Spectroscopic properties from hybrid QM, MM molecular dynamics simulation

The central aim of this thesis work is the application and further development of a hybrid quantum mechanical/molecular mechanics (QM/MM) based approach to compute spectroscopic properties of molecules in complex chemical environments from electronic structure theory. In the framework of this thesis, an existing density functional theory implementation of the QM/MM approach is first used to calculate the nuclear magnetic resonance (NMR) solvent shifts of an adenine molecule in aqueous solution. The findings show that the aqueous solvation with its strongly fluctuating hydrogen bond network leads to specific changes in the NMR resonance lines. Besides the absolute values, also the ordering of the NMR lines changes under the influence of the solvating water molecules. Without the QM/MM scheme, a quantum chemical calculation could have led to an incorrect assignment of these lines. The second part of this thesis describes a methodological improvement of the QM/MM method that is designed for cases in which a covalent chemical bond crosses the QM/MM boundary. The development consists in an automatized protocol to optimize a so-called capping potential that saturates the electronic subsystem in the QM region. The optimization scheme is capable of tuning the parameters in such a way that the deviations of the electronic orbitals between the regular and the truncated (and "capped") molecule are minimized. This in turn results in a considerable improvement of the structural and spectroscopic parameters when computed with the new optimized capping potential within the QM/MM technique. This optimization scheme is applied and benchmarked on the example of truncated carbon-carbon bonds in a set of small test molecules. It turns out that the optimized capping potentials yield an excellent agreement of NMR chemical shifts and protonation energies with respect to the corresponding full molecules. These results are very promising, so that the application to larger biological complexes will significantly improve the reliability of the prediction of the related spectroscopic properties.

Assessing the functional structure of molecular transporters by EPR spectroscopy

In this thesis, the self-assembled functional structure of a broad range of amphiphilic molecular transporters is studied. By employing paramagnetic probe molecules and ions, continuous-wave and pulse electron paramagnetic resonance spectroscopy reveal information about the local structure of these materials from the perspective of incorporated guest molecules. First, the transport function of human serum albumin for fatty acids is in the focus. As suggested by the crystal structure, the anchor points for the fatty acids are distributed asymmetrically in the protein. In contrast to the crystallographic findings, a remarkably symmetric entry point distribution of the fatty acid binding channels is found, which may facilitate the uptake and release of the guest molecules. Further, the metal binding of 1,2,3-triazole modified star-shaped cholic acid oligomers is studied. These biomimetic molecules are able to include and transport molecules in solvents of different polarity. A pre-arrangement of the triazole groups induces a strong chelate-like binding and close contact between guest molecule and metal ion. In absence of a preordering, each triazole moiety acts as a single entity and the binding affinity for metal ions is strongly decreased. Hydrogels based on N-isopropylacrylamide phase separate from water above a certain temperature. The macroscopic thermal collapse of these hydrogels is utilized as a tool for dynamic nuclear polarization. It is shown that a radical-free hyperpolarized solution can be achieved with a spin-labeled gel as separable matrix. On the nanoscale, these hydrogels form static heterogeneities in both structure and function. Collapsed regions protect the spin probes from a chemical decay while open, water-swollen regions act as catalytic centers. Similarly, thermoresponsive dendronized polymers form structural heterogeneities, which are, however, highly dynamic. At the critical temperature, they trigger the aggregation of the polymer into mesoglobules. The dehydration of these aggregates is a molecularly controlled non-equilibrium process that is facilitated by a hydrophobic dendritic core. Further, a slow heating rate results in a kinetically entrapped non-equilibrium state due to the formation of an impermeable dense polymeric layer at the periphery of the mesoglobule.

