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Quantum Mechanical Studies Of Charge Assisted Hydrogen And Halogen Bonds, Binod Nepal

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Like cement bridges one brick to another, noncovalent forces also bridge two or more molecules together to form a molecular crystal or molecular cluster. Although weaker than the covalent bond, the existence of noncovalent forces can be seen everywhere from liquid water to construction of complex biomolecules like DNA, RNA, proteins etc. An introduction of suitable charge; positive or negative, on the binding units can increase the strength of noncovalent interaction by several orders of magnitude. The primary aim of this dissertation is to explore some fundamental properties of such charge assisted noncovalent interactions which will be helpful for the …

Computational Chemistry Of Non-Covalent Interaction And Its Application In Chemical Catalysis, Vincent De Paul Nzuwah Nziko

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Known to be weaker than conventional covalent bonds, non-covalent bonds, especially hydrogen bond, has shown to be of great importance in molecular structures such as DNA, RNA, proteins and other organic frameworks. In this dissertation, we looked at non-covalent interactions other than the hydrogen bond. Replacement of the bridging hydrogen atom in a typical hydrogen bond by other atoms such a halogen, chalcogen and tetrel lead to the formation of interactions which are comparable in strength to the hydrogen bond. Unlike the hydrogen bond which arises mainly from electrostatics, these unconventional interactions mostly result from induction. Besides studying the fundamentals …

Atp Usage In The Dark-Operative Protochlorophyllide Oxidoreductase, Mark S. Soffe

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Chlorophylls are essential pigment molecules that function in photosynthesis, and serve to aid in utilizing energy from sunlight to power cellular processes in plants, and other organisms. To make chlorophyll, photosynthetic organisms devote an abundance of resources and energy to ensure their appropriate construction. This process of making chlorophylls is highlighted by the penultimate step in the pathway—the conversion of protochlorophyllide (Pchlide) to chlorophyllide a (Chlide).

This conversion can be mediated in two different ways, depending on the type of organism. The first method incorporates the use of a light-activated system called the light-dependent protochlorophyllide oxidoreductase (LPOR). This system, as …

Structural Insights Into The Regulation Of Electron Transfer In Nitrogenase, And Modulating The Reactivity Of The Isolated Iron Molybdenum Cofactor, Andrew J. Rasmussen

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

One of the most important scientific advances in the last century was the Haber-Bosch process, the industrial process of fixing nitrogen from the atmosphere to ammonia. This allowed for the commercial production and sale of nitrogen for important uses such as fertilizer for farming. The Haber-Bosch process is partially credited with the population boom that has been seen in the last century and has greatly increased the standard of living in the developed world today. While this was a great scientific breakthrough, the cost of producing the required ammonia is high, and roughly 2% of worldwide energy is used annually …

Synthesis, Structure-Activity Relationship Study, And Mode Of Action Study Of 1,4-Naphthoquinone Based Anticancer And Antimicrobial Agents, Jaya P. Shrestha

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The first three projects involve the synthesis and the mode of action study of 1,4-naphthoquinone based anticancer agents. These anticancer agents are highly potent against a wide range of cancer cell lines. These compounds showed ~8-fold selectivity towards the lung cancer cell line than the normal cell line. We also studied the mode of action and observed that generation of reactive oxygen species is the primary mode of action.

The final project involves the synthesis of multi-cationic antimicrobial agents. These compounds are active against both bacteria and fungi. These compounds are very easy to synthesize and can be scaled up …

Computational Studies Of Microscopic Superfluidity In 4he Clusters, Angeline R. Wairegi

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The onset of microscopic superfluidity has been reported in ultracold droplets of bosons (⁴He atoms or para-H₂ molecules) containing a variety of molecular dopants. The physics of these droplets involve both Bose-Einstein condensation (BEC) and superfluidity. The two phenomena, while closely related, are not exactly the same. Superfluidity is fundamentally a microscopic effect and thermodynamic limit is necessary; it is still remarkable, though, that the signature of superfluidity has been reported in doped droplets consisting of as few as 4 ⁴He atoms. The studies presented here adopt a molecular vantage point to investigate the quantum mechanics …

