Chemistry Commons^™

Rna Secondary Structures: Structure-Function Studies In Viral And Neurodegenerative Diseases, Caylee Cunningham

Electronic Theses and Dissertations

The studies within this dissertation highlight the importance of RNA structure and function, highlighting potential mechanisms in the pathogenesis of the SARS-CoV-2 virus and hallmarks of ALS. Specifically, the s2m, a 41-nt structure found within the hyper variable region of the 3’ UTR of the SARS-CoV-2 virus, was investigated as this element has no definitive role in viruses but its high conservation in several viral families warrants investigation. We used various biophysical techniques to determine if a palindromic sequence in the terminal loop could participate in dimerization activities, which may have implications in recombination and the longevity of the virus. …

Agnotology Of The E-Cigarette Industry: How The E-Cigarette Industry Continues The Tobacco Industry's Legacy Of Creating Controversy And Confusion Within The Scientific Community And The General Population, Calvin Lewis

University Honors Theses

The purpose of this paper is to determine the extent to which the e-cigarette industry follows in the footsteps of the tobacco industry's attempts to disrupt science and cause controversy. Four tactics are described that the tobacco industry uses to disrupt science: funding research that is designed to show results that support their position, criticizing and suppressing research that goes against their position, changing risk assessment and scientific research standards to fit their aims, and spreading data created by their interest groups to politicians and the nonacademic press. Evidence is found to show that both the tobacco industry and e-cigarette …

Syntheses, Characterizations And Reactions Of Acene-2,3-Dicarbaldehydes, Glen Miller, Qian Liu

Faculty Publications

Here, we report improved syntheses, detailed characterizations and reactions of a series of acene-2,3- dicarbaldehydes including tetracene-2,3-dicarbaldehyde. DFT calculations corroborate and complement the experimental results. Tetracene-2,3-dicarbaldehyde and the benchmark organic semiconductor pentacene have isoelectronic p-systems and similar HOMO–LUMO gaps. Tetracene-2,3-dicarbaldehyde is soluble in a host of organic solvents (e.g., DMF, toluene, THF, chloroform, dichloromethane) and shows excellent photooxidative resistance in solution phases exposed to light and air. Further, it is readily sublimed from the solid-state without decomposition, and can be functionalized using different chemistries. We have demonstrated the utility of acene-2,3-dicarbaldehydes as reactants in the syntheses of novel diaryl-2,3-acenedimethanols and …

Flora And Fauna Lexical Indicators Of Prehistoric Movement Of Yuman Peoples, Adam Ingwerson

Master's Theses

Amyloid fibrils are locally ordered protein aggregates characterized by a filamentous morphology held together by a hydrogen bonding motif known as cross-β structure whereby hydrogen bonds form between backbone amide bond moieties across separate protein segments. The most notable medical significance of amyloid fibrils is their central role in the etiology of Alzheimer’s disease, type 2 diabetes, and other human diseases. Although amyloid fibrils have been studied extensively, the mechanism of their formation is still not fully understood. X-ray crystallography is a leading experimental technique for resolving amyloid fibril structures from crystallized proteins; however, inherent limitations leave open the possibility …

Green Synthesis Of Carbonized Chitosan-Fe3o4-Sio2 Nano-Composite For Adsorption Of Heavy Metals From Aqueous Solutions, Dalia A. Ali Eng, Rinad Galal Ali Eng.

Chemical Engineering

Water pollution with heavy metals owing to industrial and agricultural activities have become a critical dilemma to humans, plants as well as the marine environment. Therefore, it is of great importance that the carcinogenic heavy metals present in wastewater to be eliminated through designing treatment technologies that can remove multiple pollutants. A novel green magnetic nano-composite called (Carbonized Chitosan-Fe3O4-SiO2) was synthesized using Co-precipitation method to adsorb a mixture of heavy metal ions included; cobalt (Co2+), nickel (Ni2+) and copper (Cu2+) ions from aqueous solutions. The novelty of this study was the synthesis of a new

nano-composite which was green with …

63rd Annual Rocky Mountain Conference On Magnetic Resonance

Rocky Mountain Conference on Magnetic Resonance

Final program, abstracts, and information about the 63rd annual meeting of the Rocky Mountain Conference on Magnetic Resonance, co-endorsed by the Colorado Section of the American Chemical Society and the Society for Applied Spectroscopy. Held in the Copper Conference Center, Copper Mountain, Colorado, August 4-8, 2024.