Inorganic-organic hybrid polymers: Solution-processible coating materials for defined surface functionalization

A new class of inorganic-organic hybrid polymers could successfully been prepared by the combination of different polymerization techniques. The access to a broad range of organic polymers incorporated into the hybrid polymer was realized using two independent approaches.rnIn the first approach a functional poly(silsesquioxane) (PSSQ) network was pre-formed, which was capable to initiate a controlled radical polymerization to graft organic vinyl-type monomers from the PSSQ precursor. As controlled radical polymerization techniques atom transfer radical polymerization (ATRP), as well as reversible addition fragmentation chain transfer (RAFT) polymerization could be used after defined tuning of the PSSQ precursor either toward a PSSQ macro-initiator or to a PSSQ macro-chain-transfer-agent. The polymerization pathway, consisting of polycondensation of trialkoxy-silanes followed by grafting-from polymerization of different monomers, allowed synthesis of various functional hybrid polymers. A controlled synthesis of the PSSQ precursors could successfully be performed using a microreactor setup; the molecular weight could be adjusted easily while the polydispersity index could be decreased well below 2.rnThe second approach aimed to incorporate differently derived organic polymers. As examples, polycarbonate and poly(ethylene glycol) were end-group-modified using trialkoxysilanes. After end-group-functionalization these organic polymers could be incorporated into a PSSQ network.rnThese different hybrid polymers showed extraordinary coating abilities. All polymers could be processed from solution by spin-coating or dip-coating. The high amount of reactive silanol moieties in the PSSQ part could be cross-linked after application by annealing at 130° for 1h. Not only cross-linking of the whole film was achieved, which resulted in mechanical interlocking with the substrate, also chemical bonds to metal or metal oxide surfaces were formed. All coating materials showed high stability and adhesion onto various underlying materials, reaching from metals (like steel or gold) and metal oxides (like glass) to plastics (like polycarbonate or polytetrafluoroethylene).rnAs the material and the synthetic pathway were very tolerant toward different functionalities, various functional monomers could be incorporated in the final coating material. The incorporation of N-isopropylacrylamide yielded in temperature-responsive surface coatings, whereas the incorporation of redox-active monomers allowed the preparation of semi-conductive coatings, capable to produce smooth hole-injection layers on transparent conductive electrodes used in optoelectronic devices.rnThe range of possible applications could be increased tremendously by incorporation of reactive monomers, capable to undergo fast and quantitative conversions by polymer-analogous reactions. For example, grafting active esters from a PSSQ precursor yielded a reactive surface coating after application onto numerous substrates. Just by dipping the coated substrate into a solution of a functionalized amine, the desired function could be immobilized at the interface as well as throughout the whole film. The obtained reactive surface coatings could be used as basis for different functional coatings for various applications. The conversion with specifically tuned amines yielded in surfaces with adjustable wetting behaviors, switchable wetting behaviors or as recognition element for surface-oriented bio-analytical devices. The combination of hybrid materials with orthogonal reactivities allowed for the first time the preparation of multi-reactive surfaces which could be functionalized sequentially with defined fractions of different groups at the interface. rnThe introduced concept to synthesis functional hybrid polymers unifies the main requirements on an ideal coating material. Strong adhesion on a wide range of underlying materials was achieved by secondary condensation of the PSSQ part, whereas the organic part allowed incorporation of various functionalities. Thus, a flexible platform to create functional and reactive surface coatings was achieved, which could be applied to different substrates. rn

DNA hybrid materials consisting of oligonucleotides and organic molecules: synthesis, characterization and applications

The goal of this thesis was to increase the functionality of pristine DNA scaffolds by functionalizing them with fluorescent dyes and hydrophobic moieties. Two important steps were necessary to realize this aim successfully. First, nucleic acids needed to be synthesized making use of multidisciplinary toolbox for the generation and manipulation of polynucleic acids. The most important techniques were the solid phase synthesis involving the incorporation of standard and modified phosphoramidite building blocks as well as molecular biology procedures like the polymerase chain reaction, the bacterial amplification of plasmids and the enzymatic digestion of circular vectors. Second, and evenly important, was the characterization of the novel bioorganic hybrid structures by a multitude of techniques, especially optical measurements. For studying DNA-dye conjugates methods like UV/Vis and photoluminescence spectroscopy as well as time resolved luminescence spectroscopy were utilized. While these measurements characterized the bulk behavior of an ensemble of DNA-dye hybrids it was necessary for a complete understanding of the systems to look at single structures. This was done by single-molecule fluorescence spectroscopy and fluorescence correlation spectroscopy. For complete analysis the optical experiments were complemented by direct visualization techniques, i.e. high resolution transmission electron microscopy and scanning force microscopy.

