Chemistry Commons^™

A Chemical Investigation Of Three Antarctic Tunicates Of The Genus Synoicum, Sofia Kokkaliari

USF Tampa Graduate Theses and Dissertations

Marine invertebrates, mainly sponges, tunicates and corals, have in the past few decades attracted the interest of the scientific community in regard to their secondary metabolites and their potential as leads in drug discovery. The genus Synoicum is comprised of multiple organisms found in both deep and shallow waters, tropical and cold environments around the world. The majority of the members of this genus that have been investigated can be found in shallow tropical waters due to the ease of accessing and collecting them. Of the cold environments, Antarctica is a representative of the environments where members of the Synoicum …

Chemical Investigation Of Floridian Mangrove Endophytes And Antarctic Marine Organisms, Bingjie Yang

USF Tampa Graduate Theses and Dissertations

Nature creates diseases and illnesses for mankind, however, nature also provides therapeutics by making biological systems produce secondary metabolites. Although the secondary metabolites originally play roles in chemical defense or evolution, researchers have been working on them for drug discovery. Plants, fungi and marine organisms have been mostly explored by natural products chemists over the century and contributed most drugs to the market. With the increasing need of new drugs resulting from drug resistance and pathogen evolution, the natural products area has been focused on developing innovative methodologies to achieve higher efficiency of isolating new bioactive compounds.

This dissertation herein …

Construction Of Giant 2d And 3d Metallo-Supramolecules Based On Pyrylium Salts Chemistry, Yiming Li

USF Tampa Graduate Theses and Dissertations

Pyrylium salts are a type of six-membered cationic heterocycles with one positively charged oxygen atom. Since the discovery of pyrylium salts in 1911, such salts have been underappreciated for a long time. Until 1960s, the importance of pyrylium salts has been realized as versatile precursors in a variety of organic syntheses. Due to their high reactivity towards various nucleophiles, pyrylium salts were widely used for the convenient synthesis of diverse heterocyclic compounds. Starting from 1980s, the high reactive feature of pyrylium salts were further utilized to synthesize viologen polymers with pyridinium salts in the backbones. During the past two decades, …

Breakthroughs In Obtaining Qm/Mm Free Energies, Phillip S. Hudson

USF Tampa Graduate Theses and Dissertations

The computation of free energy is pivotal to understanding the fundamental nature of chemical phenomena. That is, whether a specific molecular outcome occurs spontaneously or is inherently unfavorable. The need to do this with consistent accuracy begs for the use of quantum mechanical (QM) methods. However, techniques for directly computing free energy differences with QM or mixed QM/MM methods are untenable, as the computational expense is quite exorbitant. At present, the most feasible approach for obtaining QM/MM free energies is employing the so-called indirect cycle, which relies on accurately computing free energy differences between low (e.g., molecular mechanical, MM) and …

New Synthetic Methodology Using Base-Assisted Diazonium Salts Activation And Gold Redox Catalysis, Abiola Azeez Jimoh

USF Tampa Graduate Theses and Dissertations

Over the past two decades, homogeneous Au(I) catalysis has been a valuable synthetic tool for activating a series of unsaturated carbon-carbon bonds towards nucleophilic attack. Despite this progress, Au(I/III) redox chemistry has not been well explored. This is largely due to the challenges associated with the high oxidation potential of gold. Hence, the need for an efficient and safe method for Au oxidation.

Herein, a base-assisted diazonium salt activation has been used to facilitate Au redox reactions under mild reaction conditions. This oxidative coupling method afforded functional isoxazolines with good to excellent yields, while the alternative photoactivation method provided trace …

Laser-Induced Breakdown Spectroscopy For Elemental Analysis In Bioarchaeology And Forensic Anthropology, Kelsi N. Kuehn

USF Tampa Graduate Theses and Dissertations

Within bioarchaeology and forensic anthropology, the current processes of differentiating between individual human skeletal remains are imprecise, costly, and inefficient. A novel analytical technique within anthropology, laser-induced breakdown spectroscopy (LIBS) can aid in the identification of human remains using rapid laser ablation occurring at the micro-scale, making the technique virtually non-destructive to the sample. Considering this, LIBS could offer a superior method for materials discrimination and human identification. This research sought to examine whether LIBS can be used to obtain elemental signatures within bones to distinguish individuals from one another in a rapid, non-destructive manner. Seven human skeletal donors and …

Analyzing The Retention Of Knowledge Among General Chemistry Students, James T. Kingsepp

