Organic Chemistry Commons^™

Studies On The Synthesis, Function, And Properties Of Troponoids, John-Charles A. Baucom

Dissertations, Theses, and Capstone Projects

Troponoids are a unique class of non-benzenoid aromatic compounds with a wide range of demonstrated applications in pharmaceuticals and molecular sensing. The cycloheptatrienone scaffold possesses a noteworthy degree of tunability as a function of ring oxygenation. This manuscript describes our efforts toward a better understanding of the physical consequences of the scaffold to better utilize the motif. Chapter the first discusses our efforts at elucidating the mechanism of troponoid inhibition of the Hepatitis B virus reverse transcriptase RNAse H enzymatic domain. Using homology modeling in conjunction with traditional in vitro assays we were able to establish the likely mechanism of …

Developing Phenanthroimidazole-Based Fluorescent Sensors For Efficient Analyte Detection, Brian Kellogg

Masters Theses & Specialist Projects

The highly efficient design and synthesis of organic fluorophores with an excellent quantum yield have received extensive attention. Compared with instrumental techniques, fluorescent sensors derived from organic small molecules offer many impressive benefits, such as selective detection, lower cost, and higher efficiency. Various detection mechanisms such as colorimetric, ratiometric, and fluorescence turn on/off have been reported for single analyte detection. Developing molecular probes that are capable of detecting two (or more than two) different analytes (cations, anions, and/or biomolecules) had emerged as a new research area and attracted considerable attention in the field of chemo- and biosensors.

Phenanthroimidazole represents a …

Synthesis Of Noval Hydroxy Chalcone And Study Of Fluorescent Properties, Margaret Hilliker

Williams Honors College, Honors Research Projects

Chalcones are a class of naturally occurring compounds found in plants, which have a general structure of Ar–CO–CH=CH–Ar’. They have shown significant potential as tunable organic fluorophores due to their extended π-conjugation and structural simplicity. In this study, a 2-hydroxy-substituted chalcone featuring a terminal dimethylamino group was synthesized via a pyrrolidine-catalyzed aldol condensation and characterized for its photophysical properties. The electron-donating and -accepting ends of the molecule establish an intramolecular charge transfer (ICT) pathway, while the hydroxyl group enables excited state intramolecular proton transfer (ESIPT), leading to complex emission behavior. Room temperature fluorescence analysis revealed broad, featureless emission, while low-temperature …

Microwave Assisted Syntheses And Characterizations Of Near-Infrared Ratiometric Probes For Mitochondrial Ph Detection And Monitoring, Ronald J. Schwandt

Dissertations, Master's Theses and Master's Reports

Within the field of biochemistry, there has been a significant development of ratiometric fluorescent probes designed for mitochondrial pH detection; however, many of these probes have emissions within the visible spectrum and require long synthesis times with low-yield reactions. However, in recent years, microwave-assisted syntheses of organic molecules have led to significant increases in reaction yields and quicker reaction times. In this work, two common reactions in probe synthesis, Heck coupling, and Knoevenagel condensations are investigated using microwave-assisted synthesis. It was found the low-concentration Heck coupling reactions using palladium (II) acetate led to extremely efficient Heck coupling. Also, a novel …

Unexpected Ring Opening Reactions, Solid-State Structures, And A Chemiluminescent Reaction, L Hiscock

Theses and Dissertations (Comprehensive)

Functional π-materials involve the use of an aromatic π-system to carry out a function such as electron transport (organic electronics), absorbing and emitting photons (dyes, fluorescent materials), self-assembly (discotic liquid crystals), or sensors for various analytes. Our lab has recently published the syntheses of heteroaromatic derivatives of tetrafluoroterephthalonitrile (TFTP, 2.24) synthesised via nucleophilic aromatic substitution chemistry. The prepared derivatives have displayed fluorescent (e.g. 2.2)1 and liquid crystalline (1.0)2 properties, as well as displaying close π-π interactions in the solid state (2.8).3 As the materials we are synthesising all belong to the class of aromatic compounds, an introduction to aromaticity and …

Design, Synthesis, And Characterization Of Nqo1-Activatable Luminescent Probes, Ovini Vionika Weeratung Kankanamge

LSU Doctoral Dissertations

Being among the top ten causes of death, cancer has constantly been able to grab the attention of researchers all around the world. While several treatment methods prevail to cure cancer, the seriousness of this medical condition requires continuous work in the development of novel treatments as well as scientific advancements in order to achieve early detection of the disease. Luminescence imaging is an emerging field in both diagnosis of diseases, as well as a means to provide guidance in clinical surgeries. While there exist only a few contrasting agents approved by the Food and Drug Administration, the need for …

