Physical Sciences and Mathematics Commons^™

Development Of An Enhanced Sampling Workflow To Accelerate Molecular Docking With Sparse Biophysical Information, Zachary Stichter

Masters Theses & Specialist Projects

Rapid docking of flexible biological macromolecules remains a significant open challenge in protein structure determination. While rigid docking is relatively simple with toolkits such as TagDock, a key obstacle to rapid flexible docking is the complexity and roughness of the free energy surface associated with protein conformational motion (often termed the many-minima problem), meaning conventional molecular dynamics methods do not effectively sample protein conformations near the interaction complex in accessible timescales. Methods such as metadynamics and replica exchange molecular dynamics exist to ameliorate this obstacle, yet these methods use nonphysical biases or random swaps to enhance sampling. In contrast, high …

Real-Time Monitoring Of Paraquat Photodegradation Using Colloidal Gold Surface Enhanced Raman Spectroscopy, Nathan Wilson

Masters Theses & Specialist Projects

Monitoring chemical reactions in aqueous solution is a challenge because most instrumental techniques either are not suited for the rapid timescales, are not sensitive enough to detect products at low concentrations, or do not have sufficient structure-to-spectrum relationships. Raman spectroscopy is a promising method to monitor reactions, as it is fast, dependent on chemical structure, and has little interference from water. However, Raman scattering is generally very weak. Surface-enhanced Raman spectroscopy (SERS) improves the signal strength of Raman spectroscopy by using a metal surface plasmon, or oscillation of the surface’s electrons, to allow for highly selective and sensitive detection and …

Synthesis Of Cds/Zns Core/Shell Semiconductor Nanoparticles, Austin Skyler Antle

Masters Theses & Specialist Projects

Core/shell semiconductor nanoparticles are of great interest as photocatalysts due to their large surface area per volume and tunable band gaps. The synthesis of core/shell semiconductor nanoparticles has traditionally involved the use of binding ligands to ensure the particles do not aggregate. These binding ligands lower the surface area of the nanoparticles though, reducing their overall efficiency. Ionic liquids have been found to be capable of acting as both solvents and stabilizing agents for synthesis of catalysts with highly active surfaces. Our experiments focus on the synthesis of CdS/ZnS core/shell nanoparticles with the ionic liquid 1-butyl-3-methylimidazolium methyl sulfate, [BMIM][MeSO4], acting …

Monitoring And Identifying The Rhodamine 6g-Hydroxide Ion Reaction Using In-Situ, Surface-Enhanced Raman Spectroscopy, Ryan Lamb

Masters Theses & Specialist Projects

An effective method for monitoring chemical reactions is necessary to better understand their mechanisms and kinetics. Effective reaction monitoring requires a spectroscopy technique with fast data acquisition, high sensitivity, structure-to-spectrum correlation, and low solvent interference. Surface-enhanced Raman spectroscopy (SERS) provides these features, which makes it a valuable tool for monitoring reactions. To obtain the Raman enhancement, metallic nanostructures typically made of silver or gold are aggregated using a salt. The nanoparticles aggregates must then be stabilized using a surfactant to use this method in situ due to eventual nanoparticle precipitation. In this study, gold nanoparticles stabilized with sodium dodecyl sulfate …

Secondary Electronic And Solvent Effects On Regiospecific P-Bromination Of Aromatic Systems, Selahaddin Gumus

Masters Theses & Specialist Projects

Bromoarenes are important aromatic building blocks that are commonly used to synthesize various functional compounds in pharmaceutical, agrochemical and related industries.^1,2 This great demand for bromoarenes makes their preparation a widely studied area of synthetic organic chemistry. However, further understanding of the reactivity and regiochemistry of aromatic functionalization reactions is still necessary, as much about the secondary substitution and solvent effects remain unknown.

Resonance Theory is a widely used theoretical model to predict the regiospecifity and reactivity of the bromination of various aromatic compounds.³ The reactivity and regiospecificity of many substituted aromatic compounds is well explained using resonance …

Temperature And Electric Field Dependency Of Asymmetric Stretching Of Nitrate And Carbonate Ions, Konnor Jones

Masters Theses & Specialist Projects

Photolysis of nitrate ion in the natural environment produces NO, NO2, and O3, releasing these toxic gases into the atmosphere. Work done by other groups has shown ionic strength dependence of the ratio of products from photolysis of aqueous nitrate ion. To better understand the kinetic mechanisms of nitrate photolysis, the effects that ionic strength in solution have on nitrate ion symmetry breaking are needed. Different solvation environments induce nitrate bonding motifs that may be correlated to the product ratio. Fourier-transform infrared spectra of aqueous nitrate–ion solutions were obtained over a range of temperatures for several total electrolyte concentrations. The …

Tio2/Pdms Buoyant Photocatalyst For Water Remediation And Cu‑Rbs Organic/Inorganic Hybrid For Thermoelectric Applications, John R. Bertram

