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The Activity Of Abstraction In Physical Chemistry Problem Solving And Instruction, Jessica M. Karch

Graduate Doctoral Dissertations

Productive problem solving, concept construction, and sense making occur through the core process of abstraction. Although the capacity for domain-general abstraction is developed at a young age, the role of abstraction in increasingly complex and disciplinary environments, such as those encountered in undergraduate STEM education, is not well understood. Undergraduate physical chemistry relies particularly heavily on abstraction because it uses many overlapping and imperfect mathematical models to represent and interpret phenomena occurring on multiple scales. To reconcile these models, extract meaning from them, and recognize when to apply them in problem solving requires processes of abstraction. This dissertation aims to …

Synthesis And Characterization Of Novel Organic Ligands With Their Complexes Of Platinum, Copper And Uranium, Mustafa Adnan Yasin Aldulaimi

Dissertations

Transition metal complexes of symmetrical and asymmetrical Schiff bases have played a significant role in the field of coordination, inorganic, and bioinorganic chemistry as models for biological, analytical, industrial, and pharmaceutical applications. Over recent years a great deal of interest has developed in new transition metal complexes of Schiff base ligand. The preparation of novel organic ligands is the most important step in the development of metal complexes that exhibit unique properties and novel reactivity. To highlight the presentation of this dissertation and to provide more detailed investigations, the dissertation was separated into six chapters according to the sequence of …

Functional Π-Organogelators: From Nanoribbons To Organic Phosphors, Sae Hui Lee

UNLV Theses, Dissertations, Professional Papers, and Capstones

π-Conjugated systems have been receiving notable attention in the field of organic material chemistry due to their interesting optical properties, assembling properties, and potential application in optoelectronics. Among various self-assembly methods, organogelation has been known to allow facile and easily reproducible molecular assembly. This work focuses on creating new π-organogelators with various side group modifications which in result allow proper tuning of the optical properties along with an effective self-assembly upon gelation. The research comprises of two chapters: 1) the first chapter focuses on N-heteroacenes (NHAs) with gelation property and 2) the second chapter investigates gelation induced phosphorescence (GIP) of …

Intersection Of Redox Chemistry And Ubiquitylation: Post-Translational Modifications Required For Maintaining Cellular Homeostasis And Neuroprotection, Emma I. Kane, Kelly L. Waters, Donald E. Spratt

Chemistry

Neurodegeneration has been predominantly recognized as neuronal breakdown induced by the accumulation of aggregated and/or misfolded proteins and remains a preliminary factor in age-dependent disease. Recently, critical regulating molecular mechanisms and cellular pathways have been shown to induce neurodegeneration long before aggregate accumulation could occur. Although this opens the possibility of identifying biomarkers for early onset diagnosis, many of these pathways vary in their modes of dysfunction while presenting similar clinical phenotypes. With selectivity remaining difficult, it is promising that these neuroprotective pathways are regulated through the ubiquitin-proteasome system (UPS). This essential post-translational modification (PTM) involves the specific attachment of …

Molecular Dynamics Of Nucleic Acids, Proteins, And Their Complexes: From Atomistic And Coarse-Grained Descriptions To New Methodologies, Parth Chaturvedi

Open Access Theses & Dissertations

Computational modeling of biological macromolecules through molecular dynamics (MD) simulations is becoming increasingly useful to interpret the experimental results and guide the future experiments. Over the last decade, MD simulations have become much more powerful and accessible due to advancements in fields of structural biology, computer science and integrated chip design. In this Thesis, I utilize different MD simulation techniques to model interaction of and antiviral mechanisms. Within the framework of nucleic acid modelling, we describe first dynamics of small circular single stranded nucleic acids and highlight key dynamical differences of backbone behavior in solution between DNA and RNA and …

Synthesis Of Fullerene Derivatives For Diverse Applications: From Catalysis To Photovoltaics, Olivia Fernandez-Delgado