Preparation And Study Of Bacterial Membrane Models, Enoch Asimbisa

Electronic Theses and Dissertations

Fuel molecules are organic solvents that have disruptive effects on the bacterial membrane. This is a significant barrier in biofuel production, as it limits the fuel concentration that can be achieved through fermentation. One potential way of overcoming this barrier is to identify lipid compositions that can better withstand solvent stress, for which it is important to understand how organic solvents disrupt the membrane. Use of biophysical characterization techniques to quantify physical properties like fluidity and thickness will enable us to understand the mechanism by which solvents disrupt membranes. Native membranes are very complex, and we sought to develop in-vitro …

Biomedical Applications And Syntheses Of Selected Anthraquinone Dyes, Richard Sirard

Senior Honors Theses

Anthraquinones are aromatic organic compounds that have multiple applications in the biomedical field. Some anthraquinone-based compounds are used as fluorophores to contrast cell nuclei while others act as chemotherapeutic agents. However, there are not many fluorescent anthraquinone cell stains currently available. In this study, commercially available anthraquinone dyes, in addition to other dye families and compounds, were reviewed for their unique properties, advantages, and drawbacks. The development and characterization of three novel anthraquinone fluorophores revealed promising photophysical characteristics, like large Stokes shifts. One of the compounds, RBS3, was chosen for fixed and live cell staining and exhibited desirable biomedical properties. …

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 …

Synthesis And Self-Assembling Properties Of Peracetylated Β-1 Triazolyl Alkyl D Glucosides And D-Galactosides, Pooja Sharma, Anji Chen, Dan Wang, Guijun Wang

Chemistry & Biochemistry Faculty Publications

Carbohydrate-based low-molecular-weight gelators (LMWGs) are useful classes of compounds due to their numerous applications. Among sugar-based LMWGs, certain peracetylated sugar beta-triazole derivatives were found to be effective organogelators and showed interesting self-assembling properties. To further understand the structural influence towards molecular assemblies and obtain new functional materials with interesting properties, we designed and synthesized a library of tetraacetyl beta-1-triazolyl alkyl-D-glucosides and D-galactosides, in which a two or three carbon spacer is inserted between the anomeric position and the triazole moiety. A series of 16 glucose derivatives and 14 galactose derivatives were synthesized and analyzed. The self-assembling properties of these new …

Tumor-Targeting Fluorinated Phthalocyanines For Theranostic Applications, Erik Nathaniel Carrión

Seton Hall University Dissertations and Theses (ETDs)

Hydrocarbon-based therapeutics and imaging agents are prone to chemical oxidation and degradation resulting in loss of activity and limited functional utility. Thus, more material is required to achieve long-lasting therapeutic effects. Phthalocyanines (Pcs) and their metal complexes (PcMs) can be utilized as prodrugs requiring only renewable energy resources namely, air and light, for cancer therapy and diagnostic (theranostic) applications related to photodynamic therapy (PDT). Replacement of labile C-H bonds in the Pc scaffold with a combination of fluoro and perfluoroisopropyl groups has resulted in a stable yet reactive oxidation catalyst of biological significance and importance. For example, F₆₄PcZn, …

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 …

Determination Of Atrazine Concentration In Freshwaters Using Fluorescence Spectroscopy, Boniface Osei Amankona

Online Theses and Dissertations

Atrazine is the most widely used herbicides in USA, but its negative impact on aquatic ecosystem cannot be over-looked. Atrazine was traditionally determined through liquid/gas chromatography or IR spectroscopy. However, these methods are either time-consuming or costly, so fluorescence spectroscopy is investigated as a more cost and time efficient alternative. Literature value of the optimal wavelength of atrazine was found to be 350 nm emission. Experimental value for emission scanned of atrazine resulted in an optimal wavelength of 363 nm. Known and unknown concentrations of atrazine will be analyzed using fluorescence spectrophotometer to develop a calibration curve.

The calibration concentration …

From The Making To The Tuning To The Use Of Chlorins For Biomedical Applications, Junior Gonzales

Dissertations, Theses, and Capstone Projects

Chlorins are porphyrins missing a double bond. These pigments are optimal platforms for the development of novel dyes that display drug-like attributes such as photodynamic therapy (PDT) agents. More recently, it was demonstrated that chlorins can serve both as a PDT agent and as a modality for fluorescence or PET imaging. Thus, multifunctional chlorins eliminate the differences that may occur in specificity, uptake, and distribution between separate compounds or constructs for imaging and therapy. The overall goal of this dissertation is to take advantage of the reputed intrinsic attributes of chlorins as a viable tool in biomedical applications. In this …

Synthesis And Fluorescent Properties Of A New Flavonoid Compound, Ashley L. Ingle

