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Apart from their central role during 3D structure determination of proteins the backbone chemical shift assignment is the basis for a number of applications, like chemical shift perturbation mapping and studies on the dynamics of proteins. This assignment is not a trivial task even if a 3D protein structure is known and needs almost as much effort as the assignment for structure prediction if performed manually. We present here a new algorithm based solely on 4D [H-1, N-15]-HSQC-NOESY-[H-1, N-15]-HSQC spectra which is able to assign a large percentage of chemical shifts (73-82 %) unambiguously, demonstrated with proteins up to a size of 250 residues. For the remaining residues, a small number of possible assignments is filtered out. This is done by comparing distances in the 3D structure to restraints obtained from the peak volumes in the 4D spectrum. Using dead-end elimination, assignments are removed in which at least one of the restraints is violated. Including additional information from chemical shift predictions, a complete unambiguous assignment was obtained for Ubiquitin and 95 % of the residues were correctly assigned in the 251 residue-long N-terminal domain of enzyme I. The program including source code is available at https://github.com/thomasexner/4Dassign.
Macrocycles with quaterthiophene subunits were obtained by cyclooligomerization by direct oxidative coupling of unsubstituted dithiophene moieties. The rings were closed with high selectivity by an α,β′-connection of the thiophenes as proven by NMR spectroscopy. The reaction of the precursor with terthiophene moieties yielded the symmetric α,α′-linked macrocycle in low yield together with various differently connected isomers. Blocking of the β-position of the half-rings yielded selectively the α,α′-linked macrocycle. Selected cyclothiophenes were investigated by scanning tunneling microscopy, which displayed the formation of highly ordered 2D crystalline monolayers.
Spatio-temporal control of cellular uptake achieved by photoswitchable cell-penetrating peptides
(2016)
The selective uptake of compounds into specific cells of interest is a major objective in cell biology and drug delivery. By incorporation of a novel, thermostable azobenzene moiety we generated peptides that can be switched optically between an inactive state and an active, cell-penetrating state with excellent spatio-temporal control.
A convenient synthesis of gamma-spirolactams in only two steps was developed. Birch reduction of benzoic acids and immediate alkylation with chloroacetonitrile afforded cyclohexadienes in high yields. The products could be isolated by crystallization on a large scale in analytically pure form. Subsequent hydrogenation with platinum(IV) oxide as the catalyst reduced the nitrile functionality and the double bonds in the same step with excellent stereoselectivity. The relative configurations were determined unequivocally by X-ray analyses. Direct cyclization of the intermediary formed amino acids afforded the desired gamma-spirolactams in excellent overall yields. The procedure is characterized by few steps, cheap reagents, and can be performed on a large scale, interesting for industrial processes.
Optical biosensors based on porous silicon were fabricated by metal assisted chemical etching. Thereby double layered porous silicon structures were obtained consisting of porous pillars with large pores on top of a porous silicon layer with smaller pores. These structures showed a similar sensing performance in comparison to electrochemically produced porous silicon interferometric sensors.
Z,E-Diene sind ein häufig auftretendes Strukturmerkmal in Naturstoffen. Aus diesem Grund ist die einfache Darstellung dieser Struktureinheit von großen Interesse in der organischen Chemie.
Das erste Ziel der vorliegenden Arbeit war daher die Weiterentwicklung der Ringschlussmetathese-/ baseninduzierten Ringöffnungs-/ Veresterungssequenz (RBRV-Sequenz) zur Synthese von (2Z,4E)-Diencarbonsäureethylestern ausgehend von Butenoaten. Dazu wurde zunächst die RBRV-Sequenz optimiert. Diese aus drei Schritten bestehende Sequenz konnte in einem Eintopf-Verfahren angewendet werden. Die Ringschlussmetathese gelang mit einer Katalysatorbeladung von 1 mol% des GRUBBS-Katalysators der zweiten Generation in Dichlormethan. Für die baseninduzierte Ringöffnung des β,γ-ungesättigten δ Valerolactons wurde NaHMDS verwendet. Die Alkylierung der Carboxylatspezies gelang mit dem MEERWEIN-Reagenz. Die Anwendbarkeit der Sequenz wurde für verschiedene Substrate demonstriert.
Die Erweiterung der Methode auf α-substituierte Butenoate unterlag starken Einschränkungen. So konnte der Zugang für α Hydroxyderivate realisiert werden. Bei der Anwendung der RBRV-Sequenz auf die α-substituierten Butenoate wurde festgestellt, dass diese sich nur in moderaten Ausbeuten umsetzen ließen und zudem nicht selektiv zu den (2E,4E)-konfigurierten α-substituierten-Dienestern reagierten.
Der Einsatz von Eninen unter den Standardbedingungen der RBRV-Sequenz gelang nicht. Erst nach Modifizierung der Sequenz (höhere Katalysatorbeladung, Wechsel des Lösungsmittels) konnten die [3]Dendralen-Produkte in geringen Ausbeuten erhalten werden.
Im zweiten Teil der Arbeit wurde der Einsatz von (2Z,4E)-Diencarbonsäureethylestern in der Totalsynthese von Naturstoffen untersucht. Dazu wurden zunächst die Transformationsmöglichkeiten der Ester geprüft. Es konnte gezeigt werden, dass sich (2Z,4E)-Diencarbonsäureethylester insbesondere zur Synthese von (2Z,4E)-Aldehyden sowie zum Aufbau der (3Z,5E)-Dien-1-in-Struktur eignen.
Anhand dieser Ergebnisse wurde im Anschluss die RBRV-Sequenz in der Totalsynthese eingesetzt. Dazu wurde zunächst der (2Z,4E)-Dienester Microsphaerodiolin in seiner ersten Totalsynthese auf drei verschiedene Routen hergestellt. Im Anschluss wurden sechs verschiedene Polyacetylene mit einer (3Z,5E)-Dien-1-in-Einheit hergestellt. Schlüsselschritte in ihrer Synthese waren immer die RBRV-Sequenz zum Aufbau der Z,E-Dien-Einheit, die Transformation des Esters in ein terminales Alkin sowie die CADIOT-CHODKIEWICZ-Kupplung zum Aufbau unsymmetrischer Polyine. Alle sechs Polyacetylene wurden zum ersten Mal in einer Totalsynthese synthetisiert. Drei Polyacetylene wurden ausgehend von (S)-Butantriol enantiomerenrein dargestellt. Anhand ihrer Drehwerte konnte eine Revision der von YAO und Mitarbeitern vorgenommen Zuordnung der Absolutkonfiguration der Naturstoffe vorgenommen werden.