Feasibility Study Of Using Energy Extracted From The Process Of Electrochemically Consumed Of Al 2024 For Powering Daily Used Electric Car, Yanuar Mohamad Marda, Rini Riastuti, Muhammad Hamka Ibrahim

Journal of Materials Exploration and Findings

Usage of green energy for transportation has become important due to the contribution of transportation activity to climate change. Electrochemical energy has been used as a source of green energy. The objective of this work is to evaluate sufficiency of energy provided by electrochemically consumed Al 2024 for supplying energy to daily used PHEV electric car. Study of previous articles, observation of typical amount of energy required, electrochemical galvanic cell experiments, and simple calculations have been conducted to determine produced energy feasibility. Electrical energy produced by consuming 340 gr of Al 2024 in galvanic cells has the total lifetime of …

De Novo Synthetic Studies On Tetracyclic Triterpenoid Systems: Stereoselective Preparation, Biological Evaluation And Total Syntheses Of Euphol And Tirucallol, Joshua Nicholson

Dartmouth College Ph.D Dissertations

Tetracyclic triterpenoids have a rich history in biology, medicine, and chemistry. In terms of pharmaceutical relevance, compounds with this scaffold are one of the most successful classes with over 100 FDA approved examples. Despite this success, the vast majority of compounds within this class are prepared through semisynthesis. While this approach is undeniably successful, judged by the sheer number of medications generated, it also has limitations. Namely, semisynthesis requires the use of complex starting materials that have fixed absolute stereochemistry and often sparse functionality. One approach to address the inherent limitations with semisynthesis is through de novo synthesis. Recently, our …

Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Applications For Metabolomics, Darcy Cochran, Robert Powers

Robert Powers Publications

Metabolomics is an interdisciplinary field that aims to study all metabolites < 1500 Da that are ubiquitously found within all organisms. Metabolomics is experiencing exponential growth and commonly relies on high-resolution mass spectrometry (HRMS). Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) is a form of HRMS that is particularly well suited for metabolomics research due to its exceptionally high resolution (10⁵–10⁶) and sensitivity with a mass accuracy in parts per billion (ppb). In this regard, FT-ICR-MS can provide valuable insights into the metabolomics analysis of complex biological systems due to unique capabilities such as the easy separation of isobaric and isomeric species, isotopic fine structure analysis, spatial resolution of metabolites in cells and tissues, and a high confidence (error) in metabolite identification. Alternatively, the large and complex data sets, long acquisition times, high cost, and limited access mainly through national mass spectrometry facilities may impede the …

Knowledge Management Of Historical Data: Ontology Development For Chemical Reactions, Quynh D. Tran, Alexander Harding Bradley, Balashanmuga Priyan Rajamohan, Jonathan E. Gordon, Van D. Tran, Kiefer Lin, Erika I. Barcelos, Laura S. Bruckman, Roger H. French

Researchers, Instructors, & Staff Scholarship

Knowledge management of the literature and historical data is critical to accelerated drug and materials discovery. Currently, literature knowledge is scattered in journal articles in various formats: diagrams, texts, plots, etc. Historical data from past experiments are saved in a number of local computers under confusing folder structures with ambiguous file names. To manage and organize historical data and knowledge, our group (SDLE) at CWRU follows FAIR (Findable, Accessible, Interoperable, Reusable) principles, which outline the best practices for data stewardship and data provenance, and ontology, a formal representation of terms and concepts and their relationships, as a tool to improve …