Advances in hardware and molecular design of polarizing agents for dynamic nuclear polarization

Die Kernmagnetresonanz (NMR) ist eine vielseitige Technik, die auf spin-tragende Kerne angewiesen ist. Seit ihrer Entdeckung ist die Kernmagnetresonanz zu einem unverzichtbaren Werkzeug in unzähligen Anwendungen der Physik, Chemie, Biologie und Medizin geworden. Das größte Problem der NMR ist ihre geringe Sensitivtät auf Grund der sehr kleinen Energieaufspaltung bei Raumtemperatur. Für Protonenspins, die das größte magnetogyrische Verhältnis besitzen, ist der Polarisationsgrad selbst in den größten verfügbaren Magnetfeldern (24 T) nur ~7*10^(-5).rnDurch die geringe inhärente Polarisation ist folglich eine theoretische Sensitivitätssteigerung von mehr als 10^4 möglich. rnIn dieser Arbeit wurden verschiedene technische Aspekte und unterschiedliche Polarisationsagenzien für Dynamic Nuclear Polarization (DNP) untersucht.rnDie technische Entwicklung des mobilen Aufbaus umfasst die Verwendung eines neuen Halbach Magneten, die Konstruktion neuer Probenköpfe und den automatisierten Ablauf der Experimente mittels eines LabVIEW basierten Programms. Desweiteren wurden zwei neue Polarisationsagenzien mit besonderen Merkmalen für den Overhauser und den Tieftemperatur DNP getestet. Zusätzlich konnte die Durchführbarkeit von NMR Experimenten an Heterokernen (19F und 13C) im mobilen Aufbau bei 0,35 T gezeigt werden. Diese Ergebnisse zeigen die Möglichkeiten der Polarisationstechnik DNP auf, wenn Heterokerne mit einem kleinen magnetogyrischen Verhältnis polarisiert werden müssen.rnDie Sensitivitätssteigerung sollte viele neue Anwendungen, speziell in der Medizin, ermöglichen.

Spinpolarisierte Rastertunnelmikroskopie magnetischer Nanostrukturen am Beispiel von bcc-Co/Fe(110), Fe/Mo(110) und Kupfer-Phthalocyanin/Fe(110)

In dieser Arbeit werden, nach einer Einführung in die spinpolarisierte Rastertunnelmikroskopie und -spektroskopie als experimentelle Methode zur Untersuchung magnetischer Nanostrukturen, Ergebnisse zur spinpolarisierten elektronischen Struktur in Abhängigkeit von der Kristallstruktur am Beispiel ultradünner Co-Schichten sowie in Abhängigkeit von der Magnetisierungsrichtung für ultradünne Fe-Schichten vorgestellt. Hochaufgelöste Messungen zeigen die ortsabhängige Spinpolarisation auf einem einzelnen Kupfer-Phthalocyanin Molekül. rnrnKobalt wurde durch pseudomorphes Wachstum auf den (110)-Oberflächen der kubisch raumzentrierten Metalle Chrom und Eisen deponiert. Im Unterschied zu früheren Berichten in der Literatur lassen sich nur zwei Lagen Co in der kubisch raumzentrierten (bcc) Ordnung stabilisieren. Die bcc-Co Schichten auf der Fe(110)-Oberfläche zeigen keine Anzeichen von epitaktischen Verzerrungen. rnDickere Schichten rekonstruieren in eine dicht gepackte Struktur (hcp/fcc). Durch die bcc Ordnung wird die Spinpolarisation von Kobalt auf P=62% erhöht (hcp-Co: P=45%). rnrnDie temperaturabhängige Spinreorientierung (SRT) ultradünner Filme Fe/Mo(110) wurde mit spinpolarisierter Spektroskopie untersucht. Eine Neuausrichtung der Magnetisierung aus der senkrechten [110]-Achse in die in der Ebene liegenden [001]-Achse wird bei T=(13,2+-0,5)K festgestellt, wobei es sich um einen diskontinuierlichen Reorientierungsübergang handelt, d.h. die freie Energie weist innerhalb eines bestimmten Temperaturbereichs gleichzeitig zwei Minima auf. Weiterhin wird in der Mono- und Doppellage Fe/Mo(110 eine Abhängigkeit der elektronischen Struktur von der Ausrichtung der magnetisch leichten Achse und von der Magnetisierung beobachtet. rnrnDie Untersuchung des spinpolarisierten Ladungstransports durch ein Kupfer-Phthalocyanin-Molekül auf der Fe/Mo(110) Oberfläche liefert einen wesentlichen Beitrag zum Verständnis des Spintransports an der Grenzfläche zwischen Metall und organischem Molekül. Die HOMO-LUMO-Energielücke des freien Moleküls wird durch die Wechselwirkung mit der Metalloberfläche mit Grenzflächenzuständen gefüllt. Diese Zustände reduzieren die Spinpolarisation des durch das Molekül fließenden Tunnelstroms durch einen zusätzlichen unpolarisierten Strombeitrag um einen Faktor zwei. Spinpolarisierte hybridisierte Grenzflächenzustände mit größerem Abstand zur Fermi-Energie führen in Abhängigkeit von der Position auf dem Molekül zu weiteren Beiträgen zur effektiven Spinpolarisation. Diese Untersuchungen belegen die Möglichkeit einer effektiven Spininjektion in organische Halbleiter und damit das Potential dieser Materialien für die weitere Entwicklung von Spintronik-Bauteilen.