Open Access Theses & Dissertations

AbstractFullerene functionalization has enabled the improvement in their solubility, optoelectronic, semiconductive, chemical and physical properties that allow their use in several fields such as photovoltaics, catalysis and for biological applications. Their good electron transporting properties have been widely studied in perovskite solar cell (PSC) devices and more recently, there have been more articles focused specifically on the molecular interactions of the fullerene functional groups with the perovskite layer which has allowed to obtain high power conversion efficiencies (PCE) of 25.5%. On the other hand, fullerenes are beginning to be studied as molecular catalysts for water splitting electrocatalytic processes, resulting in …

Computational Investigation Of Nanoparticle Immersion And Selfassembly, Tara Allison Tyler Nitka

Open Access Theses & Dissertations

Both neutral and charged nanoparticles with a variety of compositions, shapes, and sizes have beenpreviously prepared. These nanoparticles have been demonstrated to self-assemble into a variety of superlattices and binary superlattices both in bulk solution and at surfaces of solutions, and the structures formed by self-assembly have been shown to depend on nanoparticle chemistry and charge as well as on whether assembly takes place at a surface or in bulk. Furthermore, the prepared isolated and self-assembled nanoparticles have a number of biomedical, nanotechnology, and industrial applications. In this Dissertation, I present my research on three general topics. First, I will …

Identification Of Fungi And Their Secondary Metabolites From Wind Cave [Poster], Kyle J. Biscoglia, Kirk Manfredi Ph.D.

Summer Undergraduate Research Program (SURP) Symposium

Eighteen fungal samples were isolated from samples of water collected in Wind Cave, South Dakota. Ten of the samples underwent chemical extraction, a growth inhibition test, and were analyzed using proton nuclear magnetic resonance spectroscopy and liquid chromatography-mass spectroscopy. All eighteen of the fungal samples were able to be identified to the genus level using the ITS region of their DNA, however confident identification of the species level was more difficult to attain just looking at one portion of the sequence.

Synthesis Of Small Molecules For The Treatment Of Infectious Diseases, Elena Bray

USF Tampa Graduate Theses and Dissertations

Drug discovery’s impact on modern healthcare cannot be measured. In the past year, the world has watched scientists all around the globe work together to help protect the public from the novel coronavirus pandemic. Although sometimes slow and costly, drug discovery is important for advancing modern society. Drug discovery is at the core of treating diseases and in particular, infectious diseases. In the first chapter an overview of drug discovery will be discussed in a brief manner.

The second chapter will introduce infectious diseases. In modern society, the development of small molecule treatments for treating bacteria, viruses, and fungi has …

Chemical Waste Management In Educational Institutions, Zuy Maria Magriotis, Adelir Aparecida Saczk, Hélvia Mara Ribeiro Salgado, Isael Aparecido Rosa

Journal of Environmental Science and Sustainable Development

Green universities and Education for Sustainable Development have an important role in reaching a sustainable society. However, there is many gaps in this area. This study aimed to report the implementation and the results of the Chemical Waste Management Program (CWMP) of the Federal University of Lavras (UFLA). The CWMP have been implemented in 2009 to solve the existing environmental problem of inadequate disposal of chemical waste generated in UFLA’s laboratories. In order to carry out the CWMP actions, the Chemical Waste Management Laboratory (CWML) was created in 2009, with the function of collecting, treating, and giving a final destination …

Pt-Containing Conjugated Polymers And Small Molecules For Bhj Photovoltaic Devices, Yunjeong Kwon

Chemistry and Chemical Biology ETDs

The current state of organic photovoltaic (OPV) devices involve series of small molecular or polymeric systems that can absorb light from the solar spectrum in concert with another material that acts as an acceptor material. Together these materials serve to generate and split bound excitation species then transport the separate charges to their respected electrode. Several limitations have restricted the widescale use of these materials. Since these devices have their genesis in organic materials the OPV devices inherit short exitonic lifetimes, narrow absorption window and a lack of precise control over the morphology. To overcome these limitations, additional molecular engineering …

