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Water-Soluble Reversible Addition-Fragmentation Chain Transfer (Raft) Agents And Their Bioconjugation To Dsdna, Dylan F. Finneran

Master's Theses and Capstones

Understanding the properties of bioconjugates and biomaterials has increasingly become the focus of pharmaceutical companies, material scientists, and academia due to their growing list of applications. Bioconjugates have found broad use in therapeutics, drug delivery, tissue engineering, and biosensing. Historically, interest in specific bioconjugates has depended on the cost-availability of the biomacromolecule, making proteins the most well studied, given their relatively low cost and ease of production. However, recent technological advances in plasmid DNA (pDNA) production from E. Coli allow for greater cost-efficiency, changing the landscape of biomaterial research. Employing alkylating agents with known chemo-selectivity to nucleophilic sites on DNA, …

Biophysical Properties Of An Antifreeze Protein And The Effects Of Ionic Liquids On The Model Protein Gb1, Korth Wade Elliott

Doctoral Dissertations

Antifreeze proteins (AFPs) are a unique class of protein characterized by their ability to depress the freezing point of water sufficient to prevent the formation of ice crystals by adsorbing to the surface of ice crystals. This unique ability allows organisms (e.g. plants, fish, insects, etc.) which live in extremely cold climates to survive. Because of these proteins’ ability to prevent and slow the rate of ice crystal formation, they have great potential in the application of cryopreservation in medicine, agriculture and food science. Antifreeze proteins have been known for over five decades, however, their exact mechanism of action is …

Photocatalysis Using Tio2 Nanoparticles Containing Surface Metal Sites, Benjamin D. Stewart

Master's Theses and Capstones

In recent years, exploration of the functionalization of nanoparticle surfaces has gained more interest. This can overcome the high energy band gap problem of a semiconductor such as TiO2. Furthermore, this kind of modification can widen the range of catalytic or other uses for the material. In this work TiO2 in various crystal forms was modified towards both degradation of water contamination as well as the reduction of CO2. Iron was covalently attached to TiO2 using a bottom up synthetic strategy incorporating a photoactive linker designed for photocatalytic applications. The resulting surface Fe(II)-terpyridine complex was characterized with techniques including microscopy …

Development Of Fluorescent Sensors Based On Molecularly Imprinted Biomimetic Polymers, Rongfang Yang

Doctoral Dissertations

Molecular recognition can be thought as the process in which two or more molecules bind to one another in specific geometry through noncovalent bonding. Bioreceptors, such as antibodies, enzymes, and DNAs can specifically bind to its target with high binding affinity and selectivity. However, the bio receptors are suffering from low stability and tolerance to extreme pH, temperature and organic solvents.

To overcome the disadvantages of the bioreceptors, novel biomimetic molecularly imprinted polymers (MIPs) were developed by Seitz group. Different from the conventional MIPs with high percentage of covalent crosslinking, the biomimetic MIPs contain less than 5% mole percent covalent …

The Development Of A Diiron Hydrogenase Mimic Catalyst For Efficient Dihydrogen Production, David S. Danico

Master's Theses and Capstones

Carbon dioxide has become an ever growing problem facing life on Earth due to the theory that the increase in CO2 levels has been the leading cause of global warming and could initiate significant climate change. Most of the CO2 produced by humans comes from the burning of fossil fuels for energy. Because of this, the development of a clean alternative fuel is a primary concern. Dihydrogen is looked at as a possible alternative because it has already demonstrated the ability to produce energy in fuel cells and could conceivably replace fossil fuels in every aspect of its use. The …

Major Fraction Of Black Carbon Is Flushed From New Hampshire Seasonal Snowpack Early In Melt, James Lazarcik

