Chemistry Commons^™

Design And Synthesis Of (-)- Englerin A Mimics, Kayleen Thompson, Dr. Merritt Andrus

Journal of Undergraduate Research

Englerin A, which comes from an East African plant, Phyllantus englari, has been found to be an impressive anti-renal cancer agent. It is even more promising than another leading natural anticancer agent, Taxol.1 Englerin A has a unique, complex structure, and its exact mode of action is currently unknown. The key features of englerin A are the cinnamate ester and glycolate ester with an intervening lipophilic cyclic hydrocarbon core. The englerin structure can be effectively mimicked with a more simplified core structure. For this project, I worked on synthesizing an analog of the anticancer agent (-)-englerin A that contains key …

Combination Of The Computational Methods: Molecular Dynamics, Homology Modeling And Docking To Design Novel Inhibitors And Study Structural Changes In Target Proteins For Current Diseases, Katherine Cristina Parra

USF Tampa Graduate Theses and Dissertations

In this thesis, molecular dynamics simulations, molecular docking, and homology modeling methods have been used in combination to design possible inhibitors as well as to study the structural changes and function of target proteins related to diseases that today are in the spotlight of drug discovery. The inwardly rectifying potassium (Kir) channels constitute the first target in this study; they are involved in cardiac problems. On the other hand, tensin, a promising target in cancer research, is the second target studied here.

The first chapter includes a brief update on computational methods and the current proposal of the combination of …

Modification Of A Gas Chromatograph For Use At An Undergraduate Laboratory, Ken Overway, Andrew Veenis

Chemistry Faculty Scholarship

Gas chromatography provides chemists with a powerful method of separating and quantitating chemicals in the gas phase. Our lab recently received two PerkinElmer Arnel AutoSystem XL Gas Chromatographs from MillerCoors Brewing Company, which were designed to sample gas directly from a pressurized source. One of the gas chromatographs (GC) uses a photoionization detector (PID), a flame ionization detector (FID) and an external sulfur chemiluminescence detector (SCD). This GC was modified so that samples could be introduced by means of a syringe and a split/split-less injector. The original gas lines were entirely reconfigured to enable dual detection using the PID and …

Reactivation Of Latent Hiv In Cd4+ T Cells Through Fdc Costimulation, Matthew Greer, Dr. Greg Burton

Journal of Undergraduate Research

I received an ORCA grant for a project entitled “Reactivation of latent HIV in CD4+ T cells through FDC costimulation.” The original hypothesis of this research was that the factor FDCs (follicular dendritic cells) produce to reactivate latent HIV in T cells is a protein signaling molecule that can be identified through analyzing the proteins FDCs produce. While this project is still proceeding, my resources during the last year since I received an ORCA grant have been dedicated to ironing out a few preliminary wrinkles to this project. Specifically, I have troubleshot and optimized the method our lab group uses …

Analysis Of The Kinetics Of Atmospherically Important Reactions, Marie Killian Chilton, Dr. Jaron Hansen

Journal of Undergraduate Research

Organic peroxy radicals react to form tropospheric ozone, which harms the health of humans and vegetation and is considered the most significant pollutant in rural areas.1 Many of the individual reactions in the overall mechanism for ozone formation involve radicals. Radicals are highly reactive and therefore it is challenging to measure their fundamental properties directly. Particularly, it is difficult to determine an accurate reaction rate constant for reactions involving radicals. This rate constant is largely dependent on the atmospheric conditions. Dr. Jaron Hansen is currently studying the effect of water vapor on the kinetic rate constant for the reaction of …

Genetic Rescue Of The Irk 2 Knockout Phenotype By Ectopic Expression Of Irk 2 Wt, Brandon Gassaway, Dr. Emily Bates

Journal of Undergraduate Research

Anderson-Tawil Syndrome (ATS) is characterized by morphological defects including clinodactyly (abnormal curvature of digits), syndactyly (fused digits), micrognathia (small jaw), cleft palate, and hypertelorism (wide-set eyes) as well as periodic paralysis and heart arrhythmia. Mutations in inwardly rectifying potassium (Irk) channels are found in patients with ATS. Expression of mutant Irk channels causes similar physiological and morphological defects in mice.1

Relativistic Wave Equations: Dirac, Ronald Lovett

Topics in Quantum Mechanics

No abstract provided.

