Chemistry Commons^™

Updating The Dual C And O Isotope—Gas-Exchange Model: A Concept To Understand Plant Responses To The Environment And Its Implications For Tree Rings, Rolf T. W. Siegwolf, Marco M. Lehmann, Gregory R. Goldsmith, Olga V. Churakova (Sidorova), Cathleen Mirande-Ney, Galina Timoveeva, Rosmarie B. Weigt, Matthias Saurer

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The combined study of carbon (C) and oxygen (O) isotopes in plant organic matter has emerged as a powerful tool for understanding plant functional responses to environmental change. The approach relies on established relationships between leaf gas exchange and isotopic fractionation to derive a series of model scenarios that can be used to infer changes in photosynthetic assimilation and stomatal conductance driven by changes in environmental parameters (CO₂, water availability, air humidity, temperature, nutrients). We review the mechanistic basis for a conceptual model, in light of recently published research, and discuss where isotopic observations do not match our …

A Streptomyces Tendae Specialized Metabolite Inhibits Quorum Sensing In Group A Streptococcus, Vanessa M. Nepomuceno, Kaitlyn M. Tylor, Skylar Carlson, Michael J. Federle, Brian T. Murphy, Tiara Perez Morales

Pacific Faculty Work

Quorum sensing (QS) is a means of bacterial communication accomplished by microbe-produced signals and sensory systems. QS systems regulate important population-wide behaviors in bacteria, including secondary metabolite production, swarming motility, and bioluminescence. The human pathogen Streptococcus pyogenes (group A Streptococcus [GAS]) utilizes Rgg-SHP QS systems to regulate biofilm formation, protease production, and activation of cryptic competence pathways. Given their reliance on small-molecule signals, QS systems are attractive targets for small-molecule modulators that would then affect gene expression. In this study, a high-throughput luciferase assay was employed to screen an Actinobacteria-derived secondary metabolite (SM) fraction library to identify small molecule inhibitors …

Dynamical Polymer Chain Heterogeneities And Their Impacts On The Glass Transition, William Forrest Drayer

USF Tampa Graduate Theses and Dissertations

The utilization of polymeric materials has endured since prehistory, at first unknowinglyin the form of natural biopolymers such as wood and leather, culminating and continuing through the development of the plastics industry in the early twentieth century. Polymers, along with other materials including silicate glasses, readily exhibit the glass transition upon quenching: a continuous but rapid change from viscous (liquid) to elastic (solid) behavior. The physics surrounding the glass transition have been studied for over a century; while considerable progress has been made, there remains no universally accepted predictive theory of the glass transition. Modern development of glassy materials consists …

Development Of Graphene And Graphene Derivative Advanced Functional Additives: Mechanism And Application In Asphalt Formulations And Thermal Interface Management Materials, Dana Pinson

Dissertations

The overarching focus of my research is the use of graphene and graphene derivatives to enhance polymer properties. My first focus area was the prevention of oxidative degradation of asphalt through the incorporation of a graphene oxide (GO) -based nanoparticle filler to enhance oxygen barrier properties. Primary amine terminated polyisobutylene was synthesized via cationic polymerization followed by post polymerization chain end modification in a range of molecular weights and covalently grafted via the primary amine to graphene oxide aerogel (aGO) to create a polyisobutylene grafted graphene oxide (PIB-g-GO) nanoparticle. PIB-g-GO was then mixed into a substitute asphalt matrix at various …

Determination And Comparison Of Freely Dissolved Pahs Using Different Types Of Passive Samplers In Freshwater, Na Yeong Kim, Bommanna G. Loganathan, Gi Beum Kim

Faculty & Staff Research and Creative Activity

Polycyclic aromatic hydrocarbons (PAHs) are well-known for their recalcitrant properties and biotoxicity in organisms, leading to serious environmental and health problems. Despite various analytical methods available, accurate determination of the bioavailable fraction is warranted in order to evaluate the precise toxic potentials of these compounds. Currently, the passive sampler is used worldwide to measure the bioavailable PAHs in the environment using the equilibrium partitioning principle. In this study, we co-deployed different types of passive samplers, which are linear low-density polyethylene (LLDPE) and low-density polyethylene (LDPE), to determine freely dissolved concentrations (Cfree) of PAHs using the performance reference compounds (PRCs) in …