Master's Theses and Capstones

Seasonal snowpacks accumulate soluble impurities derived from atmospheric aerosols and trace gases throughout the winter and release them quickly early during snow melt. Previous field and laboratory studies have shown that a snowpack can lose up to 80% of the ion burden in the first 20% of the melt, an event commonly known as an ionic pulse. Other studies have concluded that particulate impurities (e.g. black carbon (BC)) concentrate in surface layers during melt which can have important implications for snowpack albedo. To characterize snow chemistry, quantify the release of impurities, and qualify enhancement effects, we collected and analyzed near …

Linearly Extended Pyrylium Salts (Leps) And Linearly Extended Thiopyrylium Salts (Lets) As Organic Semiconductors, Jianyu Zhao

Doctoral Dissertations

Research focused on the development of a new class of n-type organic semiconductors called linearly extended pyrylium salts (LEPS) and linearly extended thiopyrylium salts (LETS). While a lot of progress has been made on p-type organic semiconductors over the last decade, less attention has been paid to n-type organic semiconductors. Pyrylium and thiopyrylium cations are aromatic structures akin to benzene but with one methine carbon (CH) replaced by either a positively charged oxygen or sulfur atom, respectively. This makes these aromatic π-systems very electron-deficient. With pentacene-like backbones, LEPS and LETS compounds combine linearly conjugated π-systems of acenes with the highly …

Synthesis Of Polycyclic Aromatic Hydrocarbons: Studies Of Aryne Cycloaddition, Acid-Catalyzed Rearrangement, And Coupling Pathways, Caitlin Hoffman

Master's Theses and Capstones

Various synthetic routes towards polycyclic aromatic hydrocarbons dibenzo[g,p]chrysene (DBC), chrysene, zethrene, and their derivatives were studied. All of these compounds are not readily available and the literature lacks facile, efficient, and scalable syntheses. Microwave flash pyrolysis (MFP) was used for the synthesis of benzyne and phenanthryne, both of which have the ability to undergo a Diels-Alder reaction at the bay region of polycyclic aromatic hydrocarbons. Phthalic anhydride was used as a benzyne precursor and 9,10-dicarboxyphenanthrene anhydride as a phenanthryne precursor. DBC was observed after the MFP of biphenyl and 9,10-dicarboxyphenanthrene anhydride, signifying phenanthryne generation. Fluoride-induced elimination and Grignard pathways were …

Evaluation Of Mercury Standard Stability For Analyzing Human Urine Using Inductively Coupled Plasma Spectrometry, Shing Lau

Master's Theses and Capstones

Quantitation of total mercury has been of great interest not only in environmental fields, but also in medical research. This is because mercury (Hg) is one of the most toxic elements, and is also a well–known global pollutant. Researchers strive to understand how toxic elements bioaccumulate in both aquatic ecosystems and terrestrial systems, along with these effect on human health. Numerous studies and analytical methods have been published for the assessment of mercury in many different sample matrices. Accurate analysis of these complex matrices is dependent on accurate and reliable analytical standards. However, the standards preparation step is time consuming. …

Development Of An Isotopic Approach For Detailing Heparin Sequences, Qing Guo

Doctoral Dissertations

Heparin/heparin sulfates are carbohydrate polyionic polymers that participate in a host of critically important biological processes such as blood anticoagulation, pathogen infection, cell differentiation, growth, migration and inflammation, to mention a few. A century has passed since heparin’s initial discovery with a fair understanding of its overall composition. Unfortunately, there has been no structural work at the detailed chemical level that might support a synthetic effort. In this study, I utilize a chemical derivatization strategy (dual permethylation) that imparts isotopic structural specificity, which can be followed by step-wise disassembly in an ion trap mass spectrometer, (MSn). A set of analytical …

Formal Synthesis Of Cj-12,954 And Cj-13,014 Using Zinc-Mediated Tandem Chain Extension-Aldol Reaction And Synthesis And Investigation Of Diastereoselectivity Of Hydroxy-Cyclopropyl Peptide Isosteres, Yashoda Naga Deepthi Bhogadhi

Doctoral Dissertations

A formal synthesis of the natural products CJ-12,954 and CJ-13,014 was successfully accomplished using the zinc-mediated tandem chain extension-aldol reaction methodology. This chemistry was performed on a chiral β-keto imide synthesized using a DCC coupling reaction. The diastereoselectivity of the aldol reaction was controlled by an Evans chiral auxiliary. Comparison between the reported and experimental spectral data for the spiroketals confirmed the structural assignment.