The Total Synthesis Of S-Equol Using Phase Transfer Catalysis, Eric Bready, Dr. Merritt Andrus

Journal of Undergraduate Research

The purpose of this project was completion of the total organic synthesis of the anti-cancer compound (S)-equol. My goal was to carry out our planned synthesis of this molecule using Phase Transfer Catalysts, (PTCs), which promote the formation of the S enantiomer as opposed to the R enantiomer of equol (S and R enantiomers are like right and left hands, which are mirror images of each other—in organic synthesis usually only one form is desired) (1). In using PTCs it was our hope that we would be able to form (S)-equol with high yield and in a timely manner. Successful …

Synthesis Of S-Equol Using Heck Coupling Reaction And Phase-Transfer Catalysis, Chelsey Hancock

Journal of Undergraduate Research

Please list all accomplishments, achievements, publications, presentations, or other scholarly productivity that resulted from your ORCA project. This may include submissions to peer-reviewed journals, conference presentations or papers, performances, exhibitions, internships, scholarships, graduate school opportunities, local presentations, or awards that followed your mentoring experience.

The Art And Science Of Living In The Present (Text And Video), Rebecca Roesner

Honorees for Teaching Excellence

No abstract provided.

Dipole Bound Excited States Of Polycyclic Aromatic Hydrocarbons Containing Nitrogen And Their Relation To The Interstellar Medium, Mallory L. Theis

Honors College Theses

Polycyclic aromatic hydrocarbons (PAHs) are the most abundant type of molecule present in the interstellar medium (ISM). It has been hypothesized that nitrogen replacement within a ring is likely for PAHs present in the ISM. Additionally, electrons, protons, and hydrogen atoms are readily added to or removed from PAHs creating a truly diverse set of chemistries in various interstellar regions. The presence of a nitrogen within a PAH (called a PANH herein) that is additionally dehydrogenated leads to a neutral radical with a large dipole moment. It has recently been shown through the use of high-level quantum chemical computations for …

Detection Of Heavy Transition Metal Cations Using Novel Chemosensors, Shannon Rhodes

Honors College Theses

Transition metals (TM) are found in the environment and living systems. When present in excess, these metals can trigger health problems, which include memory loss and cognitive functions. In this project, commercially-available compounds were used to aid in the making of novel mono- and di-triazole molecular sensors with a well-known reaction called “click chemistry”. These sensors were used efficiently and selectively to attract a specific metal like iron III, copper, and zinc. Six sensors were tested via UV-spectroscopy, NMR, and fluorescence with the cations and selectivity increased as the sensors were altered.

Photodynamic Cancer Therapy A Study Of The Photolysis Reaction Between Porphyrin And 9,10-Diphenylanthracene, James Z. Akins

Honors College Theses

Photodynamic therapy (PDT) is a method of combating cancerous tumors. PDT works when certain molecules called photosensitizers absorb light and transfer that energy to dissolved oxygen in solution. Next, this singlet oxygen will interfere with nearby molecules that are necessary for cancer cells to function. This research focuses on the kinetics (rates) of the reaction with respect to the photosensitizer, light, and the target molecule. A laser set at 514nm was used in photolysis with the photosensitizer 5,10,15,20-Tetrakis(2,3,5,6-tetrafluorophenyl)porphyrin (TPP). To mimic cancer cells and monitor the effectiveness of the chosen photosensitizer, 9,10-Diphenylanthracene (DPA) was used as the target molecule. In …

Photocatalysis And Grazing-Ion Beam Surface Modifications Of Planar Tio2 Model Systems, Timothy Luttrell

USF Tampa Graduate Theses and Dissertations

This dissertation is related to the understanding of catalytic reactions of metal oxides. For several decades, the surfaces and bulk of materials have been probed to determine additional properties that relate to photocatalytic applications. This investigation furthers these efforts by the (a) modification of a metal oxide surface to isolate known influences of chemical properties and (b) proposing and utilizing a novel methodology for attribution of photocatalytic activity to a discernable influence. For the first effort, by effectively utilizing a known technique for a new application on a metal oxide, such isolations can be made despite unfavorable states. For the …