Proteins are amphiphilic and adsorb at liquid interfaces. Therefore, they can be efficient stabilizers of foams and emulsions. β-lactoglobulin (BLG) is one of the most widely studied proteins due to its major industrial applications, in particular in food technology.
In the present work, the influence of different bulk concentration, solution pH and ionic strength on the dynamic and equilibrium pressures of BLG adsorbed layers at the solution/tetradecane (W/TD) interface has been investigated. Dynamic interfacial pressure (Π) and interfacial dilational elastic modulus (E’) of BLG solutions for various concentrations at three different pH values of 3, 5 and 7 at a fixed ionic strength of 10 mM and for a selected fixed concentration at three different ionic strengths of 1 mM, 10 mM and 100 mM are measured by Profile Analysis Tensiometer PAT-1 (SINTERFACE Technologies, Germany). A quantitative data analysis requires additional consideration of depletion due to BLG adsorption at the interface at low protein bulk concentrations. This fact makes experiments more efficient when oil drops are studied in the aqueous protein solutions rather than solution drops formed in oil. On the basis of obtained experimental data, concentration dependencies and the effect of solution pH on the protein surface activity was qualitatively analysed. In the presence of 10 mM buffer, we observed that generally the adsorbed amount is increasing with increasing BLG bulk concentration for all three pH values. The adsorption kinetics at pH 5 result in the highest Π values at any time of adsorption while it exhibits a less active behaviour at pH 3.
Since the experimental data have not been in a good agreement with the classical diffusion controlled model due to the conformational changes which occur when the protein molecules get in contact with the hydrophobic oil phase in order to adapt to the interfacial environment, a new theoretical model is proposed here. The adsorption kinetics data were analysed with the newly proposed model, which is the classical diffusion model but modified by assuming an additional change in the surface activity of BLG molecules when adsorbing at the interface. This effect can be expressed through the adsorption activity constant in the corresponding equation of state. The dilational visco-elasticity of the BLG adsorbed interfacial layers is determined from measured dynamic interfacial tensions during sinusoidal drop area variations. The interfacial tension responses to these harmonic drop oscillations are interpreted with the same thermodynamic model which is used for the corresponding adsorption isotherm.
At a selected BLG concentration of 2×10-6 mol/l, the influence of the ionic strength using different buffer concentration of 1, 10 and 100 mM on the interfacial pressure was studied. It is affected weakly at pH 5, whereas it has a strong impact by increasing buffer concentration at pH 3 and 7. In conclusion, the structure formation of BLG adsorbed layer in the early stage of adsorption at the W/TD interface is similar to those of the solution/air (W/A) surface. However, the equation of state at the W/TD interface provides an adsorption activity constant which is almost two orders of magnitude higher than that for the solution/air surface.
At the end of this work, a new experimental tool called Drop and Bubble Micro Manipulator DBMM (SINTERFACE Technologies, Germany) has been introduced to study the stability of protein covered bubbles against coalescence. Among the available protocols the lifetime between the moment of contact and coalescence of two contacting bubble is determined for different BLG concentrations. The adsorbed amount of BLG is determined as a function of time and concentration and correlates with the observed coalescence behaviour of the contacting bubbles.
Metal-containing ionic liquids (ILs) are of interest for a variety of technical applications, e.g., particle synthesis and materials with magnetic or thermochromic properties. In this paper we report the synthesis of, and two structures for, some new tetrabromidocuprates(II) with several “onium” cations in comparison to the results of electron paramagnetic resonance (EPR) spectroscopic analyses. The sterically demanding cations were used to separate the paramagnetic Cu(II) ions for EPR measurements. The EPR hyperfine structure in the spectra of these new compounds is not resolved, due to the line broadening resulting from magnetic exchange between the still-incomplete separated paramagnetic Cu(II) centres. For the majority of compounds, the principal g values (g|| and gK) of the tensors could be determined and information on the structural changes in the [CuBr4]2- anions can be obtained. The complexes have high potential, e.g., as ionic liquids, as precursors for the synthesis of copper bromide particles, as catalytically active or paramagnetic ionic liquids.
Metal-containing ionic liquids (ILs) are of interest for a variety of technical applications, e.g., particle synthesis and materials with magnetic or thermochromic properties. In this paper we report the synthesis of, and two structures for, some new tetrabromidocuprates(II) with several “onium” cations in comparison to the results of electron paramagnetic resonance (EPR) spectroscopic analyses. The sterically demanding cations were used to separate the paramagnetic Cu(II) ions for EPR measurements. The EPR hyperfine structure in the spectra of these new compounds is not resolved, due to the line broadening resulting from magnetic exchange between the still-incomplete separated paramagnetic Cu(II) centres. For the majority of compounds, the principal g values (g|| and gK) of the tensors could be determined and information on the structural changes in the [CuBr4]2- anions can be obtained. The complexes have high potential, e.g., as ionic liquids, as precursors for the synthesis of copper bromide particles, as catalytically active or paramagnetic ionic liquids.
In this thesis, a route to temperature-, pH-, solvent-, 1,2-diol-, and protein-responsive sensors made of biocompatible and low-fouling materials is established. These sensor devices are based on the sensitivemodulation of the visual band gap of a photonic crystal (PhC), which is induced by the selective binding of analytes, triggering a volume phase transition.
The PhCs introduced by this work show a high sensitivity not only for small biomolecules, but also for large analytes, such as glycopolymers or proteins. This enables the PhC to act as a sensor that detects analytes without the need of complex equipment.
Due to their periodical dielectric structure, PhCs prevent the propagation of specific wavelengths. A change of the periodicity parameters is thus indicated by a change in the reflected wavelengths. In the case explored, the PhC sensors are implemented as periodically structured responsive hydrogels in formof an inverse opal.
The stimuli-sensitive inverse opal hydrogels (IOHs) were prepared using a sacrificial opal template of monodispersed silica particles. First, monodisperse silica particles were assembled with a hexagonally packed structure via vertical deposition onto glass slides. The obtained silica crystals, also named colloidal crystals (CCs), exhibit structural color. Subsequently, the CCs templates were embedded in polymer matrix with low-fouling properties. The polymer matrices were composed of oligo(ethylene glycol) methacrylate derivatives (OEGMAs) that render the hydrogels thermoresponsive. Finally, the silica particles were etched, to produce highly porous hydrogel replicas of the CC. Importantly, the inner structure and thus the ability for light diffraction of the IOHs formed was maintained.