The diastereoselectivity of the homologation-cyclization-rearrangement-lactonization reaction of β-keto imide derived from phenyl carbamate-protected proline was studied. Tetra-n-butylammonium fluoride-mediated rearrangement of trimethylsilyl cyclopropanol demonstrated the role of chiral auxiliary and the amino acid stereocenter in controlling the …

Single Chain Technology: Toward The Controlled Synthesis Of Polymer Nanostructures, Christopher Kenneth Lyon

Doctoral Dissertations

A technique for fabricating advanced polymer nanostructures enjoying recent popularity is the collapse or folding of single polymer chains in highly dilute solution mediated by intramolecular cross-linking. We term the resultant structures single-chain nanoparticles (SCNP). This technique has proven particularly valuable in the synthesis of nanomaterials on the order of 5 – 20 nm. Many different types of covalent and non-covalent chemistries have been used to this end.

This dissertation investigates the use of so-called single-chain technology to synthesize nanoparticles using modular techniques that allow for easy incorporation of functionality or special structural or characteristic features. Specifically, the synthesis of …

Syntheses And Characterization Of Linearly Extended Tropylium Salts As N-Type Organic Semiconductors, Jinyu Yang

Master's Theses and Capstones

Organic semiconductors have been of interest to scientists since the 1970s. However, while much attention was focused on p-type organic semiconductors, n-type organic semiconductors were seldom reported. In this thesis, a series of linearly extended tropylium salts (LETS) were synthesized as n-type organic semiconductors and characterized by 1H NMR, 13C NMR spectroscopy, MALDI-TOF-Mass spectrometry and UV-Vis spectroscopy. The proposed synthetic strategy has proven highly suitable to synthesize LETS compounds. UV-Vis spectra of LETS in solution have been studied as well as their stability. Linear extension of the backbones has been found to be an effective way to improve the optical …

Syntheses And Characterizations Of Linearly Extended Thiazinium Salts As Organic Semiconductors, Yanmei Rong

Master's Theses and Capstones

Organic semiconductors have been the subject of both academic and industrial interest due to their potential advantages over inorganic semiconductors. Based on the type of charge transporting (hole or electron), organic semiconductors can be categorized as n-type (electron transporting) or p-type (hole transporting). Most attention has been concentrated on the development of p-type organic semiconductors and their development has led to dramatic enhancements in the performance of hole transporting material. However, the investigation and application of electron transporting organic semiconductors has not drawn as much attention. In this project, we focus on the exploration, design, synthesis and characterization of novel …

Covalent Attachment Of A Diimine Tricarbonyl Re(I) Catalyst On Solid State Nano-Material Surfaces For Solar Carbon Dioxide Reduction, He He

Master's Theses and Capstones

Reduction of carbon dioxide to useful chemicals and fuels is of significant interest. Transition metal complexes, such as tricarbonyl rhenium(I) compounds, are efficient molecular catalysts for photocatalytic carbon dioxide reduction. To improve the stability and catalytic activity of homogeneous catalysts, a mesoporous silica material, SBA-15, was synthesized and applied as catalyst support for immobilizing the tricarbonyl rhenium(I) compound via both covalent bonding and physical adsorption. The covalently bonded tricarbonyl rhenium(I) catalyst in SBA-15 exhibited excellent stability and good activity during the photocatalytic reduction process, compared with its homogeneous counterpart and the physically absorbed one. Another solid-state nano-material, Kaolin, was also …

Identification And Stoichiometric Analysis Of The Monosomal Translational Complex, Xin Wang

