Design, synthesis and application of ultrastable rylene dyes for fluorescent labeling of biomolecules

Studies of organic fluorescent dyes are experiencing a renaissance related to the increasing demands posed by new microscopy techniques for high resolution and high sensitivity. While in the last decade single molecule equipment and methodology has significantly advanced and in some cases reached theoretical limits (e.g. detectors approaching unity quantum yields) unstable emission from chromophores and photobleaching become more and more the bottleneck of the advancement and spreading of single-molecule fluorescence studies. The main goal of this work was the synthesis of fluorophores that are water-soluble, highly fluorescent in an aqueous environment, have a reactive group for attachment to a biomolecule and posses exceptional photostability. An approach towards highly fluorescent, water-soluble and monofunctional perylene-3,4,9,10-tetracarboxdiimide and terrylene-3,4:11,12-tetra carboxidiimide chromophores was presented. A new synthetic strategy for the desymmetrization of perylenetetracarboximides was elaborated; water-solubility was accomplished by introducing sulfonyl substituents in the phenoxy ring. Two strategies have been followed relying on either non-specific or site specific labeling. For this purpose a series of new water-soluble monofunctional perylene and terrylene dyes, bearing amine or carboxy group were prepared. The reactivity and photophysical properties of these new chromophores were studied in aqueous medium. The most suitable chromophores were further derivatized with amine or thiol reactive groups, suitable for chemical modification of proteins. The performance of the new fluorescent probes was assessed by single molecule enzyme tracking, in this case phospholipase acting on phospholipid supported layers. Phospholipase-1 (PLA-1) was labeled with N-hydroxysuccinimide ester functionalized perylene and terrylene derivatives. The purification of the conjugates was accomplished by novel convenient procedure for the removal of unreacted dye from labeled enzymes, which involves capturing excess dye with a solid support. This novel strategy for purification of bioconjugates allows convenient and fast separation of labeled proteins without the need for performing time consuming chromatographic or electrophoretic purification steps. The outstanding photostability of the dyes and, associated therewith, the extended survival times under strong illumination conditions allow a complete characterization of enzyme action on its natural substrates and even connecting enzyme mobility to catalytic activity. For site-specific attachment of the rylene dyes to proteins the chromophores were functionalized with thioesters or nitrilotriacetic acid groups. This allowed attachment of the emitters to the N-terminus of proteins by native chemical ligation or complexation with His-tagged polypeptides at the N- or C-termini, respectively. The synthesis of a water-soluble perylenebis (dicarboximide) functionalized with a thioester group was presented. This chromophore exhibits an exceptional photostability and a functional unit for site-specific labeling of proteins. The suitability of the fluorophore as a covalent label was demonstrated via native chemical ligation with protein containing N-terminal cystein residue. We exploited also oligohisitidine sequences as recognition elements for site-selective labeling. The synthesis of a new water-soluble perylene chromophore, containing a nitrilotriacetic acid functional group was demonstrated, using solution-phase and solid-phase approaches. This chromophore combines the exceptional photophysical properties of the rylene dyes and a recognition unit for site-specific labeling of proteins. An important feature of the label is the unchanged emission of the dye upon complexation with nickel ions.