Hydrogen-Bonding Trends In A Bithiophene With 3- And/Or 4-Pyridyl Substituents, Alison M. Costello, Rebekah Duke, Stephanie Sorensen, Nadeesha Kothalawala, Moses Ogbaje, Nandini Sarkar, Doo Young Kim, Chad Risko, Sean Parkin, Aron J. Huckaba

UK CARES Faculty Publications

To improve the charge-carrier transport capabilities of thin-film organic materials, the intermolecular electronic couplings in the material should be maximized. Decreasing intermolecular distance while maintaining proper orbital overlap in highly conjugated aromatic molecules has so far been a successful way to increase electronic coupling. We attempted to decrease the intermolecular distance in this study by synthesizing cocrystals of simple benzoic acid coformers and dipyridyl-2,2′- bithiophene molecules to understand how the coformer identity and pyridine N atom placement affected solid-state properties. We found that with the 5-(3-pyridyl)-5′-(4-pyridyl)-isomer, the 4- pyridyl ring interacted with electrophiles and protons more strongly. Synthesized cocrystal powders …

Fate And Distribution Of Orally-Ingested Ceo2-Nanoparticles Based On A Mouse Model: Implication For Human Health, Xingmao Ma, Xiaoxuan Wang, Lei Xu, Honglan Shi, Hu Yang, Kerstin K. Landrock, Virender K. Sharma, Robert S. Chapkin

Chemistry Faculty Research & Creative Works

The use of nanoparticles in agrichemical formula and food products as additives has increased their chances of accumulation in humans via oral intake. Due to their potential toxicity, it is critical to understand their fate and distribution following oral intake. Cerium oxide nanoparticle (CeO2NP) is commonly used in agriculture and is highly stable in the environment. as such, it has been used as a model chemical to investigate nanoparticle's distribution and clearance. based on their estimated human exposure levels, 0.15–0.75 mg/kg body weight/day of CeO2NPs with different sizes and surface charges (30–50 nm with negative charge and <25 >nm with positive …

Copper-Indazolate Nanojars: Synthesis And Characterization, Nicholas Alexander Rudell

Masters Theses

The field of synthetic supramolecular chemistry has exploded since the first syntheses of crown ethers by Charles Pedersen in the 1960s, leading to further development in the area of macrocycles and incorporation into a vast array of metal-organic structures. Supramolecular chemistry came to the forefront of science with the 1987 Nobel Prize in Chemistry, awarded jointly to Donald J. Cram, Jean-Marie Lehn, and Charles Pedersen “for their development and use of molecules with structure-specific interactions of high selectivity.”

Nanojars are supramolecular metal-organic complexes with a high affinity for hydrophilic anions and can efficiently transfer such anions from water into organic …

Supramolecular Design Of 3d-Printable Hydrogels For Functional Materials, Miao Tang

Dartmouth College Ph.D Dissertations

Additive manufacturing, more commonly known as 3D-printing, is bringing about a grand technological transformation in material design and fabrication. In contrast to traditional fabrication techniques, 3D-printing features rapid prototyping, complex and customized 3D structural designs, and multi-material integration. Among current 3D-printing systems, direct-ink-writing (DIW) exhibits unique functionalities due to its mild operation conditions and the ability to integrate various organic and inorganic entities. Although supramolecular binding motifs are increasingly utilized in 3D-printing designs, the optimization of 3D-printable inks remains largely empirical. In this thesis, we present two strategies to rationally design supramolecularly crosslinked 3D-printable hydrogels, including (1) micro-crystallization and (2) …

Covalent Adaptable Networks For Wood Coatings, Jachin Boaz Clarke

Materials Engineering

Wood swells and shrinks causing problems with seasonal humidity. Applying thick coatings of reactive finishes based on cross-linked polyurethane, epoxy, or polyesters can slow moisture-vapor exchange. However, the use of thick coatings leads to cracking and crazing sooner than thin finishes. This research proposes the addition of 3.3 mol % triazabicyclodecene, a conventionally used covalent adaptable network catalyst, in a commercially available polyester-based wood coating. The self-healing of the wood coating is tested using DMA stress relaxation and compression molding. The result from DMA renders inconclusive and compression molding indicates the novel wood coating oxidizes at elevated temperatures. The wood …