Investigation Of The Prevalence Of Fentanyl Analogs In A Drug Testing Population Using Liquid Chromatography Tandem Mass Spectrometry (Lc-Ms-Ms), Ivan Cordova

Student Theses

This study serves to determine the prevalence of novel fentanyl analogs that are present within a drug testing population in New York State. Samples were analyzed using liquid chromatography tandem mass spectrometry (LC-MS/MS) to qualitatively determine the presence of various possible fentanyl analogs. The sample preparation of this assay consisted of a simple dilute and shoot. This method of sample preparation can be quicker, eliminating sample preparation times as well as being less financially strenuous to clinical laboratories as it eliminates the need for various solvents and solid/liquid phase cartridges. The assay was aimed to see if analytes can be …

I. Degradable Polymers And Networks Based On Furan-Maleimide Diels-Alder Reactions Of Silyl Ether Derivatives And Maleimides, And Ii. The Michael Addition Of Amines To 1,3,5-Triacryloylhexahydro-1,3,5-Triazine (Tat) As A Synthetic Route To Novel Chelating Agents, Reyad Alkhazalah

Chemistry Theses and Dissertations

Degradable Polymers and Networks Based on Furan-Maleimide Diels-Alder Reactions of Silyl Ether Derivatives and Maleimides. I.

I. Part 1. Two groups of silyl ether monomers, A and B, were synthesized, each containing four different monomers. The monomers of group A were obtained by reacting furfuryl alcohol with four dichlorosilanes with varying siloxane spacers. The monomers of group B were obtained by reacting n-(2-hydroxyethyl)maleimide (HEMI-1c) with the same four dichlorosilanes. Each monomer from group A was individually reacted with each monomer from group B via a Diels-Alder reaction to produce a series of sixteen degradable linear polymers with a variety …

Optimizing The Protein Yield Of The Collagen Mimetic Peptide: Col108, Fahmida Akter

Theses and Dissertations

Abstract

The fibril-forming collagen mimetic peptide Col108, produced in E. Coli, has shown potential for innovative biomaterial applications. However, further research is constrained by its limited yield. My study aims to enhance the experimental parameters and has successfully pinpointed rifampicin as an efficient method to boost the production of Col108.

Settingsorder Article Reprints Open Accessarticle A Model To Account For The Effects Of Load Ratio And Hydrogen Pressure On The Fatigue Crack Growth Behavior Of Pressure Vessel Steels, Ashok Saxena, Kip O. Findley

Mechanical Engineering Faculty Publications and Presentations

A phenomenological model for estimating the effects of load ratio R and hydrogen pressure P_H2 on the hydrogen-assisted fatigue crack growth rate (HA-FCGR) behavior in the transient and steady-state regimes of pressure vessel steels is described. The "transient regime" is identified with crack growth within a severely embrittled zone of intense plasticity at the crack tip. The "steady-state" behavior is associated with the crack growing into a region of comparatively lower hydrogen concentration located further away from the crack tip. The model treats the effects of R and P_H2 as being functionally separable. In the transient …

Stimuli-Responsive Phosphate Hydrogel: A Study On Swelling Behavior, Mechanical Properties, And Application In Expansion Microscopy, Yokly Leng, Collin N. Britten, Fatema Tarannum, Kayla Foley, Christopher Billings, Yingtao Liu, Keisha B. Walters

Chemical Engineering Faculty Publications and Presentations

Phosphorus-based stimuli-responsive hydrogels have potential in a wide range of applications due to their ionizable phosphorus groups, biocompatibility, and tunable swelling capacity utilizing hydrogel design parameters and external stimuli. In this study, poly(2-methacryloyloxyethyl phosphate) (PMOEP) hydrogels were synthesized via aqueous activators regenerated by electron transfer atomic transfer radical polymerization using ascorbic acid as the reducing agent. Swelling and deswelling behaviors of PMOEP hydrogels were examined in different salt solutions, pH conditions, and temperatures. The degree of swelling in salt solutions followed CaCl₂ < MgCl₂ < KCl < NaCl with a decrease in swelling rate at higher concentrations until reaching a saturation point. In water, the degree of swelling increased significantly around neutral pH and remained constant at basic pH values. The effects of polymerization conditions, including pH, temperature (30, 40, 50 °C), and MOEP concentration (40, 50, 60% v/v MOEP/H₂O), on the hydrogel swelling behavior in various salt solutions were also investigated. PMOEP hydrogels …