In Vitro Activation Of Human Follicular Dentritic Cells And Its Effects On Human Immunodeficiency Virus Infection, Sean Llewellyn, Dr. Gregory F. Burton

Journal of Undergraduate Research

HIV is known to survive on follicular dendritic cells (FDCs) for many months and is believed to contribute to persisting HIV infection. FDCs protect HIV from degradation, thereby prolonging the infectivity of the virus. Moreover, when virus is trapped on FDCs, it escapes the ability of neutralizing antibodies (NtAb) to block infection of CD4+ T cells and subsequent removal of virus from the body. We postulate that FDC CD32 and/or CD21 contribute to maintaining virus infectivity and permitting infection in the presence of NtAb. Furthermore, when HIV forms an immune complex with antibodies and binds to CD32 and/or CD21, the …

Design & Synthesis Of Peptidomimetics Adopting Secondary Structures For Inhibition Of P53/Mdm2 Protein-Protein Interaction And Multiple Myeloma Cell Adhesion, Hyun Joo Kil

USF Tampa Graduate Theses and Dissertations

The protein-protein interactions (PPIs) occur when two or more proteins are bound together. Also, this protein-protein interactions (PPIs) cause the various biological processes in the body. Due to this reason, abilities of controlling or inhibiting PPIs can give us promising advantages like (1) better understanding of biological systems, (2) development of new diagnostic approaches for health or disease, and (3) establishment of novel molecular therapeutics. Many proteins adopt the secondary structures, where most of protein-protein interactions take place. -Helices and -sheets are the prevalent secondary conformations, but there are extended secondary structures such as -hairpins, -turns, 310 helix, and so …

Effect Of Multivalent Ions On The Swelling And Mechanical Behavior Of Superabsorbent Polymers (Saps) For Mitigation Of Mortar Autogenous Shrinkage, Qian Zhu

Open Access Theses

The chemical and physical structure-property relationships of model superabsorbent polymer (SAP) hydrogels were characterized with respect to swelling behavior and mechanical properties in different ionic solutions (Na+ , Ca2+ , and Al3+ ). The model hydrogels were composed of poly(sodium acrylate-acrylamide) (PANa-PAM) copolymer with varying concentrations of PANa (0, 17, 33, 67, and 83 wt.%) and covalent crosslinking densities of 1, 1.5, and 2 wt.%. By synthesizing the hydrogels in-house, systems with independently tunable amounts of covalent crosslinking and anionic functional groups were created, allowing for the relative effects of covalent and ionic crosslinking on the properties of the hydrogels …

Nanoalloying And Phase Transformations During Thermal Treatment Of Physical Mixtures Of Pd And Cu Nanoparticles, Vineetha Mukundan, Jun Yin, Pharrah Joseph, Jin Luo, Shiyao Shan, Dmitri N. Zakharov, Chuan-Jian Zhong, Oana Malis

Chemistry Faculty Scholarship

Nanoscale alloying and phase transformations in physical mixtures of Pd and Cu ultrafine nanoparticles are investigated in real time with in situ synchrotron-based x-ray diffraction complemented by ex situ high-resolution transmission electron microscopy. The combination of metal-support interaction and reactive/non-reactive environment was found to determine the thermal evolution and ultimate structure of this binary system. At 300 degrees C, the nanoparticles supported on silica and carbon black intermix to form a chemically ordered CsCl-type (B2) alloy phase. The B2 phase transforms into a disordered fcc alloy at higher temperature (> 450 degrees C). The alloy nanoparticles supported on silica and …

Exploring Diphosphene Synthesis With Trimethylsilylated And Imidazolidine Reductants, Katherine Miller

