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 …

Towards The Quantification Of Estrone And 17Β-Estradiol Conjugates In Dairy Cattle Urine Sorptive Stir Bar Extraction And Gas Chromatography-Mass Spectometry, S.M. Istiak Ahmed

Masters Theses & Specialist Projects

The global concern regarding the presence of compounds with estrogenic properties in the environment has grown significantly. Endocrine-disrupting compounds (EDCs) are environmental pollutants that disrupt the endocrine systems of both wildlife and humans. Estrogens, with their potent estrogenic effects, are particularly noteworthy among the various substances with endocrine-disrupting properties. They are of concern due to their prevalence in the environment, especially due to dairy waste contamination. These lipophilic compounds can accumulate in livestock fat tissues, potentially entering the human food chain. Sulfated forms of estrone and β- estriol, which exhibit a higher degree of saturation than their non-conjugated counterparts, have …

Liquid Chromatography Mass Spectrometry Method Development For The Determination Of Β–Defensins In Bovine Milk, Elisha Ogbebor

Masters Theses & Specialist Projects

Bovine mastitis is caused by a wide range of pathogens which results in a substantial economic loss for the dairy cattle livestock industry. β-defensins are a part of the innate immune system and act as the first line of defense against mastitis in bovine. β-defensins (~6- 10kDa) are antimicrobial peptides that contain about 28 to 67 amino acids, the presence of six cysteine residues results in their three disulfide bonds and a β-sheet structure. A few β- defensins have been identified in cows based on the site of occurrence and time of expression in tissue, but not in milk. A …

Towards Deposition Of Iron & Nickel Onto Cadmium Selenide/Cadmium Sulfide Nanorods, Rajib Nath

Masters Theses & Specialist Projects

Metal-semiconductor hybrids have been studied extensively as photocatalysts for the watersplitting reaction to generate hydrogen gas and oxygen gas to use as a renewable energy source. The semiconductor component converts light into electrochemical energy, while the metal component provides a site for chemical reactions with water. Here, the choice of metal can have a significant impact on the efficiency of the catalyst. Platinum efficiently catalyzes the watersplitting reaction and is therefore commonly used in metal-semiconductor hybrids to generate hydrogen. Platinum is very expensive, which motivates research into improving less costly metals like iron or nickel that do not have nearly …

Carbon Cycling And Critical Zone Dynamics In An Urbanized Karst Groundwater System, Amy Hourigan

Masters Theses & Specialist Projects

Increasing atmospheric CO₂ concentrations are correlated to rising global temperatures. Investigating the cumulative global carbon cycling processes is important to understand and quantify the global carbon cycle. By investigating basic geochemical parameters, EpCO₂, DIC, and δ¹³C_DIC, at four sites along Lost River Cave (LRC), in Bowling Green, Kentucky, concentrations, fluxes and sources of C dissolved in groundwater were determined. Urban karst groundwater systems, compared to more natural karst landscapes, typically exhibit widespread impervious, heat-absorbing surfaces, urban heat island effects, and increased anthropogenic groundwater inputs and localized CO₂ emissions. Carbonate hydrogeochemical …

Evaluation Of Silver Nanoparticles Attached To Methylene Blue As An Antimicrobial Agent And Its Cytotoxicity, Somon Hakimov

Masters Theses & Specialist Projects

Antibiotics resistance is considered as one of the greatest public health challenges of our time. In this work, we have synthesized silver nanoparticles (Ag NPs) using pulsed liquid ablation in different medium of growth and later combined with methylene blue (MB) to evaluate its potential as an effective photodynamic therapy agent. Ag NPs were synthesized by pulsed laser ablation technique in Polyvinylpyrrolidone (PVP), citrate, and Polyvinyl alcohol (PVA). The Ag NPs were characterized using transmission electron microscopy (TEM), UV-Visible (UV-Vis), and photoluminescence (PL) spectra. Next, Ag NPs were coupled with MB and used to deactivate the Gram-negative bacteria, Escherichia coli …