Masters Theses & Specialist Projects

Two novel materials have been developed: TiO2/poly(dimethylsiloxane) (PDMS) beads as buoyant photocatalyst materials for water remediation, and copper rhodamine‑B silane (Cu‑RBS) as an n ‑type organic/inorganic hybrid for thermoelectric applications. The approach to incorporate TiO2 into low‑density PDMS beads addresses many of the challenges traditionally encountered when creating buoyant photocatalysts, an area which is crucial for wide‑spread remediation of water resources, including natural bodies of water. The performance and reusability of the buoyant photocatalyst materials, demonstrated by using methylene blue as a model degradation target, is strong enough for environmental application. The use of a kinetic model and the introduction …

Regiospecific P-Bromination Of Activated Aromatic Systems – Greener Approach, Elnaz Jalali

Masters Theses & Specialist Projects

The halogenated derivatives of heterocyclic compounds (haloarenes) are highly utilized in many fields of chemistry, including drug discovery, medicinal, and material chemistry. There are a variety of ways to functionalize an aromatic system and introduce halogen substituent into the ring. However, electrophilic aromatic substitution (EAS) has been the focus of growing attention, particularly for electronrich substrates.

Electrophilic aromatic bromination protocols are one of the most important electrophilic aromatic substitution reactions. However, preparation of bromoarenes classically recommends the use of highly oxidative agents along with utilizing various metal catalysts in a halogenated solvent. The corrosive and toxic nature of these reagents …

Environmentally Friendly Synthesis Of Transition Metalorganic Hybrid Nanocomposites, Aubrey N. Penn

Masters Theses & Specialist Projects

Research on metal nanoparticles (MNPs) synthesis and their applications for optoelectronic devices has been a recent interest in the fields of nanoscience and nanotechnology Photovoltaics are one of such systems in which MNPs have shown to be quite useful, due to unique physical, optical, magnetic, and electronic properties, including the metal nanoparticles synthesized in this research.

Owing to the challenges with the most common physical and chemical methods of preparing MNPs, including the use of high temperatures, toxic reducing agents, and environmentally hazardous organic solvents, there is a critical need for a benign synthesis procedure for MNPs. In this work, …

In Situ Ion Exchange In A Micro-Porous Transition Metal Silicate Framework, Jason M. Lively

Masters Theses & Specialist Projects

Ion selectivity of minerals has traditionally been utilized in industry as a catalyst, metal separation, and environmental reclamation/sequestration tool. There is an increased interest in understanding ion selectivity mechanisms of micro-porous minerals and mineral-like structures and how they can be applied in various industries: environmental and, potentially, pharmaceutical. This study seeks to understand the ion exchange mechanisms in micro-porous zirconosilicates using time-resolved Raman spectroscopy and X-ray diffraction. The thesis material was exchanged with H+, Na+, K+, and Cs+ in order to better understand structural changes as well as the influence of the H+-bonding during the exchange process. It is hypothesized …

Metal-Organic Hybrid Nanocomposites For Energy Harvesting Applications, Thulitha Madawa Abeywickrama

Masters Theses & Specialist Projects

Various synthetic methods have been developed to produce metal nanostructures including copper and iron nanostructures. Modification of nanoparticle surface to enhance their characteristic properties through surface functionalization with organic ligands ranging from small molecules to polymeric materials including organic semiconducting polymers is a key interest in nanoscience. However, most of the synthetic methods developed in the past depend widely on non-aqueous solvents, toxic reducing agents, and high temperature and high-pressure conditions. Therefore, to produce metal nanostructures and their nanocomposites with a simpler and greener method is indeed necessary and desirable for their nano-scale applications. Hence the objective of this thesis …

Enhancing The Photovoltaic Efficiency Of A Bulk Heterojunction Organic Solar Cell, Swapnil Ashok Sahare

Masters Theses & Specialist Projects

Active layer morphology of polymer-based solar cells plays an important role in improving power conversion efficiency (PCE). In this thesis, the focus is to improve the device efficiency of polymer-based solar cells. In the first objective, active layer morphology of polymer-solar cells was optimized though a novel solvent annealing technique. The second objective was to explore the possibility of replacing the highly sensitive aluminum cathode layer with a low-cost and stable alternative, copper metal. Large scale manufacturing of these solar cells is also explored using roll-to-roll printing techniques.

Poly (3-hexylthiophene) (P3HT) and phenyl-C61-butyric acid methyl (PCBM) were used as the …

Fused-Molecular Systems For Organic Light Emitting Diodes, Avinash Jami

Masters Theses & Specialist Projects

Organic light emitting diodes (OLEDs) are electronic devices made by sandwitching organic light emissive materials between two electrodes. When voltage is applied across the two conductors, a bright light is generated. The color of the emitting light depends on the band gap of the semiconducting material. The work described here focuses on designing and synthesizing narrow band gap molecular systems derived from fused-arene derivatives for producing organic blue light emitting diodes. Three molecular systems derived from anthracene, pyrene, and carbazole, were designed and synthesized. Two molecular systems of anthracen-9-ylmethyl anthracene-9- carboxylate and pyren-1-ylmethyl 4-bromobenzoate were synthesized through Steglich esterification reaction …

