Organic Chemistry Commons^™

Lighting Up The Cell: Developing A Luminescent Lanthanide Probe For Detecting Rnas, Jonathan Savell

Honors Projects

An anion detecting luminescent probe, Tb:DO2A-Cs124, was repurposed for use in RNA imaging. Potential RNA aptamers were identified for the molecule using Capture-SELEX and MinION sequencing. Fluorimetry data revealed these aptamers did not allow for the probe to luminesce in the presence of target RNAs due to adenosine monophosphate’s ability to quench the emission signal.

The Importance Of Atomic Charges For Predicting Site-Selective Ir-, Ru-, And Rh-Catalyzed C-H Borylations, Shannon M. Stephens, Kyle M. Lambert

Chemistry & Biochemistry Faculty Publications

A supervised machine learning model has been developed that allows for the prediction of site selectivity in late-stage C-H borylations. Model development was accomplished using literature data for the site-selective (≥95%) C-H borylation of 189 unique arene, heteroarene, and aliphatic substrates that feature a total of 971 possible sp² or sp³ C-H borylation sites. The reported experimental data was supplemented with additional chemoinformatic descriptors, computed atomic charges at the C-H borylation sites, and data from parameterization of catalytically active tris-boryl complexes resulting from the combination of seven different Ir-, Ru-, and Rh-based precatalysts with eight different ligands. Of the over …

Investigations Into The Expansion Of Breslow-Type Intermediate Reactivity Via Radical C-N Bond Homolysis, Jacklyn J. Kubik

Graduate Theses and Dissertations

The Breslow intermediate is a key intermediate in catalytic transformations like the benzoin condensation and Stetter reaction. These intermediates were first postulated by Ronald Breslow in 1958. Since then, a number of researchers have sought to prove their existence and expand upon the reactions possible using these intermediates. In the sixty plus years since this intermediate was first postulated the reaction scope has expanded significantly, Breslow and breslow-type intermediates have expanded to encompass benzothiazoles, imidazoles, benzoimidazoles, triazoles, thiadiazoles, diamino type structures, and most recently pyridine structures. The expansion of these reactions has opened up new avenues of exploration and previously …

The Investigation Of The Antimicrobial And Biofilm-Disrupting Properties Of Synthesized Hemibastadin Derivatives, Antonio Harvey, Andrew A. Yeagley

Longwood Senior Thesis Proposal

We want to investigate structural changes to the core hemibastadin structure while attempting to make these derivatives biologically safer. Since these modifications have never been done before, we will need to design a synthesis of these new molecules. Due to the nature of the molecules (dimers), a divergent synthesis that allows for the creation of both halves simultaneously seems most appropriate. A successful synthesis of these compounds will allow us to further investigate these derivatives for their antimicrobial and biofilm-disrupting properties.

Synthesis Of Phosphonate-Based Diimide Ligands, Kenya V. Medina

Honors Program Theses and Research Projects

There has been a resurged interest in the synthesis of metal-organic frameworks because of their potential applications in energy production and drug delivery. Although diimides are insoluble in aqueous solutions, the addition of phosphonic acid allows the complex to be water soluble, which greatly increases their application. Therefore, the creation of a hybrid metal-organic complex by the addition of phosphonic groups to diimide ligands can result in a polar porous compound. In this project the ligand design included the use of dianhydrides including pyromellitic dianhydride, naphthalenetetracarboxylic dianhydride, perylenetetracarboxylic dianhydride, and biphenyl-tetracarboxylic acid dianhydride. These dianhydride precursors were refluxed under argon …

Recent Studies On The Synthesis Of Medicinal Molecules., Paige Monsen

Electronic Theses and Dissertations

Medicinal chemistry interfaces synthetic organic chemistry, natural product chemistry and chemical biology, with a goal of yielding therapeutic agents. Natural products or compounds derived from natural sources such as plants, animals, and microorganisms, are often biologically active and render that compound a likely drug lead. For thousands of years humankind has utilized natural products for medicinal purposes and consequently scientists take advantage of both these compounds’ core structural characteristics and their modes of actions on selected targets as inspiration to develop therapeutics. Because the total synthesis of such complex molecules can be cumbersome and expensive, semi-synthetic methods on isolated natural …

Investigation Of Factors Influencing Recombination Versus Disproportionation Of Complex Radicals Formed By C-N Homolysis Of Breslow Type Intermediates And Related Compounds, Taylor Burnett

