Chemistry Commons^™

Determination Of Antibiotic Release From Electrospun Nanofibers, John P. O'Brien Iii

Honors Theses

Decreasing the risk of infection following surgery for traumatic bone breaks is a major focus of the medical and scientific community. Drug delivery devices are emerging as powerful solutions for combating infection following these procedures. Current devices, however, suffer several drawbacks including poor antibiotic release rate and control the devices themselves not being biodegradable. This thesis studies the \textit{in vitro} release rate for antibiotics tobramycin and vancomycin from a biodegradable medical implant. Antibiotics, collagen, and bone growth factors are incorporated into Poly(lactide-co-glycolide)-based electrospun nanofibers by local company eSpin for development. The drug-loaded nanofibers are immersed in phosphate buffered saline (PBS) …

Modifications Of Lysozyme By Substituted Benzoquinones, Hendrik J. Greve

Honors Theses

Amyloidosis, which involves the precipitation of mis-folded protein aggregates, is a prominent process that occurs in many neurodegenerative conditions such as Alzheimer's disease and Parkinson's disease; the protein aggregates being amyloid-β for Alzheimer’s disease and α-synuclein for Parkinson’s disease. This study has focused on lysozyme modifications induced by metabolites of the commonly found pollutants known as polycyclic aromatic hydrocarbons (PAHs). PAHs are found in substances ranging from grilled meats to cigarette smoke to cosmetics, and they can be metabolized into a family of biological toxins known as benzoquinones. The molecules of interest for this study were 1,4-benzoquinone (pBQ), 2-chloro-1,4-benzoquinone (CBQ), …

Ribonuclease A Modification Induced By 1,2-Naphthoquinone And 2-Hydroxy-1,4-Naphthoquinone, Michelle Dawn Smith

Honors Theses

Protein modifications may occur upon exposure to environmental toxins such as polycyclic aromatic hydrocarbon (PAH) molecules or their metabolites. In this context, our laboratory was interested in investigating protein modifications in the presence of select naphthoquinones, which were 2-hydroxy-1,4-naphthoquinone (HNQ) and 1,2-naphthoquinone (o-NQ). The effects of HNQ and o-NQ on the protein Ribonuclease A (RNase) were investigated through a variety of conditions. These modified incubation conditions included pH variation and the addition of metal ions to further mimic physiological conditions. Documentation of results was carried out through sodium dodecyl sulfate polyacrylamide gel electrophoretic analysis (SDS-PAGE). Of the two quinones, o-NQ …

Exploration Of Protein-Protein Interactions Involving Deinococcus Radiodurans Pria, Dnab And Ssb, Christopher S. Morrow

Honors Theses

Deinococcus radiodurans is a species of bacteria that has sparked a lot of interest since its discovery due to its incredible resistance to ionizing radiation. When exposed to ionizing radiation the genome of D. radiodurans will sustain over one hundred double stranded breaks. D. radiodurans demonstrates the ability to repair its genome and restart replication after sustaining, typically lethal, DNA damage. This project examined the mechanism of replication restart in D. radiodurans by investigating primosome protein PriA interacting with replicative helicase DnaB and single stranded binding protein. Many different types of gel electrophoresis were employed to investigate potential protein complex …

Synthesis Of Potential Phosphorus-Nitrogen Containing Flame Retardants, Colin Kloock

Honors Theses

Production of extremely efficient flame retardants is ideal because, in many instances, the amount of flame retardants that are added to pre-production to the mixture are so large that they can have an effect on the physical properties of the material. In addition, these types of polymers, when added during production, are homogenously mixed throughout the mixture which means not only uniform distribution and therefore function, but a less concentration of the retardants need to be used. Using Phosphorus-Nitrogen containing flame retardants in mixtures can have two means by which they function. First is the ability of P-N compounds to …

Synthesis Of Phosphorus-Based Hemiacetals For Potential Flame Retardants, Sara Alakkad

Honors Theses

Flame retardants which contain a phosphorus moiety attached to a carbohydrate backbone were developed. To synthesize the flame retardants, carbohydrates and polyols were used as the starting materials which occur in nature and are environmentally and toxicologically safe materials. The two target structures include one with a triose substructure and one with a pentose substructure. For both situations, however, multiple steps were taken for the synthesis of the flame retardant, as the carbohydrate needed to be generated into its protected form. The protected carbohydrate then interacted with a dialkyl phosphite, resulting in a phosphorous hemiacetal. This hemiacetal was then deprotected …

Kinetic Characterization Of B-Carotene In N-Hexane At Various Oxygen Concentrations, Katelyn Mary Arnold

Honors Theses

We have characterized the photo – degradation of ẞC in oxygenated and deoxygenated n–hexane solvent and in the solid phase using broadband (BB; λ ≥ 200 nm) and 313 nm filtered output of a 100 W Hg Arc lamp. Oxygen concentrations of 0, 10, 20, and 100% were used in the solution phase studies. ẞC(s) did not photo – degrade upon exposure to BB light under air atmospheres; the mass and appearance of the samples, TLC chromatograms, and the absorption spectra were all identical pre- and post-irradiation. In the solution phase, the order of the photo – degradation with respect …