Senior Honors Projects

Various reducing agents were tested to try and find a new way to synthesize the diphosphene DmpP=PDmp (Dmp = 2,6-dimesitylphenyl). The reducing agents tested were an organosilicon-based compound, 1-methyl-3,6-bis(trimethylsilyl)-1,4-cyclohexadiene (MBTCD), 3,6-bis(trimethylsilyl)1,4-cyclohexadiene (BTCD), and 1,3,1’,3’-tetraethyl-bis(2,2’-imidazolidine). Through the use of dimesitylphenyl phosphorous dichloride (DmpPCl₂), it is thought that the chemistry exhibited by these reducing agents on similar compounds could be applied to compounds with PCl₂ groups, such as DmpPCl₂, in the hopes of creating the diphosphene DmpP=PDmp.

Nanopowder Synthesis And Characterization Of The Natural Superlattice (Bi2)M(Bi2te3)N For Prospective Thermoelectric Materials, Brian Washburne

Senior Honors Projects

The goal of this study was to synthesize nanocrystals of bismuth telluride (Bi­₂Te₃) through scalable bottom-up, wet-chemical methods. Rapid nanocrystal growth is accomplished through microwave stimulation of organically dissolved bismuth and tellurium precursors within the time of one minute. Elemental analysis of our product using Inductively Coupled Plasma Spectroscopy indicated that our samples have excess Bi. Together with structure analysis using Powder X-ray Diffraction, these compounds were found to have Bi:Te ratios of 2:1.

Effects Of Oxidative Stress On J774 Macrophages, Katelyn Chessier

Senior Honors Projects

No abstract provided.

The Biochemical Mechanism Of Dimethyloxalylglycine In The Prevention Of Retinopathy Of Prematurity, Rebecca Brown

Senior Honors Projects

Retinopathy of prematurity (ROP), a retinal disease characterized by neovascularization and vasoobliteration, is becoming more prevalent in premature infants as technological advances succeed in better sustaining the life of infants that are the result of premature birth. Dimethyloxalylglycine (DMOG) has been proven to lessen the severity of the symptoms of ROP in mice through the inhibition of prolyl hydroxylase, an enzyme crucial to the degradation of hypoxia inducible growth factor (HIF). The identification of DMOG as a potential novel therapeutic treatment for ROP has brought the mechanism by which DMOG functions into question. To further define this mechanism, wild-type (WT) …

(Η5‐Cyclopentadienyl)Tricarbonylmanganese(I) Complexes, Patrick N. Kirk, Michael P. Castellani

Chemistry Faculty Research

Since the initial preparation of (η⁵‐C₅H₅)Mn(CO)₃ by Fischer and Jira in 1954, many methods have been developed for the synthesis of this compound (often referred to as “cymantrene”) and its C₅ substituted derivatives. Interestingly, each of these preparations has at least one significant drawback from a preparative perspective (thallium reagents, high pressures, poor yields, or reactants that require significant preparative investment). Surprisingly missing from this collection of preparative methods is the direct reaction between commercially available Mn(CO)₅Br and NaC₅H₅. In 1988, however, Smart and coworkers found …

Case Study Of A Successful Educational Partnership: University Of Illinois At Urbana-Champaign And The Illinois Mathematics And Science Academy, Dave Devol

Faculty Publications & Research

This article describes partnerships between an NCSSSMST member institution and a research university and the use of student-generated survey data as a means of both professional self-reflection and asking further questions. As a chemist, I have been trained to write in the style of scientists, and in fact I teach a course at the Illinois Mathematics and Science Academy on the methods of science and scientific writing. This article is intentionally not written in a scientific style; rather is written to convey a story of how a partnership between institutions naturally progressed into my current area of research into motivational …

Designing Conical Intersections For Light-Driven Single Molecule Rotary Motors: From Precessional To Axial Motion, Michael Filatov, Massimo Olivucci

Chemistry Faculty Publications

In the past, the design of light-driven single molecule rotary motors has been mainly guided by the modification of their ground-state conformational properties. Further progress in this field is thus likely to be achieved through a detailed understanding of light-induced dynamics of the system and the ways of modulating it by introducing chemical modifications. In the present theoretical work, the analysis of model organic chromophores and synthesized rotary motors is used for rationalizing the effect of electron-withdrawing heteroatoms (such as a cationic nitrogen) on the topography and branching plane of mechanistically relevant conical intersections. Such an analysis reveals how the …