Designer synthesis of monodisperse heterodimer and ferrite nanoparticles

The work presented in this doctoral thesis is a facile procedure, thermal decomposition, forrnthe synthesis of different types of monodisperse heterodimer M@iron oxide (M= Cu, Co, Nirnand Pt) and single ferrites, MFe2O4 (M= Cu and Co), nanoparticles. In the following chapter,rnwe study the synthesis of these monodiperse nanoparticles with the similar iron precursorrn(iron pentacarbonyl) and different transition metal precursors such as metalrnacetate/acetylacetonate/formate precursors in the presence of various surfactants and solvents.rnAccording to their decomposition temperatures and reducing condition, a specific and suitablernroute was designed for the formation of Metal@Metal oxide or MFe2O4 nanoparticlesrn(Metal/M=transition metal).rnOne of the key purposes in the formation of nanocrystals is the development of syntheticrnpathways for designing and controlling the composition, shape and size of predictedrnnanostructures. The ability to arrange different nanosized domains of metallic and magneticrnmaterials into a single heterodimer nanostructure offers an interesting direction to engineerrnthem with multiple functionalities or enhanced properties of one domain. The presence andrnrole of surfactants and solvents in these reactions result in a variety of nanocrystal shapes. Therncrystalline phase, the growth rate and the orientation of growth parameters along certainrndirections of these structures can be chemically modulated by using suitable surfactants. In allrnnovel reported heterodimer nanostructures in this thesis, initially metals were preformed andrnthen by the injection of iron precursor in appropriate temperature, iron oxide nanoparticlesrnwere started to nucleate on the top or over the surfaces of metal nanoparticles. Ternary phasesrnof spherical CuxFe3-xO4 and CoFe2O4 ferrites nanoparticles were designed to synthesis just byrnlittle difference in diffusion step with the formation of mentioned phase separated heterodimerrnnanoparticles. In order to use these magnetic nanoparticles in biomedical and catalysisrnapplications, they should be transferred into the water phase solution, therefore they werernfunctionalized by a multifunctional polymeric ligand. These functionalized nanoparticles werernstable against aggregation and precipitation in aqueous media for a long time. Magneticrnresonance imaging and catalytic reactivities are two promising applications which have beenrnutilized for these magnetic nanoparticles in this thesis.rnThis synthetic method explained in the following chapters can be extended to the synthesis ofrnother heterostructured nanomaterials such as Ni@MnO or M@M@iron oxide (M=transitionrnmetal) or to use these multidomain particles as building blocks for higher order structures.

Synthesis of carbolines and analogues via rhodhium-catalyzed [2+2+2] cycloaddition with alkynyl-ynamides : application to the total synthesis of alkaloids

The main research theme of this dissertation is the synthesis of g- and b-carbolines using a metal-catalyzed [2+2+2] cycloaddition strategy of tethered alkynyl-ynamides (diynes) with nitriles. g- and b-carbolines form the core of a large group of natural product and represent important targets for organic chemists. Many of these carbolines showed pharmacological effects ranging from anti-tumor to anxiolytic and anti-HIV activity. A model study with N-Ethynyl-N-tosyl-2-(2-phenylethynyl)aniline and methyl cyanoformate showed that rhodium-based catalysts promote efficiently the reaction. A further optimization showed that the regioselectivity of the reaction can be tuned by the choice of the solvent or by the catalytic system. Application to a larger scope of diynes showed that the regioselectivity strongly depends on the type of substitution of the alkynyl moieties, giving regioselectivities in the range g:b = 1/0 to g:b = 0/1. This [2+2+2] cycloaddition approach for the synthesis of the g- and b-carboline cores was successfully applied to the first total synthesis of Isoperlolyrine and the total synthesis of Perlolyrine. Extension of this strategy to heterocumulenes as cycloaddition partners allowed the synthesis of a g-carbolinone, a thiopyrano[3,4-b]indol-3-imine and thiopyranothiones.

Morphology control in metallocene-catalyzed polyolefin synthesis

The main aim of the work presented in this dissertation was the morphology control in metallocene-catalyzed polyolefin synthesis. This was studied by selective immobilization techniques on a variety of supports such as porous polyurethane particles (Chapter 3), electrospun fibers (Chapter 4 and 5), inorganic-organic hybrid core-shell particles (Chapter 6) and hollow silica particles (Chapter 7). Another aspect of this dissertation was modulating a catalytic activity by controlling a size of boron-based cocatalysts (Chapter 8).

Bio-inspired polymer-supported nitrido molybdenum(VI) complexes for ammonia synthesis − reactivity towards protons and electrons : EPR investigations on paramagnetic molybdenum(V) and copper(II) complexes