USF Tampa Graduate Theses and Dissertations

General chemistry is a survey course meant to form a foundation for students’ to build upon as they progress into chemistry sub-disciplines. The effectiveness of this foundation rests heavily on students’ abilities to retain or relearn concepts from the course. This study seeks to investigate the utility of a measure of general chemistry students’ knowledge retention across the time period of one semester. This approach was enacted in five different courses of either first or second semester general chemistry. The results showed that one-quarter to one-half of students exhibited a high rate of retention across the semester. A smaller group, …

Optimization Of A Digital Ion Trap To Perform Isotope Ratio Analysis Of Xenon For Planetary Studies, Timothy Vazquez

USF Tampa Graduate Theses and Dissertations

Ion trap mass spectrometers present a powerful analytical tool which not only enables mass spectrometric determination of analyte species but also has the added feature of being able to act as an ion storage device. As a mass spectrometer, ion traps can achieve a reasonable mass range with flexible mass resolution while boasting a considerably smaller footprint when compared to conventional time-of-flight or magnetic sector instruments. Due to their smaller geometries, high-pressure tolerance, and ability to perform tandem mass spectrometry, ion trap mass spectrometers are ideal candidates for portable applications such as deployment to another planetary body. While ideal candidates …

Asking Why: Analyzing Students' Explanations Of Organic Chemistry Reaction Mechanisms Using Lexical Analysis And Predictive Logistic Regression Models, Amber J. Dood

USF Tampa Graduate Theses and Dissertations

In order to evaluate student understanding of chemical reactions and reaction mechanisms, it is necessary to ask students to construct written or oral explanations of mechanistic representations. Studies have shown that students can reproduce pictorial representations of organic chemistry mechanisms without understanding the meaning of the representations. Grading written assessments is time-consuming, which limits their use in large-lecture courses. To address this limitation, lexical analysis and logistic regression techniques can be used to develop models that predict human scoring for constructed-response items. In this dissertation, students’ responses to constructed-response items about what is happening and why in organic chemistry reaction …

Advancing Equity Amongst General Chemistry Students With Variable Preparations In Mathematics, Vanessa R. Ralph

USF Tampa Graduate Theses and Dissertations

Reducing the inequities propagating the lack of representation in Science, Technology, Engineering, and Mathematics (STEM) careers has become a national imperative made increasingly complex given the inequitable preparations in science and mathematics students experience before college. A common institutional-level approach to promoting equity is the use of math and science prerequisites to prepare students who seek to enroll in lower-level STEM coursework. However, the literature does not support the efficacy of this approach, finding no substantive improvement to student performance despite considerable financial and time costs to students, instructors, and universities alike. Set in first-semester General Chemistry courses taken early …

Differential Mobility Spectrometry-Mass Spectrometry (Dms-Ms) For Forensic And Nuclear-Forensic Applications, Ifeoluwa Ayodeji

USF Tampa Graduate Theses and Dissertations

In forensics and nuclear-forensics, the current lab-based analytical technique employed can be laborious, time consuming, and less suitable for in-situ and real time screening. However, it is important to develop fast and fieldable instrumental technique, without a tradeoff for its high throughput, for drug screening and radionuclear analysis. The underlying factors to be considered in the instrument development ranges from: high potency of samples, even at very low concentration; complex nature of samples in the surrounding environment; real-time chemical composition variation; and instrument size, weight and power (SWAP) consideration. Differential mobility spectrometry (DMS), also known as field asymmetric waveform ion …

Chemical Tools And Treatments For Neurological Disorders And Infectious Diseases, Andrea Lemus

USF Tampa Graduate Theses and Dissertations

Neurological disorders have multiple etiologies such as genetics and age. Stress related disorders are becoming more common and diagnosed more often. Mental health disorders are no longer being treated as purely psychological. Mechanisms into the underlying factors of these disorders continue to bring this area to new frontiers. Chapter 2 of this dissertation focuses on the efforts made to prove the association of the protein FKBP51 to the stress response. We synthesized and used a molecular tool to discover and prove these interactions.

The study of neurodegenerative diseases is of continued importance as the world reaches record numbers of an …

Antarctic Deep Sea Coral And Tropical Fungal Endophyte: Novel Chemistry For Drug Discovery, Anne-Claire D. Limon

USF Tampa Graduate Theses and Dissertations

Considered the pulse controlling the biological interactions and contributing to the ecological survival of organisms, natural products have intrigued, challenged, and stimulated the scientific and non-scientific minds for millennia. Drug resistance and the lack of suitable potent drugs against neglected tropical diseases further motivate the biological activity assessment of these secondary metabolites, when possible.