Biomaterials With Structural Hierarchy And Controlled 3d Nanotopography Guide Endogenous Bone Regeneration, Shixuan Chen, Hongjun Wang, Valerio Luca Mainardi, Giuseppe Talò, Alec Mccarthy, Johnson V. John, Matthew J. Teusink, Liu Hong, Jingwei Xie

Department of Chemistry: Faculty Publications

Biomaterials without exogenous cells or therapeutic agents often fail to achieve rapid endogenous bone regeneration with high quality. Here, we reported a class of three-dimensional (3D) nanofiber scaffolds with hierarchical structure and controlled alignment for effective endogenous cranial bone regeneration. 3D scaffolds consisting of radially aligned nanofibers guided and promoted the migration of bone marrow stem cells from the surrounding region to the center in vitro. These scaffolds showed the highest new bone volume, surface coverage, and mineral density among the tested groups in vivo. The regenerated bone exhibited a radially aligned fashion, closely recapitulating the scaffold’s architecture. The organic …

Method Development Of Standard Dilution Analysis On Molecules And Dissolution Studies Of Ibuprofen Tablets Along With Common Beverage Constituents, Scott Richardson

Master of Science in Chemical Sciences Theses

The United States Pharmacopeia sets the standards for the manufacturing, storage, and analysis of medicinal formulations. One analysis, dissolution testing evaluates the rate at which the medicinal formulation forms a solution to predict in vivo drug release. Dissolution testing on ibuprofen tablets alone and in the presence of ascorbic acid or caffeine was performed to mimic the administration using orange juice or caffeinated soft drinks to assess their impact on the dissolution rate of ibuprofen. Results using the external calibration method produced a dissolution rate of ibuprofen that decreased 4% in the presence of ascorbic acid and increased 1% in …

Degumming Of Hemp Fibers Using Combined Microwave Energy And Deep Eutectic Solvent, Bulbul Ahmed

LSU Master's Theses

Hemp is considered as one of the sustainable agricultural fiber materials. Degumming or surface modification of hemp bast is needed to produce single fibers for ensuing textile and industrial applications. The traditional degumming process necessitates a high amount of alkali, which causes detrimental environmental pollution. This study offers a new method to degum hemp fibers with reduced use of harmful alkali and precious water resources. In this work, hemp bast fibers were degummed by using combined microwave energy and deep eutectic solvent (DES). The properties of hemp fibers manufactured by this method were investigated and compared with the traditional alkali …

Morphology Transformation Of Foldamer Assemblies Triggered By Single Oxygen Atom On Critical Residue Switch, Byung-Chang Oh, Eunyoung Yoon, Jintaek Gong, Jaewook Kim, Russell W. Driver, Yongjun Kim, Woo Youn Kim, Hee-Seung Lee

Chemistry and Physics Faculty Articles

The synthesis of morphologically well-defined peptidic materials via self-assembly is challenging but demanding for biocompatible functional materials. Moreover, switching morphology from a given shape to other predictable forms by molecular modification of the identical building block is an even more complicated subject because the self-assembly of flexible peptides is prone to diverge upon subtle structural change. To accomplish controllable morphology transformation, systematic self-assembly studies are performed using congener short β-peptide foldamers to find a minimal structural change that alters the self-assembled morphology. Introduction of oxygen-containing β-amino acid (ATFC) for subtle electronic perturbation on hydrophobic foldamer induces a previously inaccessible solid-state …

Motif Wfyy Of Human Primpol Is Crucial To Stabilize The Incoming 3′-Nucleotide During Replication Fork Restart, Patricia R. Calvo, María I. Martínez-Jiménez, Marcos Díaz, Gorazd Stojkovic, Kazutoshi Kasho, Susana Guerra, Sjoerd Wanrooij, Juan Méndez, Luis Blanco