Doctoral Dissertations

The identification of the components involved in translational complexes has relied primarily on in vitro studies. Determining which proteins associate together in these complexes, under what conditions they do so, and how the composition of the complexes change under different conditions have became the key issues of in vivo studies. After a one-step affinity purification, using a novel technique of analytical ultracentrifugation with a fluorescence detection system (AU-FDS) I have identified a 77S monosomal translational complex in the yeast Saccharomyces cerevisiae. Major components of the 77S complex include the 80S ribosome, mRNA, and components of the closed-loop structure, eIF4E, eIF4G1/eIF4G2 …

The Identification And Characterization Of The Interaction Between Upf1 And Pab1 During Nonsense-Mediated Decay & The Identification Of Novel Protein Complexes Associated With Translation Termination Factor Erf1, Roy Richardson

Doctoral Dissertations

There are still many protein interactions that occur during translation termination that are poorly understood. One of the important termination pathways still under investigation is nonsense-mediated decay (NMD), which rapidly degrades mRNAs that contain a premature stop codon (PTC). I identified that the interaction between Upfl, which is required for NMD, and PAB1 occurs via the RRM1 domain of PAB1 in the yeast Saccharomyces cerevisiae. Determining the role of this interaction during NMD was performed with pulse-chase assays using a PGKlpG mRNA. These assays revealed that the interaction between Upfl and PAB1 is required for a shift from distributive to …

I The Tandem Chain Extension-Acylation Reaction Ii Synthesis Of Papyracillic Acid A: Application Of The Tandem Homologation-Acylation Reaction Iii Synthesis Of Tetrahydrofuran-Based Peptidomimetics, Carley Meredith Spencer

Doctoral Dissertations

A zinc-mediated tandem chain extension-acylation reaction was successfully developed. This reaction was optimized with the use of beta-keto esters, amides, and imides as well as a variety of acylating agents. The tandem homologation-acylation reaction was successfully applied towards the total synthesis of papyracillic acid A.

Use of a tandem chain extension-aldol reaction, followed by a reductive cyclization, allowed for the synthesis of tetrahydrofuran-based peptidomimetics. A variety of amino acid derived beta-keto imides and aldehydes were used during the initial tandem homologation-aldol reaction. High diastereocontrol was achieved during reductive cyclization when a cis relationship was present between the substituents on the …

Regulation Of The Catalytic And Allosteric Properties Of Photoreceptor Phosphodiesterase (Pde6) By The Glutamic Acid-Rich Protein-2 (Garp2), Wei Yao

Doctoral Dissertations

The photoreceptor phosphodiesterase (PDE6) must be precisely regulated to control the sensitivity, amplitude, and kinetics of the photoresponse during excitation, termination and adaptation to light stimulation in rod and cone photoreceptors. The central hypothesis of this thesis is that one PDE6 binding partner, the glutamic acid-rich protein (GARP2), may regulate PDE6 to reduce its "dark noise", enhance its sensitivity and conserve metabolic energy during rod photoresponse saturation.

The first aim of this research is to better understand the unique biochemical and biophysical characteristics of GARP2 in order to reveal its functional attributes for regulating PDE6 during phototransduction in rod photoreceptors. …

Patterns Of Cytosine Methylation In The Genome Of Caenorhabditis Elegans, Kazufusa Okamoto

Doctoral Dissertations

Recent large-scale comparative analysis of cytosine DNA methylation across diverse eukaryotes suggest that early features of DNA methylation present in the last common ancestor of all eukaryotes some 1.6 to 1.8 billion years ago included the methylation of gene bodies and transposable elements (Zemach, McDaniel et al. 2010; Parfrey, Lahr et al. 2011). These potentially ancient patterns may reflect a primitive role of methylation in transcriptional fidelity and as a mechanism to protect the germ line from transposon, or repeat, mediated mutation. Because spurious transcription and mutation are hypothesized to be among the critical limiting factors to genome size, an …

Synthesis Of Adjacent-Bridged Benzo-Annelated Cyclam And Studies Of Mono- And Di-Benzo-Annelated Cyclam Derivatives, Amanuel B. Ghidey

Master's Theses and Capstones

A new synthetic methodology for the preparation of a novel adjacent-bridged benzoannelated cyclam is presented. This methodology utilizes reductive ring expansion followed by deallylation to give the desired adjacent-bridged benzo-annelated cyclam. This novel ligand is designed to complex metal cations with a trans coordination geometry. Derivatives of this ligand can be prepared by attaching pendant arms on the nitrogens which can aid as coordinating arms and linkers for potential use of this ligand as bifunctional chelator (BFC).