The IOH membrane was shown to have interconnected pores with a diameter as well as interconnections between the pores of several hundred nanometers. This enables not only the detection of small analytes, but also, the detection of even large analytes that can diffuse into the nanostructured IOH membrane. Various recognition unit – analyte model systems, such as benzoboroxole – 1,2-diols, biotin – avidin and mannose – concanavalin A, were studied by incorporating functional
comonomers of benzoboroxole, biotin and mannose into the copolymers. The incorporated recognition units specifically bind to certain low and highmolar mass biomolecules, namely to certain saccharides, catechols, glycopolymers or proteins.
Their specific binding strongly changes the overall hydrophilicity, thus modulating the swelling of the IOH matrices, and in consequence, drastically changes their internal periodicity. This swelling is amplified by the thermoresponsive properties of the polymer matrix. The shift of the interference band gap due to the specific molecular recognition is easily visible by the naked eye (up to 150 nm shifts). Moreover, preliminary trial were attempted to detect even larger entities. Therefore anti-bodies were immobilized on hydrogel platforms via polymer-analogous esterification. These platforms incorporate comonomers made of tri(ethylene glycol) methacrylate end-functionalized with a carboxylic acid. In these model systems, the bacteria analytes are too big to penetrate into the IOH membranes, but can only interact with their surfaces. The selected model bacteria, as Escherichia coli, show a specific affinity to anti-body-functionalized hydrogels. Surprisingly in the case functionalized IOHs, this study produced weak color shifts, possibly opening a path to detect directly living organism, which will need further investigations.
In complement to the well-established zwitterionic monomers 3-((2-(methacryloyloxy)ethyl)dimethylammonio)propane-1-sulfonate (“SPE”) and 3-((3-methacrylamidopropyl)dimethylammonio)propane-1-sulfonate (“SPP”), the closely related sulfobetaine monomers were synthesized and polymerized by reversible addition-fragmentation chain transfer (RAFT) polymerization, using a fluorophore labeled RAFT agent. The polyzwitterions of systematically varied molar mass were characterized with respect to their solubility in water, deuterated water, and aqueous salt solutions. These poly(sulfobetaine)s show thermoresponsive behavior in water, exhibiting upper critical solution temperatures (UCST). Phase transition temperatures depend notably on the molar mass and polymer concentration, and are much higher in D2O than in H2O. Also, the phase transition temperatures are effectively modulated by the addition of salts. The individual effects can be in parts correlated to the Hofmeister series for the anions studied. Still, they depend in a complex way on the concentration and the nature of the added electrolytes, on the one hand, and on the detailed structure of the zwitterionic side chain, on the other hand. For the polymers with the same zwitterionic side chain, it is found that methacrylamide-based poly(sulfobetaine)s exhibit higher UCST-type transition temperatures than their methacrylate analogs. The extension of the distance between polymerizable unit and zwitterionic groups from 2 to 3 methylene units decreases the UCST-type transition temperatures. Poly(sulfobetaine)s derived from aliphatic esters show higher UCST-type transition temperatures than their analogs featuring cyclic ammonium cations. The UCST-type transition temperatures increase markedly with spacer length separating the cationic and anionic moieties from 3 to 4 methylene units. Thus, apparently small variations of their chemical structure strongly affect the phase behavior of the polyzwitterions in specific aqueous environments.
Water-soluble block copolymers were prepared from the zwitterionic monomers and the non-ionic monomer N-isopropylmethacrylamide (“NIPMAM”) by the RAFT polymerization. Such block copolymers with two hydrophilic blocks exhibit twofold thermoresponsive behavior in water. The poly(sulfobetaine) block shows an UCST, whereas the poly(NIPMAM) block exhibits a lower critical solution temperature (LCST). This constellation induces a structure inversion of the solvophobic aggregate, called “schizophrenic micelle”. Depending on the relative positions of the two different phase transitions, the block copolymer passes through a molecularly dissolved or an insoluble intermediate regime, which can be modulated by the polymer concentration or by the addition of salt. Whereas, at low temperature, the poly(sulfobetaine) block forms polar aggregates that are kept in solution by the poly(NIPMAM) block, at high temperature, the poly(NIPMAM) block forms hydrophobic aggregates that are kept in solution by the poly(sulfobetaine) block. Thus, aggregates can be prepared in water, which switch reversibly their “inside” to the “outside”, and vice versa.
Diese Arbeit zu Grunde liegenden Forschung zielte darauf ab, neue schmelzbare Acrylnitril-Copolymere zu entwickeln. Diese sollten im Anschluss über ein Schmelzspinnverfahren zur Chemiefaser geformt und im letzten Schritt zur Carbonfaser konvertiert werden. Zu diesem Zweck wurden zunächst orientierende Untersuchungen an unterschiedlichen Copolymeren des Acrylnitril aus Lösungspolymerisation durchgeführt. Die Untersuchungen zeigten, dass elektrostatische Wechselwirkungen besser als sterische Abschirmung dazu geeignet sind, Schmelzbarkeit unterhalb der Zersetzungstemperatur von Polyacrylnitril zu bewirken. Aus der Vielzahl untersuchter Copolymere stellten sich jene mit Methoxyethylacrylat (MEA) als am effektivsten heraus. Für diese Copolymere wurden sowohl die Copolymerisationsparameter bestimmt als auch die grundlegende Kinetik der Lösungspolymerisation untersucht. Die Copolymere mit MEA wurden über Schmelzspinnen zur Faser umgeformt und diese dann untersucht. Hierbei wurden auch Einflüsse verschiedener Parameter, wie z.B. die der Molmasse, auf die Fasereigenschaften und -herstellung untersucht. Zuletzt wurde ein Heterophasenpolymerisationsverfahren zur Herstellung von Copolymeren aus AN/MEA entwickelt; dadurch konnten die Materialeigenschaften weiter verbessert werden. Zur Unterdrückung der thermoplastischen Eigenschaften der Fasern wurde ein geeignetes Verfahren entwickelt und anschließend die Konversion zu Carbonfasern durchgeführt.