Elevating Commodity Polymers To Advanced Applications In Polymer Photonics And Polymer-Derived Porous Materials, Mark Robertson

Dissertations

Since the inception of synthetic polymers, polymer-derived materials have permeated into essentially all aspects of our daily lives. The most commonly thought of examples of polymer materials involve single-use, disposable products to increase shelf lives of perishable items, act as personal protective equipment, or provide some degree of convenience for the consumer. However, as we have furthered our understanding of polymer chemistry and polymer physics to develop increasingly sophisticated polymer systems, polymer materials have been employed in incredibly advanced applications. These include solid electrolytes for energy storage, matrices for aerospace grade carbon fiber-reinforced composites, membranes for liquid and gas separations, …

Catalytic Hydrogenation Of Co2 In Water And Ionic Liquids Using Platinum On Carbon, Kristin Collins

Masters Theses & Specialist Projects

Platinum-on-carbon (Pt/C) is a commercially-available catalyst that has been used in the literature to benchmark the performance of catalysts produced using platinum/cobalt alloy nanoparticles. Initially, we intended to build upon this example by synthesizing shape-controlled platinum/cobalt alloy nanoparticles in ionic liquids and compare their ability to catalyze the hydrogenation of CO₂ to methanol against Pt/C as a benchmark, with the idea that ionic liquids may improve catalysis. However, we found that Pt/C was unable to catalyze the hydrogenation of CO₂ to methanol. In an attempt to track the source of this discrepancy, Pt/C was characterized using thermogravimetric analysis …

Enhanced Rate Capability And Capacity Of Lib Full Cells Achieved Through Aerosol Jet Printing, Rodrigo Rodriguez, L. Jay Deiner, Bang-Hung S. Tsao, Joseph P. Fellner

Publications and Research

Thick lithium-iron phosphate (LFP) cathodes (31 mg cm−2) with rationally engineered pore structure and tortuosity were manufactured with an aerosol jet (AJ) printer. Cathode pore structuring was tuned by controlling the rate at which the printed ink dried. Slow-drying prints yielded smoother cathodes while fast-drying prints resulted in mesoscale structuring with substantial surface roughness. X-ray tomography further revealed that the rapid drying of AJ printed LFP cathodes produced low-tortuosity pore channels which were preserved after calendering. Full cells comprised of AJ print optimized LFP cathodes, with 30 mg cm−2 active material loadings, and capacity-matched, AJ printed lithium titanate anodes were …

High-Resolution Ion Mobility Analysis Of Isomeric Bile Acids Using Structures For Lossless Ion Manipulations (Slim) Im-Ms, Emmaleigh D. Efird

All Theses

Bile acids are an essential part of the human digestion system and play an important role in lipid absorption, bacteria movement in the small intestine, and regulation of the farnesoid X receptor (FXR) and G protein-coupled bile acid receptors (GPBAR) responsible for homeostasis. They are synthesized in the liver, stored in the gallbladder and the excess is carried on to the small intestine. Many liver and intestinal diseases are diagnosed based on bile acid metabolism pathways and the structures of those bile acids. Therefore, the bile acid structure determines the function of the molecule. Many bile acids are similar in …

Structure-Function Relationships In Neurodegenerative And Infectious Diseases: Biophysical Characterization Of Rna Secondary Structures By Computational Techniques, Kendy Guarinoni

Electronic Theses and Dissertations

The research described in this dissertation focuses on the investigation of the structure and dynamics of regions of RNA implicated in two diseases: COVID-19 and amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD). Both studies sought to create experimentally corroborated models that were used to characterize the structure and dynamics of the C9orf72 repeat expansion and the s2m region in coronaviruses, respectively and provided the foundation for future work. In our work involving the s2m region of SARS-CoV-2, the virus responsible for COVID-19, we determined that the homology modeling approach commonly used to derive atomistic structures when no coordinates are available yields a …