Graduate Theses and Dissertations

Electron rich enamines are capable of C-N bond homolysis and subsequent recombination and/or disproportionation. It is unclear what causes these radicals to undergo recombination or disproportionation. Density Functional Theory (DFT) calculations do not provide a transition state for the recombination and disproportionation processes and therefore they cannot be used to predict the favorable reaction. Breslow intermediates formed by deprotonation of thiazolium salts and reaction with aromatic aldehydes are examples of electron rich enamines. These breslow intermediates can undergo C-N bond homolysis to form a radical pair the either recombine or disproportionate. Upon investigation of the factors influencing recombination and disproportionation, …

Emergent Photophysics In Diketopyrrolopyrrole Superstructures, Andrew Levine

Dissertations, Theses, and Capstone Projects

Organic semiconductors have received substantial attention as active components in optoelectronic devices because of their processability and customizable electronic properties. Tailoring the organic active layer in these devices to exhibit desirable optoelectronic properties requires understanding the complex and often subtle structure-property relationships governing their photophysical response to light. Both structural organization and frontier molecular orbitals (FMO) play pivotal roles in energy relaxation processes, and complex interplay between organization and orbital energies are difficult to anticipate based upon the molecular structure of the components alone, especially in systems comprised of multiple components. In pursuit of design rules, there is a need …

Applications Of Sodium Azide In The Synthesis Of Tetrazines And Hydrolysis Reactions, My Le

Honors Theses

The inverse electron demand Diels−Alder cycloadditions of heterocyclic azadienes have provided a robust methodology for synthesizing highly substituted and functionalized heterocycles. It is widely used in organic synthesis and the pharmaceutical industry in the divergent construction of screening libraries and bioorthogonal conjugation. Each heterocyclic azadiene was found to possess a unique reactivity toward different classes of dienophiles, display predictable modes of cycloaddition, and exhibit substantial substituent electronic effects impacting their intrinsic reactivity and cycloaddition regioselectivity. Synthesis of 1,2,4,5-tetrazine has been reported in the literature since the late 19th century, showing scientists' tremendous interest in its application.

Herein we attempt to …

Nitro Group Reduction For Use In Organic, Cathodic Materials, Brock G. Goeden

Honors Thesis

The industrial demand for higher capacity, light-weight battery materials has skyrocketed in recent years due to heavy investments in portable electronics, electronic vehicles, and renewable energy sources. However, rechargeable battery technology has seen little improvement since the invention of the Lithium-Ion battery in the 1980s. The low energy density of the traditionally utilized LiCoO2 cathodic material (specific capacity: 272 mAh g-1), has limited its potential to meet these increasing demands. To solve this problem, our research group is investigating new types of lightweight, organic, polymeric materials with conductive backbones as a possible replacement for the cathodic materials in Lithium-Ion batteries. …

Indolizine Donor-Based Dyes For Applications In Fluorescence Biological Imaging, William Meador

Honors Theses

NIR emissive fluorophores are intensely researched due to their potential to replace modern imaging procedures. Many molecular strategies have been employed in the literature to optimize fluorophores for deeper NIR absorption and emission, biocompatibility, and higher fluorescence quantum yields. Amongst the fluorophores studied to date, proaromatic indolizine donors are attractive alternatives to traditional alkyl amine and indoline based donors due to their 1) lower energy absorption and emission facilitated by proaromaticity, 2) large Stokes shifts due to increased dihedral angles about the π-system, 3) ease of functionalization and capacity for bioconjugation at the phenyl ring, and 4) potential for further …

Influence Of Conformational Restriction On The Antibacterial Activity And Ribosomal Selectivity Of Aminoglycoside Antibiotics, Michael Gabriel Pirrone

Wayne State University Dissertations

The ever-increasing threat posed by multidrug-resistant infectious bacteria necessitates

the development of novel antibiotics. Aminoglycoside antibiotics are growing in interest due to

their broad spectrum of activity, lack of known drug related allergies, low manufacturing cost,

and their well-studied mechanism of action. The simplification of rational drug design due to the

well-studied mechanism of action is the key to overcoming the issues presented by these drugs,

namely ototoxicity and nephrotoxicity.

A study of the effect of the conformation of the aminoglycoside ring I side chain is

described wherein it was discovered that an increase in a particular conformation augments the …

A Brief Introduction To The Applications Of Small Organic Molecules As Food Additives, Zhou Zhou

Open Educational Resources

A new chapter in Introductory Organic Chemistry course. Lecture PowerPoint file and laboratory document are also included in this work.