Ab-initio study of hydrogen technology materials for hydrogen storage and proton conduction

This dissertation deals with two specific aspects of a potential hydrogen-based energy economy, namely the problems of energy storage and energy conversion. In order to contribute to the solution of these problems, the structural and dynamical properties of two promising materials for hydrogen storage (lithium imide/amide) and proton conduction (poly[vinyl phosphonic acid]) are modeled on an atomistic scale by means of first principles molecular dynamics simulation methods.rnrnrnIn the case of the hydrogen storage system lithium amide/imide (LiNH_2/Li_2NH), the focus was on the interplay of structural features and nuclear quantum effects. For these calculations, Path-Integral Molecular Dynamics (PIMD) simulations were used. The structures of these materials at room temperature were elucidated; in collaboration with an experimental group, a very good agreement between calculated and experimental solid-state 1H-NMR chemical shifts was observed. Specifically, the structure of Li_2NH features a disordered arrangement of the Li lattice, which was not reported in previous studies. In addition, a persistent precession of the NH bonds was observed in our simulations. We provide evidence that this precession is the consequence of a toroid-shaped effective potential, in which the protons in the material are immersed. This potential is essentially flat along the torus azimuthal angle, which might lead to important quantum delocalization effects of the protons over the torus.rnrnOn the energy conversion side, the dynamics of protons in a proton conducting polymer (poly[vinyl phosphonic acid], PVPA) was studied by means of a steered ab-initio Molecular Dynamics approach applied on a simplified polymer model. The focus was put on understanding the microscopic proton transport mechanism in polymer membranes, and on characterizing the relevance of the local environment. This covers particularly the effect of water molecules, which participate in the hydrogen bonding network in the material. The results indicate that these water molecules are essential for the effectiveness of proton conduction. A water-mediated Grotthuss mechanism is identified as the main contributor to proton conduction, which agrees with the experimentally observed decay on conductivity for the same material in the absence of water molecules.rnrnThe gain in understanding the microscopic processes and structures present in this materials can help the development of new materials with improved properties, thus contributing to the solution of problems in the implementation of fuel cells.

Synthese und Charakterisierung von multivalenten kationischen Tensiden und Polymeren

