By Ph And Polarity And Their Biological Effects On Plant Growth, Rachel L. Sleighter, Paolo Caricasole, Kristen M. Richards, Terry Hanson, Patrick G. Hatcher

Chemistry & Biochemistry Faculty Publications

Background: Humic substances are ubiquitous in the environment, complex mixtures, and known to be beneficial to plant growth. To better understand and identify components responsible for plant growth stimulation, a terrestrial aquatic DOM sample was fractionated according to pH and polarity, obtaining acid-soluble and acid-insoluble portions, as well as acid-soluble hydrophobic and hydrophilic fractions using C18. The various fractions were characterized then evaluated for their biological effects on plant growth using bioassays with corn at two carbon rates.

Results: Approximately 43% and 57% of the carbon, and 31% and 69% of the iron, was found in the acid-insoluble and acid-soluble …

Indolinyl-Thiazole Based Inhibitors Of Scavenger Receptor-Bi (Sr-Bi)-Mediated Lipid Transport, Chris Dockendorff, Patrick W. Faloon, Miao Yu, Willmen Youngsaye, Marsha Penman, Thomas J.F. Nieland, Partha P. Nag, Timothy A. Lewis, Jun Pu, Melissa Bennion, Joseph Negri, Conor Paterson, Garrett Lam, Sivaraman Dandapani, José R. Perez, Benito Munoz, Michelle A. Palmer, Stuart L. Schreiber, Monty Krieger

Chemistry Faculty Research and Publications

A potent class of indolinyl-thiazole based inhibitors of cellular lipid uptake mediated by scavenger receptor, class B, type I (SR-BI) was identified via a high-throughput screen of the National Institutes of Health Molecular Libraries Small Molecule Repository (NIH MLSMR) in an assay measuring the uptake of the fluorescent lipid DiI from HDL particles. This class of compounds is represented by ML278 (17–11), a potent (average IC₅₀ = 6 nM) and reversible inhibitor of lipid uptake via SR-BI. ML278 is a plasma-stable, noncytotoxic probe that exhibits moderate metabolic stability, thus displaying improved properties for in vitro …

Cellulose, Chitosan, And Keratin Composite Materials. Controlled Drug Release, Chieu D. Tran, Tamutsiwa Moven Mututuvari

Chemistry Faculty Research and Publications

A method was developed in which cellulose (CEL) and/or chitosan (CS) were added to keratin (KER) to enable [CEL/CS+KER] composites to have better mechanical strength and wider utilization. Butylmethylimmidazolium chloride ([BMIm⁺Cl^–]), an ionic liquid, was used as the sole solvent, and because the [BMIm⁺Cl^–] used was recovered, the method is green and recyclable. Fourier transform infrared spectroscopy results confirm that KER, CS, and CEL remain chemically intact in the composites. Tensile strength results expectedly show that adding CEL or CS into KER substantially increases the mechanical strength of the composites. We found …

Synthetic Studies Of Ambruticin: Preparation Of The C1-C8 Tetrahydropyran And The C17-C24 Dihydropyran Segments, Luping Liu, Julie L. Wondergem, William A. Donaldson

Chemistry Faculty Research and Publications

The C1-C8 tetrahydropyran and the C17-C24 dihdropyran segments of ambruticin were prepared from L-arabinose in 11 steps, 7.6% overall yield and from (S)-ethyl lactate in 8 steps, 22.2% overall yield respectively.

The Role Of Hydroxyl Channel In Defining Selected Physicochemical Peculiarities Exhibited By Hydroxyapatite, Vuk Uskoković

Pharmacy Faculty Articles and Research

Mysteries surrounding the most important mineral for the vertebrate biology, hydroxyapatite, are many. Perhaps the Greek root of its name, απαταo, meaning ‘to deceive’ and given to its mineral form by the early gem collectors who confused it with more precious stones, is still applicable today, though in a different connotation, descriptive of a number of physicochemical peculiarities exhibited by it. Comparable to water as the epitome of peculiarities in the realm of liquids, hydroxyapatite can serve as a paradigm for peculiarities in the world of solids. Ten of the peculiar properties of hydroxyapatite are sketched in this review piece, …

Nanoceria Exposure To Kidney Beans (Phaseolus Vulgaris): Implications On Plant Physiology, Nutrition And Their Transfer To Next Trophic Level, Sanghamitra Majumdar

Open Access Theses & Dissertations

Previous studies investigating the effects of cerium oxide nanoparticles (nanoceria, nCeO2) on plants have primarily focused on the physiological and biochemical changes at early growth stages. Comprehensive information on the effects of nCeO2 through the entire life cycle of plants and the nutritional quality of the edible tissues is limited. No studies have been reported on the interactions between nCeO2 and common beans (Phaseolus vulgaris). Common beans are leguminous crops, which are societally important due to their nutritional benefits. The beans are rich in proteins and essential nutrients like folate, iron, zinc, molybdenum and magnesium, and are consumed worldwide. This …

Investigation Of Solvent-Dependent Properties Of Donor And Acceptor Materials For Photovoltaic Applications, Anna L. Foote

Browse all Theses and Dissertations

The choice of solvent and additive has been shown to affect efficiency of organic solar cell devices. To gain a basic understanding of the role of solvents in influencing overall device performance, we present a comparative study on the physical properties of donor: acceptor mixtures in different solvents. Investigations have been carried out for P3HT (poly(3-hexylthiophene-2,5-diyl)), PTB7 (poly[4,8-bis[(2-ethylhexyl)oxy]benzo[1,2-b:4,5-b']-dithiophene-2,6-diyl][3-fluro-2-[2-ethylhexyl)carbonyl[thieno[3,4-b]thiophenediyl]]), PC61BM ([6,6]-phenyl-C60-butyric acid methyl ester), and PC71BM ([6,6]-phenyl-C70-butyric acid methyl ester). The physical properties reported are based on UV-Vis absorption spectroscopy, resistance measurements, cyclic voltammetry measurements, and surface energy characterizations of the organic films. The solvents used to prepare the organic films …

Method Development For Mass Spectrometric Characterization Of Ultra-Small Nanomolecules And Mass Spectrometry Imaging Of Selected Biomolecules, Nuwan K. Kothalawala

Electronic Theses and Dissertations

High sensitivity, selectivity and remarkable identification capabilities facilitate the applicability of mass spectrometry (MS) in diverse fields. This dissertation outlines how this cutting edge technology is used to determine the chemical composition of the ultra-small nanomolecules (NMs) to atomic precision and obtain spatial resolution of selected biomolecules using mass spectrometry imaging (MSI). Chapter I includes introduction to electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI) MS used in my PhD research. Chapter II explains how high resolution ESI-MS methods were developed to analyze the polar water-soluble NMs. These new methods express how ESI-MS parameters need to be optimized …