A Ph Switchable Responsive Surface For The Trapping And Release Of A Hydrophobic Substance, Ali Esmail Karim

Masters Theses & Specialist Projects

Solid phase extraction is one of the most widely used techniques to trap and release compounds in a solution. A hydrophobic substance will stick efficiently to a hydrophobic surface (the “like dissolves like” principle). With an introduced response (i.e. pH change), a responsive surface can change from hydrophobic to hydrophilic, weakening the hydrophobic substance’s attraction and thus facilitate in an easy removal. A surface has been prepared having a terminal anthranilic acid (AA) moiety on silica gel particles, microscope slides, and TLC plates in three steps. First, a vinyl group was attached to the surface. Then, this vinyl group was …

Corrosion Behaviors Of Coated Aluminum Alloys In Simulated Corrosive Environment, Jingyi Yue

Masters Theses & Specialist Projects

This study investigated the corrosion of an aluminum alloy with and without coatings under simulated corrosive environments. Coatings were selected and applied from commercial materials and techniques, consisting of microceramic, epoxy primer, and topcoat. The experiments for coated specimens were carried out under various corrosive conditions, specifically, hydrodynamic flow, immersion in salt water and DI water, varying temperatures, and simulated sun light. The hydrodynamic conditions were simulated using a rotating cylinder electrode (RCE) with rotational speeds of 200, 400, 600, 800, and 1000 rpm. The immersion in saltwater and sunlight illumination tests were applied for 8 hours, and the simulated …

Syntheses, Structures And Properties Of Metal-Organic Frameworks, Xin Liu

Masters Theses & Specialist Projects

Mercury is one of the most serious heavy metal pollution sources that threaten people’s health. For decades, people have developed many technologies and materials to capture mercury from flue gas of coal-fired plant. Currently, the most effective material for mercury absorption is powdered activated carbon, which shows increased efficiency when modified with halogen functional groups such as bromine. Metal-organic frameworks (MOFs) have potential applications in mercury capture due to their fantastic properties such as high porosity and high thermal stability. More important, their pore sizes and topology structures can be controlled through choosing different organic ligands in the syntheses. However, …

Electrically Controlled Formation And Release Of Admicelles For Solid Phase Extraction, Sukyeon Lee

Masters Theses & Specialist Projects

Solid phase extraction is one of the most widely used methods to concentrate diluted compounds in a solution. Substances can be extracted into admicelles and hemimicelles, which are surface adsorbed micelles and surfactant monolayers, respectively. Investigations of the electrical control of surfactants on surfaces for the purpose of analyte preconcentration prior to chromatographic analysis are presented. The surfactant layer serves as the “stationary phase” in a solid phase extraction sorbent scenario. Analytes are adsorbed on this layer, and then released from the solid phase via surfactant removal. The attachment and removal of the surfactant are controlled by means of an …

Solar Energy Conversion And Control Using Organic Photovoltaic Cells, Kurt Wade Woods

Masters Theses & Specialist Projects

Organic photovoltaic (OPV) cells are advanced, newly emerging technologies that are lightweight, mechanically flexible devices with highthroughput processes from low cost material in a variety of colors. Rathnayake et al. of Western Kentucky University have developed a nanostructure-based OPV cell. Presented in this thesis is a model and simulation of a generalized PV powered system that can predict the performance of solar arrays in various environmental conditions. The simulation has been carried out in Matlab/Simulink, and upon entering the cell’s parameters, it provides key electrical characteristics such as the cell’s I-V curve and efficiency information. The total system that is …

Synthesis And Computational Studies Of A New Class Of Lanthanide Niobate Cluster : [Ln4(H2O)8(So4)5(Nbo3)2]+3h2O; Ln= Dy, Tb, Brady D. Garabato

Masters Theses & Specialist Projects

Polyoxoniobates (PONbs) are a small family of highly electron-rich clusters. The development of new solids composed of these clusters have applications in green energy and electronics. However, the high charge environment of PONbs typically requires alkaline synthetic conditions that are unsuitable for introducing other metals and organic molecules, making synthesis of new systems difficult. To date, very few transition metals and organic ligands have been incorporated into these PONb solids, and lanthanide metal inclusion, which generally improves photoconductivity due to longlived f-orbital excitations, has not yet been fully realized. Here, the synthesis of a new class of lanthanide niobate cluster …

Fused Arenes-Based Molecular And Polymeric Materials For Organic Field Effect Transistors, Harista Irugulapati

Masters Theses & Specialist Projects

In the past decade, tremendous progress has been made in organic field effect
transistors. Fused oligothiophenes and anthracene molecules are fascinating
macromolecules having unique optoelectronic properties. These compounds are successfully employed as active components in optoelectronic devices including field effect transistors. Our goal is to design and synthesize conjugated molecular materials, which are highly functionalized through structural modifications in order to enhance their electronic, photonic, and morphological properties. The main desire is to synthesize novel organic fused-arenes having efficient charge carrier mobilities, as well as to optimize optical properties for organic field effect transistors (OFETs). Novel series of fused arene …