Physikalische Hydrogele gewinnen derzeit als Zellsubstrate zunehmend an Interesse, da Viskoelastizität oder Stressrelaxation ein bedeutender Parameter in der Mechanotransduktion ist, der bisher vernachlässigt wurde. In dieser Arbeit wurden multi-funktionelle Polyurethane entworfen, die über einen neuartigen Gelierungsmechanismus physikalische Hydrogele bilden. In Wasser bilden die anionischen Polyurethane spontan Aggregate, welche durch elektrostatische Abstoßung in Lösung gehalten werden. Eine schnelle Gelierung kann von hier aus durch Ladungsabschirmung erreicht werden, wodurch die Aggregation voranschreitet und ein Netzwerk ausgebildet wird. Dies kann durch die Zugabe von verschiedenen Säuren oder Salzen geschehen, sodass sowohl saure (pH 4 - 5) als auch pH-neutrale Hydrogele erhalten werden können. Während konventionelle Hydrogele auf Polyurethan-Basis in der Regel durch toxische isocyanat-haltige Präpolymere hergestellt werden, eignet sich der hier beschriebene physikalische Gelierungsmechanismus für in situ Anwendungen in sensitiven Umgebungen. Sowohl Härte als auch Stressrelaxation der Hydrogele können unabhängig voneinander über einen breiten Bereich eingestellt werden. Darüberhinaus zeichnen sich die Hydrogele durch exzellente Stressregeneration aus.
The title compounds, [(1R,3R,4R,5R,6S)-4,5-bis(acetyloxy)-7-oxo-2-oxabicyclo-
[4.2.0]octan-3-yl]methyl acetate, C14H18O8, (I), [(1S,4R,5S,6R)-5-acetyloxy-7-
hydroxyimino-2-oxobicyclo[4.2.0]octan-4-yl acetate, C11H15NO6, (II), and
[(3aR,5R,6R,7R,7aS)-6,7-bis(acetyloxy)-2-oxooctahydropyrano[3,2-b]pyrrol-5-
yl]methyl acetate, C14H19NO8, (III), are stable bicyclic carbohydrate derivatives.
They can easily be synthesized in a few steps from commercially available
glycals. As a result of the ring strain from the four-membered rings in (I) and
(II), the conformations of the carbohydrates deviate strongly from the ideal
chair form. Compound (II) occurs in the boat form. In the five-membered
lactam (III), on the other hand, the carbohydrate adopts an almost ideal chair
conformation. As a result of the distortion of the sugar rings, the configurations
of the three bicyclic carbohydrate derivatives could not be determined from
their NMR coupling constants. From our three crystal structure determinations,
we were able to establish for the first time the absolute configurations of all new
stereocenters of the carbohydrate rings.
The title compounds, [(1R,3R,4R,5R,6S)-4,5-bis(acetyloxy)-7-oxo-2-oxabicyclo[4.2.0]octan-3-yl]methyl acetate, C14H18O8, (I), [(1S,4R,5S,6R)-5-acetyloxy-7-hydroxyimino-2-oxobicyclo[4.2.0]octan-4-yl acetate, C11H15NO6, (II), and [(3aR,5R,6R,7R,7aS)-6,7-bis(acetyloxy)-2-oxooctahydropyrano[3,2-b]pyrrol-5-yl]methyl acetate, C14H19NO8, (III), are stable bicyclic carbohydrate derivatives. They can easily be synthesized in a few steps from commercially available glycals. As a result of the ring strain from the four-membered rings in (I) and (II), the conformations of the carbohydrates deviate strongly from the ideal chair form. Compound (II) occurs in the boat form. In the five-membered lactam (III), on the other hand, the carbohydrate adopts an almost ideal chair conformation. As a result of the distortion of the sugar rings, the configurations of the three bicyclic carbohydrate derivatives could not be determined from their NMR coupling constants. From our three crystal structure determinations, we were able to establish for the first time the absolute configurations of all new stereocenters of the carbohydrate rings.
The novel combination of infrared matrix-assisted laser dispersion and ionization (IR-MALDI) with ion mobility (IM) spectrometry makes it possible to investigate biomolecules in their natural environment, liquid water. As an alternative to an ESI source, the IR-MALDI source was implemented in an in-house-developed ion mobility (IM) spectrometer. The release of ions directly from an aqueous solution is based on a phase explosion, induced by the absorption of an IR laser pulse (lambda = 2.94 mu m, 6 ns pulse width), which disperses the liquid as nano- and micro-droplets. The prerequisites for the application of IR-MALDI-IM spectrometry as an analytical method are narrow analyte ion signal peaks for a high spectrometer resolution. This can only be achieved by improving the desolvation of ions. One way to full desolvation is to give the cluster ions sufficient time to desolvate. Two methods for achieving this are studied: the implementation of an additional drift tube, as in ESI-IM-spectrometry, and the delayed extraction of the ions. As a result of this optimization procedure, limits of detection between 5 nM and 2.5 mu M as well as linear dynamic ranges of 2-3 orders of magnitude were obtained for a number of substances. The ability of this method to analyze simple mixtures is illustrated by the separation of two different surfactant mixtures.
Infrared matrix-assisted laser dispersion and ionization (IR-MALDI) in combination with ion mobility (IM) spectrometry enables the direct analysis of biomolecules in aqueous solution. The release of ions directly from an aqueous solution is based on a phase explosion, induced by the absorption of an IR laser pulse, which disperses the liquid as vapor, nano-and micro-droplets. The ionization process is characterized initially by a broad spatial distribution of the ions, which is a result of complex fluid dynamics and desolvation kinetics. These processes have a profound effect on the shape and width of the peaks in the IM spectra. In this work, the transport of ions by the phase explosion-induced shockwave could be studied independently from the transport by the electric field. The shockwave-induced mean velocities of the ions at different time scales were determined through IM spectrometry and shadowgraphy. The results show a deceleration of the ions from 118 m.s(-1) at a distance of 400 mu m from the liquid surface to 7.1 m.s(-1) at a distance of 10 mm, which is caused by a pile-up effect. Furthermore, the desolvation kinetics were investigated and a first-order desolvation constant of 325 +/- 50 s(-1) was obtained. In the second part, the IR-MALDI-IM spectrometer is used as an HPLC detector for the two-dimensional separation of a pesticide mixture.