Chemistry and Physics Faculty Articles

PrimPol is the second primase in human cells, the first with the ability to start DNA chains with dNTPs. PrimPol contributes to DNA damage tolerance by restarting DNA synthesis beyond stalling lesions, acting as a TLS primase. Multiple alignment of eukaryotic PrimPols allowed us to identify a highly conserved motif, WxxY near the invariant motif A, which contains two active site metal ligands in all members of the archeo-eukaryotic primase (AEP) superfamily. In vivo and in vitro analysis of single variants of the WFYY motif of human PrimPol demonstrated that the invariant Trp⁸⁷ and Tyr⁹⁰ residues are essential …

Bridging The 12-6-4 Model And The Fluctuating Charge Model, Pengfei Li

Chemistry: Faculty Publications and Other Works

Metal ions play important roles in various biological systems. Molecular dynamics (MD) using classical force field has become a popular research tool to study biological systems at the atomic level. However, meaningful MD simulations require reliable models and parameters. Previously we showed that the 12-6 Lennard-Jones nonbonded model for ions could not reproduce the experimental hydration free energy (HFE) and ion-oxygen distance (IOD) values simultaneously when ion has a charge of +2 or higher. We discussed that this deficiency arises from the overlook of the ion-induced dipole interaction in the 12-6 model, and this term is proportional to 1/r …

Structural And Biochemical Characterization Of The Flavin-Dependent Siderophore-Interacting Protein From Acinetobacter Baumannii, Hannah Valentino, David A. Korasick, Tabbetha J. Bohac, Justin A. Shapiro, Timothy A. Wencewicz, John J. Tanner, Pablo Sobrado

Chemistry Faculty Research & Creative Works

Acinetobacter baumannii is an opportunistic pathogen with a high mortality rate due to multi-drug-resistant strains. The synthesis and uptake of the iron-chelating siderophores acinetobactin (Acb) and preacinetobactin (pre-Acb) have been shown to be essential for virulence. Here, we report the kinetic and structural characterization of BauF, a flavin-dependent siderophore-interacting protein (SIP) required for the reduction of Fe (III) bound to Acb/pre-Acb and release of Fe(II). Stopped-flow spectrophotometric studies of the reductive half-reaction show that BauF forms a stable neutral flavin semiquinone intermediate. Reduction with NAD(P)H is very slow (kobs, 0.001 s-1) and commensurate with the rate of reduction by photobleaching, …

Structure-Guided Microbial Targeting Of Antistaphylococcal Prodrugs, Justin J. Miller, Ishaan T. Shah, Jayda Hatten, Yasaman Barekatain, Elizabeth A. Mueller, Ahmed M. Moustafa, Rachel L. Edwards, Cynthia S. Dowd, Geoffrey C. Hoops, R Jeremy Johnson

Scholarship and Professional Work - LAS

Carboxy ester prodrugs are widely employed to increase oral absorption and potency of phosphonate antibiotics. Prodrugging can mask problematic chemical features that prevent cellular uptake and may enable tissue-specific compound delivery. However, many carboxy ester promoieties are rapidly hydrolyzed by serum esterases, limiting their therapeutic potential. While carboxy ester-based prodrug targeting is feasible, it has seen limited use in microbes as microbial esterase-specific promoieties have not been described. Here we identify the bacterial esterases, GloB and FrmB, that activate carboxy ester prodrugs in Staphylococcus aureus. Additionally, we determine the substrate specificities for FrmB and GloB and demonstrate the structural basis …

Health Disparity And Covid-19—A Retrospective Analysis, Sanjay Sarkar, Archie Taylor, Pratik Dutta, Bidisha Sengupta, Debarshi Roy

Faculty Publications

Background and Aims

According to the World Health Organization (WHO), more than 75.7 million confirmed cases of coronavirus disease 2019 (COVID-19), a global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), have been reported so far. Researchers are working relentlessly to find effective solutions to this catastrophe, using genomic sequence-based investigation, immunological analysis, and more. The role of health disparity has also emerged as an intriguing factor that made a huge impact on the lives of people.