Coupling chemistry studies have been carried out in an attempt to increase the lipophilicity of a dibenzo-annelated tetracyclic bisaminal and to functionalize at …

Theoretical Analysis Of The Reaction Of Peroxymethyl Radical With Atomic Hydrogen And Of Dibenzofuran With Atomic Chlorine, Mikhail Zhukovskiy

Master's Theses and Capstones

Experimental determination of rate constants for gas phase radical reactions is challenging. When rate constants necessary for modeling complex processes in atmospheric and combustion science are unknown, theoretical predictions are useful. We used Variational Transition State Theory with Multidimensional Tunneling (VTST/MT) with Density Functional Theory (DFT) to calculate the rate constant and isotope effects for reaction between the peroxymethyl radical and the hydrogen atom.

Polychlorinated dibenzofurans (PCDFs) are a group of extremely toxic compounds formed during waste incineration. Currently, their chemical degradation in the atmosphere is poorly understood. While some experimental and theoretical results regarding the reaction of PCDFs with …

Novel Synthesis Of Sulfur Based Ligands Used In Modeling Biological Hydrogen Bonding Interactions, Tyler Jesse Jacinto

Master's Theses and Capstones

Heme-thiolate proteins are known to have hydrogen bond donors proximal to the axial thiolate ligand. The specific roles of these conserved H-bond donors have not yet been elucidated. However, various sources agree upon the positive influence that increased X-H···S interactions have on protein redox potentials. For example, synthetic modeling studies of the cytochromes P450 show similar positive shifts in potential in iron-porphyrin-thiolate model systems. The ligands used in modeling the H-bonding interactions in the P450 cytochromes included a series of 2,6-substituted thiophenols, -S(2,6-(CX3CONH)2C6H3), where X = H, F, CH3. The current synthetic route to these ligands is vague and employs …

Spectroscopic Investigations Of The Photochemical Properties Of I. Spiropyran On Y Zeolite For Photochromic Applications Ii. Rhenium(I) Bipyridyl Tricarbonyl On Mesoporous Zsm-5 Zeolite And Silica For Photocatalytic Reduction Of Carbon Dioxide, Kevin Dubois

Master's Theses and Capstones

Immobilization of photoactive molecules on porous and nano-sized solid supports provides unique interactions which affect photophysical properties. In situ diffuse reflectance FTIR and UV-vis spectroscopies were primarily used to investigate the properties of surface functionalized materials. Spectroscopic characterization of photochromic spiropyran molecules physically adsorbed on Y zeolite revealed the importance of surface water in controlling kinetics and reversibility of photoswitching by stabilizing the merocyanine isomer. Re(bpy)(CO)3C1 was both physically adsorbed on a mesoporous ZSM-5 zeolite and covalently bound via the bipyridyl ligand on fumed silica to generate photocatalytic CO2 reduction materials. Upon light irradiation of the solids in the presence …

Cavity Ring Down: Construction, Validation And Experiments Measuring The Optical Extinction Of Pure Clays And Their Mixtures With Salts And Carboxylic Acids Under A Range Of Atmospherically Relevant Conditions, Alexis Rae Attwood