Williams Honors College, Honors Research Projects

Flavonoids are highly luminescent compounds that are used in diagnosing and treating certain diseases.They are composed of two aromatic rings (ring A and ring B) and a six-membered heterocyclic pyran ring (ring C) that contains a carbonyl and hydroxyl group, which are responsible for unique photophysical characteristics associated with flavonoids. The target flavonoids (compound 1, or 1, and compound 2 or 2) were synthesized, purified and characterized by NMR spectroscopy. The photophysical properties of the flavonoid were investigated in varying solvents by using UV-vis and fluorescence spectroscopy. Such properties include Excited State Intramolecular Proton Transfer (ESIPT), Intramolecular Charge …

Influence Of Shelling Temperature And Time On The Optical And Structural Properties Of Cuins2/Zns Quantum Dots, Colette Robinson

Graduate Theses and Dissertations

CIS/ZnS core/shell QDs are an important class of nanomaterials for optoelectronic, photovoltaic and photoluminescence applications. They consist of lower toxicity materials than the prototypical II-VI Cd-based QDs and show long fluorescence lifetimes, which generates prospective in biological imaging applications. It is vital to develop reproducible synthetic methods for this new class of nanomaterials in order to maintain small sizes with high QYs. CIS core QDs have been shelled with ZnS at various temperatures from 90-210°C for reaction times ranging from 20-140 minutes to examine the role of thermodynamics and kinetics on the shell growth. Using HR-TEM and ICP-MS, it was …

A Structurally-Tunable 3-Hydroxyflavone Motif For Visible Light-Induced Carbon Monoxide-Releasing Molecules (Corms), Stacey N. Anderson, Jason M. Richards, Hector J. Esquer, Abby D. Benninghoff, Atta M. Arif, Lisa M. Berreau

Chemistry and Biochemistry Faculty Publications

Molecules that can be used to deliver a controlled amount of carbon monoxide (CO) have the potential to facilitate investigations into the roles of this gaseous molecule in biology and advance therapeutic treatments. This has led to the development of light-induced CO-releasing molecules (photoCORMs). A goal in this field of research is the development of molecules that exhibit a combination of controlled CO release, favorable biological properties (e.g., low toxicity and trackability in cells), and structural tunability to affect CO release. Herein, we report a new biologically-inspired organic photoCORM motif that exhibits several features that are desirable in a next-generation …

Design And Development Of Bodipy-Based Fluorescent Probes For Sensing And Imaging Of Cyanide, Zn (Ii) Ions, Lysosomal Ph And Cancer Cells, Jingtuo Zhang

Dissertations, Master's Theses and Master's Reports - Open

BODIPY (4,4-Difluoro-3a,4a-diaza-s-indacene) dyes have gained lots of attention in application of fluorescence sensing and imaging in recent years because they possess many distinctive and desirable properties such as high extinction coefficient, narrow absorption and emission bands, high quantum yield and low photobleaching effect. However, most of BODIPY-based fluorescent probes have very poor solubilities in aqueous solution, emit less than 650 nm fluorescence that can cause cell and tissue photodamages compared with bio-desirable near infrared (650-900 nm) light. These undesirable properties extremely limit the applications of BODIPY-based fluorescent probes in sensing and imaging applications. In order to overcome these drawbacks, we …

Optical Characterization And Distribution Of Chromophoric Dissolved Organic Matter (Cdom) In Soil Porewater From A Salt Marsh Ecosystem, Catherine D. Clark, Paige Aiona, Jason K. Keller, Warren J. De Bruyn

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

To characterize chromophoric dissolved organic matter (CDOM) in marsh porewaters and its contribution as a carbon source, optical properties (absorbance, fluorescence indices, 3-dimensional excitation-emission matrices [EEMs]) of soil porewater and surface water were measured in a southern Californian salt marsh. Absorption coefficients and fluorescence intensities were higher in porewater than in overlying surface waters, consistent with higher CDOM concentration at depth. Humic-type peaks A and C were observed in EEMs in all samples, and peak M was observed in surface waters and shallow porewater to -5 cm depth. Fluorescence:absorbance (flu:abs) ratios and spectral slopes (S) decreased across the surface interface, …

Molecular Probes For The Detection Of Zn2+ And Fe3+ Ions, Erendra Manandhar

Dissertations

A number of molecular probes have been designed and synthesized for the detection of Zn²⁺ and Fe³⁺ ions. Two types of functional groups have been incorporated into the molecular scaffolds to utilize different fluorescent mechanisms. The first class of receptors contains a pyrene moiety. These molecular probes use the excimer mechanism for the detection of Zn²⁺ ion. The probes work well in an organic solvent with a detection limit of 20 nM (one ppb). Alternatives are made to make them water soluble, but this proved to be difficult. An interesting ion-induced self-assembly system will also be discussed. …

