Chemistry Commons^™

Studies Toward Provenance Determination For Indigo Dyes, Erin Kibby

Undergraduate Honors Thesis Projects

Species of indigo-producing plants have been used to color textiles for thousands of years all over the globe. Natural indigo-producing species have historically been harvested in regions of Asia, North Africa, and North and South America. This study is an exploration of methods that can be used to determine the provenance (origin) of the indigo dye in a textile through the extraction and isolation of indigoids, flavonoids, and other compounds from the natural dyestuff. There is no accepted method of extracting flavonoids from indigo-dyed textiles specifically, and there is little investigation of the regionally different species. If a method is …

Sustainable Polymers: Upcycling Poly(Vinyl Chloride) And Mimicking Low Density Polyethylene, Ian Baxter

Theses and Dissertations

In this research, increasing the sustainability of polymers was investigated through two main methods. The upcycling of poly(vinyl chloride) and the creation of polymer mimics to create degradable low-density polyethylene. In the first chapter, an overview of the sustainability issues of polymers is presented and approaches are described on how their sustainability may be increased through the upcycling of polymers or the synthesis of degradable polymers that mimic the properties of petrol-based polymers.

Chapter 2 contains the progress on the upcycling of PVC using high oleic soybean oil. Soybean oil can soften PVC making it less brittle than pure PVC. …

Photophysics And Electronic Properties Of Photochromic Metal-Organic Frameworks, Corey R. Martin

Theses and Dissertations

Modulation of materials properties through light-based illumination has the capability to expand the technology sector due to stimuli-responsive dynamic behavior that cannot be achieved in traditional materials. For example, reversibly tuning photophysical profiles of such materials allows for switching between discrete states that is a key aspect for the developing logic gates, spatially- and temporally-resolved sensors, and on-demand drug delivery systems. My efforts have focused on employment of metal-organic frameworks (MOFs) as a versatile platform for the material development which contain photochromic moieties allowing for tailoring their electronic properties. Our group has expanded this direction to include heterometallic and actinide-containing …

Understanding The Hydrolytic Activity Of Papiliotrema Laurentii On Polyester Polyurethane Coatings, Ariana L. Santos

Honors Theses

Though plastic polymers such as polyester polyurethanes have many applications from electronics to aircraft coatings, their resistance to natural degradation presents an environmental concern. Therefore, elucidating the mechanism of degradation from microorganisms that were discovered breaking down the coating of a cargo aircraft may offer insights into a method of bioremediation. To explore this, the fungus Papiliotrema laurentii (one microorganism isolated from the consortium) was cultured in several different media types at different pH levels in order to understand how it adjusts its protein secretion patterns to environmental changes. 2D gel electrophoresis, isoelectric focusing (IEF) and a variety of gel …

College Of Natural Sciences Newsletter, March & April 2022, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 3, Issue 3

Page 1 Dean's Message
Page 2-3 Awards and Recognition
Page 4 2022 URSCAD - CNS Snaps
Page 5 Geography Convention Recap
Page 6 Attention Students!
Page 7-8 Media Coverage of CNS
Page 9 Spring Break Outreach, Adopt the Pantry,
Page 10 Discovery on Tap Event
Page 11 CNS Students Visit State Capital
Page 12 Celebrating 50 Years of Sally
Page 13 Open PRAIRIE Data
Page 14 Grants Awarded and Bio-Micro Day of Scholars
Page 15 -17 2022 Geography Convention Snaps
Page 18 Sally Krueger's 50th Work Anniversary

1st Place Contest Entry: Designing Hollow Nanogels For Drug Delivery Applications, Mo Hijazi

Kevin and Tam Ross Undergraduate Research Prize

This is Mo Hijazi's submission for the 2022 Kevin and Tam Ross Undergraduate Research Prize, which won first place. It contains their essay on using library resources, their bibliography, and a summary of their research project on hollow-core nanogels.

Mo is a second-year student at Chapman University, majoring in Biological Sciences. Their faculty mentor is Dr. Molla Islam.

