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A Raman Spectroscopic And Computational Study Of The Effects Of Halogen Bonding On Pyrimidine Containing Systems, Peyton Lindsey Reves
A Raman Spectroscopic And Computational Study Of The Effects Of Halogen Bonding On Pyrimidine Containing Systems, Peyton Lindsey Reves
Honors Theses
This thesis involves the study of the effects of halogen bonding on pyrimidine containing systems. Halogen bonding is a type of non-covalent interaction that can occur when a Lewis base interacts with an iodine, bromine, or chlorine atom in a second molecule. The phenomenon of halogen bonding is explained by the presence of a localized region of positive electrostatic potential that exists on the halogen. This positive region is referred to as the σ-hole, and gives halogen bonding its other common name, σ-hole bonding. The magnitude of the positive σ-hole depends on both the type of halogen molecule involved in …
The Effect Of Polyamines On I-Motif Thermal Stablity, Shelby Claire Liddell
The Effect Of Polyamines On I-Motif Thermal Stablity, Shelby Claire Liddell
Honors Theses
Polyamines are present inside cells at varying concentrations anywhere between 10 mM and 60 mM, and because of their molecular structure they contribute a positive charge to the interior of the cell. There has been previous evidence that the concentrations of polyamines have an effect on the stability of the DNA strands, which can affect the cellular processes. The particular DNA conformation studied is the i-motif, which is formed by intermolecular folding in cytosine rich strands. The i-motif studied is C20T, which is found in the promoter region of the oncogene, c-myc. Stabilization of c-myc can have an effect on …
Pro-Aromatic Dye Components For Dye-Sensitized Solar Cells: Thienothiophene And Indolizine, George A. Puneky
Pro-Aromatic Dye Components For Dye-Sensitized Solar Cells: Thienothiophene And Indolizine, George A. Puneky
Honors Theses
Four D-π-A dyes based on a 3,4-thienothiophene Ï€-bridge were synthesized for use in dye-sensitized solar cells (DSCs). The pro-aromatic building block 3,4-thienothiophene has been reported to stabilize dye excited-state oxidation potentials. This lowering of excited-state energy levels permits for increased absorption into the near-infrared (NIR) region using relatively low molecular weight dyes. Strong donor functionality based on triaryl- and diarylamines are employed in the dye designs to raise both the ground and excited-state oxidation potentials to values capable of generating DSC devices with good open-circuit voltages. Solubility, aggregation, and TiO2 surface protection were addressed by examining an ethylhexyl alkyl chain …
Breastfeeding: Physiological And Cultural Influences, Alison R. Cegielski
Breastfeeding: Physiological And Cultural Influences, Alison R. Cegielski
Honors Theses
Within a biological perspective, breasts are indisputably for the use of nourishment of the young. This can be seen by how mammary glands are used by every other species other than humans. Humans are the only species that also looks at breasts within a cultural perspective, and that perspective is where the debate of breastfeeding occurs. There is really no debate that if given the option to breastfeed, breastfeeding is the best choice for the development of infants due to the fact that breast milk has been adapted for the human physique. In spite of the health benefits associated with …
Effects Of Synthetic Blood Plasma On Calcium Dependent Dimerization Of Ncad12, Brent Treadway
Effects Of Synthetic Blood Plasma On Calcium Dependent Dimerization Of Ncad12, Brent Treadway
Honors Theses
Neural Cadherin (NCAD) is one of three Type 1 vertebral classical cadherins that function as the primary transmembrane component in cell-to-cell interactions at adherens junctions. Adhesive interactions mediated by this protein are calcium dependent with three calcium-binding sites between each of its five extracellular domains. NCAD is very important in many cell-to-cell interactions because of its function in development and in immune and neurological synapses. Generally, in vitro studies of calcium dependent dimerization of NCAD are conducted in a nonphysiological buffer (NaCl + HEPES: SEC buffer). In order to study dimerization in more physiologically relevant conditions, I created a synthetic …