An ellipsometric approach towards the description of inhomogeneous polymer-based Langmuir layers
(2016)
The applicability of nulling-based ellipsometric mapping as a complementary method next to Brewster angle microscopy (BAM) and imaging ellipsometry (IE) is presented for the characterization of ultrathin films at the air-water interface. First, the methodology is demonstrated for a vertically nonmoving Langmuir layer of star-shaped, 4-arm poly(omega-pentadecalactone) (PPDL-D4). Using nulling-based ellipsometric mapping, PPDL-D4-based inhomogeneously structured morphologies with a vertical dimension in the lower nm range could be mapped. In addition to the identification of these structures, the differentiation between a monolayer and bare water was possible. Second, the potential and limitations of this method were verified by applying it to more versatile Langmuir layers of telechelic poly[(rac-lactide)-co-glycolide]-diol (PLGA). All ellipsometric maps were converted into thickness maps by introduction of the refractive index that was derived from independent ellipsometric experiments, and the result was additionally evaluated in terms of the root mean square roughness, R-q. Thereby, a three-dimensional view into the layers was enabled and morphological inhomogeneity could be quantified.
The influence of terminal functionalization of oligo(epsilon-caprolactone)s (OCL) with phenylboronic acid pinacol ester or phenylboronic acid on the enzymatic degradation behavior at the air-water interface is investigated by the Langmuir monolayer degradation technique. While the unsubstituted OCL immediately degrades after injection of the enzyme lipase from Pseudomonas cepacia, enzyme molecules are incorporated into the films based on end-capped OCL before degradation. This incorporation of enzymes does not inhibit or suppress the film degradation, but retards it significantly. A specific binding of lipase to the polymer monolayer allows studying the enzymatic activity of bound proteins and the influence on the degradation process. The functionalization of a macromolecule with phenyl boronic acid groups is an approach to investigate their interactions with diol-containing biomolecules like sugars and to monitor their specified impact on the enzymatic degradation behavior at the air-water interface.
WavePacket
(2016)
WavePacket is an open-source program package for the numerical simulation of quantum-mechanical dynamics. It can be used to solve time-independent or time-dependent linear Schrödinger and Liouville–von Neumann-equations in one or more dimensions. Also coupled equations can be treated, which allows to simulate molecular quantum dynamics beyond the Born–Oppenheimer approximation. Optionally accounting for the interaction with external electric fields within the semiclassical dipole approximation, WavePacket can be used to simulate experiments involving tailored light pulses in photo-induced physics or chemistry. The graphical capabilities allow visualization of quantum dynamics ‘on the fly’, including Wigner phase space representations. Being easy to use and highly versatile, WavePacket is well suited for the teaching of quantum mechanics as well as for research projects in atomic, molecular and optical physics or in physical or theoretical chemistry. The present Part I deals with the description of closed quantum systems in terms of Schrödinger equations. The emphasis is on discrete variable representations for spatial discretization as well as various techniques for temporal discretization. The upcoming Part II will focus on open quantum systems and dimension reduction; it also describes the codes for optimal control of quantum dynamics. The present work introduces the MATLAB version of WavePacket 5.2.1 which is hosted at the Sourceforge platform, where extensive Wiki-documentation as well as worked-out demonstration examples can be found.
Optical biosensors based on porous silicon were fabricated by metal assisted chemical etching. Thereby double layered porous silicon structures were obtained consisting of porous pillars with large pores on top of a porous silicon layer with smaller pores. These structures showed a similar sensing performance in comparison to electrochemically produced porous silicon interferometric sensors.
Responsive inverse opal hydrogels functionalized by boroxole moieties were synthesized and explored as sensor platforms for various low molar mass as well as polymeric diols and polyols, including saccharides, glycopolymers and catechols, by exploiting the diol induced modulation of their structural color. The underlying thermoresponsive water-soluble copolymers and hydrogels exhibit a coil-to-globule or volume phase transition, respectively, of the LCST-type. They were prepared from oligoethylene oxide methacrylate (macro)monomers and functionalized via copolymerization to bear benzoboroxole moieties. The resulting copolymers represent weak polyacids, which can bind specifically to diols within an appropriate pH window. Due to the resulting modulation of the overall hydrophilicity of the systems and the consequent shift of their phase transition temperature, the usefulness of such systems for indicating the presence of catechols, saccharides, and glycopolymers was studied, exploiting the diol/polyol induced shifts of the soluble polymers’ cloud point, or the induced changes of the hydrogels’ swelling. In particular, the increased acidity of benzoboroxoles compared to standard phenylboronic acids allowed performing the studies in PBS buffer (phosphate buffered saline) at the physiologically relevant pH of 7.4. The inverse opals constructed of these thermo- and analyte-responsive hydrogels enabled following the binding of specific diols by the induced shift of the optical stop band. Their highly porous structure enabled the facile and specific optical detection of not only low molar mass but also of high molar mass diol/polyol analytes such as glycopolymers. Accordingly, such thermoresponsive inverse opal systems functionalized with recognition units represent attractive and promising platforms for the facile sensing of even rather big analytes by simple optical means, or even by the bare eye.
Extraction of model contaminants from solid surfaces by environmentally compatible microemulsions
(2016)
In the present contribution, we evaluate the efficiency of eco-friendly microemulsions to decontaminate solid surfaces by monitoring the extraction of non-toxic simulants of sulfur mustard out of model surfaces. The extraction process of the non-toxic simulants has been monitored by means of spectroscopic and chromatographic techniques. The kinetics of the removal process was analyzed by different empirical models. Based on the analysis of the kinetics, we can assess the influence of the amounts of oil and water and the microemulsion structure on the extraction process. (C) 2016 Elsevier Inc. All rights reserved.
We report on an extension of the previously established concept of oligospiroketal (OSK) rods by replacing a part or all ketal moieties by thioketals leading to oligospirothioketal (OSTK) rods. In this way, some crucial problems arising from the reversible formation of ketals are circumvented. Furthermore, the stability of the rods toward hydrolysis is considerably improved. To successfully implement this concept, we first developed a number of new oligothiol building blocks and improved the synthetic accessibility of known oligothiols, respectively. Another advantage of thioacetals is that terephthalaldehyde (TAA) sleeves, which are too flexible in the case of acetals can be used in OSTK rods. The viability of the OSTK approach was demonstrated by the successful preparation of some OSTK rods with a length of some nanometers.