• The goal of this chapter is to cover the basic ground of the food additives from the perspective of organic chemistry. This chapter has three parts.
  • Part one: Introduction of the food additive industry including the history, definition and the purposes of food additives.
  • Part two: The terminology in food additives and in organic chemistry, how to locate trustworthy data sheets for chemicals, and how to interpret the toxicity data.
  • Part three: Different families of organic compounds used as food …

C(Sp2)-C(Sp3) Cross-Coupling Of Aryl Halides And Active C(Spp3)-H Bonds Via Dual Catalysis: Organic Photocatalysis/Nickel Redox Catalysis, Nicholas Armada

Department of Chemistry: Dissertations, Theses, and Student Research

Convenient catalytic methodologies that can facilitate the formation of C-C bonds are undoubtedly of great interest in synthetic organic chemistry. Recent reports in literature have showcased hybrid catalytic methods that couple Ni-redox catalysis and photocatalysis to enable C-H activation of tetrahydrofuran (THF) and subsequent cross-coupling with aryl halides in appreciable yields and under relatively mild reaction conditions.^1-2 However, these studies used expensive, heavy metal-containing photocatalysts and both report difficulty obtaining low-specificity across their scopes of aryl-halides. The following report will shed light on a class of photo-excitable small organic molecules that – in conjunction with a catalytic Ni-redox cycle …

Do Paraben Derivatives Alter T Cell Immunity?, Hailey Kintz

Spring Presentation of Undergraduate Research

T cells immunity is linked to a complex system of cytokines that determine differentiation of naïve T cells into Th1, Th2, Th17, and Treg cells. Estrogen production or periods of elevated production have been correlated with an anti-inflammatory state in which Th2 and Treg cells are up-regulated. Such responses in the immune system are capable of supporting pre-cancerous activity. We are investigating the tie between the xenoestrogen compounds found in cosmetics, parabens, and their ability to regulate T cell immunity. Testing parabens and paraben derivatives with weaker estrogen receptor association will allow for a better understanding of the interplay between …

Higher Energy Gap Control Of Fluorescence In Conjugated Polymers, Chien-Hung Chiang

LSU Doctoral Dissertations

Chemo- and biosensors based on fluorescent conjugated polymer benefit from greater detection sensitivity due to amplification of the electronic perturbations produced by analyte binding. This amplification stems from the exciton-transporting properties of conjugated polymers. A conventional design paradigm relies on the analyte binding events which generate sites of lower energy relative to the polymer energy: either fluorescence quenching sites (turn-off sensors) or bathochromically shifted fluorophores (turn-on sensors). In both type sensors, the excitons migrate to the lower-energy site created by analyte binding.

This dissertation primarily focused the investigation of an alternative paradigm when analyte binding creates higher energy gap sites …

Reducing Dynamic Disorder In Small-Molecule Organic Semiconductors By Suppressing Large-Amplitude Thermal Motions, Steffen Illig, Alexander S. Eggeman, Alessandro Troisi, Lang Jiang, Chris Warwick, Mark Nikolka, Guillaume Schweicher, Stephen G. Yeates, Yves Henri Geerts, John E. Anthony, Henning Sirringhaus

Chemistry Faculty Publications

Thermal vibrations and the dynamic disorder they create can detrimentally affect the transport properties of van der Waals bonded molecular semiconductors. The low-energy nature of these vibrations makes it difficult to access them experimentally, which is why we still lack clear molecular design rules to control and reduce dynamic disorder. In this study we discuss the promising organic semiconductors rubrene, 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothio-phene and 2,9-di-decyl-dinaphtho-[2,3-b:20,30-f]-thieno-[3,2-b]-thiophene in terms of an exceptionally low degree of dynamic disorder. In particular, we analyse diffuse scattering in transmission electron microscopy, to show that small molecules that have their side chains attached along the long axis of their …

Synthesis And Characterization Of Neo-Confused Porphyrins And Related Systems, Arwa Salem Almejbel

Theses and Dissertations

Carbaporphyrins have been the focus of many studies, and a wide variety of related carbaporphyrinoid systems have been reported. N-confused porphyrins are a class of carbaporphyrins where one pyrrole unit has been inverted. In this work, a newly discovered family of porphyrin isomers where one of the pyrrolic subunits is connected to the meso-bridges in a 1,3-fashion, called neo-confused porphyrins, has been investigated.