Towards The Determination Of Estrone And 17Β-Estradiol In Dairy Cattle Waste Using Solid Phase And Stir Bar Sorptive Extractions With Liquid Chromatography-Mass Spectrometry And Gas Chromatography-Mass Spectrometry, Pallavi Ragi

Masters Theses & Specialist Projects

Steroidal hormones are naturally produced as a part of many physiological processes and are excreted in the urine and feces of animals and humans. Farm animals in concentrated animal feeding operations (CAFOs) are routinely implanted with synthetic and natural hormones to enhance growth and production, contributing significantly to environmental steroid hormone contamination. Every year around 49 tons of estrogens are generated by livestock waste in the United States alone. Due to rainfall and runoff, these steroid hormones reach the environment when animal waste is applied as manure. Studies show that estrogens and other steroidal hormones present in the surface waters …

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 …

Liquid Chromatography With Tandem Mass Spectrometry Method Development For The Determination Of Β–Defensins In Bovine Milk, Symone T. Whalin

Masters Theses & Specialist Projects

Bovine mastitis, caused by a wide array of pathogens, results in a substantial economic loss for the dairy cattle livestock industry. β-defensins are a part of the bovine’s innate immune system and act as the first line of defense against mastitis. Only foundational research has been done on β-defensins’ ability to treat and prevent mastitis. There have been no analytical methods reported in the literature for analyzing β-defensins in bovine milk. This research aims to create an analytical approach to determine β-defensins in bovine milk. It is challenging to determine an analyte in a complex sample matrix, and milk is …

Towards Semiconductor Nanorods With Nickel/Iron Cocatalyst., Kehinde Ayorinde

Masters Theses & Specialist Projects

The adverse effects associated with the utilization of fossil fuels has led to the need to provide an alternative cleaner energy. Photocatalytic hydrogen evolution reaction via water splitting provides a renewable pathway to generating energy. Our photocatalyst system includes a semiconductor component (CdSe/CdS core/shell nanorods) to capture light and an attached metal (cocatalyst) for the hydrogen evolution reaction. Platinum is an effective metal catalyst for this reaction due to strong proton binding energy that easily facilitates the reduction of water to produce hydrogen gas. However, due to the high cost of platinum, there is a need to find a less …

Synthetic, Photophysical, And Catalytic Studies Of Light-Harvesting Macrocyclic Complexes, Fox Bratcher

Masters Theses & Specialist Projects

Chromophores are an important class of compounds in Nature and industry, with several hundred thousand tons produced annually as dyes and pigments. Alone, these compounds absorb light unto themselves; however, several of these compounds can be combined to produce a beneficial cascading transfer of energy to a core chromophore.

In this study, photophysical properties of several covalent and axially borondipyrromethene (BODIPY)-conjugated complexes of porphyrin and salphen scaffolds have been evaluated in a series of emission and catalytic studies. In the porphyrin systems, a beneficial excited energy transfer (EET) from the BODIPY moieties to the porphyrin core was observed; however, only …

Functionalized Ionic Liquids For Improved Co2 Hydrogenation Catalysts, Amol Nanduji Jaybhaye

Masters Theses & Specialist Projects

Climate change is one of the biggest problems we are facing today, and anthropogenic greenhouse gases contribute significantly to it. Among greenhouse gasses, carbon dioxide emission is increased drastically and affecting majorly for increasing global temperature, and anything we can do to mitigate carbon dioxide emission will be helpful. A carbon dioxide hydrogenation reaction is a promising technique that can convert carbon dioxide into value-added chemicals, but the reaction rate is slow, and for that, we can use catalysts that will accelerate the reaction rate. Platinum-based nanoparticles have sparked research related to energy and environmental catalysts. Catalytic properties are depending …

Design Of Antioxidant Monomer, Augustine Osilamah Yusuf

Masters Theses & Specialist Projects

Reactive oxygen species such as hydrogen peroxide are present at the sites of inflammation in the body. Degradable polymeric nanoparticles have shown great promise in a range of biomedical applications which include preferential delivery of therapeutics to such inflamed sites. We are working towards a new class of materials expected to have tunable degradation rates in the presence of hydrogen peroxide. These new materials consist of three parts: degradable linkages, antioxidant groups, and unreactive filler monomers such as methylmethacrylate. We have synthesized a polymerization initiator with a degradable linkage, and we have shown that using this initiator to synthesize another …