Suspension Electrospinning Carbon Nanotube Doped Poly (Vinyl Alcohol) Nanowires, Ryan Hensleigh

Honors Theses

The synthesis, characterization and application of carbon nanotubes (CNTs) have received substantial attention in recent years, particularly in the field of polymer nanomaterial composites (PNCs). CNTs possess impressive thermal, electrical and mechanical properties, and PNCs incorporating them have shown multitude increases in these same properties with relatively low percolation thresholds [1]. Electrospinning is an effective and tunable materials synthesis platform for the manufacture of micro and nanofibers that has shown particular promise in the fields of carbon nanotube PNC processing due to the favorable isotropic alignment CNTs undergo due to the electrospinning process [2]. CNT alignment has been shown to …

Generation Of 2-Adamantylidenecarbene From A Phenanthrene-Based Precursor, Christine E. Wamsley

Honors Theses

This thesis examines the generation of 2-adamantylidenecarbene from a phenanthrene-based precursor. A three-step synthetic procedure was used to generate the 2-adamantylidenecarbene precursor, which subsequently underwent photolysis to produce 2-adamantylidenecarbene. This product was trapped with cyclohexene. No evidence of a ring expansion to 4-homoadamantyne was observed. It was also noted that the target precursor underwent rearrangement during photolysis, leading to the formation of an isomer containing a seven-membered ring. This isomer did not photolyze. Additionally, computational studies were performed using Gaussian 09. Geometries were initially optimized and then, the single point energies of the singlet and triplet carbene states were calculated. …

Experimental And Computational Investigation Of Selected Β-Hydroxy Carbenes, Joseph D. Deangelo

Honors Theses

The photolytic precursor to the sterically hindered β-bis(tert)-butanol carbene, 3-(1a,9b-dihydro-1H-cyclopropa[l]phenanthren-1-yl)-2,2,4,4-tetramethylpentan-3-ol was prepared in three steps from phenanthrene. Photolysis of the precursor generates the desired β-hydroxy carbene, an intermediate, which subsequently rearranges into two different observed products from an intramolecular C-H insertion and alkyl shift. Four intramolecular mechanisms were ultimately considered to account for the possible rearrangement pathways. Computational studies using density functional theory are also presented.

In addition, the photolytic precursors to two cyclic β-hydroxy carbenes, 1-(1a,9b-dihydro-1H-cyclopropa[l]phenanthren-1-yl)cyclopropan-1-ol and 1-(1a,9b-dihydro-1H-cyclopropa[l]phenanthren-1-yl)cyclobutan-1-ol, were also prepared through different synthetic routes from phenanthrene. …

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

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 …

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 …

The Effects Of Hg2+ On Secondary Structures Formed By T-Rich Dna, Zachary Boynton

Honors Theses

Single stranded DNA that forms secondary structures has been a popular area of research in recent years. Much research has also been done in the field of heavy metals binding to DNA. Recently, it has been discovered that mercury in the presence of thymines will form T-HgII-T bonds. It is our hypothesis that single stranded DNA rich in thymine residues will form into a structure similar to i-motifs, formed from C-rich single strands, in the presence of mercury. Based on spectral changes during a mercuric titration, it is evident that mercury induces a structural change in T-rich DNA. We then …

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 …

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 …

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 …

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]. …

A Computational Investigation Of Halogen Bonding With Halomethanes And Their Group 14 Analogues, William Kretz

Honors Theses

It is known that halogen bonding is supported by so-called sigma holes on halides that interact with bases, but what are the limits of that interaction? How does the interaction depend on the group to which the halogen atom is bonded? To answer these questions, complexes of the form MH3X---Y (where M=C, Si, Ge, Sn, Pb; X= F, Cl, Br, I and Y are Lewis bases) were optimized and their energetics and relative stability were assessed. The Lewis bases range from NH3 to the more complicated pentafluroropyridine (F-py). Calculations were performed entirely at the MP2(full) level of theory, including frequency …

The Application Of Formyl Group Activation Of Brompyrrole Esters To A Formal Synthesis Of Lycogarubin C, Jon Patteson

Honors Theses

Lycogarubln C is a member of an interesting family of marine natural products, which contains two indole groups appended to a pyrrole scaffold at the 3 and 4 positions. Such compounds are proposed to be biosynthetically related to the important antitumor agent, Staurosporine. Recent work in our lab involving the use of Suzuki cross-coupling reactions of an ortho activated bromoformylpyrrole ester has provided key intermediates for the synthesis of pyrrole natural products and pyrolle-based analogues.

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 …

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 …

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 …

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 …

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 …

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 …

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. …

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 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 …