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Articles 211 - 240 of 285
Full-Text Articles in Chemistry
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 …
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]. …
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 …
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 …
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 …
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 …
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
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
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
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 …
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 …
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.
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 …
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 …
Exploration Of Novel Synthetic Utility Of Lithioacetonitirile, Rambabu Sankranti
Exploration Of Novel Synthetic Utility Of Lithioacetonitirile, Rambabu Sankranti
Electronic Theses and Dissertations
No abstract provided.
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 …
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 …
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 …
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 …
Atmospheric Mercury Species In Northern Mississippi: Concentrations, Sources, Temporal Patterns, And Soil-Air Exchange, Yi Jiang
Electronic Theses and Dissertations
Mercury is a highly toxic element that is found both naturally and as an introduced contaminant in the environment. The majority of Mercury released to the environment is into the atmosphere, where because of its high volatility and long residence time is dispersed globally. In order to better understand the factors controlling the distribution and temporal patterns of atmospheric Mercury species, as well as the sources of airborne Mercury in the mid-south region, concentrations of gaseous elemental mercury (gem), gaseous oxidized mercury (gom), and particulate-bound mercury (pbm), along with meteorological parameters and other ancillary data, were collected for more than …
Noncovalent Interactions Involving Microsolvated Networks Of Trimethylamine N-Oxide, Kristina Andrea Cuellar
Noncovalent Interactions Involving Microsolvated Networks Of Trimethylamine N-Oxide, Kristina Andrea Cuellar
Electronic Theses and Dissertations
This thesis research focuses on the effects of the formation of hydrogen-bonded networks with the important osmolyte trimethylamine N-oxide (TMAO). Vibrational spectroscopy, in this case Raman spectroscopy, is used to interpret the effects of noncovalent interactions by solvation with select hydrogen bond donors such as water, methanol, ethanol and ethylene glycol in the form of slight changes in vibrational frequencies. Spectral shifts in the experimental Raman spectra of interacting molecules are compared to the results of electronic structure calculations on explicit hydrogen bonded molecular clusters. The similarities in the Raman spectra of microsolvated TMAO using a variety of hydrogen bond …
Structural Analysis Of Bulky Thiolate-Protected Gold Nanomolecules, David Walton Crasto
Structural Analysis Of Bulky Thiolate-Protected Gold Nanomolecules, David Walton Crasto
Electronic Theses and Dissertations
Routine preparation of thiolate-protected gold nanomolecules involves, most commonly, straight-chain organic thiolate ligands for which the sulfhydryl `head' group is bound to a primary carbon atom. The primary connectivity of these sulfur atoms, such as for the case of n-hexanethiol and phenylethanethiol, allows for even packing, and the relative ease of formation of gold-thiolate oligomers about the surface monolayer in the formation of Au-SR bonds. Moreover, these straight-chain ligands routinely support the formation of an icosahedron-based series of core-size gold nanomolecules. Within this series of nanoparticles, Au25(SR)18 and Au38(SR)24 are among the most commonly studied core-sizes; Au25(SR)18 is situated upon …
On Harmonic Vibrational Frequency Convergence To The Complete Basis Set Limit In Water Dimers And Hydrogen Fluoride Dimers, Amanda Hardwick
On Harmonic Vibrational Frequency Convergence To The Complete Basis Set Limit In Water Dimers And Hydrogen Fluoride Dimers, Amanda Hardwick
Honors Theses
This work focuses on the convergence of harmonic vibrational frequencies in the water dimer (H2O)2 and the hydrogen fluoride dimer (HF)2 to the complete basis set (CBS) limit. It also evaluates the effect of counterpoise (CP) correction procedures and the effect of sequentially removing diffuse functions from specific basis sets on the harmonic vibrational frequencies of these dimers. Computations were run using second-order Møller-Plesset perturbation theory (MP2) with large, flexible correlation consistent basis sets. This research aims to determine if removing diffuse functions can increase the speed of harmonic vibrational frequency computations without sacrificing accuracy. Results indicate that CP-correction procedures …
Raman Spectroscopic And Computational Analysis Of The Effects Of Noncovalent Interactions On Dmso, Ashton T. Nicholson
Raman Spectroscopic And Computational Analysis Of The Effects Of Noncovalent Interactions On Dmso, Ashton T. Nicholson
Honors Theses
Dimethyl sulfoxide (DMSO) is a widely used chemical in synthetic chemistry and also has unique and important biological applications. In the pure liquid, DMSO forms chain like structures of alternating sulfur and oxygen atoms due to its high self-association. However, it is known that DMSO/water mixtures form solutions with unique physical characteristics depending on the mole ratio. For instance, at a 1:2 ratio of DMSO/water a eutectic mixture forms with a freezing point of-70 C. Vibrational spectroscopy allows us to study the effects of noncovalent interactions when water and DMSO interact in solution. Spectral shifts can be analyzed in order …
Synthesis Of An Unsymmetrical Ccc-Nhc Pincer Ligand Precursor, Brian Spurlock
Synthesis Of An Unsymmetrical Ccc-Nhc Pincer Ligand Precursor, Brian Spurlock
Honors Theses
The purpose of this study was to synthesize a 3-butyl-1-(3-(3-butyl-1H-imidazol-3-ium-1-yl)phenyl)-4,5-dichloro-1H-imidazol-3-ium salt using an Ullmann-type copper coupling reaction. This salt would subsequently be metallated and evaluated for C-H bond activation and luminescence. However, NMR and MS spectra did not show evidence of conversion to the desired product under standard conditions so a model reaction was designed making use of recent findings concerning the Ullmann-type coupling of imidazoles to aryl halides. Specifically, an activated aryl halide with a larger leaving group was used with a more soluble base and a ligand for the copper. The desired product appears by ESI-MS to have …
Evaluating The Efficacy Of Small Basis Sets And The Counterpoise Procedure To Reproduce Complete Basis Set Limit Higher-Order Correlation Corrections For Weakly Bound Molecular Clusters, Cara M. Thorne
Honors Theses
The efficacy of small basis sets and the counterpoise procedure to accurately reproduce higher-order correlation corrections, which are routinely employed to estimate CCSD(T) interaction energies at the complete basis set (CBS) limit using an additive scheme, was examined through the study of four dispersion-dominated dimer systems. The dimers of acetylene (HCCH), cyanogen (NCCN), diphosphorous (P2) and 1,4-diphosphabutadiyne (PCCP) were studied in three different configurations: cross, parallel-displaced and t-shaped at the intermolecular distance corresponding to the minimum point on the CCSD(T) potential energy curve (PEC) for each system using MP2, CCSD and CCSD(T) methods in conjunction with eight basis sets from …