Visible Light Generation And Mechanistic Investigation Of High-Valent Metal-Oxo Species Supported By Different Ligands, Seth Ellis Klaine

Masters Theses & Specialist Projects

Numerous transition metal catalysts have been designed as biomimetic model compounds for the active site of metalloenzymes found throughout Nature, most notably cytochrome P450 monooxygenases that carry out the oxidative transformations of organic substrates with near-perfect chemo-, regio-, and stereo-selectivity. The primary active oxidants in catalytic and enzymatic cycles are fleeting high-valent metal-oxo intermediates where the oxo ligand can transfer to an organic substrate in a process known as oxygen atom transfer (OAT).

In the present work, porphyrin-manganese(III), salen-chromium(III), and salenmanganese( III) derivatives were successfully synthesized and spectroscopically characterized using 1H NMR and UV-Vis spectroscopies. A facile photochemical approach was …

Synthesis And Catalytic Oxidation Of Organic Substrates By Light-Harvesting Metalloporphyrins, Christian Alcantar

Masters Theses & Specialist Projects

note: Some notation in this abstract may not appear exactly as formatted in the thesis.

In this work, ruthenium, iron, and manganese light-harvesting metalloporphyrins have been successfully synthesized to serve as biomimetic models of the active site of Cytochrome P450 for the development of a green and efficient oxidation catalyst. The covalent introduction of light-harvesting boron-dipyrrin (BODIPY) fluorophores on the porphyrin macrocycle allows for the absorption of a broader range of visible light in addition to that captured by the porphyrin aromatic system alone. It is expected that this core-antenna system will increase the absorbed light energy and transfer it …

Developing Novel Tale-Based Rapid Detection Of Pathogenic Dna Utilizing 2d Graphene Oxide Nanosheets And Quantum Dots, Narayan Neupane

Masters Theses & Specialist Projects

A faster method of quantitative detection of specific dsDNA of pathogenic bacteria such as the Shiga toxin 2 gene (stx2) present in E. coli O157:H7 is of great importance. There is a need for a simple and facile method for sensitive detection of pathogenic gene which is crucial for the prevention and earlier treatment of any infectious diseases. A Transcriptional Activator-Like Effector (TALE) is a novel class of DNA-binding proteins with the unique modularity, flexibility and easy programmability compared to previously discovered DNA- binding proteins. TALEs can bind to any DNA sequences through its unique variable di- residues …

Solvent-Free Synthesis Of Metal Coordination Compounds Using Ball Mills, Jenna Cantway

Masters Theses & Specialist Projects

Mechanochemistry utilizes mechanical energy to promote chemical reactions to completion. Samples ground with a ball mill are placed under consistent pressure and temperature, which allows for increased surface area, shorter reaction times and overall better control of reaction conditions compared to the use of a mortar and pestle. Many synthetic techniques to prepare metal coordination compounds use a solvent. The solvent promotes the reactions by providing a route for reagents to interact. While solvents facilitate reactions, there is interest in reducing or eliminating solvents altogether during the synthesis process due to potential instability of a solvent under certain experimental conditions …

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 …

Mercury And Other Trace Metal Analysis In Bat Guano, Amanda Lee Houchens

Masters Theses & Specialist Projects

Heavy metal pollution in the environment pose risks to ecosystems and the populations that reside in them. Mercury, lead, and cadmium negatively impact humans by way of neurological disorders, various cancers, and damage the reproductive organs, kidneys, and lungs. Bats have been studied as a bioindicator species to identify possibly elevated levels of these metals in the environment. Previous studies have identified correlation between metal concentrations within bat tissues and fur. Many bat species are endangered or at risk due to white-nose syndrome so collection of tissues and fur for analysis can impose stress on bat colonies. This study investigates …

Synthesis And Molecular Mechanics Study Of Platinum Triamine Complex With N-Acetyl-L-Methionine And Guanosine 5’Monophosphate, Nitin Tanajirao Katare