Dna I-Motif Stabilization By Ligand Binding To Loop Regions, Harrison Reed Davis
Dna I-Motif Stabilization By Ligand Binding To Loop Regions, Harrison Reed Davis
Honors Theses
DNA i-motifs are a secondary structure of DNA that can be useful in a variety of ways, but this experiment investigates the maximum potential to stabilize i-motifs artificially with a small molecule binding to loop regions. DNA with different position and number of loops was tested to see to what extent the i-motif could be stabilized . A drug, Actinomycin D, was used for its known high affinity for a particular DNA sequence, which we used to make the loops of the i-motif. The binding constant for the drug to the DNA was determined through fluorescense spectroscopy while the presence …
Non-Covalent Ineteractions Of Trimethylamine N-Oxide (Tmao) And Urea In Water, John Prather
Non-Covalent Ineteractions Of Trimethylamine N-Oxide (Tmao) And Urea In Water, John Prather
Honors Theses
TMAO and urea are important osmolytes. Osmolytes help maintain cell volume with their presence inside and outside cells. Urea is used by kidney cells to neutralize strong osmotic gradients caused by excretion of hypertonic waste. Although urea is for volume- maintaining purposes, it is also known to be a strong denaturant of cellular proteins. The method by which urea destabilizes folded proteins is a debated topic. There is evidence that urea binds directly to amino acid side chains to make protein folding less thermodynamically favored. It has also been suggested that urea acts indirectly to denature proteins by destabilizing the …
A Computational Comparison Of The Hydrophobic Pocket Of Neural And Epithelial Cadherins For The Purpose Of Identifying A Selective Inhibitor, Ross E. Straughan
A Computational Comparison Of The Hydrophobic Pocket Of Neural And Epithelial Cadherins For The Purpose Of Identifying A Selective Inhibitor, Ross E. Straughan
Honors Theses
Classical cadherins are a subfamily of calcium-dependent cellular adhesion molecules that play an important role in the formation of cellular junctions in many tissues. The extracellular portion of cadherins consists of five tandem-repeated domains (EC1-EC5). The critical first step in cadherin-mediated cellular adhesion occurs at the interface between two adjacent EC1 domains in which the transition from monomer to dimer is accomplished by docking the W2 residue of the N-terminal β-strand of one EC1 domain into the hydrophobic pocket of its partner domain. Cancer and many other diseases have been linked to the aberrant expression of Epithelial (E-cad) and Neural …
Effect Of Biochar And Activated Carbon Amendments On Gaseous Mercury Emissions Of Soil And Mercury Methylation Rates In Sediment, Ryan Sessums
Honors Theses
Mercury is a pervasive global contaminant with a complex biogeochemical cycle. In this biogeochemical cycle, methylmercury (MeHg+) tends to biomagnify and concentrate in fish and seafood consumed by humans. This study examines the effect of sorbent amendments on both the mercury emission from soils and the methylation rates of mercury in sediments, both of which are believed to be major contributors to the global cycle. Biochar and activated carbon were used to treat soils and sediments to explore their effects. It was found that biochar and activated carbon reduced gaseous mercury emission by 25% and 49%, respectively. Methylation rates in …
Effective Tuning Of Bimetallic Composition Of Gold-Copper Nanomolecules And The Emergence Of Plasmon-Like Feature In Optical Spectra, Asantha Champika Dharmaratne
Effective Tuning Of Bimetallic Composition Of Gold-Copper Nanomolecules And The Emergence Of Plasmon-Like Feature In Optical Spectra, Asantha Champika Dharmaratne
Electronic Theses and Dissertations
Au144-xCux(SR)60 alloy nanomolecules were synthesized and characterized by using ESI-MS to atomic precision. A maximum of 23 copper atoms replace the gold atoms; when the number of copper atoms is higher than eight, a surface plasmon-like peak appears at ∼520 nm. Based on the fundamental, elemental properties of Au and Cu, we predict a mixed atomic ordering and incorporation into the Au12 and Au 42 shells of the proposed icosahedral structured model. Alloy nanomolecules reported here could have potential applications in the field of catalysis and optical sensors.