Synthesis And Characterization Of Enantioenriched Deuterated And Fluorinated Small Molecules, Mitchell D. Mills

Master's Theses (2009 -)

The development of novel deuterated and fluorinated bioisosteres has significantly impacted the pharmaceutical and agricultural industry and created a growing demand for new synthetic methodology. Both deuterated and fluorinated small molecules exist at the forefront of drug discovery due to their unique ability to attenuate the pharmacokinetic properties of new and currently existing drugs. Selective, high-throughput methods for deuteration and fluorination are scarce in the literature, especially methods that introduce D or F atoms asymmetrically. Benzylic CH bonds are oftentimes key sites for enzymatic manipulation in metabolic processes, alteration of CH bonds to CD or CF bonds at the benzylic …

Intrinsic Photodynamic Study On Photocatalytic Materials, Wenhui Hu

Dissertations (1934 -)

To relieve the global energy crisis and environmental pollution caused by the combustion of traditional fossil fuels, developing an environmental-friendly renewable energy to replace fossil fuel is urgent. Among the possible energy sources, solar energy has attracted numerous attentions because of the abundant storage. However, it is challenging to efficiently utilize and store solar energy. One attractive strategy to address this challenge is to convert solar energy to fuel through artificial photosynthesis (e.g. photocatalytic water splitting to generate H2). A technologically significant solar-driven water splitting system requires an efficient photocatalytic system that can not only effectively harvest light but also …

Well–Defined Donor–Acceptor Materials, Gabrielle A. Leith

Theses and Dissertations

The modularity of multivariant scaffolds such as covalent–organic frameworks (COFs) provides an unprecedented level of control in the alignment of donor (D) and acceptor (A) units, a demand that is driven by the production of optoelectronic, photonic, and spintronic devices. The foray into novel motifs bearing D-A ensembles in frameworks has been applied towards material property modulation for device performance enhancement. This dissertation presents an emerging trend in the development of D-A interfaces by highlighting recent advances probing D-A interactions in porous crystalline matrices and co-crystals, with a focus on energy transfer (ET) and charge transfer (CT) processes in pre-designed …

Prefusion Spike Protein Conformational Changes Are Slower In Sars-Cov-2 Than In Sars-Cov-1, Vivek Govind Kumar, Dylan S. Ogden, Ugochi H. Isu, Adithya Polasa, James Losey, Mahmoud Moradi

Chemistry & Biochemistry Faculty Publications and Presentations

Within the last 2 decades, severe acute respiratory syndrome coronaviruses 1 and 2 (SARS-CoV-1 and SARS-CoV-2) have caused two major outbreaks; yet, for reasons not fully understood, the coronavirus disease 2019 pandemic caused by SARS-CoV-2 has been significantly more widespread than the 2003 SARS epidemic caused by SARS-CoV-1, despite striking similarities between these two viruses. The SARS-CoV-1 and SARSCoV-2 spike proteins, both of which bind to host cell angiotensin-converting enzyme 2, have been implied to be a potential source of their differential transmissibility. However, the mechanistic details of prefusion spike protein binding to angiotensin-converting enzyme 2 remain elusive at the …

A Proposed Treatment Of Mixed Connective Tissue Disease By Competitive Inhibition Of Autoantibodies, Thomas Russell

Senior Honors Theses

Mixed Connective Tissue Disease is an autoimmune disease characterized by Raynaud’s phenomenon and arthritis among other symptoms. It is primarily caused by antibodies that target the U1-RNP 70K peptide. The treatment proposed in this paper uses competitive inhibition to prevent the binding of the anti-U1-RNP 70K antibodies with the U1-RNP 70K peptide. A method for testing the designed treatment in silico is proposed using AutoDock Vina docking software.