The construction of a low-cost potentiostat and an electrochemical cell are described. Both have been used for the potentiostatic deposition of conducting polymers on FTO-coated glass. According to a reported procedure from literature an electrochromic window has been prepared and tested. Furthermore a novel window containing an additional electrodeposited polymer layer that shows a more pronounced electrochromism than the literature example is described for the first time. The required chemicals are inexpensive as well as the entire electrochemical equipment.
Herein we present an efficient synthesis of a biomimetic probe with modular construction that can be specifically bound by the mannose binding FimH protein - a surface adhesion protein of E. coli bacteria. The synthesis combines the new and interesting DBD dye with the carbohydrate ligand mannose via a Click reaction. We demonstrate the binding to E. coli bacteria over a large concentration range and also present some special characteristics of those molecules that are of particular interest for the application as a biosensor. In particular, the mix-and-measure ability and the very good photo-stability should be highlighted here.
The mechanism of nanotriangle formation in multivesicular vesicles (MMV) is investigated by using time-dependent SAXS measurements in combination with UV-vis spectroscopy, light, and transmission electron microscopy. In the first time period 6.5 nm sized spherical gold nanoparticles are formed inside of the vesicles, which build up soft nanoparticle aggregates. a) In situ SAXS experiments show a linear increase of the volume and molar mass of nanotriangles in the second time period. The volume growth rate of the triangles is 16.1 nm(3)/min, and the growth rate in the vertical direction is only 0.02 nm/min. Therefore, flat nanotriangles with a thickness of 7 nm and a diameter of 23 nm are formed. This process can be described by a diffusion limited Ostwald ripening growth mechanism. TEM micrographs visualize soft coral-like structures with thin nanoplatelets at the periphery of the aggregates, which disaggregate in the third time period into nanotriangles and spherical particles. The 16 times faster growth of nanotriangles in the lateral than that in the vertical direction is related to the adsorption of symmetry breaking components, i.e., AOT and the polyampholyte PalPhBisCarb, on the {111} facets of the gold nanoplatelets in combination with confinement effects of the vesicular template phase.
In this study, a new reliable, economic, and environmentally-friendly one-step synthesis is established to obtain carbon nanodots (CNDs) with well-defined and reproducible photoluminescence (PL) properties via the microwave-assisted hydrothermal treatment of starch and Tris-acetate-EDTA (TAE) buffer as carbon sources. Three kinds of CNDs are prepared using different sets of above mentioned starting materials. The as-synthesized CNDs: C-CND (starch only), N-CND 1 (starch in TAE) and N-CND 2 (TAE only) exhibit highly homogenous PL and are ready to use without need for further purification. The CNDs are stable over a long period of time (>1 year) either in solution or as freeze-dried powder. Depending on starting material, CNDs with PL quantum yield (PLQY) ranging from less than 1% up to 28% are obtained. The influence of the precursor concentration, reaction time and type of additives on the optical properties (UV-Vis absorption, PL emission spectrum and PLQY) is carefully investigated, providing insight into the chemical processes that occur during CND formation. Remarkably, upon freeze-drying the initially brown CND-solution turns into a non-fluorescent white/slightly brown powder which recovers PL in aqueous solution and can potentially be applied as fluorescent marker in bio-imaging, as a reduction agent or as a photocatalyst.
DNA origami nanostructures are a versatile tool to arrange metal nanostructures and other chemical entities with nanometer precision. In this way gold nanoparticle dimers with defined distance can be constructed, which can be exploited as novel substrates for surface enhanced Raman scattering (SERS). We have optimized the size, composition and arrangement of Au/Ag nanoparticles to create intense SERS hot spots, with Raman enhancement up to 1010, which is sufficient to detect single molecules by Raman scattering. This is demonstrated using single dye molecules (TAMRA and Cy3) placed into the center of the nanoparticle dimers. In conjunction with the DNA origami nanostructures novel SERS substrates are created, which can in the future be applied to the SERS analysis of more complex biomolecular targets, whose position and conformation within the SERS hot spot can be precisely controlled.
The folding of single-stranded telomeric DNA into guanine (G) quadruplexes is a conformational change that plays a major role in sensing and drug targeting. The telomeric DNA can be placed on DNA origami nanostructures to make the folding process extremely selective for K+ ions even in the presence of high Na+ concentrations. Here, we demonstrate that the K+-selective G-quadruplex formation is reversible when using a cryptand to remove K+ from the G-quadruplex. We present a full characterization of the reversible switching between single-stranded telomeric DNA and G-quadruplex structures using Förster resonance energy transfer (FRET) between the dyes fluorescein (FAM) and cyanine3 (Cy3). When attached to the DNA origami platform, the G-quadruplex switch can be incorporated into more complex photonic networks, which is demonstrated for a three-color and a four-color FRET cascade from FAM over Cy3 and Cy5 to IRDye700 with G-quadruplex-Cy3 acting as a switchable transmitter.
Polysarcosine (Mn = 3650–20 000 g mol−1, Đ ∼ 1.1) was synthesized from the air and moisture stable N-phenoxycarbonyl-N-methylglycine. Polymerization was achieved by in situ transformation of the urethane precursor into the corresponding N-methylglycine-N-carboxyanhydride, when in the presence of a non-nucleophilic tertiary amine base and a primary amine initiator.
The excitation of localized surface plasmons in noble metal nanoparticles (NPs) results in different nanoscale effects such as electric field enhancement, the generation of hot electrons and a temperature increase close to the NP surface. These effects are typically exploited in diverse fields such as surface-enhanced Raman scattering (SERS), NP catalysis and photothermal therapy (PTT). Halogenated nucleobases are applied as radiosensitizers in conventional radiation cancer therapy due to their high reactivity towards secondary electrons. Here, we use SERS to study the transformation of 8-bromoadenine (8BrA) into adenine on the surface of Au and AgNPs upon irradiation with a low-power continuous wave laser at 532, 633 and 785 nm, respectively. The dissociation of 8BrA is ascribed to a hot-electron transfer reaction and the underlying kinetics are carefully explored. The reaction proceeds within seconds or even milliseconds. Similar dissociation reactions might also occur with other electrophilic molecules, which must be considered in the interpretation of respective SERS spectra. Furthermore, we suggest that hot-electron transfer induced dissociation of radiosensitizers such as 8BrA can be applied in the future in PTT to enhance the damage of tumor tissue upon irradiation.