Method Development For Mass Spectrometric Characterization Of Ultra-Small Nanomolecules And Mass Spectrometry Imaging Of Selected Biomolecules, Nuwan K. Kothalawala
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 …
Efficient Utilization Of Solar Energy In Dye-Sensitized Solar Cells And In The Photocatalytic Reduction Of Carbon Dioxide, Aron Joel Huckaba
Efficient Utilization Of Solar Energy In Dye-Sensitized Solar Cells And In The Photocatalytic Reduction Of Carbon Dioxide, Aron Joel Huckaba
Electronic Theses and Dissertations
One of the most important questions humanity will face in the next 100 years is going to be "What will happen when oil runs out?" This dissertation describes efforts to utilize solar energy to improve renewable energy technology in two ways: First, through the improvement of dye sensitized solar cells by theimprovement of D-π-A dye subunits, the development of practical sensitizers, and progress towards stable, tunable redox shuttles. A novel indolizine donor subunit was synthesized that was shown to be the strongest reported donor. Dyes made from this novel donor and devices using the Γ-/I 3- reached up to 5.4% …
Gold Nanomolecules : Developing Synthetic Protocols, Characterization And Investigation Of Ligand Effects On Structure And Properties, Praneeth Reddy Nimmala
Gold Nanomolecules : Developing Synthetic Protocols, Characterization And Investigation Of Ligand Effects On Structure And Properties, Praneeth Reddy Nimmala
Electronic Theses and Dissertations
The term "Nano" in chemistry refers to particles/molecules in the size range 1 to 100 nm. Gold nanoparticles were used in ancient times in making decorative glass as they produce vibrant, size dependent, colors upon interaction with light. Gold is a preferred choice of metal for the synthesis of nanoparticles mainly due to its inertness to atmospheric conditions and most chemicals. Gold thiolate nanomolecules, which is the primary focus of this dissertation research, are chemical molecules with a fixed number of gold atoms and organo-thiolate ligands. They are of the form Aux(SR)y and possess molecule-like properties as a result of …
Synthetic Study Of Karlotoxins And Investigation Of Alpha-Diaminoboryl Carbanion Chemistry, Yusuke Takahashi
Synthetic Study Of Karlotoxins And Investigation Of Alpha-Diaminoboryl Carbanion Chemistry, Yusuke Takahashi
Electronic Theses and Dissertations
Karlotoxins (KmTxs), produced by a toxic marine/estuarine phytoplankton, the dinoflagellate Karlodinium veneficum, are known to be ichthyotoxic, thus being associated with numerous fish deaths events worldwide. They have also been reported to show a variety of biological activities such as hemolytic, cytotoxic, and anti-fungal activities. Recently, the Hamann group successfully assigned the absolute configurations of KmTx2, the first complete structure elucidation among the congeners. In a structural sense, karlotoxins are a family of linear polyketides with three distinctive regions; a bis-tetrahydropyran core fragment, a long, highly oxygenated carbon chain, and a lipophilic chlorodiene unit. Such potent biological activities as well …
Accurate Computation Of Molecular Properties From Novel Applications Of Quantum Mechanical Wavefunction Methods, James Coleman Howard
Accurate Computation Of Molecular Properties From Novel Applications Of Quantum Mechanical Wavefunction Methods, James Coleman Howard
Electronic Theses and Dissertations
High-accuracy quantum mechanical (qm) wavefunction methods have been applied to compute molecular properties of weakly-bound clusters. This work focuses on both extending the applicability of robust theoretical methods to larger systems and also determining the inherent accuracy of ab initio methods when compared to experimentally measured properties. Described here is the development of an efficient many-body approach that offers the ability to reduce both the time and the computational resources normally required to compute these properties reliably. The n-body:many-body qm:qm technique has been extended to compute harmonic vibrational frequencies of clusters. Applying this methodology to small hydrogen-bonded clusters demonstrates that …
Progress Toward The Total Synthesis Of The Natural Product Herbicide Ascaulitoxin Aglycone, Jeffery Brian Morgan
Progress Toward The Total Synthesis Of The Natural Product Herbicide Ascaulitoxin Aglycone, Jeffery Brian Morgan