Exploring The Kinetics And Thermodynamics Of O–H Bond Activation By Tripodal Tris(Nitroxide) Aluminum And Gallium Complexes, Joseph S. Scott , '22

Senior Theses, Projects, and Awards

Aluminum is one of earth’s most abundant and cheapest metals, and it is also nontoxic and environmentally friendly. This makes it an ideal candidate to be implemented in organometallic chemistry as a greener alternative to metal-based systems based on heavy and/or precious metals. One of the realms in which aluminum and other group 13 elements show promise is metal-ligand cooperative chemistry, which can afford transition metal-reminiscent small molecule activation chemistry. Our studies of organic ligands with nitroxide-functionalities within Al and Ga coordinative systems has led us to the discovery of tripodal tris(nitroxide) Al and Ga complexes with abilities to engage …

Synthesis And Characterization Of Aluminum Complexes Implementing Redox-Active Nitroxide Bidentate Ligands, Omar Saleh , '22

Senior Theses, Projects, and Awards

Aluminum is an abundant, sustainable, and non-toxic metal, which would be a great candidate to be used in redox and catalytic chemistry in lieu of the currently used heavy metals. However, aluminum can only exist over one stable oxidation state, which is a major obstacle in this pursuit. To tackle this issue, the Graves Lab has been focusing on incorporating redox active ligands into aluminum complexes. Nitroxide (NO⁻) is an exceptionally important functional group, as it can reversibly exist over three stable oxidation states. In this work, I synthesized and characterized neutral aluminum complexes, [(^(OMe)pyNO)AlMe₂]₂ (1b) and [(^(OMe)pyNO)AlMe₂]AlMe₃ (2b), with …

Mathematica Assessment Of Spatial Reasoning Development After Virtual Reality Collaboration, Arthur Odenheimer

Honors Capstones

No abstract provided.

Observing Reactive Events At The Aqueous Graphene Oxide Interface Using Deep Neural Network Potentials, Lukas Kim

Honors Capstones

No abstract provided.

Expression And Purification Of Tag-Free Chlamydia Trachomatis Scc4 For Improved Nmr Structural Studies, Peter Howard

Honors Capstones

No abstract provided.

Datadescription-Detection Of Sulfur Dioxide By Broadband Cavity-Enhanced Absorption Spectroscopy (Bbceas), Ryan Thalman, Nitish Bhardwaj, Callum Flowerday, Jaron C. Hansen

ScholarsArchive Data

Files archived include the following:

Figure1.txt This file contains all the data used to make Figure 1 in the paper.

Figure4.txt This file contains all the data used to make Figure 4 in the paper.

Figure5.txt This file contains all the data used to make Figure 5 in the paper.

Figure6.txt This file contains all the data used to make Figure 6 in the paper.

Figure7.txt This file contains the code, written in Igor, that was used to generate this figure.

Figure8.txt This file contains all the data used to make Figure 8 in the paper.

Figure9.txt This file contains …

The Development Of Inhibitors For Sars-Cov-2 Orf8, My Thanh Thao Nguyen

CSB and SJU Distinguished Thesis

An unexpected outbreak of SARS-CoV-2 caused a worldwide pandemic in 2020. Many repurposed drugs were tested, but there are currently only three FDA approved antivirals (Merck’s antiviral Molnupiravir, Pfizer’s antiviral Paxlovid, and Remdisivir).1 Most of the antiviral drugs tested SARS-CoV-2 main protease and RNA-dependent RNA polymerase. However, it is important to explore different drug targets of SARS-CoV-2 to prepare for the virus mutations of the future. This research looks at an alternative approach in which SARSCoV- 2 Open Reading Frame 8 (ORF8), which has been shown to be a rapidly evolving hypervariable gene, was chosen to be the protein of …

Sars-Cov-2 Main Protease Inhibitors Repurposed For Hiv-1 Protease Binding, Jacob Minkkinen

CSB and SJU Distinguished Thesis

Severe acute respiratory syndrome (SARS-CoV-2) led to the COVID-19 global pandemic, with over 460 million cases of infection and over 6 million deaths since the start of the pandemic. SARS-CoV-2 is a retrovirus that utilizes a main protease (Mpro). Mpro is a catalytic cys/his protease. Several treatments were proposed to stop the pandemic including repurposing drugs to inhibit the Mpro. Another retrovirus that uses a protease is human immunodeficiency virus (HIV-1) which has been a global epidemic for 40 years and is a devastating disease that attacks the immune system. HIV-1 has infected 79.5 million people and has killed an …

Block Copolymer Directed Self-Assembly: Exploring The Efficacy Of Applications In Semiconductor Fabrication, Jakin Bryce Delony