Metals And Metal Complexes In Diseases With A Focus On Covid-19: Facts And Opinions, Agnieszka Ścibior, Manuel Aureliano, Alvin A. Holder, Juan Llopis

Chemistry & Biochemistry Faculty Publications

In the present Special Issue on “Metals and Metal Complexes in Diseases with a Focus on COVID-19: Facts and Opinions”, an attempt has been made to include reports updating our knowledge of elements considered to be potential candidates for therapeutic applications and certain metal-containing species, which are extensively being examined towards their potential biomedical use due to their specific physicochemical properties. The Special Issue compiles data on the role of metals in COVID-19 and focuses on other illnesses and biological processes that affect metal metabolism. It consists of eight manuscripts, including five review articles and three original research papers (Figure …

Synthesis And Study Of High-Spin Stable Organic Radicals For Electrical Conductors And Mannosamine Nitroxide For Mri Contrast Agents, Shuyang Zhang

Department of Chemistry: Dissertations, Theses, and Student Research

In the first project, we describe the synthesis of an ambient stable high spin organic diradical 4 based on the Blatter moiety. The high-spin (S = 1) organic diradical 4, which consists of two Blatter radical moieties in a conjugated structure, exhibits a nearly exclusive population (88%) on triplet ground state at room temperature as a consequence of a large single-triplet energy gap (ΔEST = 0.5 kcal/mol). The target diradical molecule is synthesized over five steps with structural confirmation by single-crystal X-ray diffraction. The thermogravimetric analysis (TGA) shows the onset of decomposition at ~264 oC, indicating the diradical molecule has …

Addressing The Embeddability Problem In Transition Rate Estimation, Curtis Goolsby, James Losey, Ashkan Fakharzadeh, Yuchen Xu, Marie-Christine Düker, Mila Getmansky Sherman, David S. Matteson, Mahmoud Moradi

Chemistry & Biochemistry Faculty Publications and Presentations

Markov State Models (MSM) and related techniques have gained significant traction as a tool for analyzing and guiding molecular dynamics (MD) simulations due to their ability to extract structural, thermodynamic, and kinetic information on proteins using computationally feasible MD simulations. The MSM analysis often relies on spectral decomposition of empirically generated transition matrices. This work discusses an alternative approach for extracting the thermodynamic and kinetic information from the so-called rate/generator matrix rather than the transition matrix. Although the rate matrix itself is built from the empirical transition matrix, it provides an alternative approach for estimating both thermodynamic and kinetic quantities, …

Analysis Of Polymer-Coated Bullets Using Spectroscopic Methods, Liana R. Albano

Student Theses

Polymer-coated bullets have gained popularity because they can reduce the user’s exposure to heavy metals in the ammunition. The synthetic jacket, which surrounds the lead core, is advantageous because it prevents metal-on-metal contact between the bullet and the bore. A challenge for firearms identification is that polymer-coated bullets do not retain unique markings that can be used to identify the gun, the way standard metal-coated bullets do. However, metal-coated bullets will result in a similar challenge if the bullet is too deformed once it is recovered. Another issue is that the composition of the polymer coating was never disclosed by …

Identification Of Different Hair Dyes In Dyed Hair Using Attenuated Total Reflectance (Atr Ft-Ir), Surface Enhancing Raman Spectroscopy (Sers) Techniques, Nicholas Lovera

Student Theses

This investigation compares the ability of Attenuated Total Reflection Fourier Transfer Infrared Spectroscopy (ATR FT-IR) and Surface Enhance Raman Spectroscopy (SERS) to identify and differentiate different hair dye brands on dyed hair samples. Hair is a common type of trace evidence found at crime scenes and can provide numerous information through forensic hair analysis. Cosmetic hair treatment such as dying the hair different colors has grown and became popular, thus it can be a very common type of trace evidence. This study can provide a forensic scientist an additional method for analyzing dyed hair samples. The goal was to compare …