Antimicrobial And Chemical Characterization Of Cold Atmospheric-Pressure Plasmas, Dalton Albert Miller

Boise State University Theses and Dissertations

Microbial contamination of food processing facilities is a major cause of human disease and economic loss. There are approximately 48,000,000 cases of foodborne illness in the United States annually, leading to 128,000 hospitalizations and 1,300 deaths. The total economic damages are estimated at $36 billion each year, including productive hours, medical expenses, and the disposal of contaminated foodstuffs. Current methods to reduce contamination on food processing surfaces utilize steam or concentrated chemicals (hydrogen peroxide, hypochlorite, strong acids, strong bases) that are hazardous to workers and required large volumes of water to remove prior to resuming contact with food. Ongoing outbreaks …

Investigating The Applications Of Peps To The Measurement Of The Stabilities Of Staphylococcal Nuclease (Stw) And Human Acidic Fibroblast Growth Factor (Hfgf1), Motolani Omolade Matthew

Graduate Theses and Dissertations

This dissertation presents a detailed investigation into the applications of Protein Equilibrium Population Snapshot H/D Exchange Electrospray Ionization Mass Spectrometry (PEPS-H/D exchange or PEPS) method. This method is based on protein equilibrium unfolding, and its fundamental capability is to capture a "snapshot" of the protein's state, allowing us to monitor the ratio of the unfolded to folded populations at different chemical denaturant concentrations. First, to increase the accuracy of PEPS data analysis for assessing protein stability, the traditional linear extrapolation method (LEM) was replaced. Instead of using LEM, which calculates free energy change based on the peak ratio of unfolded …

Quantum Modeling & Experimental Studies Of Radical Chemistry, Justin Michael Barrett

Graduate Theses and Dissertations

This work describes two projects centered around radical chemical mechanisms. The first investigation generalized the utility of a C-N bond homolysis followed by a [1,3] – rearrangement synthetic strategy found possible in N-alkylated thiazole & benzothiazole species onto analogous systems. Computational investigation guided the inquiry on structurally analogous systems that would favor a radical, [1,3] – rearrangement. Herein, we describe the implementation of that mechanism to transform Breslow Intermediate-like substrates into tertiary alcohol and amide products under facile conditions. We confer on the proficiency of this strategy with 2-pyridinemethanol and the problematic implementation with 2-(aminomethyl)pyridine. The second investigation solved a …

Engineering Central Substitutions In Heptamethine Dyes For Improved Fluorophore Performance, Lei Guo, Meek Yang, Bin Dong, Seth Lewman, Alex Van Horn, Shang Jia

Chemistry & Biochemistry Faculty Publications and Presentations

As a major family of red-shifted fluorophores that operate beyond visible light, polymethine dyes are pivotal in light-based biological techniques. However, methods for tuning this kind of fluorophores by structural modification remain restricted to bottom-up synthesis and modification using coupling or nucleophilic substitutions. In this study, we introduce a two-step, late-stage functionalization process for heptamethine dyes. This process enables the substitution of the central chlorine atom in the commonly used 4′-chloro heptamethine scaffold with various aryl groups using aryllithium reagents. This method borrows the building block and designs from the xanthene dye community and offers a mild and convenient way …

Development Of A Flow Cytometry Method For The Identification And Enumeration Of Enterococcus Faecalis, Riza Magbitang

Master's Theses

A multi-color flow cytometry method coupled with fluorescent staining was developed to detect and quantify E. faecalis concentrations in coastal waters as an alternative to the traditional membrane filtration method. The developed method was used to characterize E. faecalis during batch growth and yielded consistent results across the various physiological states of the cells. Additionally, the application of propidium iodide (i.e., a viability stain), afforded the method the ability to differentiate between cells with intact and compromised cell membranes, which raises the potential of quantifying cells that are in viable-but-non-culturable (VBNC) state. Initial field test using natural seawater samples spiked …