USF Tampa Graduate Theses and Dissertations

Over the course of the past 80 years, semiconductor devices have become increasingly ubiquitous in everyday life.From constructing mainframes that encompassed entire rooms during the 1940s, to inventing personal computers in the 1980s, to developing progressively faster smartphones and wearable technology in the 2010s, the primary driving force behind the Digital Revolution has been increasing transistor counts, and thus computing power, via incremental improvements in optical lithography. In 1965, Intel co-founder Gordon Moore boldly predicted that the transistor density of semiconductor devices would double approximately every 18-24 months. While this prediction -- now colloquially referred to as Moore's Law -- …

Metal Free Bond Activation By Carboranyl Phosphines, Gayathri B. Gange

Theses and Dissertations

In the past few decades, main group-based catalysts have attracted increasing attention as an alternative approach to overcome the most prevailing issues of transition metal catalysts such as high cost, toxicity, and low abundance. Among these main groupbased catalysts, Phosphine based compounds have shown a variety of bond activations due to the strong nucleophilicity from their congener species. To the contrary, unique electron deficient boron-based clusters have the tendency to accept two electrons reversibly due to their electron deficiency. In this study, we have synchronized the electron donor ability of the phosphine with the electron acceptor ability of the ortho …

Synthesis Of Carborane Pincer Complexes And Exploration Of The Reactivity Of Metal-Boron Bonds, Hindurangalage Don Asela Chathumal Jayaweera

Theses and Dissertations

Exploration of transition metal complexes with metal-boron bonds for the cooperative bond activation of small molecules in catalysis is one of the recent developments in novel synthetic strategies. The use of boron clusters as a modular platform for the formation of metal-boron bond has been successfully utilized by our and other groups. Carboranes are icosahedral boron-carbon molecular clusters that have gained attraction as multifunctional ligands due to their unique geometry, electronic properties, and versatility of functionalization methods. Their 3-D structure exerts a steric bulk around the exohedral substituent, either metal or non-metal center. Furthermore, due to the cluster geometry, five …

Tailored Nanomaterials For Advancing Fast-Charge Research, Wessel Van Den Bergh

Theses and Dissertations

The demand for fast, energy-dense storage has driven research into nanoscale intercalation materials. Nanoscale materials not only accelerate kinetics but also can modify reaction path thermodynamics, intercalant solubility, and diffusivity. Pioneering works have revealed such nanoscale changes, often without the need to separately probe each fundamental transport process. While electrodes can be designed to have one transport processes dominant, there remain opportunities to better understand energy-dense designs with multiple concomitant transport constraints. The contents herein highlight emerging an method using tailored, energy-dense nanomaterials and the process of elimination to clearly correlate architectural features to performance. For example, this method revealed …

Adsorption Of Microcystins To Sediment Affects Their Bioavailability And Remediation, Ashley Womer

Theses and Dissertations

The freshwater harmful algae Microcystis spp produces a family of toxins called microcystins1. These species of algae are known to release microcystins from their cells directly into the surrounding water2. This creates an array of human health risks depending on the fate and transport of the toxins in the water column3,4. Risk modelling and previous literature has shown that sediment is a sink for free microcystin, microcystin can be stably adsorbed to sediment for hundreds of years, and its adsorption to sediment is determined by the sediment adsorption partitioning coefficient (Kd)5,6,7. In this work it is hypothesized that the sediment …

Mechanistic Understanding Of Catalytic Processes For Sustainable Chemical Transformations, Pooja J. Ayare

Theses and Dissertations

The current field of catalysis is notably advanced in terms of both conceptual and technical innovation. There is a constant need to design new catalysts and develop catalytic processes to improve the scope, efficiency, and selectivity of various chemical transformations. It is also imperative to design catalytic systems which are effective, truly-recyclable and energy efficient for a sustainable future. This can be done through comprehensive knowledge and understanding of catalyst behavior, reaction kinetics and process designing.