This thesis describes the chemical investigation of two marine organisms and the elucidation of eight novel structures.

The study of a deep sea Antarctic coral unveils six novel terpenoid structures from three different molecular classes: sesquiterpenoid alcyopterosins, a triterpene steroid, and three prostaglandins. While mass availability …

Effect Of Atypical Protein Kinase C Inhibitor (Dnda) On Cell Proliferation And Migration Of Lung Cancer Cells, Raja Reddy Bommareddy

USF Tampa Graduate Theses and Dissertations

Lung cancer is the second most common cancer, and it is the leading cause of cancer death in both men and women. Elevated levels of PKC-ι and FAK are implicated in the progression of lung cancer and involved in cell proliferation, apoptosis, cell survival, and cell migration processes. Lung cancer diagnosis typically occurs in the late stages, which limits the treatment options. Hence, there is a dire need to develop drugs that are effective and safe to treat lung cancers. We used a novel aPKC inhibitor named DNDA (3,4-amino-2,7 napthalene disulfonic acid) to study the role of atypical PKCs (aPKCs) …

The Activity And Structure Of Cu2+-Biomolecules In Disease And Disease Treatment, Darrell Cole Cerrato

USF Tampa Graduate Theses and Dissertations

Despite its relatively low concentration in the human body, copper is an essential transition metal ion. Under normal circumstances, it is a well-regulated trace element that is introduced via diet or environment depending on the organism. Its strong reactivity and binding to some biologically essential chemicals can be detrimental to the host organism. Herein the oxidative chemistry of copper and its possible prevention in humans and agricultural organisms is discussed, as well as the potential avenues as metal-targeting disease treatment via novel-peptide and peptoid products.

In the first study, copper is implicated in the progression and onset of Alzheimer’s disease. …

Construction Of G-Quadruplexes Via Self-Assembly: Enhanced Stability And Unique Properties, Ying He

USF Tampa Graduate Theses and Dissertations

This dissertation mainly contains three parts: 1) The construction of well-defined G8-octamers through the monomer conformational design. 2) The construction of cross-layer interactions in the G8-octamer for enhanced stability in H-bond competitive solvents. 3) Design and synthesis of 8-triazole guanosine with photoluminescent properties.

Through the structural conformational design, we have developed a new class of guanosine derivatives with modification on guanine (8-aryl) and ribose (2’,3’-isopropylidene). This unique design has led to the formation of the first discrete G8-octamer with structure characterized by NMR, MS and single crystal X-ray diffraction. The selectivity between monovalent (K+) and divalent cat-ions (Ba2+ and Sr2+) …

Self-Assembly Of 2d And 3d Metallo-Supramolecules With Increasing Complexity, Bo Song

USF Tampa Graduate Theses and Dissertations

Synthetic organic chemistry played a crucial role in the construction of molecules through the formation and dissociation of covalent bonds. However, the laborious synthetic procedures as well as the low yield after multiple steps have restricted the pursuit of complicated giant molecules with high efficiency. Being complementary to organic synthesis, self-assembly provided an alternative route to achieving the giant architectures using weak non-covalent interactions in high efficiency, which is in analog to natural systems such as DNA, peptide, and protein. Among the various interactions, coordination has shown unique advantages in terms of directionality, reversibility and strength. Serving as a bottom-up …

Biomimetic Light Harvesting In Metalloporphyrins Encapsulated/Incorporated Within Metal Organic Frameworks (Mofs)., Abdulaziz A. Alanazi

USF Tampa Graduate Theses and Dissertations

The Global energy supply relies mostly on fossil fuels and only 10% comes from renewable energy. These places humankind in an unsafe situation as the fossil fuel resources won’t last forever. More efficient use of renewable energy is required sooner than later to meet the growing energy need. A promising approach is to utilize light harvesting chromophores (e.g., porphyrin derivatives) to advance organic photovoltaics and increase its efficiency or to improve photocatalysts. Metal-organic frameworks (MOFs) can be employed to aid the self-assembly of the porphyrin chromophores in a large light-harvesting system comparable to the natural photosystem. The advantage of using …

Development Of Α-Aa Peptides As Peptidomimetics For Antimicrobial Therapeutics And The Discovery Of Nanostructures, Sylvia E. Singh