N-Methylmesoporphyrin Ix Fluorescence As A Reporter Of Strand Orientation In Guanine Quadruplexes, Navin C. Sabharwal , '14, V. Savikhin, Joshua R. Turek-Herman , '16, John Michael Nicoludis , '12, V. A. Szalai, Liliya A. Yatsunyk

Chemistry & Biochemistry Faculty Works

Guanine quadruplexes (GQ) are four-stranded DNA structures formed by guanine-rich DNA sequences. The formation of GQs inhibits cancer cell growth, although the detection of GQs invivo has proven difficult, in part because of their structural diversity. The development of GQ-selective fluorescent reporters would enhance our ability to quantify the number and location of GQs, ultimately advancing biological studies of quadruplex relevance and function. N-methylmesoporphyrin IX (NMM) interacts selectively with parallel-stranded GQs; in addition, its fluorescence is sensitive to the presence of DNA, making this ligand a possible candidate for a quadruplex probe. In the present study, we investigated the effect …

Thioflavin T As A Fluorescence Light-Up Probe For G4 Formation, A. R. De La Faverie, A. Guédin, A. Bedrat, Liliya A. Yatsunyk, J.-L. Mergny

Chemistry & Biochemistry Faculty Works

Thioflavin T (ThT) becomes fluorescent in the presence of the G-quadruplex structure such as that formed by the human telomeric motif. In this report, we extend and generalize these observations and show that this dye may be used as a convenient and specific quadruplex probe. In the presence of most, but not all, G4-forming sequences, we observed a large increase in ThT fluorescence emission, whereas the presence of control duplexes and single strands had a more limited effect on emission. This differential behavior allowed us to design a high-throughput assay to detect G4 formation. Hundreds of different oligonucleotides may be …

The Determination Of Mercury Levels In Aquatic Avian Populations Using Atomic Spectroscopy Techniques, Peter M. Klaeser

All Capstone Projects

Mercury contamination has been shown to have a negative impact in fish-eating birds, including impacts on behavior, reproductive success, and their overall survival. Higher than normal mercury levels have been detected in birds who depend on fish for their food. High levels of mercury have been detected in the bird’s blood and feathers using analytical techniques. The present accepted method of determining levels of mercury in feathers and blood is the use of atomic spectroscopy. The amount of mercury in feathers appears to depend on the growth of the feathers with more growth associated with lower levels of mercury contamination. …

Method Development And Analysis For Pharmaceuticals And Personal Care Products In Surface Water, Victoria Ruelas

All Capstone Projects

Pharmaceuticals and Personal Care Products (PPCP) in surface waters is a worldwide concern. Effluent from waste water treatment plants have tested positive for PPCP. Method development for a liquid chromatographic method was derived using columns with fused core technology. Analysis of spiked samples as direct injection and after solid phase extraction indicated detection of acetaminophen, caffeine, bisphenol-A and triclosan. Confirmation of acetaminophen, caffeine, bisphenol-A and triclosan was achieved using Agilent 1100 HPLC with Agilent MST Trap XCT. Solid phase extraction using Oasis HLB indicated reproducibility at 0.05ppm.

The Roles Of Phosducin-Like Protein 1 And Programmed Cell Death Protein 5 As Molecular Co-Chaperones Of The Cytosolic Chaperonin Complex, Christopher M. Tracy

Theses and Dissertations

A fundamental question in biology is how proteins, which are synthesized by the ribosome as a linear sequence of amino acids, fold into their native functional state. Many proteins require the assistance of molecular chaperones to maneuver through the folding process to protect them from aggregation and to help them reach their native state in the very concentrated protein environment of the cell. This study focuses on the roles of Phosducin-like Protein 1 (PhLP1) and Programmed Cell Death Protein 5 (PDCD5) as molecular co-chaperones of the Cytosolic Chaperonin Complex (CCT).Signaling in retinal photoreceptors is mediated by canonical G protein pathways. …