Reaction of pyrrole-3-carbaldehydes with acetoxymethylpyrroles and NaH in DMF gave neo-confused dipyrrylmethane dialdehydes. The resulting dialdehydes underwent an acid catalyzed condensation with a dipyrrylmethane to give neo-confused phlorins, and following oxidation with FeCl3 afforded new neo-confused porphyrins. …

Methodology Development In Green Chemistry: Oxoammonium Salt Oxidations And Fluoroform Incorporation, Rebecca J. Wiles

University Scholar Projects

Central to the advancement of small molecule synthesis is the ability to develop methodologies that reimagine well known chemistry in a new, environmentally friendly manner. In this thesis two central themes emerge: oxoammonium salt oxidations and trifluoromethyl incorporation using fluoroform gas. Several projects have been developed surrounding oxoammonium salt chemistry, which are featured by their mild conditions, ease of use, and the metal-free, recyclable nature of the oxidant. Trifluoromethylation using fluoroform gas finds its utility in the use of a potent greenhouse gas waste product as a benchtop reagent.

Methodology Development In Green Chemistry: Oxoammonium Salt Oxidations And Fluoroform Incorporation, Rebecca J. Wiles

Honors Scholar Theses

Central to the advancement of small molecule synthesis is the ability to develop methodologies that reimagine well known chemistry in a new, environmentally friendly manner. In this thesis two central themes emerge: oxoammonium salt oxidations and trifluoromethyl incorporation using fluoroform gas. Several projects have been developed surrounding oxoammonium salt chemistry, which are featured by their mild conditions, ease of use, and the metal-free, recyclable nature of the oxidant. Trifluoromethylation using fluoroform gas finds its utility in the use of a potent greenhouse gas waste product as a benchtop reagent.

Photogenerated O-Azaxylylenes: Mechanistic Studies And Synthetic Applications, William Cole Cronk

Electronic Theses and Dissertations

This research sets out to build upon excited state o-azaxylylene cycloaddition. The mechanism behind the excitation and cycloaddition process of photogenerated o-azaxylylenes was determined experimentally. Time-correlated single-photon counting, steady-state spectroscopy, triplet quenching experiments, and quantum yield studies provided evidence suggesting that excited state intramolecular proton transfer is followed by intersystem crossing and stepwise addition to the tethered unsaturated pendant.

In keeping with the principles of diversity oriented synthesis, a modular approach was taken to gain access to a diverse array of N,O,S-Polyheterocycles which were modified postphotochemically via Suzuki coupling to yield fused biaryls. Cycloaddition products, outfitted with halogens …

Investigating The Synthesis Of Heterocycles Via Gold Catalyzed Cyclizations And Cyclo-Dehydrating Reactions, Katherine L. Childers

Undergraduate Honors Thesis Projects

The goal of this project was to study novel synthetic procedures for heterocycles. This was achieved through a two-part investigation. In the first part, a variety of conditions for the gold catalyzed cyclization of allenes were studied. This work was focused on the lesser studied intermolecular reactions of allenes. A variety of allenes were synthesized, and then reacted with 1,3-dipoles and a gold catalyst. These reactions were determined to be unsuccessful through the analysis of nuclear magnetic resonance spectroscopy data. In the second part of this study, the synthesis of 1,3,4-oxadiazoles was investigated. Several cited procedures were examined to determine …

The Synthesis Of A Bisbenzothiophene (Bbt) Based Organic Semiconductor With Increased Function And Increased Solubility, Mary England

Senior Honors Theses

Organic semiconductors are growing in applications for use in modern technology.¹ The main interest in these molecules can be attributed to their low cost (compared to silicon) and their ability to be used on flexible substrates. There are four features that make a good organic semiconductor. First, the molecule should be conjugated, having alternating single and double bonds (lone electron pairs act similarly to double bonds). Secondly, the molecule should be planar, or flat, in shape. Thirdly, the molecule should have a narrow band gap to increase the overall conductivity. Lastly, the molecule should be soluble to ease application. …

Studies Toward The Total Synthesis Of Antascomicin B, David Ross Clay

Graduate Theses and Dissertations

The following dissertation describes synthetic efforts toward the synthesis of the C21-C34 fragment of antascomicin B. Our initial enzymatic approach is detailed as well as an asymmetric transfer hydrogenation (ATH) strategy that will be used in the eventual total synthesis of the molecule. Several investigations into anomalies observed during (ATH) reactions are also discussed.