USF Tampa Graduate Theses and Dissertations

For decades it has been convention to use antibiotics for the treatment of bacterial infections. Due to the overuse and misuse of these drugs, bacteria are becoming resistant to these treatments. This phenomenon has led to the search for alternative antibiotics, and in the study of Host Defense Peptides (HDPs). HDPs are the body’s innate immune response to infection. They are known to modulate immune system response and kills bacterial using various methods causing them to be less susceptible to bacterial resistance. The method by which we can mimic these biological peptides is called peptidomimetics. Various research shows the use …

The Chemical Ecology And Drug Discovery Potential Of The Antarctic Red Alga Plocamium Cartilagineum And The Antarctic Sponge Dendrilla Membranosa, Andrew Jason Shilling

USF Tampa Graduate Theses and Dissertations

Chemical ecology is the study of chemical interactions between organisms and their environment mediated by small molecules involved in nonessential physiological functions, known as secondary metabolites. These compounds can be crucial to survival of the organism, and have also provided the field of medicine with some of history’s most influential drugs, referred to in that context as natural products. Antarctica is a dynamic and understudied environment, which affords the opportunity to examine the chemical ecology of unique organisms while simultaneously evaluating their novel chemistry for potential therapeutic properties as natural products.

Plocamium cartilagineum is a red macroalgal species found in …

Design, Synthesis, And Self-Assembly Of Supramolecular Fractals Based On Terpyridine With Different Transition Metal Ions, Lei Wang

USF Tampa Graduate Theses and Dissertations

Fractals have existed in a variety of natural forms, and the concept of "fractal geometry" has been developed in many areas by humankind, including art, economics, mathematics, physics, chemistry, material science, and etc. In the field of chemistry, researchers have endeavored great efforts to express the concept using molecules either by theoretical prediction or using synthetic methods in the past few decades, and one successful example is the “Sierpiński triangle”. Challenge still remains to achieve other fractal geometries as well as high generation of fractals with precisely controlled shape and size. Coordination-driven self-assembly has witnessed a wide array of well-defined …

Formulation To Application: Thermomechanical Characterization Of Flexible Polyimides And The Improvement Of Their Properties Via Chain Interaction, Alejandro Rivera Nicholls

USF Tampa Graduate Theses and Dissertations

In this work, Polyimides were synthesized by incorporating an aromatic diamine monomer with a methylene linker, 4,4'-methylenebis(2,6-dimethylaniline) (MBDMA), to make a robust main chain along with aliphatic polyetherdiamine backbone linkers to reduce rigidity. The polymers were designed to exhibit thermal properties in between those of conventional aromatic polyimides and polymers with wholly aliphatic ether diamine links. Through dynamic mechanical analysis and differential scanning calorimetry, it is shown that control of the molar ratios of the aromatic MBDMA and the composition and size of the aliphatic polyetherdiamine can be used to tune the glass transition temperature. The materials were characterized and …

Thermo-Oxidative Degradation Of Hdpe Geomembranes: Effect Of Phenolic Antioxidant And Hindered Amine Light Stabilizer Concentrations, Yasin Kocak

USF Tampa Graduate Theses and Dissertations

High density polyethylene (HDPE) geomembrane is most common geomembrane which is mainly used for civil engineering applications. However, HDPE geomembrane loses its properties under oxidative degradation progress. This study aims to assess geomembranes which have different percentage of phenolic antioxidant and hindered amine light stabilizer (HALS) with under the six months of the thermal-oxidative degradation. The interactions between phenolic antioxidant, HALS and carbon black can affect the mechanical, physical and chemical properties. To monitor these properties, Differential Scanning Calorimetry (DSC), Fourier-transform Infrared Spectroscopy (FTIR), Thermogravimetric Analysis (TGA), Scanning Electron Microscopy coupled with Energy Dispersive X-ray spectroscopy (SEM/EDX), Melt Index tests, …

Evaluating The Evidence Base For Evidence-Based Instructional Practices In Chemistry Through Meta-Analysis, Md Tawabur Rahman

USF Tampa Graduate Theses and Dissertations

Investigating the effectiveness of instructional practices provides an evidence base to inform instructional decisions. Synthesizing research studies on instructional effectiveness provides an estimate of the generalizability of effectiveness across settings, along with an exploration of factors that may moderate the impact, which cannot be achieved within individual studies. This study sought to provide a synthesis of evidence- based instructional practices (EBIPs) particular to chemistry through meta-analysis. 99 studies were analyzed comprising a broader view of chemistry specific studies than past meta-analyses. The results showed that EBIPs feature a demonstrably positive impact on students’ academic performance in chemistry, although assessment topic …