Doctoral Dissertations

Aerosols interact directly with solar radiation by scattering and absorbing incident light to affect the Earth's climate system. Models indicate that aerosols cool the Earth counterbalancing greenhouse gases, but contribute the largest uncertainty to anthropogenic effects on climate. To address these uncertainties, a cavity ring down spectrometer (CRD) was built and performance tests were conducted to validate its capabilities for measuring optical properties of laboratory generated, atmospherically relevant aerosols over a range of conditions. The CRD provides an absolute and unbiased in situ measurement of total extinction and can reduce uncertainties associated with aerosols having unusual chemical and physical properties. …

Morphological Study Of Composite Latex Particles And Water Interaction With Polymer Chains, Bo Jiang

Doctoral Dissertations

The primary purpose of this research was the morphological study of composite polymer (2 or more) nano-particles in an aqueous dispersed system. This included synthesis, characterization and mathematical/numerical modeling. For a composite latex particle, the morphology can play an important role in determining the final application properties, and the structure depends on many factors which are active during and after polymerization. Among these are the penetration of oligomeric chains into the latex particles, mixing of the two composite polymers, and eventual phase separation of such mixtures. These actions depend upon the materials used in the polymerization and the process by …

Ratiometric Copper(Ii) Indicators Based On Poly(N-Isoproprylacrylamide) And Fluorescence Resonance Energy Transfer, Shaojun Yao

Doctoral Dissertations

An approach to ratiometric fluorescence detection of Cu(II) ions was devised by copolymerizing N-isopropylacrylamide with small percentages of bipyridine and amine monomers. The copolymer was divided into two portions. The amine group on one portion was functionalized with AlexaFluor555 (donor fluorophore) and the other with AlexaFluor647 (acceptor fluorophore). The indicator consists of a mixture of these two portions. Aggregation above the lower critical solution temperature (LCST) of this copolymer brings about a large increase in fluorescence resonance energy transfer (FRET). Addition of Cu(II) to the aggregated copolymer introduces charge onto the backbone, causing the copolymer to deaggregate with a resulting …

Nonideality In High Concentration Solutions, Ronald Toth

Doctoral Dissertations

Our current understanding of molecular interactions, the kinetics, equilibria, and thermodynamics of biochemical reactions, is based mostly on research conducted in dilute solutions. Recent interest in the implications of true physiological concentrations has led to the development of new tools and techniques. In vivo biological systems differ so significantly from dilute solutions that a model is required to conceptualize them. The excluded volume theory is one such model. In this framework macromolecules are regarded as hard spherical volumes, holding only the property of size, and not those of shape or charge. Alternatively, the proximity energy framework considers molecules as having …

Detection Of Trehalose In Porphyra Extracts Using Mass Spectrometry And Gas Chromatography-Mass Spectrometry, Ying Huo

Master's Theses and Capstones

It is known that trehalose helps many plants to survive under desiccated environment26. This property of trehalose has also been proposed to explain why Porphyra could survive desiccation when left on dry land for a long period of time25. However, after extensive study25, effort at identifying trehalose in Porphyra has been unsuccessful, leaving the question of whether trehalose really exists in Porphyra unanswered. In my thesis research, in collaboration with Dr. Anita Klein, I set out to use ion-trap mass spectrometry and gas chromatography coupled with mass spectrometry to identify and quantify the amount of trehalose in Porphyra extracts. Using …

The Road Less Traveled: New Chemistry Of Old Reactive Intermediates, Erin Carcella Mclaughlin

Master's Theses and Capstones

Conditions were optimized to utilize benzyl alcohol and acetate substrates in Friedel-Crafts electrophilic aromatic substitution reactions. Anhydrous iron (III) chloride (20 mol%) was shown to be an efficient catalyst when using benzene in a microwave reactor. Rapid reactions and minimal further purification make this procedure suitable for chemical library generation. We attempted to develop a synthetic route to the little known intermediate, ortho-xylallene. Though work to date has been unsuccessful, we have determined that traditional routes via allene formation may be viable. Rearrangements of terphenyls, phenyl-naphthalene, and 1,1'-binaphthalene by ipso-arenium cations were studied using triflic acid in 1,2-dichloroethane. Preferred formation …