Lipid Content And Biomass Analysis In Autotrophic And Heterotrophic Algal Species, Addie M. Lauder, Daniel P. Jones, Thomas E. Walker, Todd Allen

Montview Journal of Research & Scholarship

Biofuels are a form of renewable energy derived from living matter, typically plants. The push for biofuels began in order to decrease the amount of carbon dioxide (CO2) released into the atmosphere, as biofuels are essentially carbon neutral. The idea is the same amount of CO2 the plants took in to perform photosynthesis will then be released in the burning of the biofuels. Algae is an excellent source of biofuels because it grows quickly and is versatile in terms of the type of fuel it can produce. The two most common mechanisms for algae growth are heterotrophic or photoautotrophic. Heterotrophically …

H-Bonding And Stacking Interactions Between Chloroquine And Temozolomide, Okuma Emile Kasende, Vincent De Paul Nzuwah-Nziko, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The interactions between temozolomide and chloroquine were examined via Dispersion-Corrected Density Functional Theory and MP2 methods. Chloroquine was considered in both its lowest energy structure and in a local minimum where its aromatic system and secondary amine group are free to interact directly with temozolomide. The accessibility of these two components to intermolecular interaction makes the lowest energy dimer of this local monomer minimum competitive in total energy with that involving chloroquine’s most stable monomer geometry. In either case, the most stable heterodimer places the aromatic ring systems of the two molecules parallel and directly above one another in a …

Ph Dependence Of The Spectral Distribution Of Hydrogen Peroxide Quantum Yields, Juliana R. Laszakovits

Departmental Honors & Graduate Capstone Projects

Dissolved natural organic matter (DOM) is an important natural photosensitizer, which produces a variety of reactive oxygen species including singlet oxygen, hydroxyl radical, superoxide (O2-) and hydrogen peroxide (H2O2). H2O2 is formed primarily through the dismutation of O2-. Previous work has suggested that neither singlet oxygen nor excited triplet states of DOM are responsible for H2O2 production. Rather, reducing DOM intermediates likely form O2-, which in turn produce H2O2. One such intermediate may be a charge-separated DOM species (DOM+/-) formed by charge transfer (CT) relaxation of excited singlet states. In the CT model, the electron transfer is believed to occur …

Synthesis Of The Stereoismomers Of Dehp And Mehp From Kinetically Resolved 2-Ethyl-1-Hexanol, Lonnie Alexander Harris

Departmental Honors & Graduate Capstone Projects

Di(2-ethylhexyl) phthalate (DEHP) is a known chiral persistent organic pollutant found in many different consumer products, and the toxicities of its stereoisomers and their metabolites are not well known. To determine their adverse health effects, each enantiomer has to be synthesized. Using lipase PS from Burkholderia cepacia in dichloromethane at 0˚C for 48 hours, 2-ethyl-1-hexyl acetate was obtained in 55% yield (75:25 e.r.), while (R)-2-ethyl-1-hexanol (1) was obtained in 29% yield (96:4 e.r.). The acetate was then hydrolyzed to recover the (S) enriched alcohol (82% yield). The enriched alcohol was acylated a second time to yield (S)-(1) in 39% yield …

Synthetic Methods For The Preparation Of 1,3-S,O-Esters, Α-Phosphonovinyl Triflates, And Α-Alkynylphosphonates, David P. Kercher

Master of Science in Chemical Sciences Theses

A broad and systematic study was conducted on synthetic methods to efficiently synthesize 1,3-S,O-esters, α-phosphonovinyl triflates, and α-alkynylphosphonates under mild reaction conditions. The master’s thesis is composed of two projects; the first project is titled “Synthesis of 1,3-S,O-Esters” and the second project is titled “Synthesis of α-Phosphonovinyl Triflates and α-Alkynylphosphonates.” The first project outlines a synthetic route to conveniently prepare novel α-functionalized 1,3-S,O-esters via an acid-promoted hydrolysis of α-functionalized α-oxoketene dimethylthioacetals. The second project, unrelated to the first project, primarily focuses on extensive synthetic methodology developed to prepare …