Masters Theses & Specialist Projects

Cisplatin and its analogues have been used and tested over decades for cancer treatment, but because of the serious side effects, it is important to find ways to overcome those side effect by synthesizing a novel platinum molecule. We have synthesized triamine complex and conducted its reaction with biomolecules such as 5’GMP and Methionine in the lab as well as conducted molecular mechanics (MM). MM methods are used for predicting and designing new structures and properties, and to model geometries of small molecules. MM and dynamics calculations have been used to study the 9 Ethylguanine and N-Ac-Lmethionine complexes with platinum …

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 …

Leaving Ligand Effects On Reactivity And Solubility Of Monofunctional Platinum(Ii) Anticancer Complexes, Heidi Linn Hruska Millay

Masters Theses & Specialist Projects

Monofunctional platinum(II) complexes, such as phenanthriplatin and pyriplatin, have notably different characteristics from the bifunctional anticancer complexes, such as cisplatin and oxaliplatin, which have detrimental toxicities and resistance associated with them. The unique properties of the monofunctional complexes may be exploited to target cancer cells without producing the toxic side effects associated with the current FDA-approved platinum-based anticancer drugs. To advance the understanding of these monofunctional platinum(II) complexes, this study replaced the chloride leaving ligand with an acetate group, which should increase solubility and alter the rate of reactivity with key amino acid and nucleotide targets. Phenanthriplatin and pyriplatin compounds …

Interaction Of A Platinum Triamine Complex Having A Seven-Membered Chelate Ring With N-Acetyl-Lmethionine And Guanosine 5'-Monophosphate, Jae Ko

Masters Theses & Specialist Projects

In the 1960s, Rosenberg and his colleagues confirmed the anti-cancer activity of cisplatin. Although cisplatin was capable of killing testicular cancer cells there were also serious side effects. It was necessary to find alternate ways of overcoming side effects, and soon many researchers have discovered novel platinum compounds that show similar reactivity. Recently, replacing one chloride group to a heterocyclic amine group showed significant cytotoxicity with a different binding activity than cisplatin. Previously in our lab, [Pt(Me5dien)(NO3)]+ and [Pt(Et2dien)Cl]+ have been synthesized and reacted with NAcetyl- L-methionine (N-AcMet) and Guanosine 5’-monophosphate (5’-GMP) showed unusual reactivity. Unlike most previously studied platinum …

Synthesis Of Bis(Imino)Pyridine Iron(Ii) Complexes And Development Of Bis(Imino)Pyridine Iron(Ii) Catalyzed Carbene Transfer Reactions, Ban Wang

Masters Theses & Specialist Projects

Metal catalysis of symmetric and asymmetric carbene transfer reactions has been widely applied in natural product synthesis and material science over years. Metal carbene can be easily generated from the extrusion of nitrogen under the catalysis of metal complexes to further undergo various organic reactions, O/N/C-H insertions, cycloadditions, and ylide formations. Currently, the dominant effective catalysts for carbene reactions are built with expensive precious metal, for example, rhodium, ruthenium, palladium, gold. Notably, the effective reactivity and enantioselectivity of the dirhodium(II) catalysts are researched and established over the decades. However, the use of precious metal catalysts is the major source of …

The Development Of An Integrated Simulation Model On Understandings On The Interaction Between Electromagnetic Waves And Nanoparticles, Xiaojin Wang

Masters Theses & Specialist Projects

To investigate the interaction between nanoparticles and electromagnetic waves, a numerical simulation model based on FEM was built in this thesis. Numerical simulation is an important auxiliary research method besides experiments. The optical properties of nanoparticles consist of scattering, absorption, and extinction, and in the case of nanoparticle suspension, the transmission is also involved. This thesis addressed two typical applications based on the established model, one was regarding the nanofluids for solar energy harvesting, and the other was regarding the optical properties of atmospheric soot. In the case of the nanofluids solar energy harvesting, the established model provided a convenient …