Methods

We analyzed various factors that triggered the health disparity in the United States of America along with the rate of …

Hydrochloric Acid Modification And Lead Removal Studies On Naturally Occurring Zeolites From Nevada, New Mexico, And Arizona, Garven M. Huntley, Rudy Luck, Michael Mullins, Nick Newberry

Michigan Tech Publications, Part 1

Four naturally occurring zeolites were examined to verify their assignments as chabazites AZLB-Ca and AZLB-Na (Bowie, Arizona) and clinoptilolites NM-Ca (Winston, New Mexico) and NV-Na (Ash Meadows, Nevada). Based on powder X-ray diffraction, NM-Ca was discovered to be mostly quartz with some clinoptilolite residues. Treatment with concentrated HCl (12.1 M) acid resulted in AZLB-Ca and AZLB-Na, the chabazite-like species, becoming amorphous, as confirmed by powder X-ray diffraction. In contrast, NM-Ca and NV-Na, which are clinoptilolite-like species, withstood boiling in concentrated HCl acid. This treatment removes calcium, magnesium, sodium, potassium, aluminum, and iron atoms or ions from the framework while leaving …

Visualizing Amino Acid Substitutions In A Physicochemical Vector Space, Louis R. Nemzer

Chemistry and Physics Faculty Articles

A three-dimensional representation of the twenty proteinogenic amino acids in a physicochemical space is presented. Vectors corresponding to amino acid substitutions are classified based on whether they are accessible via a single-nucleotide mutation. It is shown that the standard genetic code establishes a “choice architecture” that permits nearly independent tuning of the properties related with size and those related with hydrophobicity. This work sheds light on the metarules of evolvability that may have shaped the standard genetic code to increase the probability that adaptive point mutations will be generated. An illustration of the usefulness of visualizing amino acid substitutions in …

Stereocontrolled Mannosylation By Hydrogen-Bond-Mediated Aglycone Delivery, Catherine Alex

Dissertations

Stereocontrolled Mannosylation by Hydrogen-Bond-Mediated Aglycone Delivery

Carbohydrates are the essential bio-molecules of life as they form the forefront of interactions with receptors, proteins, pathogens, or neighboring cells. On cell-surfaces, carbohydrates are mostly found as linear or branched glycoconjugates, and a majority of them are linked via either 1,2-cis or 1,2-trans O-glycosidic linkages. There is no template-driven pathway for achieving the synthesis of glycans unlike other biomolecules like proteins and nucleic acids. The synthesis of 1,2-trans glycosides can be reliably achieved via the neighboring group assistance. The synthesis of 1,2-cis glycosides is difficult because, beyond weak anomeric effects, there are …

Enrolling Reactive Oxygen Species In Photon-To-Chemical Energy Conversion: Fundamentals, Technological Advances, And Applications, Irving D. Rettig, Theresa M. Mccormick

Chemistry Faculty Publications and Presentations

In theory, oxygen (O2) is an ideal chemical reagent because of its high relative abundance and negligible environmental toxicity. In practice however, by the nature of its ground state electronic configuration, many chemical reactions involving O2 are spin forbidden which dramatically decreases its reactivity and thus its utility in applications. More reactive forms of O2 can be achieved by changing its electronic configuration through the use of photochemical and photophysical methods. This review highlights the roll of photon-to-chemical energy conversion in two of these reactive oxygen species (ROS): superoxide (O2−) and singlet oxygen (1O2), which can be accessed through a …

Experimental Evidence That Metapopulation Structure Can Accelerate Adaptive Evolution, Partha Pratim Chakraborty, Louis R. Nemzer, Rees Kassen

Chemistry and Physics Faculty Articles

Whether the spatial arrangement of a population influences adaptive evolution has been a long-standing question in population genetics. In contrast to standard population genetic models, evolutionary graph theory (EGT) predicts certain topologies amplify (increase) the probability that a beneficial mutation will spread in the population relative to a well-mixed population. Here, we test these predictions empirically by tracking the fixation dynamics of an antibiotic resistant mutant under positive selection as it spreads through networks of different topologies both in vitro and in silico. We show that star-like topologies involving bi-directional dispersal between a central hub and peripheral leaves can …