Syntheses Of Carbon Paper Supported High-Index Faceted Pt Nanoparticles And Their Performance In Direct Formic Acid Fuel Cells, Long Huang, Mei Zhan, Yu-Cheng Wang, Yan-Fen Lin, Shuo Liu, Ting Yuan, Hui Yang, Shi-Gang Sun

Journal of Electrochemistry

Direct formic acid fuel fuels (DFAFCs) are promising energy source for portable electronic devices. Palladium (Pd) is more active than platinum (Pt) for the formic acid electrooxidation. However, the stability of Pd is much poorer than that of Pt. Unfortunately, the ultra-low natural abundance of the Pt makes it extremely expensive and limits its application as a fuel cell catalyst. Boosting both the activity and stability of Pt nanoparticles to enhance their efficiency is urgent. As previous works illustrated, nanoparticles enclosed with high-index facets usually bare a higher activity toward fuel cell related reactions than those nanoparticles with low-index facet. …

The Influence Of Dissolved Organic Matter (Dom) On Sodium Regulation And Nitrogenous Waste Excretion In The Zebrafish (Danio Rerio), Hassan A. Al-Reasi, Scott D. Smith, Chris M. Wood

Chemistry Faculty Publications

Dissolved organic matter (DOM) is both ubiquitous and diverse in composition in natural waters, but its effects on the branchial physiology of aquatic organisms have received little attention relative to other variables (e.g. pH, hardness, salinity, alkalinity). Here, we investigated the effects of four chemically distinct DOM isolates (three natural, one commercial, ranging from autochthonous to highly allochthonous, all at ∼6 mg C l⁻¹) on the physiology of gill ionoregulation and nitrogenous waste excretion in zebrafish acclimated to either circumneutral (7.0–8.0) or acidic pH (5.0). Overall, lower pH tended to increase net branchial ammonia excretion, net K^{+ …}

Binding Of Oxygen To Human Hemoglobin Within The Erythrocyte Using Icam Spectrophotometry, Kyle K. Hill

Department of Chemistry: Dissertations, Theses, and Student Research

Many of the spectrophotometric techniques used to determine the properties of intracellular human hemoglobin cannot be utilized due to the turbidity of erythrocyte suspensions. An Integrating Cavity Absorption Meter, or ICAM, allows for absorption measurements of strongly scattering samples in the visible-light region of the spectrum. The spectrum of oxygenated hemoglobin within erythrocytes is significantly different from the absorption spectrum of oxygenated hemoglobin in solution. Studies of the oxygen binding to hemoglobin in erythrocytes allowed the four sequential binding constants (Adair constants) to be determined and compared with those of hemoglobin in solution. The Adair constants for hemoglobin in solution …

Catalytic Transfer Hydrogenation Of Nitroalkenes To Primary Amines, Brendan Phillips

Chemistry Honors Papers

This work describes synthetic methodology development in organic chemistry. The goal of this work is to demonstrate new ways of making biologically-relevant molecules that are in line with the principles of green chemistry (chemical practices which seek to be, regarding human and environmental health, benign by design). To this end, a new method has been developed toward the introduction of primary amine functionalities into organic molecules from readily-available aldehydes, via reduction of nitroalkene intermediates. Traditional methods of reducing nitroalkenes to primary amines require harsh conditions, often produce stoichiometric amounts of metal salt waste, and present significant safety challenges to the …

Effects Of Creatine, Leucine, And Ethanol On Glial Cell Line-Derived Neurotrophic Factor In C2c12 Skeletal Muscle Cells, Daniel Waters