Sers For The Detection Of Trace Materials, Omari Kirkland

Dissertations, Theses, and Capstone Projects

In this dissertation are presented three projects that contribute to the body of research on SERS in the forensic, heritage, and semiconductor fields. The first project, Charge-Transfer mapping on GaN/Ag, a silver-decorated nanopillar semiconductor substrate fabricated from the GaN is used with the Raman probe Rhodamine 6 G (R6G) to map the effect of the nanofeatures on the CT resonance. The second project, in collaboration with Marco Leona from the Metropolitan Museum of Art, explores the use of AgNIFs to identify colorants used on textile fiber samples from four 19th century works of Japanese art. The final project analyzes the …

A Typological And Chemical Analysis Of Roman Oil Lamps From Poggio Del Molino, Brandon Tejo

Dissertations, Theses, and Capstone Projects

Terracotta lamps, known to the Romans as lucernae, are small, handheld, often decorated objects which provided ancient people light. To modern researchers, they serve as tools for dating stratigraphy and iconographic studies. Beyond their immediately apparent aesthetic and symbolic value, the chemical compositions of the clay of these lamps reflect their origin. This study complements archaeological typologies with chemometric analyses to describe 16 Late Republican and Imperial Roman lamps recovered from the villa at Poggio del Molino (PdM), Tuscany. These finds were recovered from the 2021 and 2022 PdM excavations. The combined approach of typology with X-ray Diffraction (XRD) …

The Effect Of The Carbon Nanotubes’ Surface Area On The Morphology And Performance Of Cellulose Acetate Nanocomposite Membranes In Nanofiltration Applications, Nouran Elbadawi

Theses and Dissertations

Population increase and climate change have significantly affected the availability of fresh water for consumption. Studies by UNESCO showed that more than 28% of the world population didn’t have access to clean safe drinking water in 2020. This situation is expected to get more serious over the coming 30 years with the limited availability of natural fresh water sources. The need to find solutions from alternative non-freshwater resources for drinking or irrigation is becoming a necessity. Within the context of desalination technologies, thousands of investigations are conducted to find the cheapest most efficient way of water treatment aiming at expanding …

Fog Harvesting Using Chemically Functionalized Porous Membranes, Afra Saif Alhumaidi

Theses

This work explores the use of chemically functionalized porous membranes for fog harvesting. Fog water has emerged as a valuable alternative water source in regions where traditional freshwater resources are scarce. However, conventional fog harvesting techniques often suffer from low collection efficiency and limited scalability. To address these challenges, this research investigates the potential of chemically functionalized porous membranes for enhanced fog water collection. The study focuses on the development and characterization of specialized membranes with surface properties optimized for efficient fog droplet capture.
/="/">The current study proposes the use of aluminum mesh for fog collection, as it stands …

The Kappa Opioid Receptor Agonist 16-Bromo Salvinorin A Has Anti-Cocaine Effects Without Significant Effects On Locomotion, Food Reward, Learning And Memory, Or Anxiety And Depressive-Like Behaviors, Ross Van De Wetering, Amy Ewald, Susan Welsh, Lindsay Kornberger, Samuel E. Williamson, Bryan D. Mcelroy, Eduardo R. Butelman, Thomas E. Prisinzano, Bronwyn M. Kivell

Markey Cancer Center Faculty Publications

Kappa opioid receptor (KOR) agonists have preclinical antipsychostimulant effects; however, adverse side effects have limited their therapeutic development. In this preclinical study, conducted in Sprague Dawley rats, B6-SJL mice, and non-human primates (NHPs), we evaluated the G-protein-biased analogue of salvinorin A (SalA), 16-bromo salvinorin A (16-BrSalA), for its anticocaine effects, side effects, and activation of cellular signaling pathways. 16-BrSalA dose-dependently decreased the cocaine-primed reinstatement of drug-seeking behavior in a KOR-dependent manner. It also decreased cocaine-induced hyperactivity, but had no effect on responding for cocaine on a progressive ratio schedule. Compared to SalA, 16-BrSalA had an improved side effect profile, with …