An Insight Into The Biological Functions, The Molecular Mechanism And The Nature Of Interactions Of A Set Of Biologically Important Proteins., Adam A. Aboalroub

USF Tampa Graduate Theses and Dissertations

Characterization of protein structural properties is crucial to determine its role in normal and pathological conditions. In this dissertation, we have employed NMR spectroscopy in a combination of other biochemical and biophysical techniques to investigate the catalytic function, the molecular mechanism, and nature of the interactions of bmAANAT3, Cdc37, and TIMP2, respectively.

In the first project, we have employed an arylalkylamine N-acetyltransferases (AANATs) from Bombyx mori (bmAANAT3) to determine the role of the acetyl-group in coordinating the catalytic cycle in this family of enzymes. We have found that the occupancy of the acetyl-moiety in the catalytic funnel of these enzymes …

Design And Synthesis Of Novel Agents For The Treatment Of Tropical Diseases, Linda Corrinne Barbeto

USF Tampa Graduate Theses and Dissertations

Infectious diseases have had an impact on populations since the beginning of humanity. Despite huge advances in the fight against these conditions, they continue to be the leading cause of death and disability for a large portion of the world’s populace. Those most adversely affected predominately live in the more improvised areas of the developing world. Often treatments are made inaccessible to these areas due to cost, complicated administration requirements, severe side effects, and / or compound instability. Even when treatments are available the accelerated development of resistance has created an urgent need for the creation of new molecules with …

Simulation And Software Development To Understand Interactions Of Guest Molecules Inporous Materials, Douglas M. Franz

USF Tampa Graduate Theses and Dissertations

The effect of inclusion of explicit polarization is investigated through several theoret- ical studies of crystalline porous materials herein. In addition to the use of Monte Carlo simulation for such studies, a robust molecular dynamics software is presented which is suitable for analyzing time dependent properties of gases or other molecules in porous materials and other condensed phase systems. Metal-organic frameworks (MOFs) are the main focus of the work included here, a relatively young class of materials originally in- troduced in the early 1990s. These are usually three dimensional crystalline nanoporous materials that exhibit unique properties such as gas separation, …

Synthesis, Discovery And Delivery Of Therapeutic Natural Products And Analogs, Zachary P. Shultz

USF Tampa Graduate Theses and Dissertations

Small molecule drug discovery relies heavily on synthetic organic chemistry to develop novel chemical entities that elicit desirable therapeutic effects. The development of targeted chemical syntheses is of paramount importance to access molecules for biological evaluation and is usually considered the bottleneck in most drug discovery campaigns. Targets for chemical syntheses commonly draw inspiration from molecules of natural origin. Nature harbors a wealth of chemical diversity that has established itself over millions of years through chemical and biological evolution. Organisms have an inherent ability to protect themselves from predators and harmful environments. In doing so, many of them evolve to …

Functional Porous Materials: Applications For Environmental Sustainability, Briana Amaris Aguila

USF Tampa Graduate Theses and Dissertations

Resource depletion, clean water shortages, and global climate change have led to environmental sustainability being of primary concern for both governmental and industrial practices. Current methods to address these challenges typically come as a double-edged sword, fixing one problem while contributing to another. As introduced in chapter one of this dissertation, adsorbent materials are seen as a promising alternative remediation system due to their low energy consumption and minimal chemical waste production. However, many traditional adsorbents, such as activated carbon, metal oxides, and resins, are hindered in practice. This is because they lack the structural tunability to have long-term effectiveness …

The Potential Of Marine Microbes, Flora And Fauna In Drug Discovery, Santana Alexa Lavonia Thomas

USF Tampa Graduate Theses and Dissertations

Natural products are chemical compounds synthesized by a living organism. These compounds have been utilized by humans from ancient times to the present for their pharmacological and biological activities. Terrestrial organisms are considered a lucrative source of bioactive compounds and chemical diversity. Within the past 60 years, the marine environment has presented its potential as a validated source for structural diversity and biologically active compounds. Technology has given access from shallow waters down to the abyssal plane for exploration and investigation of the inhabitants. Marine organisms have displayed their benefits in the pharmaceutical industry with the approval of several marine-derived …