Honors Theses

Glial Cell Line-Derived Neurotrophic Factor (GDNF) is a protein expressed throughout the mammalian nervous system that serves several protective functions. Originally discovered in the brain, where it supports the survival of dopaminergic neurons, GDNF has since been shown to be expressed in skeletal muscle and is vital for the maintenance of motor neurons. The relationship between muscle hypertrophy, and GDNF is not well understood. The purpose of this study was to examine the relationship between hypertrophy and GDNF by inducing hypertrophy in C2C12 skeletal muscle cells using leucine and creatine, inhibiting hypertrophy using ethanol and measuring GDNF content. As measured …

Molecular Mechanism Of Protein Kinase Recognition And Sorting By The Hsp90 Kinome-Specific Cochaperone Cdc37, Dimitra Keramisanou, Adam Aboalroub, Ziming Zhang, Wenjun Liu, Devon Marshall, Andrea Diviney, Randy W. Larsen, Ralf Landgraf, Ioannis Gelis

Chemistry Faculty Publications

Despite the essential functions of Hsp90, little is known about the mechanism that controls substrate entry into its chaperone cycle. We show that the role of Cdc37 cochaperone reaches beyond that of an adaptor protein and find that it participates in the selective recruitment of only client kinases. Cdc37 recognizes kinase specificity determinants in both clients and nonclients and acts as a general kinase scanning factor. Kinase sorting within the client-to-nonclient continuum relies on the ability of Cdc37 to challenge the conformational stability of clients by locally unfolding them. This metastable conformational state has high affinity for Cdc37 and forms …

From Mollusks To Medicine: A Venomics Approach For The Discovery And Characterization Of Therapeutics From Terebridae Peptide Toxins, Aida Verdes, Prachi Anand, Juliette Gorson, Stephen Jannetti, Patrick Kelly, Abba Leffler, Danny Simpson, Girish Ramrattan, Mandë Holford

Publications and Research

Animal venoms comprise a diversity of peptide toxins that manipulate molecular targets such as ion channels and receptors, making venom peptides attractive candidates for the development of therapeutics to benefit human health. However, identifying bioactive venom peptides remains a significant challenge. In this review we describe our particular venomics strategy for the discovery, characterization, and optimization of Terebridae venom peptides, teretoxins. Our strategy reflects the scientific path from mollusks to medicine in an integrative sequential approach with the following steps: (1) delimitation of venomous Terebridae lineages through taxonomic and phylogenetic analyses; (2) identification and classification of putative teretoxins through omics …

Microwave Assisted Synthesis Of Tri-Substituted Pyridazine Exploration, Austin Wright

GS4 Student Scholars Symposium

Pyridazines are nitrogen-containing compounds that have been found to show a number of pharmaceutical applications. They exhibit antimicrobial, antifungal, and antibacterial properties to name a few. In particular: 3,4,6-triphenylpyridazine derivatives are known to possess anticancer properties. The purpose of this project is to synthesize tri-substituted pyridazine derivatives using microwave-assisted reactions, and to check its biological applications. Microwave synthesis will help shorten reaction times and produce high, efficient yields. Various catalysts, bases, reaction times, and temperatures will be explored to study the scope of the reactions.

Titanocene−Gold Complexes Containing N‑Heterocyclic Carbene Ligands Inhibit Growth Of Prostate, Renal, And Colon Cancers In Vitro, Yiu Fung Mui, Jacob FernáNdez-Gallardo, Benelita T. Elie, Ahmed Gubran, Irene Maluenda, Mercedes Sanau, Marıá Contel

Publications and Research

We report on the synthesis, characterization, and stability studies of new titanocene complexes containing a methyl group and a carboxylate ligand (mba = −OC(O)-p-C6H4-S−) bound to gold(I)−N-heterocyclic carbene fragments through the thiolate group: [(η5-C5H5)2TiMe(μ-mba)Au(NHC)]. The cytotoxicities of the heterometallic compounds along with those of novel monometallic gold−N-heterocyclic carbene precursors [(NHC)Au(mbaH)] have been evaluated against renal, prostate, colon, and breast cancer cell lines. The highest activity and selectivity and a synergistic effect of the resulting heterometallic species was found for the prostate and colon cancer cell lines. The colocalization of both titanium and gold metals (1:1 ratio) in PC3 prostate cancer …