Ganglioside Alters Phospholipase Trafficking, Inhibits Nf-Κb Assembly, And Protects Tight Junction Integrity, John J. Miklavcic, Qun Li, Jordan Skolnick, Alan B. R. Thomson, Vera C. Mazurak, Michael Tom Clandinin

Food Science Faculty Articles and Research

Background and Aims: Dietary gangliosides are present in human milk and consumed in low amounts from organ meats. Clinical and animal studies indicate that dietary gangliosides attenuate signaling processes that are a hallmark of inflammatory bowel disease (IBD). Gangliosides decrease pro-inflammatory markers, improve intestinal permeability, and reduce symptoms characteristic in patients with IBD. The objective of this study was to examine mechanisms by which dietary gangliosides exert beneficial effects on intestinal health.

Methods: Studies were conducted in vitro using CaCo-2 intestinal epithelial cells. Gangliosides were extracted from milk powder and incubated with differentiated CaCo-2 cells after exposure to pro-inflammatory stimuli. …

Tp-5801 In Vitro Kinase Screen Data, Joshua Andersen

ScholarsArchive Data

In vitro kinase screen data for TP-5801 to accompany Chan and Egbert et al., Nature Communications, 2021 (in press)

Preparation And Characterization Of Single Layer Conducting Polymer Electrochromic And Touchchromic Devices, Sharan Kumar Indrakar

USF Tampa Graduate Theses and Dissertations

Electrochromic devices (ECDs) have triggered great interest because of their potential applicability in energy-efficient buildings and low power display systems, including reflective type smart windows/mirrors and wearable-flexible devices. In the past decades, electrochromic technologies with different device structures and materials have been proposed. The idea of employing a simple device structure with a durable, cost effective electrolyte is crucial to designing and manufacturing high-performance ECDs. With this idea in mind, this thesis describes the various efforts to develop a simple ECD comprising of a composite single active layer gel electrolyte, sandwiched between two transparent conducting electrodes, lasting over 10,000 cycles …

Electrochemical Reduction Of Hexavalent Chromium In Acetonitrile Using Glassy Carbon Electrodes, Temitope Jegede

LSU Master's Theses

Hexavalent chromium Cr(VI), a form of chromium mainly generated through industrial processes, has attracted great research interests due to its severe toxicity to biological systems. A common way to remove hexavalent chromium from industrial wastes is through reduction to the non-toxic trivalent state. To this end, methods such as chemical reduction, chemical precipitation and coagulation have been used. However, these methods are limited by poor removal efficiency, formation of secondary pollutants (sludge), and are mostly applicable to aqueous solutions. Recently, electrochemical methods have been investigated for reducing hexavalent chromium, but there is a lack of data on the reduction of …

Local And 2-Local Derivations On Octonion Algebras, Allayar Allambergenov

Karakalpak Scientific Journal

The present paper is devoted to study of local and 2-local derivations on octonion algebras. We shall give a general form of local derivations on the real octonion algebra \[{\mathbb{O}_\mathbb{R}}.\] This description implies that the space of all local derivations on \[{\mathbb{O}_\mathbb{R}}\] when equipped with Lie bracket is isomorphic to the Lie algebra \[\mathfrak{s}{\mathfrak{o}_7}(\mathbb{R})\] of all real skew-symmetric \[7 \times 7\]-matrices. We also consider \[2\]-local derivations on an octonion algebra \[{\mathbb{O}_\mathbb{F}}\] over an algebraically closed field \[\mathbb{F}\] of the characteristic zero and prove that every \[2\]-local derivation on \[{\mathbb{O}_\mathbb{F}}\] is a derivation. Further, we apply these results to similar problems …