Electronic Theses and Dissertations
Ascaulitoxin aglycone is a structurally unique bis-amino acid isolated from the fungal species Ascochyta caulina, with herbicidal activity against Chenopodium album. Ascaulitoxin aglycone's potent herbicidal activity coupled with an unknown but novel mechanism of action makes it a perfect candidate for further study in the pursuit of new natural product herbicides. This dissertation research will illustrate three synthetic strategies towards the total synthesis of ascaulitoxin aglycone from chiral pool building blocks. Strategy 1 invokes the use of the Henry reaction as a key step for the construction of the central C4-C5 cis-aminohydroxy group, which was moderately successful, but abandoned in …
The Spectroscopic Characterization Of Newly Developed Emissive Materials And The Effects Of Environment On Their Photophysical Properties, Louis Edward Mcnamara
The Spectroscopic Characterization Of Newly Developed Emissive Materials And The Effects Of Environment On Their Photophysical Properties, Louis Edward Mcnamara
Electronic Theses and Dissertations
The development of new materials capable of efficient charge transfer and energy storage has become increasingly important in many areas of modern chemical research. This is especially true for the development of emissive optoelectronic devices and in the field of solar to electric energy conversion. The characterization of the photophysical properties of new molecular systems for these applications has become critical in the design and development of these materials. Many molecular building blocks have been developed and understanding the properties of these molecules at a fundamental level is essential for their successful implementation and future engineering. This dissertation focuses on …
Mercury Methylation Potentials In Sediments An Ancient Cypress Wetland Using Species-Specific Isotope Dilution-Gc-Icp-Ms: Analytical Method Development And The Effect Of Sorbent Amendments, Derek Davin Bussan
Electronic Theses and Dissertations
A novel method was developed to measure mercury (Hg) directly in environmental solids using inductively coupled plasma mass spectrometry (ICP-MS) with online sample ashing. The method combines a direct mercury analyzer (DMA) that is based on sample combustion, Hg pre-concentration by amalgamation with gold, and atomic absorption spectrometry (AAS), with a high resolution ICP-MS. Unlike AAS, the ICP-MS is capable of individual isotope measurements allowing for accurate quantitation by isotope dilution mass spectrometry (IDMS) and for isotope tracer experiments. The method was validated using certified reference materials including sediment (NIST 2709), leaves (NIST 1547), and fish-muscle (DORM-3), with recoveries within …
Method Development For The Detection And Quantitation Of Illicit Drugs In Fingerprints Using Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry, Madison Roussel
Honors Theses
The purpose of this research was to develop a method for the detection and quantitation of caffeine and 11-nor-9-carboxy-Δ9- tetrahydrocannabinol in fingerprints using matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). The matrix used was 2,5-dihydroxybenzoic acid (DHB). The presence of the analytes was confirmed by analysis using liquid chromatography-mass spectrometry (LC-MS). 11-nor-9-carboxy-Δ9- tetrahydrocannabinol was chosen as the drug of interest because it is the major metabolite of tetrahydrocannabinol, the main psychoactive component of marijuana. Marijuana's popularity as a recreational drug continues to increase with its legalization and decriminalization across the country. It is critical to establish methods for the quantification …
From Lazarus To Theophilus: How Manuscript Digitization Led To The Historical, Chemical, And Technological Understanding Of Iron Gall Ink And Its Counterparts, Meredith Oliver
Honors Theses
This paper examines the physical and chemical composition of iron gall ink, how such composition has changed throughout its use in history, and the current chemical, digital, and multi-spectral methods by which the digital humanities use to preserve ancient texts inscribed with such ink. By using spectral technology, I hypothesized it possible to date and locate the geographic origin of ink based on its chemical composition. Uv-vis, fluorescence, and micro-XRF spectrometry were used to analyze elemental composition. Ink samples were made to simulate the ink on ancient manuscripts for UV-vis and fluorescence spectral analysis. Micro-XRF was performed on the Vercelli …