Agonist-Mediated Activation Of Sting Induces Apoptosis In Malignant B Cells, Chih-Hang Anthony Tang, Joseph A. Zundell, Sujeewa Ranatunga, Cindy Lin, Yulia Nefedova, Juan R. Del Valle, Chih-Chi Andrew Hu

Chemistry Faculty Publications

Endoplasmic reticulum (ER) stress responses through the IRE-1/XBP-1 pathway are required for the function of STING (TMEM173), an ER-resident transmembrane protein critical for cytoplasmic DNA sensing, IFN production, and cancer control. Here we show that the IRE-1/XBP-1 pathway functions downstream of STING and that STING agonists selectively trigger mitochondria-mediated apoptosis in normal and malignant B cells. Upon stimulation, STING was degraded less efficiently in B cells, implying that prolonged activation of STING can lead to apoptosis. Transient activation of the IRE-1/XBP-1 pathway partially protected agonist-stimulated malignant B cells from undergoing apoptosis. In Eμ-TCL1 mice with chronic lymphocytic leukemia, injection of …

Selective Incarceration And Extraction Of Oxoanion Contaminants From Aqueous Media By Self-Assembled Nanojars, Basil Ahmed

Research and Creative Activities Poster Day

Selective binding and extraction of anions by artificial receptors is one of the most far‐reaching areas of supramolecular chemistry, with implications in chemical, biological and environmental sciences. The extraction of kosmotropic anions from aqueous media is challenging, due to their large hydration energies (affinity for water). We have recently shown that a class of toroidal copper(II)‐hydroxide/pyrazolate complexes (nanojars), with the formula [Cu(OH)(pz)]_n (n = 27−36), totally incarcerate kosmotropic anions with an unprecedented strength. Lined by H‐bond donors on the inside and hydrophobic on the outside, these ~2 nm sized assemblies selectively extract kosmotropic anions from mixtures with chaotropic anions …

Ion Transfer Stripping Voltammetry Method Using Conductive Polymer To Low Concentration Detection Of Environmental Contaminants, Dinusha Udari Ranawaka Arachchige

Student Theses and Dissertations

Detecting environmental contaminants such as Selective serotonin reuptake inhibitors (SSRIs) and Cr (VI) compounds is essential since they are highly toxic contaminants of many drinking water supplies leading to adverse health effects. Selective serotonin reuptake inhibitors are common antidepressants therapeutics and fluoxetine; Prozac®, citalopram; Celexa® and sertraline; Zoloft® were successfully detected in this study. Ion transfer stripping voltammetry (ITSV) was applied to detect those as cations at nanomolar concentrations using an inexpensive and disposable pencil lead electrode, with a lower detection limit of 30 nM. The pencil lead electrode was modified using the conducting polymer Poly (3, 4-ethylenedioxythiophene) (PEDOT-C14) and …

Big Changes For Small Noncovalent Dimers: Revisiting The Potential Energy Surfaces Of (P2)2 And (Pccp)2 With Ccsd(T) Optimizations And Vibrational Frequencies, Eric Van Dornshuld, Gregory S. Tschumper

Chemistry Faculty Research & Creative Works

This article details the re-examination of low-lying stationary points on the potential energy surfaces (PESs) of two challenging noncovalent homogeneous dimers, (P₂)₂ and (PCCP)₂. The work was motivated by the rather large differences between MP2 and CCSD(T) energetics that were recently reported for these systems (J. Comput. Chem. 2014, 35, 479-487). The current investigation reveals significant qualitative and quantitative changes when the CCSD(T) method is used to characterize the stationary points instead of MP2. For example, CCSD(T) optimizations and harmonic vibrational frequency computations with the aug-cc-pVTZ basis set indicate that the parallel-slipped (PS) structure is …

Chiral Boro-Phosphates In Asymmetric Catalysis: 1,4-Reduction Of Enones And Reductive Aldol, Susana Sorina Lopez