Synthesis And Characterization Of Fluorophores For The Detection Of Lanthanides And Actinides, Robinson I. Roacho

Open Access Theses & Dissertations

A series of fluorophores based in the boron dipyrromethene (BODIPY) family were synthesized and characterized. These fluorophores have the capacity of being introduced to a carbamoyl methyl phosphine oxide (CMPO) lanthanide/actinide extractant. These blue, green and red emission fluorophores show high thermal/moisture stability and high fluorescence efficiencies. The fluorescence intensity seems to be dependent on the restricted rotation about the C(8)-C bond in 8-Ph-BODIPY. By taking advantage of this feature, a hydroxyl- containing BODIPY with high fluorescence intensity was synthesized to be incorporated to a CMPO carboxylic acid via esterification. Unfortunately, we did not observe an optical response upon the …

Visible-Light Photocatalyzed Cross-Linking Of Diacetylene Ligands By Quantum Dots To Improve Their Aqueous Colloidal Stability, Marion G. Götz, Hiroko Takeuchi, Matthew J. Goldfogel, Julia M. Warren, Brandon D. Fennel, Colin D. Heyes

Chemistry & Biochemistry Faculty Publications and Presentations

Ligand cross-linking is known to improve the colloidal stability of nanoparticles, particularly in aqueous solutions. However, most cross-linking is performed chemically, in which it is difficult to limit interparticle cross-linking, unless performed at low concentrations. Photochemical cross-linking is a promising approach but usually requires ultraviolet (UV) light to initiate. Using such high-energy photons can be harmful to systems in which the ligand–nanoparticle bond is fairly weak, as is the case for the commonly used semiconductor quantum dots (QDs). Here, we introduce a novel approach to cross-link thiolated ligands on QDs by utilizing the photocatalytic activity of QDs upon absorbing visible …

Molecular Level Interaction Of Human Fibroblast Growth Factor-1 (Hfgf-1) With Phloridzin, Rammohan Paripelly

Masters Theses & Specialist Projects

Fibroblast growth factors (FGFs) are a family of growth factors which includes twenty three proteins. FGFs work as modulators for various cellular activities like mitosis, differentiation and survival. Among the FGF family, human fibroblast growth factor-1 (hFGF-1), which is also known as acidic fibroblast growth factor, is a potent angiogenic agent, involved in the formation of new blood vessels in various tissues. hFGF-1 is regarded as a prototype of the FGF family. It serves as one of the potential targets in tumor inhibition and obesity due to its involvement in new blood vessel formation in cancerous regions and adipose tissues. …

Development Of A Bio-Molecular Fluorescent Probe Used In Kinetic Target-Guided Synthesis For The Identification Of Inhibitors Of Enzymatic And Protein-Protein Interaction Targets, Katya Pavlova Nacheva

USF Tampa Graduate Theses and Dissertations

Abstract

Fluorescent molecules used as detection probes and sensors provide vital information about the chemical events in living cells. Despite the large variety of available fluorescent dyes, new improved fluorogenic systems are of continued interest. The Diaryl-substituted Maleimides (DMs) exhibit excellent photophysical properties but have remained unexplored in bioscience applications. Herein we present the identification and full spectroscopic characterization of 3,4-bis(2,4-difluorophenyl)-maleimide and its first reported use as a donor component in Forster resonance energy transfer (FRET) systems. The FRET technique is often used to visualize proteins and to investigate protein-protein interactions in vitro as well as in vivo. The analysis …

Aneuploidy Frequencies In Semen Fractions From Ten Oligoasthenoteratozoospermic Patients Donating Sperm For Intracytoplasmic Sperm Injection, Jerome Pfeffer, Myung-Geol Pang, Stanton F. Hoegerman, Christopher J. Osgood, M. W. Stacey, Jacob Mayer, Sergio Oehninger, William G. Kearns

Biological Sciences Faculty Publications

Objective: To determine aneuploidy frequencies in pellet and swim-up semen fractions from 10 infertile men with severe oligoasthenoteratozoospermia (OAT) who were donating sperm for intracytoplasmic sperm injection and to determine whether the swim-up isolation method would successfully separate aneuploid from haploid sperm.

Design: Prospective study.

Setting: Infertility clinic and molecular genetics laboratory.

Patient(s): Ten patients with severe OAT.

Intervention(s): Cytogenetic analyses by fluorescence in situ hybridization to determine aneuploidy frequencies for chromosomes 1, 13, 18, 21, X, and Y in sperm from swim-up and pellet fractions.

Main Outcome Measure(s): Gametic aneuploidy was scored in sperm fractions separated by the swim-up …