Quantification Of Tylosin Antibiotics In Cattle Waste, Appala Keerthi

Masters Theses & Specialist Projects

Antibiotics are used as prophylactic agents to promote growth and for treating infections in animals. However, the irrational use of antibiotics in livestock management is a significant cause of the development of antibioticresistant genes in the environment. Each year 2 million people suffer from the infections caused by bacteria which are resistant to antibiotics and 23,000 of these people are estimated to die because of antibiotic resistance. New drugs are continually coming into the market but are at the risk of developing resistance. Thus, there is a need for the development of analytical methods which can be used to monitor …

Developing A New Sensing Technology For Double-Stranded Dna Detection Utilizing Engineered Zinc Finger Proteins And Nanomaterials, Dat Thinh Ha

Masters Theses & Specialist Projects

A specific double-stranded DNA sensing system is of great interest for diagnostic and other biomedical applications. Zinc finger domains, which recognize double-stranded DNA, can be engineered to form custom DNA-binding proteins for recognition of specific DNA sequences. As a proof of concept, a sequence-enabled reassembly of TEM-1 β- lactamase system (SEER-LAC) was previously demonstrated to develop zinc finger protein (ZFP) arrays for the detection of a double-stranded bacterial DNA sequence. Here, we implemented the SEER-LAC system to demonstrate the direct detection of pathogenspecific DNA sequences present in E. coli O157:H7 on the lab-on-a chip. ZFPs customdesigned to detect shiga toxin …

Synthesis Of A Platinum Triamine Complex And Its Interactions With Guanosine 5’- Monophosphate And N-Acetylmethionine, Manal El Masri

Masters Theses & Specialist Projects

Cisplatin (cis-diamminedichloroplatinum(II)) and its analogs are known to form 1,2-intrastrand cross-links with guanine bases that lead to DNA distortion and are responsible for cytotoxicity. Reaction with proteins, especially at methionine residues, could also be responsible for cytotoxicity (Sandlin, R. D. et al. 2010). A new tridentate platinum(II) complex with a piperazine ring was successfully designed and synthesized. In this complex, the platinum is coordinating to all three nitrogens of (1,2- dimethylaminoethylpiperazine), which makes it a Platinum triamine compound. A series of chemical reactions of this compound with guanosine 5’-monophosphate (5’-GMP) and N-acetylmethionine (N-AcMet) were conducted under different conditions. Reactions with …

Synthesis And Characterization Of Graphene-Family Mesoporous Nanomaterials For Themal Energy Harvesting And Sensing Applications, Romney Meek

Masters Theses & Specialist Projects

Graphene-family nanomaterials (GFNs) have attracted a great deal of attention both in academia and in industry for a range of applications relevant for homeland security. In this thesis, an array of graphene-based hybrid materials and aerogels are synthesized for use as novel thermo-electrochemical energy harvesters and for ascorbic acid biosensing devices. The graphene-family nanomaterials include graphene oxide-GO, thermally reduced GO-rGOth, nitrogenated functionalized graphene-NFG, graphene aerogel-GA, nitrogen-doped graphene aerogel-NGA, multi-walled carbon nanotube aerogel-MWCNT, single-walled carbon nanotube aerogel-SWCNT, graphene and nanotube combined ‘hybrid’ aerogels-Gr:(SW/MW)CNT of various ratios, along with multilayered nanostructured architectures such as gold (AuNP) and silver nanoparticles (AgNP) decorated NFG …

Photochemical Investigation Of High-Valent Metal-Oxo Intermediates Containing Corrole And Light-Harvesting Porphyrin Ligands, Jonathan Malone

Masters Theses & Specialist Projects

In enzymatic and synthetic catalytic oxidations, high-valent iron-oxo intermediates play a vital role as the active oxidant. In this regard, many synthetic metal catalysts are designed as biomimetic models to resemble the active site of Cytochrome P450 enzymes (P450) which are the predominant oxidation catalysts in nature. Vitamin B12 cofactors, with a corrole-like structure corrin, are also utilized in some of the more difficult reactions in nature such as rearrangement and reductase reactions.

In this work, application of the promising photochemical method to corrolecontaining ligands systems showed much success in the generation of manganese(V)-oxo corrole intermediates using two electron-deficient corrole …