USF Tampa Graduate Theses and Dissertations

The biological activity of the pharmaceutical drugs often depends on how it fits with a receptor making stereochemistry a key component. Selective reactions can limit or avoid the mixture of enantiomers obtained. One such reaction is the selective reduction of a carbon-carbon double bond in the presence of a carbonyl. Although efficient, current asymmetric synthesis methods have limitations such as harsh reaction conditions, the high costs of chiral catalysts and the toxicity of the metal-based catalysts. Catalysts derived from small organic molecules have become an attractive alternative which have been explored more rigorously in recent years. Using a BINOL-derived boro-phosphate …

Photocatalytic Reduction Of Fumarate To Succinate On Zns Mineral Surfaces, Ruixin Zhou, Marcelo I. Guzman

Chemistry Faculty Publications

The reductive tricarboxylic acid (rTCA) cycle is an important central biosynthetic pathway that fixes CO₂ into carboxylic acids. Among the five reductive steps in the rTCA cycle, the two-electron reduction of fumarate to succinate proceeds nonenzymatically on the surface of photoexcited sphalerite (ZnS) colloids suspended in water. This model reaction is chosen to systematically study the surface photoprocess occurring on ZnS in the presence of [Na₂S] (1–10 mM) hole scavenger at 15 °C. Experiments at variable pH (5–10) indicate that monodissociated fumaric acid is the primary electron acceptor forming the monoprotic form of succinic acid. The following …

Effects Of Macromolecular Crowding On Ferredoxin And Ferredoxin-Nadp+ Reductase Kinetics, Danielle Bautista, David W. Seybert Ph.D.

Undergraduate Research and Scholarship Symposium

Macromolecular crowding refers to the intrinsic occurrence of high concentrations of macromolecules found within cells, which may alter biomolecular properties of other macromolecules. Simulating these environments in vitro should enable a more accurate understanding of these modifications. We have employed in vitro studies to specifically examine the effects of macromolecular crowding on biological redox reactions. The iron-sulfur protein ferredoxin (Fdx) and the FAD-containing flavoprotein ferredoxin-NADP+ reductase (FNR), from Spinacea oleracea, were utilized as a model electron transfer system. Utilizing NADPH as a reductant, the Fdx-FNR complex reduces mammalian cytochrome c as a surrogate electron acceptor. Reduction of the heme moiety …

Macromolecular Crowding Effects Of Ldh, Sadiq Ali Shaik

Undergraduate Research and Scholarship Symposium

No abstract provided.

The Use Of Synthetic Mixture Based Libraries To Identify Hit Compounds For Eskape Pathogens, Leishmaniasis, And Inhibitors Of Palmitoylation, Marcello Giulianotti

USF Tampa Graduate Theses and Dissertations

The goal of this work is to demonstrate the utility of using systematically formatted mixture based libraries as part of the drug discovery processes. While there are a number of different valid approaches for identifying hit and tool compounds, systematically formatted mixture based libraries, such as those described in this study, offer the ability to develop a significant amount of structure activity relationship data from the testing of very few samples. In support of this claim a review of recent developments in the area of systematically formatted mixture based libraries as well as three case studies are presented. The three …

Co(Ii)-Based Metalloradical Catalysis For Asymmetric Radical Cyclopropanation, Qigan Cheng

USF Tampa Graduate Theses and Dissertations

Metal-catalyzed cyclopropanation of olefins with diazo reagents is one of the most general and efficient method to prepare cyclopropanes. The resulting cyclopropyl units are found as a basic structural element in a wide range of naturally occurring compounds and biologically active compounds, and can serve as versatile synthetic intermediates in the synthesis of multifunctionalized cycloalkanes and acyclic compounds. Since Co(II) complexes of D₂-symmetric chiral amidoporphyrins [Co(D₂-Por*)] were first introduced in 2004, Co(II)-metalloradical catalysis (MRC) have emerged as a new platform for asymmetric cyclopropanation. These metalloradical catalysts have been shown to be highly effective for asymmetric intermolecular …