Cpsrp43 Is Both Highly Flexible And Stable: Structural Insights Using A Combined Experimental And Computational Approach, Mitchell Benton, Mercede Furr, Vivek Govind Kumar, Adithya Polasa, Feng Gao, Colin David Heyes, Thallapuranam Krishnaswamy Suresh Kumar, Mahmoud Moradi

Chemistry & Biochemistry Faculty Publications and Presentations

The novel multidomain protein, cpSRP43, is a unique subunit of the post-translational chloroplast signal recognition particle (cpSRP) targeting pathway in higher plants. The cpSRP pathway is responsible for targeting and insertion of light-harvesting chlorophyll a/b binding proteins (LHCPs) to the thylakoid membrane. Upon emergence into the stroma, LHCPs form a soluble transit complex with the cpSRP heterodimer, which is composed of cpSRP43 and cpSRP54. cpSRP43 is irreplaceable as a chaperone to LHCPs in their translocation to the thylakoid membrane and remarkable in its ability to dissolve aggregates of LHCPs without the need for external energy input. In previous studies, cpSRP43 …

The Alternating Access Mechanism In Mammalian Multidrug Resistance Transporters And Their Bacterial Homologs, Shadi A. Badiee, Ugochi H. Isu, Ehsaneh Khodadadi, Mahmoud Moradi

Chemistry & Biochemistry Faculty Publications and Presentations

Multidrug resistance (MDR) proteins belonging to the ATP-Binding Cassette (ABC) transporter group play a crucial role in the export of cytotoxic drugs across cell membranes. These proteins are particularly fascinating due to their ability to confer drug resistance, which subsequently leads to the failure of therapeutic interventions and hinders successful treatments. One key mechanism by which multidrug resistance (MDR) proteins carry out their transport function is through alternating access. This mechanism involves intricate conformational changes that enable the binding and transport of substrates across cellular membranes. In this extensive review, we provide an overview of ABC transporters, including their classifications …

The Development Of Novel Radioimmunoconjugates For The Pet Imaging And Radioimmunotherapy Of Cancer, Samantha M. Sarrett

Dissertations, Theses, and Capstone Projects

Antibodies have long played a vital role in nuclear medicine for both the diagnosis and therapy of various malignancies. The role and development of antibodies in nuclear medicine can be broadly separated into three different categories: 1) bioconjugation strategies, 2) immunoPET imaging, and 3) radioimmunotherapy. This dissertation will attempt to comprehensively cover each of these categories through a series of studies, protocols, and reviews. For the bioconjugation strategies, we will describe the development of a novel site-selective bioconjugation strategy using an innovative lysine-targeting reagent, PFP-bisN₃, to prepare [⁸⁹Zr]Zr-^SSKDFO-pertuzumab for visualizing HER2+ breast cancer. Further, …

Design, Synthesis, And Kinetic Study Of The First Generation Phenyloxadiazole Compounds And The Second Generation Phenyloxadiazole Compounds And Highly Selective Hydroboration Of Alkenes, Ketones And Aldehydes Catalyzed By A Well-Defined Manganese Complex, Haisu Zeng

Dissertations, Theses, and Capstone Projects

This thesis focuses on two projects. In the first project, my goal was to discover a new variant of phenyloxadiazole compounds that could exhibit increased thiol-reactivity during bioconjugation processes. To achieve this, I synthesized several phenyloxadiazole derivatives and subjected them to NMR kinetic studies to assess their reactivity with a model thiol. Based on the results, I was able to identify a phenyloxadiazole analog that demonstrated enhanced reactivity, which included a chlorine atom located in the meta-position of the phenyl ring.