Die biologische Stickstofffixierung durch Molybdän-haltige Nitrogenasen sowie die Erforschung des zugrundeliegenden komplexen Mechanismus (N2-Aktivierung an Metall-Zentren, 6-fache Protonierung und Reduktion, N–N Bindungsspaltung unter Bildung von Ammoniak) ist von erheblichem Interesse. Insbesondere Molybdän-Komplexe wurden bereits erfolgreich als Modellverbindungen für die Untersuchung elementarer Einzelschritte der N2-Aktivierung eingesetzt. Durch die Verwendung von Triamidoamin-Liganden ist es Schrock et al. sogar gelungen mehrere Katalysezyklen zu durchlaufen und einen Mechanismus zu formulieren. Trotz der sterisch anspruchsvollen Substituenten in den Schrock-Komplexen ist die Umsatzrate dieses homogenen Katalysators, aufgrund Komplex-Deaktivierung infolge intermolekularer Reaktionen wie Dimerisierung und Disproportionierung, limitiert. In der vorliegenden Arbeit wurden einige dieser Herausforderungen angegangen und die aktiven Spezies auf einer Festphase immobilisiert, um intermolekulare Reaktionen durch räumliche Isolierung der Komplexe zu unterdrücken.rnEin Polymer-verankertes Analogon des Schrock Nitrido-Molybdän(VI)-Komplexes wurde auf einem neuen Reaktionsweg synthetisiert. Dieser beinhaltet nur einen einzigen Reaktionsschritt, um die funktionelle Gruppe „MoN“ einzuführen. Protonierung des immobilisierten Nitrido-Molybdän(VI)-Komplexes LMoVIN (L = Polymer-verankerter Triamidoamin-Ligand) mit 2,6-Lutidinium liefert den entsprechenden Imido-Molybdän(VI)-Komplex. Durch anschließende Ein-Elektronen-Reduktion mit Cobaltocen wird der Polymer-angebundene Imido-Molybdän(V)-Komplex erhalten, bewiesen durch EPR-Spektroskopie (g1,2,3 = 1.989, 1.929, 1.902). Durch die Immobilisierung und die effektive räumliche Separation der Reaktionszentren auf der Festphase werden bimolekulare Nebenreaktionen, die oft in homogenen Systemen auftreten, unterdrückt. Dies ermöglicht zum ersten Mal die Darstellung des Imido-Molybdän(V)-Intermediates des Schrock-Zyklus.rnEPR-Spektren des als Spin-Label eingeführten immobilisierten Nitrato-Kupfer(II)-Komplexes wurden unter verschiedenen Bedingungen (Lösungsmittel, Temperatur) aufgenommen, wobei sich eine starke Abhängigkeit zwischen der Zugänglichkeit und Reaktivität der immobilisierten Reaktionszentren und der Art des Lösungsmittels zeigte. Somit wurde die Reaktivität von LMoVIN gegenüber Protonen und Elektronen, welches zur Bildung von NH3 führt, unter Verwendung verschiedener Lösungsmittel untersucht und optimiert. Innerhalb des kugelförmigen Polymers verläuft die Protonierung und Reduktion von LMoVIN stufenweise. Aktive Zentren, die sich an der „äußeren Schale“ des Polymers befinden, sind gut zugänglich und reagieren schnell nach H+/e− Zugabe. Aktive Zentren im „Inneren des Polymers“ hingegen sind schlechter zugänglich und zeigen langsame diffusions-kontrollierte Reaktionen, wobei drei H+/e− Schritte gefolgt von einer Ligandenaustausch-Reaktion erforderlich sind, um NH3 freizusetzen: LMoVIN  LMoVNH  LMoIVNH2  LMoIIINH3 und anschließender Ligandenaustausch führt zur Freisetzung von NH3.rnIn einem weiteren Projekt wurde der Bis(ddpd)-Kupfer(II)-Komplex EPR-spektroskopisch in Hinblick auf Jahn−Teller-Verzerrung und -Dynamik untersucht. Dabei wurden die EPR-Spektren bei variabler Temperatur (70−293 K) aufgenommen. Im Festkörperspektrum bei T < 100 K erscheint der Kupfer(II)-Komplex als gestreckter Oktaeder, wohingegen das EPR-Spektrum bei höheren Temperaturen g-Werte aufzeigt, die einer pseudo-gestauchten oktaedrischen Kupfer(II)-Spezies zuzuordnen sind. Diese Tatsache wird einem intramolekularen dynamischen Jahn−Teller Phänomen zugeschrieben, welcher bei 100 K eingefroren wird.