Development Of Methods For Determining Dry Deposition Of Mercury Using An Ion-Exchange Membrane: Relative Rates Of Mercury Dry Deposition At Sardis, Enid, And Grenada Lakes, Ruiqi Feng
Honors Theses
This research focuses on studies developing methods to measure dry deposition of mercury (Hg) using an ion-exchange (IX) membrane to capture gaseous mercury species in the air. Mercury is a toxic heavy metal that is spread globally through the atmosphere. Atmospheric Hg deposits to terrestrial and aquatic ecosystems through wet and dry deposition. While routine methods have been developed to study wet deposition of Hg, measuring dry deposition of Hg is more problematic and often overlooked. In this study, we developed an inexpensive means to deploy a polyethersulfone cation exchange membrane in the field by dangling it within a polycarbonate …
Using Technology To Engage Students In The Stem Field, April Elizabeth Steen
Using Technology To Engage Students In The Stem Field, April Elizabeth Steen
Honors Theses
The United States is currently facing a shortage of qualified STEM professionals in the workforce and in research fields. Part of this lack of professionals can be traced back to lack of interest and lack of proficiency in mathematics and science at the secondary level of education as well as STEM major attrition at the college level. In an effort to increase student interest in STEM fields and increase retention of STEM majors, technology was employed to engage student interest. At the high school level, a physical chemistry demonstration on the spectroscopy of light was created. The demonstration was presented …
A Study Of The Impact Of Ph On The Structure And Stability Of Epithelial Cadherin, Catherine Abadie
A Study Of The Impact Of Ph On The Structure And Stability Of Epithelial Cadherin, Catherine Abadie
Honors Theses
Epithelial (E-) cadherin is a transmembrane protein whose function lies in cell-to-cell adhesion. It is a transmembrane component of adherens junctions of epithelial tissues, thereby connecting the actin cytoskeletons of adhered cells. It has five extracellular domains, a small transmembrane portion, and a cytoplasmic tail. The molecule must bind calcium in order to form an adhesive dimer with a cadherin molecule emanating from an adjacent cell. Cancer of the epithelial tissue, carcinoma, is accompanied by acidification of the tissue and a loss in cell adhesion. The long-term goal of this project is to determine the effect of a decrease in …
An Investigation Into The Synthesis Of A Four-Armed Diamino Swallowtail, Christopher Carter Barnett
An Investigation Into The Synthesis Of A Four-Armed Diamino Swallowtail, Christopher Carter Barnett
Honors Theses
Perylenebisimides (PBIs) complex with quadruplex DNA and may influence the formation of telomeres. PBIs with amine groups are ionized at neutral pH and therefore soluble in water [1]. Swallowtails are long alkyl chains usually attached to PBIs to inhibit self-aggregation by pi-stacking [2]. Past attempts to create a PBI with swallowtails containing extra nitrogens were unsuccessful due to purification issues and methylene connectors. The purpose of this research is to investigate the synthesis of a diamino swallowtail with a methine connector. The first step is to create 1,3-bis(dibenzylamino)propan-2-one by way of an SN2 substitution reaction using 1,3-dichloroacetone and dibenzylamine [3]. …
An Investigation Of Protein-Dna Binding Characteristics By Fluorescence Anisotropy, Danna Nobile
An Investigation Of Protein-Dna Binding Characteristics By Fluorescence Anisotropy, Danna Nobile
Honors Theses
Recent studies have illustrated the presence of several secondary, non-B DNA structures that are associated with the promoter regions of several oncogenes, such as the intensely studied MYC gene. Two such secondary structures, G-quadruplexes and i-Motifs, have become topics of interest due to their prevalence within oncogenic promoters and their potential accessibility for future drug targeting due to their globular natures. Though fairly extensive research has been conducted to understand different factors affecting G-quadruplex formation and stability, similar studies for i-Motifs, particularly related to thermodynamics, are still evolving. One factor known to contribute to the additional energy required for duplex …