I provided a detailed description of the synthesis and characterization of the newly discovered phenyloxadiazole analog and demonstrate its …

Enhanced Methods In Forensic Mass Spectrometry For Targeted And Untargeted Drug Analysis, Dina M. Swanson

USF Tampa Graduate Theses and Dissertations

Forensic science has long used mass spectrometry for the analysis of drugsand metabolites. Traditionally, screening methods consisted of color tests or immunoassay and confirmation methods used gas chromatography with mass spectrometry, which was considered the gold standard for identification. In the last several decades, advances in liquid chromatography with mass spectrometry (LCMS) have brought this technology to the forefront of forensic drug identification. Drug identification in forensic drug chemistry and forensic toxicology has become increasingly challenging due to the rapid increase in illicit drug analogs including novel opioids such as fentanyl analogs. Traditional screening methodologies are often unable to identify …

Bismuth And Lanthanides In Mixed Metal Oxides To Metal– Organic Frameworks: Synthesis, Cherectarization, And Photocatalytic Performance, Reem H. Alzard

Dissertations

Known as rare–earth elements (REE), lanthanides (Ln) found in f–blocks of the periodic table, have gained much interest because of their unique characteristics including magnetism, photoluminescence and catalysis. Having a diverse range of coordination geometries, lanthanides can result in different complexes and materials. Herein, three classes of materials containing selected lanthanides such as lanthanide bismuth mixed metal oxides (Ln–Bi oxides), 1D lanthanide coordination polymers (Ln–CPs) and lanthanide metal–organic frameworks (Ln–MOFs) were investigated. Simple route sol– gel method was used to prepare Ln–Bi oxides while Ln–CPs and MOFs were prepared by solvothermal condition. The materials were characterized using multiple analytical, spectroscopic …

Fabrication, Characterization And Analytical Applications Of Planar Solid Metal And Planar Cavity Electrodes, Fatima Salmeen Alnuaimi

Theses

The present thesis describes the design, construction, and applications of a versatile flow cell (VFC) for used with different types of planar working electrodes. These included the commercially available planar 3-electrode screen-printed electrode chips (SPECs), custom planar metallic electrodes (PMEs), and cavity-type electrodes (CTEs). The PMEs are fabricated from platinum, titanium, stainless steel and copper rods inserted in a rectangular-PEEK housing, respectively. The dimensions of the PEEK blocks were 13.5 mm width x 39 mm length x 12.5 mm height. The VFC was constructed from a cell cover and base machined from acrylic sheets. The cover incorporated a built-in Ag/AgCl/Cl …

Preparation Of Copper Oxide Nano-Architectures For Fog Harvesting Applications, Ola M. Abu Draz

Theses

The issue of limited freshwater resources is a significant problem for humans, especially in desert areas where water scarcity poses a serious risk to human survival. In nature, there are several species that harvest fog based on their tuned surface structure, e.g.., Cactus, desert beetles, etc. In addition to surface hydrophilic/hydrophobic architecture, another key factor in effective water collection is the porosity of the surface, which helps droplets to form, grow, and be removed. To address the challenge of water scarcity, we inspired, from nature, to design surfaces that have features that favor water collection. In this aspect, we introduced …

Synthesis, Characterization, And Photocatalytic Activity Of Photoactive Mofs And M-Hof Under Simulated Visible Light Irradiation, Lamia Ali Siddig

Dissertations

The increasing global energy demand has resulted in environmental issues, leading to a shift in research towards sustainable and renewable energy sources. Among these, solar energy is the most abundant natural resource available. One of the most profitable ways to utilize sunlight is through chemical transformation using photocatalysts. In this regard, we reported the synthesis of different stable porous materials, such as metal-organic frameworks (MOFs) and metal hydrogen-bonded organic frameworks (M-HOFs). The MOF photocatalysts are bismuth-gallate (Bi-gallate), a mixed ligand manganese-based MOF (Mn^II₃(tp)_6/2(bpy)₂. (dmf)) and a new hexagonal layer manganese MOF compound named …

V-Shaped Temperature Dependences And Pressure Dependence Of Elementary Reactions Of Hydroxyl Radicals With Several Organophosphorus Compounds, Xiaokai Zhang

Dissertations

Organophosphorus compounds have brought increasing attention since they are widely used as flame-retardants, which can take effect in combustion via reactions with reactive radicals. These reactions are influenced by variables such as temperature and pressure, resulting in a temperature and pressure dependent rate constant. Studying this reaction kinetics has great importance in both combustion reaction and atmospheric environment.

This study is focused on kinetics of several elementary reactions of combustion importance. The kinetics of hydroxyl radicals were studied using pulsed laser photolysis coupled to transient UV-vis absorption spectroscopy over the 295 - 837 K temperature range and the 1 - …