For most industrial processes, the preferred catalysts are heterogeneous because these solid catalysts can be easily separated from the final product. However, they often …

Fragmentation Method For Computing Quantum Mechanics And Molecular Mechanics Gradients For Force Matching: Validation With Hydration Free Energy Predictions Using Adaptive Force Matching, Dong Zheng, Ying Yuan, Feng Wang

Chemistry & Biochemistry Faculty Publications and Presentations

A fragmentation approach referred to as a simple overlapping region method for force matching (SORForM) is presented. SORForM is designed to enable efficient computation of quantum mechanical (QM) forces for large molecules and is validated in the framework of adaptive force matching (AFM) to develop solute models in water. The SORForM method divides a molecule into overlapping QM regions with each region containing a gradient zone and a buffer zone. The buffer zone ensures that the atoms in the gradient zone have their surroundings unchanged with fragmentation. The performance of the method is validated with mefenamic acid and linalyl acetate …

A Comparative Study Of Two Nickel-Based Suzuki-Miyaura Hybrid Molecular Catalysts, Mollie Morrow

Senior Theses

Two molecular nickel-based catalysts, (2,2’bipyridine-4,4’-carboxylic acid)nickel(II) chloride and (2,2'-bipyridine-4,4'-diamidopropylsilatrane)nickel(II) chloride, were synthesized and subsequently attached to a solid support in the form of amorphous silicon dioxide to create two hybrid molecular/heterogeneous catalysts. Characterization using ICP-MS and ATR-FTIR confirms that both catalysts are bonded to the SiO₂ support. The catalysts were both able to catalyze a Suzuki-Miyarua cross-coupling which their molecular counterparts were unable to; the carboxylate catalyst was able to achieve yields of 10% and the silatrane catalyst achieved yields of up to 50%. Post-reaction analysis indicated that while some catalyst desorption occurred in both complexes, active catalytic species …

Modification Of Active Sites In Catalytic Materials For Gas-Phase Heterogeneous Catalysis, Deependra Man Shakya

Theses and Dissertations

Heterogeneous catalysis remains at the core of chemical manufacturing industries with 80-90 % of chemical processes relying on the use of catalysts. Unlike homogeneous catalyst that has extremely well-defined active sites, active sites in heterogeneous catalysis are complex and show dynamic behavior under reaction conditions, and change their structures, composition, particle size. The complexity associated with these systems has made the rational design of the catalyst a difficult problem. Highly crystalline metalorganic frameworks (MOFs) as heterogeneous catalysts present the unique opportunity to systematically modify the geometries, ensemble sizes, and compositions of highly dispersed active sites due to their tailorable, and …

Design And Application Of Membrane Nanodiscs For Biophysical Studies Of Influenza A Proteins, Aye K. Kyaw , '22

Senior Theses, Projects, and Awards

Membrane proteins play a range of important roles in biological systems, yet they are underrepresented in the data base of high-resolution structures of all proteins. There is intense interest in developing new methodologies for studying membrane proteins. An essential step to membrane protein method development is devising reliable membrane mimics in which to embed membrane proteins. The goal of this thesis was to develop and apply nanodisc membrane mimics to the study of an influenza A membrane protein called M2. Nanodiscs provide a lipid bilayer environment with access to both sides of the bilayer and are smaller than commonly used …

Geochemistry Of Mafic-Intermediate Intrusive Rocks From The Twangiza-Namoya Gold Belt, Eastern Democratic Republic Of Congo: Trace Element Constraints On Their Origin, Petrogenesis And Tectonic Setting, Gerald L. Chuwa, Charles H. Kasanzu

Tanzania Journal of Science

Bulk geochemical data for the Twangiza-Namoya Gold Belt, Democratic Republic of Congo, are presented in order to classify the rock assemblages, elucidate their petrogenesis and tectonic settings. Nb/Yb and Zr/Ti constraints reveal two suites for the rocks: sub-alkaline to andesitic basalts (Suite-1); and alkaline basalts (Suite-2).  Ratios of Ti/Zr = 22–70; Zr/Hf = 35–42; Nb/Ta = 12–13; Nb/Th = 1–2 and La/Nb = 2.4–3.8 suggest arc-generated mantle melts with crustal inputs and arc-fluids metasomatism for Suite-1. The samples have positive LILE and negative Nb, Ta, Ti anomalies, enrichments in the LREE over middle and HREE (La/Yb)CN = 3.6–8.9 with negative …