Der Einsatz von den Polyelektrolytkomplexen von DNA / RNA mit Polykationen oder Lipiden in der Gen-Therapie ist für Wissenschaftler von besonderem Interesse, da sie als Träger für den Transport von genetischem Material in lebende Zellen fungieren können. Interessant ist auch die Komplexbildung aus Gadolinium und Polykation, hier können die stabil gebildeten Aggregate als Kontrastmittel zur Anwendung in der Magnetresonanztomographie eingeführt werden. Ziel der vorliegenden Arbeit war es, strukturdefinierte, positiv geladene, polyvalente sperminanaloge Polymere zu synthetisieren. Durch die polyelektrolytische Natur erlauben solche Polymere die Komplexierung von mehr Gadolinium-Polyoxometalaten und wären deshalb sehr gut als Kontrastmittel geeignet. Aufbauend auf den Vorarbeiten, wurde insbesondere die Komplexbildung von kationischem Polymer mit der Green Fluorescent Protein DNA in physiologischem Salzgehalt untersucht. Die Beschreibung der Synthese im Rahmen dieser Arbeit zeigt, dass es mit dem entwickelten Syntheseprinzip, also unter Einsatz von orthogonaler Schutzgruppenchemie und funktionaler Transformation gelungen ist, durch einfache nukleophile Substitution die Kopplung der Elementareinheiten zu komplexeren, auch ionischen Tensiden durchzuführen. Die Komplexierung von Gadolinium-Polyoxometalat mit kationisch geladenem Polymer in reinem Wasser und in physiologischem Salzgehalt hat gezeigt, dass bei einem Ladungsverhältnis von ungefähr 2:1 stabile sphärische Komplexe gebildet werden. HeLa-Zellen zeigen keine hohe Empfindlichkeit gegenüber Polykation-POM-Komplexen, da deren toxische Wirkung nur einen Anteil toter Zellen von maximal 24 % zur Folge hatte. Die Bildqualität einer MRT-Aufnahme der gebildeten Polykation-POM-Komplexe wurde im Vergleich zu den reinen Gadolinium-Polyoxometalat-Lösungen erheblich verbessert. Die Komplexierung von DNA mit dem im Überschuss vorliegenden kationisch geladenen Polymer wurde mittels Rasterkraftmikroskopie, statischer sowie dynamischer Lichtstreuung untersucht. Die Molmasse und Größe der Polykation-DNA-Komplexe geben eindeutige Hinweise darauf, dass sich in physiologischer Salzlösung Multi-Ketten-Komplexe bilden. Neben der Untersuchung der Polymer-Komplexe wurde eine Reihe neuartiger multivalenter kationischer Tenside hergestellt, wobei ihre Eigenschaften beispielsweise mit Tensid B (C12N4), Tensid C (EG8N4) und Tensid F (EG8C12N4) in wässriger Lösung bei verschiedener Salzkonzentration im Vordergrund stehen.

Organic lasing: correlation between molecular structure, optical and optoelectronic properties

In this thesis mainly two alternating indenofluorene-phenanthrene copolymers were investigated with a variety of spectroscopic and optoelectronic experiments. The different experimental techniques allowed to retrieve deeper insights into their unique optical as well as optoelectronic properties. The motivation of the research presented in this work was to correlate their photophysical properties with respect to their application in electrically pumped lasing. This thesis begins with the description of optical properties studied by classical absorption and emission spectroscopy and successively describes an overall picture regarding their excited state dynamics occurring after photoexcitation studied by time-resolved spectroscopy. The different spectroscopic methods do not only allow to elucidate the different optical transitions occurring in this class of materials, but also contribute to a better understanding of exciton dynamics and exciton interaction with respect to the molecular structure as well as aggregation and photooxidation of the polymers. Furthermore, the stimulated emission properties were analyzed by amplified spontaneous emission (ASE) experiments. Especially one of the investigated materials, called BLUE-1, showed outstanding optical properties including a high optical gain, a low threshold for ASE and low optical losses. Apart from the optical experiments, the charge carrier mobility was measured with the time-of-flight technique and a comparably high hole mobility on the order of 1 x 10-² cm²/(Vs) was determined for BLUE-1 which makes this material promising for organic lasing. The impact of the high charge carrier mobility in this material class was further analyzed in different optoelectronic devices such as organic LEDs (OLEDs) and organic solar cells.