X-Dimer Mutations And Their Effects On The Folding Stability And Assembly Of Ecad12 At The K14-D138 Interface, Martha Kaitlyn Coghlan
X-Dimer Mutations And Their Effects On The Folding Stability And Assembly Of Ecad12 At The K14-D138 Interface, Martha Kaitlyn Coghlan
Honors Theses
Classical cadherins were first identified by their function in mediating calcium-dependent cellular adhesion and constitute a large family of cellular adhesion receptor proteins whose differential binding is central to the development and maintenance of tissue architecture. The interface underlying the binding interaction reveals that all classical cadherins share a common adhesive interface in which the portion of the β-A strand closest to the N-terminus is swapped between EC1 domains of the adhesive partner protomers. A second dimeric configuration, known as the 'X-dimer', is the face-to-face association of two protomers in which their orientation is dictated by three symmetrical noncovalent interactions …
Characterization Of Epithelial Cadherin Domain 1, Molly Edmondson
Characterization Of Epithelial Cadherin Domain 1, Molly Edmondson
Honors Theses
Cadherins are a family of cell-surface glycoproteins that aid in cell adhesion between two proximal cells. The characteristic cadherin extracellular structure consists of five ~100 amino acid domains connected by seven-residue linker regions. Cadherins mediate adhesion via adherens junctions by forming a strand-swapped structure between identical protomers from apposing cells. Upon calcium binding, the swapping of the N- terminal strands between protomers allows for the symmetrical docking of a conserved tryptophan residue in the N-terminal strand into the hydrophobic pocket of its partner protomer. The two most-well-studied members of the classical cadherin family are Neural- (N-) and Epithelial- (E-) cadherin. …
Properties Of A Fluorescent Deoxycytidine Analog In I-Motif Dna, Sara E. Wingate
Properties Of A Fluorescent Deoxycytidine Analog In I-Motif Dna, Sara E. Wingate
Honors Theses
Experiments to determine fluorescence lifetimes and fluorescence quenching constants were performed using oligonucleotides of DNA containing PdC, a fluorescent analog of cytidine, at five different locations in the i-motif. My experiments were chosen in order to better understand the structural characteristics of i-motif DNA, which are thought to have biological importance in cancer and drug delivery. Fluorescent lifetime experiments were carried out using an ISS K2 fluorescence instrument with a modulated LED light source in order to determine if the cytidine bases in DNA replaced by PdC were paired or unpaired in the i-motif structure. The resulting data allowed us …
The Dimerization Kinetics Of Ncad12 With A Mutated Cis-X-Pro Bond, Victoria Mcclearn
The Dimerization Kinetics Of Ncad12 With A Mutated Cis-X-Pro Bond, Victoria Mcclearn
Honors Theses
VICTORIA RAE McCLEARN: DIMERIZATION KINECTICS OF NCAD12 P16A (Under the direction Dr. Susan Pedigo) Calcium binding causes a conformational change into a strand swapped dimer for the cadherins. However, regardless of the sequence similarity for Epithelial Cadherin (ECAD) and Neural Cadherin (NCAD), they respond to the presence of calcium differently. For NCAD, the rate of assembly and disassembly depends upon the presence of calcium, whereas for ECAD the rate of exchange is independent of calcium. Studies into a kinetic model to explain the differences between the rates have been recently conducted. It is believed that ECAD uses an X-dimer intermediate …
Towards The Synthesis Of A Swallowtailed Perylene Monoimide, Wyatt S. Whicker
Towards The Synthesis Of A Swallowtailed Perylene Monoimide, Wyatt S. Whicker
Honors Theses
This project was initiated in conjunction with Dr. Justin Youngblood from the University of North Texas. The goal was to synthesize a molecule to be used in solar cell testing. The target molecule involved combining donor and acceptor groups to make a combination that would be able to transfer electricity in a unilateral direction to increase efficiency in solar cells. My project involved the donor portion, a perylene monoimide donor with a long alkyl swallowtail to impart solubility. While the final molecule was not synthesized, the proposed procedure for making such a molecule was improved upon. A perylene tetracarboxylic dianhydride …