Macrocycles based on L-cystine were synthesized by ring-closing metathesis (RCM) and subsequently polymerized by entropy-driven ring-opening metathesis polymerization (ED-ROMP). Monomer conversion reached ∼80% in equilibrium and the produced poly(ester-amine-disulfide-alkene)s exhibited apparent molar masses (Mappw) of up to 80 kDa and dispersities (Đ) of ∼2. The polymers can be further functionalized with acid anhydrides and degraded by reductive cleavage of the main-chain disulfide.
Proteins are natural polypeptides produced by cells; they can be found in both animals and plants, and possess a variety of functions. One of these functions is to provide structural support to the surrounding cells and tissues. For example, collagen (which is found in skin, cartilage, tendons and bones) and keratin (which is found in hair and nails) are structural proteins. When a tissue is damaged, however, the supporting matrix formed by structural proteins cannot always spontaneously regenerate. Tailor-made synthetic polypeptides can be used to help heal and restore tissue formation.
Synthetic polypeptides are typically synthesized by the so-called ring opening polymerization (ROP) of α-amino acid N-carboxyanhydrides (NCA). Such synthetic polypeptides are generally non-sequence-controlled and thus less complex than proteins. As such, synthetic polypeptides are rarely as efficient as proteins in their ability to self-assemble and form hierarchical or structural supramolecular assemblies in water, and thus, often require rational designing. In this doctoral work, two types of amino acids, γ-benzyl-L/D-glutamate (BLG / BDG) and allylglycine (AG), were selected to synthesize a series of (co)polypeptides of different compositions and molar masses.
A new and versatile synthetic route to prepare polypeptides was developed, and its mechanism and kinetics were investigated. The polypeptide properties were thoroughly studied and new materials were developed from them. In particular, these polypeptides were able to aggregate (or self-assemble) in solution into microscopic fibres, very similar to those formed by collagen. By doing so, they formed robust physical networks and organogels which could be processed into high water-content, pH-responsive hydrogels. Particles with highly regular and chiral spiral morphologies were also obtained by emulsifying these polypeptides. Such polypeptides and the materials derived from them are, therefore, promising candidates for biomedical applications.
Surface-enhanced Raman scattering (SERS) is a promising tool to obtain rich chemical information about analytes at trace levels. However, in order to perform selective experiments on individual molecules, two fundamental requirements have to be fulfilled. On the one hand, areas with high local field enhancement, so-called “hot spots”, have to be created by positioning the supporting metal surfaces in close proximity to each other. In most cases hot spots are formed in the gap between adjacent metal nanoparticles (NPs). On the other hand, the analyte has to be positioned directly in the hot spot in order to profit from the highest signal amplification. The use of DNA origami substrates provides both, the arrangement of AuNPs with nm precision as well as the ability to bind analyte molecules at predefined positions. Consequently, the present cumulative doctoral thesis aims at the development of a novel SERS substrate based on a DNA origami template. To this end, two DNA-functionalized gold nanoparticles (AuNPs) are attached to one DNA origami substrate resulting in the formation of a AuNP dimer and thus in a hot spot within the corresponding gap. The obtained structures are characterized by correlated atomic force microscopy (AFM) and SERS imaging which allows for the combination of structural and chemical information.
Initially, the proof-of principle is presented which demonstrates the potential of the novel approach. It is shown that the Raman signal of 15 nm AuNPs coated with dye-modified DNA
(dye: carboxytetramethylrhodamine (TAMRA)) is significantly higher for AuNP dimers arranged on a DNA origami platform in comparison to single AuNPs. Furthermore, by attaching single TAMRA molecules in the hot spot between two 5 nm AuNPs and optimizing the size of the AuNPs by electroless gold deposition, SERS experiments at the few-molecule level are presented. The initially used DNA origami-AuNPs design is further optimized in many respects. On the one hand, larger AuNPs up to a diameter of 60 nm are used which are additionally treated with a silver enhancement solution to obtain Au-Ag-core-shell NPs. On the other hand, the arrangement of both AuNPs is altered to improve the position of the dye molecule within the hot spot as well as to decrease the gap size between the two particles. With the optimized design the detection of single dye molecules (TAMRA and cyanine 3 (Cy3)) by means of SERS is demonstrated. Quantitatively, enhancement factors up to 10^10 are estimated which is sufficiently high to detect single dye molecules.
In the second part, the influence of graphene as an additional component of the SERS substrate is investigated. Graphene is a two-dimensional material with an outstanding combination of electronical, mechanical and optical properties. Here, it is demonstrated that
single layer graphene (SLG) replicates the shape of underlying non-modified DNA origami
substrates very well, which enables the monitoring of structural alterations by AFM imaging.
In this way, it is shown that graphene encapsulation significantly increases the structural
stability of bare DNA origami substrates towards mechanical force and prolonged exposure
to deionized water.
Furthermore, SLG is used to cover DNA origami substrates which are functionalized with a
40 nm AuNP dimer. In this way, a novel kind of hybrid material is created which exhibits
several advantages compared to the analogue non-covered SERS substrates. First, the fluorescence background of dye molecules that are located in between the AuNP surface and SLG is efficiently reduced. Second, the photobleaching rate of the incorporated dye molecules is decreased up to one order of magnitude. Third, due to the increased photostability of the investigated dye molecules, the performance of polarization-dependent series measurements on individual structures is enabled. This in turn reveals extensive information about the dye molecules in the hot spot as well as about the strain induced within the graphene lattice.
Although SLG can significantly influence the SERS substrate in the aforementioned ways, all
those effects are strongly related to the extent of contact with the underlying AuNP dimer.
Ionothermal carbon materials
(2016)
Alternative concepts for energy storage and conversion have to be developed, optimized and employed to fulfill the dream of a fossil-independent energy economy. Porous carbon materials play a major role in many energy-related devices. Among different characteristics, distinct porosity features, e.g., specific surface area (SSA), total pore volume (TPV), and the pore size distribution (PSD), are important to maximize the performance in the final device. In order to approach the aim to synthesize carbon materials with tailor-made porosity in a sustainable fashion, the present thesis focused on biomass-derived precursors employing and developing the ionothermal carbonization.