Coating of surfaces of composite materials with enzymatically formed biosilica

Die Bildung kieselsäurehaltiger Spicula in marinen Schwämmen ist nur möglich durch die enzymatische Aktivität des Silicatein- in Verbindung mit der stöchiometrischen Selbstassemblierung des Enzyms mit anderen Schwammproteinen. Die vorliegende Arbeit basiert auf einem biomimetischen Ansatz mit dem Ziel, unterschiedliche Oberflächen für biotechnologische und biomedizinische Anwendungen mit Biosilica und Biotitania zu beschichten und zu funktionalisieren. Für biotechnologische Anwendungen ist dabei das Drucken von Cystein-getaggtem Silicatein auf Gold-Oberflächen von Bedeutung, denn es ermöglichte die Bildung definierter Biotitania-Strukturen (Anatas), welche als Photokatalysator den Abbau eines organischen Farbstoffs bewirkten. Des Weiteren zeigte sich die bio-inspirierte Modifikation von Tyrosin-Resten an rekombinantem Silicatein-(via Tyrosinase) als vielversprechendes Werkzeug zur Beschleunigung der Selbstassemblierung des Enzyms zu mesoskaligen Filamenten. Durch eine solche Modifikation konnte Silicatein auch auf der Oberfläche von anorganischen Partikeln immobilisiert werden, welches die Assemblierung von anorganisch-organischen Verbundwerkstoffen in wäßriger Umgebung förderte. Die resultierenden supramolekularen Strukturen könnten dabei in bio-inspirierten und biotechnologischen Anwendungen genutzt werden. Weiterhin wurde in der vorliegenden Arbeit die Sekundärstruktur von rekombinantem Silicatein- (Monomer und Oligomer) durch Raman Spektroskopie analysiert, nachdem das Protein gemäß einer neu etablierten Methode rückgefaltet worden war. Diese Spektraldaten zeigten insbesondere Änderungen der Proteinkonformation durch Solubilisierung und Oligomerisierung des Enzyms. Außerdem wurden die osteoinduzierenden und osteogenen Eigenschaften unterschiedlicher organischer Polymere, die herkömmlich als Knochenersatzmaterial genutzt werden, durch Oberflächenmodifikation mit Silicatein/Biosilica verbessert: Die bei der Kultivierung knochenbildender Zellen auf derart oberflächenbehandelten Materialien beobachtete verstärkte Biomineralisierung, Aktivierung der Alkalischen Phosphatase, und Ausbildung eines typischen zellulären Phänotyps verdeutlichen das Potential von Silicatein/Biosilica für der Herstellung neuartiger Implantat- und Knochenersatzmaterialien.

Field-free control of magnetism in nanostructured materials probed with high resolution X-ray microscopy

Magnetic memories are a backbone of today's digital data storage technology, where the digital information is stored as the magnetic configuration of nanostructured ferromagnetic bits. Currently, the writing of the digital information on the magnetic memory is carried out with the help of magnetic fields. This approach, while viable, is not optimal due to its intrinsically high energy consumption and relatively poor scalability. For this reason, the research for different mechanisms that can be used to manipulate the magnetic configuration of a material is of interest. In this thesis, the control of the magnetization of different nanostructured materials with field-free mechanisms is investigated. The magnetic configuration of these nanostructured materials was imaged directly with high resolution x-ray magnetic microscopy. rnFirst of all, the control of the magnetic configuration of nanostructured ferromagnetic Heusler compounds by fabricating nanostructures with different geometries was analyzed. Here, it was observed that the magnetic configuration of the nanostructured elements is given by the competition of magneto-crystalline and shape anisotropy. By fabricating elements with different geometries, we could alter the point where these two effects equilibrate, allowing for the possibility to tailor the magnetic configuration of these nanostructured elements to the required necessities.rnThen, the control of the magnetic configuration of Ni nanostructures fabricated on top of a piezoelectric material with the magneto-elastic effect (i.e. by applying a piezoelectric strain to the Ni nanostructures) was investigated. Here, the magneto-elastic coupling effect gives rise to an additional anisotropy contribution, proportional to the strain applied to the magnetic material. For this system, a reproducible and reversible control of the magnetic configuration of the nanostructured Ni elements with the application of an electric field across the piezoelectric material was achieved.rnFinally, the control of the magnetic configuration of La0.7Sr0.3MnO3 (LSMO) nanostructures with spin-polarized currents was studied. Here, the spin-transfer torque effect was employed to achieve the displacement of magnetic domain walls in the LSMO nanostructures. A high spin-transfer torque efficiency was observed for LSMO at low temperatures, and a Joule-heating induced hopping of the magnetic domain walls was observed at room temperatures, allowing for the analysis of the energetics of the domain walls in LSMO.rnThe results presented in this thesis give thus an overview on the different field-free approaches that can be used to manipulate and tailor the magnetization configuration of a nanostructured material to the various technological requirements, opening up novel interesting possibilities for these materials.