Single Charge Carrier Dynamics In A Single Polymer Chain, Ming Lei

All Dissertations

Understanding how charge carrier move through conjugated polymers is crucial for optimizing the functionality and efficiency of various applications, from organic solar cells and light-emitting diodes (LEDs) to field-effect transistors. Previous studies have demonstrated that tracking the fluorescence centroid displacement provides a method to determine the position of single charge carriers in a conjugated polymer nanoparticle. This method allows the observation of charge carrier trajectories over time and allow researchers to obtain insights into the dynamic processes. In addition, a detailed map of the energy landscape can be constructed by analyzing the fluorescence spectrum. These techniques were previously applied to …

Modeling Study Of Si3N4 Waveguides On A Sapphire Platform For Photonic Integration Applications, Diandian Zhang, Shui-Qing Yu, Gregory J. Salamo, Richard A. Soref, Wei Du

Electrical Engineering and Computer Science Faculty Publications and Presentations

Sapphire has various applications in photonics due to its broadband transparency, high-contrast index, and chemical and physical stability. Photonics integration on the sapphire platform has been proposed, along with potentially high-performance lasers made of group III–V materials. In parallel with developing active devices for photonics integration applications, in this work, silicon nitride optical waveguides on a sapphire substrate were analyzed using the commercial software Comsol Multiphysics in a spectral window of 800~2400 nm, covering the operating wavelengths of III–V lasers, which could be monolithically or hybridly integrated on the same substrate. A high confinement factor of ~90% near the single-mode …

Design Of Engineered Nanomaterials For Pfas Adsorption And Catalytic Degradation From Relevant Environmental Conditions, Sheng Yin

Open Access Theses & Dissertations

Poly- and per-fluoroalkyl substances (PFAS) are a class of artificially made chemicals whose carbon chains are fully or partially fluorinated. Due to their persistent and pervasive distribution and their adverse effects on human health, the removal of PFAS from the environment has been the focus of current research. This project explores the use of engineered nanomaterials for the effective removal of PFAS through various adsorption and catalytic degradation methods. First, a comprehensive review of recent studies highlights the significant potential of various nanomaterials, including carbon-based, non-metal, single-metal, and multi-metal nanomaterials, for PFAS remediation. These materials are evaluated for their performance, …

Method Development For The Quantification Of Critically Valuable Elements In Permian Basin Produced Waters, Carley Oliver

Open Access Theses & Dissertations

Produced waters (PW) are a major byproduct of the oil and gas industrial hydraulic fracturing processes that create a major waste disposal issue with a need for disposal, treatment, and reuse method developments. The current primary disposal method is subsurface injection, which can lead to high pressures in the subsurface. PWs are often highly saline from mineral leaching due to long residence in subsurface reservoirs. According to the USGS National Minerals Information Center, bromine, calcium chloride, iodine, lithium, magnesium, and sodium chloride have been found in and extracted from these domestic subsurface brines, suggesting that there may be other economically …

Performance And Enhanced Efficiency Induced By Cold Plasma On Sapo-34 Membranes For Co2 And Ch4 Mixtures, Fnu Gorky, Vashanti Storr, Grace Jones, Apolo Nambo, Jacek B. Jasinski, Maria L. Carreon

Chemical Engineering Faculty Publications and Presentations

In this study, we investigate the influence of cold-plasma-induced enhanced performance and efficiency of SAPO-34 membranes in the separation of CO₂ and CH₄ mixtures. Placing the herein presented research in a broader context, we aim to address the question of whether cold plasma can significantly impact the membrane performance. We subjected SAPO-34 membranes to plasma mild disturbances and analyzed their performance in separating CO₂ and CH₄. Our findings reveal a notable enhancement in membrane efficiency and sustained performance when exposed to cold plasma. The pulsed plasma separation displayed improved structural integrity, and the experimental results …