During the ionothermal carbonization, a salt melt simultaneously serves as solvent and porogen. Typically, eutectic mixtures containing zinc chloride are employed as salt phase. The first topic of the present thesis addressed the possibility to precisely tailor the porosity of ionothermal carbon materials by an experimentally simple variation of the molar composition of the binary salt mixture. The developed pore tuning tool allowed the synthesis of glucose derived carbon materials with predictable SSAs in the range of ~ 900 to ~ 2100 m2 g-1. Moreover, the nucleobase adenine was employed as precursor introducing nitrogen functionalities in the final material. Thereby, the chemical properties of the carbon materials are varied leading to new application fields. Nitrogen doped carbons (NDCs) are able to catalyze the oxygen reduction reaction (ORR) which takes place on the cathodic site of a fuel cell. The herein developed porosity tailoring allowed the synthesis of adenine derived NDCs with outstanding SSAs of up to 2900 m2 g-1 and very large TPV of 5.19 cm3 g-1. Furthermore, the influence of the porosity on the ORR could be directly investigated enabling the precise optimization of the porosity characteristics of NDCs for this application. The second topic addressed the development of a new method to investigate the not-yet unraveled mechanism of the oxygen reduction reaction using a rotating disc electrode setup. The focus was put on noble-metal free catalysts. The results showed that the reaction pathway of the investigated catalysts is pH-dependent indicating different active species at different pH-values. The third topic addressed the expansion of the used salts for the ionothermal approach towards hydrated calcium and magnesium chloride. It was shown that hydrated salt phases allowed the introduction of a secondary templating effect which was connected to the coexistence of liquid and solid salt phases. The method enabled the synthesis of fibrous NDCs with SSAs of up to 2780 m2 g-1 and very large TPV of 3.86 cm3 g-1. Moreover, the concept of active site implementation by a facile low-temperature metalation employing the obtained NDCs as solid ligands could be shown for the first time in the context of ORR.
Overall, the thesis may pave the way towards highly porous carbon with tailor-made porosity materials prepared by an inexpensive and sustainable pathway, which can be applied in energy related field thereby supporting the needed expansion of the renewable energy sector.
In the interest of producing functional catalysts from sustainable building-blocks, 1, 3-dicarboxylate imidazolium salts derived from amino acids were successfully modified to be suitable as N-Heterocyclic carbene (NHC) ligands within metal complexes. Complexes of Ag(I), Pd(II), and Ir(I) were successfully produced using known procedures using ligands derived from glycine, alanine, β-alanine and phenylalanine. The complexes were characterized in solid state using X-Ray crystallography, which allowed for the steric and electronic comparison of these ligands to well-known NHC ligands within analogous metal complexes.
The palladium complexes were tested as catalysts for aqueous-phase Suzuki-Miyaura cross-coupling. Water-solubility could be induced via ester hydrolysis of the N-bound groups in the presence of base. The mono-NHC–Pd complexes were seen to be highly active in the coupling of aryl bromides with phenylboronic acid; the active catalyst of which was determined to be mostly Pd(0) nanoparticles. Kinetic studies determined that reaction proceeds quickly in the coupling of bromoacetophenone, for both pre-hydrolyzed and in-situ hydrolysis catalyst dissolution. The catalyst could also be recycled for an extra run by simply re-using the aqueous layer.
The imidazolium salts were also used to produce organosilica hybrid materials. This was attempted via two methods: by post-grafting onto a commercial organosilica, and co-condensation of the corresponding organosilane. The co-condensation technique harbours potential for the production of solid-support catalysts.
Due to the adsorption of biomolecules, the control of the biodistribution of nanoparticles is still one of the major challenges of nanomedicine. Poly(2-ethyl-2-oxazoline) (PEtOx) for surface modification of nanoparticles is applied and both protein adsorption and cellular uptake of PEtOxylated nanoparticles versus nanoparticles coated with poly(ethylene glycol) (PEG) and non-coated positively and negatively charged nanoparticles are compared. Therefore, fluorescent poly(organosiloxane) nanoparticles of 15 nm radius are synthesized, which are used as a scaffold for surface modification in a grafting onto approach. With multi-angle dynamic light scattering, asymmetrical flow field-flow fractionation, gel electrophoresis, and liquid chromatography-mass spectrometry, it is demonstrated that protein adsorption on PEtOxylated nanoparticles is extremely low, similar as on PEGylated nanoparticles. Moreover, quantitative microscopy reveals that PEtOxylation significantly reduces the non-specific cellular uptake, particularly by macrophage-like cells. Collectively, studies demonstrate that PEtOx is a very effective alternative to PEG for stealth modification of the surface of nanoparticles.
2-Fluoroadenine ((2F)A) is a therapeutic agent, which is suggested for application in cancer radiotherapy. The molecular mechanism of DNA radiation damage can be ascribed to a significant extent to the action of low-energy (<20 eV) electrons (LEEs), which damage DNA by dissociative electron attachment. LEE induced reactions in (2F)A are characterized both isolated in the gas phase and in the condensed phase when it is incorporated into DNA. Information about negative ion resonances and anion-mediated fragmentation reactions is combined with an absolute quantification of DNA strand breaks in (2F)A-containing oligonucleotides upon irradiation with LEEs. The incorporation of (2F)A into DNA results in an enhanced strand breakage. The strand-break cross sections are clearly energy dependent, whereas the strand-break enhancements by (2F)A at 5.5, 10, and 15 eV are very similar. Thus, (2F)A can be considered an effective radiosensitizer operative at a wide range of electron energies.
In this study, a new reliable, economic, and environmentally-friendly one-step synthesis is established to obtain carbon nanodots (CNDs) with well-defined and reproducible photoluminescence (PL) properties via the microwave-assisted hydrothermal treatment of starch and Tris-acetate-EDTA (TAE) buffer as carbon sources. Three kinds of CNDs are prepared using different sets of above mentioned starting materials. The as-synthesized CNDs: C-CND (starch only), N-CND 1 (starch in TAE) and N-CND 2 (TAE only) exhibit highly homogenous PL and are ready to use without need for further purification. The CNDs are stable over a long period of time (> 1 year) either in solution or as freeze-dried powder. Depending on starting material, CNDs with PL quantum yield (PLQY) ranging from less than 1% up to 28% are obtained. The influence of the precursor concentration, reaction time and type of additives on the optical properties (UV-Vis absorption, PL emission spectrum and PLQY) is carefully investigated, providing insight into the chemical processes that occur during CND formation. Remarkably, upon freeze-drying the initially brown CND-solution turns into a non-fluorescent white/slightly brown powder which recovers PL in aqueous solution and can potentially be applied as fluorescent marker in bio-imaging, as a reduction agent or as a photocatalyst.