A molecular dynamics study of the influence of chain branching on the properties of polymer systems

Die vorliegende Arbeit beschäftigt sich mit dem Einfluß von Kettenverzweigungen unterschiedlicher Topologien auf die statischen Eigenschaften von Polymeren. Diese Untersuchungen werden mit Hilfe von Monte-Carlo- und Molekular-Dynamik-Simulationen durchgeführt.Zunächst werden einige theoretische Konzepte und Modelle eingeführt, welche die Beschreibung von Polymerketten auf mesoskopischen Längenskalen gestatten. Es werden wichtige Bestimmungsgrößen eingeführt und erläutert, welche zur quantitativen Charakterisierung von Verzweigungsstrukturen bei Polymeren geeignet sind. Es wird ebenso auf die verwendeten Optimierungstechniken eingegangen, die bei der Implementierung des Computerprogrammes Verwendung fanden. Untersucht werden neben linearen Polymerketten unterschiedliche Topolgien -Sternpolymere mit variabler Armzahl, Übergang von Sternpolymeren zu linearen Polymeren, Ketten mit variabler Zahl von Seitenketten, reguläre Dendrimere und hyperverzweigte Strukturen - in Abhängigkeit von der Lösungsmittelqualität. Es wird zunächst eine gründliche Analyse des verwendeten Simulationsmodells an sehr langen linearen Einzelketten vorgenommen. Die Skalierungseigenschaften der linearen Ketten werden untersucht in dem gesamten Lösungsmittelbereich vom guten Lösungsmittel bis hin zu weitgehend kollabierten Ketten im schlechten Lösungsmittel. Ein wichtiges Ergebnis dieser Arbeit ist die Bestätigung der Korrekturen zum Skalenverhalten des hydrodynamischen Radius Rh. Dieses Ergebnis war möglich aufgrund der großen gewählten Kettenlängen und der hohen Qualität der erhaltenen Daten in dieser Arbeit, insbesondere bei den linearen ketten, und es steht im Widerspruch zu vielen bisherigen Simulations-Studien und experimentellen Arbeiten. Diese Korrekturen zum Skalenverhalten wurden nicht nur für die linearen Ketten, sondern auch für Sternpolymere mit unterchiedlicher Armzahl gezeigt. Für lineare Ketten wird der Einfluß von Polydispersität untersucht.Es wird gezeigt, daß eine eindeutige Abbildung von Längenskalen zwischen Simulationsmodell und Experiment nicht möglich ist, da die zu diesem Zweck verwendete dimensionslose Größe eine zu schwache Abhängigkeit von der Polymerisation der Ketten besitzt. Ein Vergleich von Simulationsdaten mit industriellem Low-Density-Polyäthylen(LDPE) zeigt, daß LDPE in Form von stark verzweigten Ketten vorliegt.Für reguläre Dendrimere konnte ein hochgradiges Zurückfalten der Arme in die innere Kernregion nachgewiesen werden.

Quantum effects and dynamics in hydrogen-bonded systems: a first-principles approach to spectroscopic experiments

Computer simulations have become an important tool in physics. Especially systems in the solid state have been investigated extensively with the help of modern computational methods. This thesis focuses on the simulation of hydrogen-bonded systems, using quantum chemical methods combined with molecular dynamics (MD) simulations. MD simulations are carried out for investigating the energetics and structure of a system under conditions that include physical parameters such as temperature and pressure. Ab initio quantum chemical methods have proven to be capable of predicting spectroscopic quantities. The combination of these two features still represents a methodological challenge. Furthermore, conventional MD simulations consider the nuclei as classical particles. Not only motional effects, but also the quantum nature of the nuclei are expected to influence the properties of a molecular system. This work aims at a more realistic description of properties that are accessible via NMR experiments. With the help of the path integral formalism the quantum nature of the nuclei has been incorporated and its influence on the NMR parameters explored. The effect on both the NMR chemical shift and the Nuclear Quadrupole Coupling Constants (NQCC) is presented for intra- and intermolecular hydrogen bonds. The second part of this thesis presents the computation of electric field gradients within the Gaussian and Augmented Plane Waves (GAPW) framework, that allows for all-electron calculations in periodic systems. This recent development improves the accuracy of many calculations compared to the pseudopotential approximation, which treats the core electrons as part of an effective potential. In combination with MD simulations of water, the NMR longitudinal relaxation times for 17O and 2H have been obtained. The results show a considerable agreement with the experiment. Finally, an implementation of the calculation of the stress tensor into the quantum chemical program suite CP2K is presented. This enables MD simulations under constant pressure conditions, which is demonstrated with a series of liquid water simulations, that sheds light on the influence of the exchange-correlation functional used on the density of the simulated liquid.

Characterization of structure and dynamics of submicrometric systems via fluorescence correlation spectroscopy

The presented thesis revolves around the study of thermally-responsive PNIPAAm-based hydrogels in water/based environments, as studied by Fluorescence Correlation Spectroscopy (FCS).rnThe goal of the project was the engineering of PNIPAAm gels into biosensors. Specifically, a gamma of such gels were both investigated concerning their dynamics and structure at the nanometer scale, and their performance in retaining bound bodies upon thermal collapse (which PNIPAAm undergoes upon heating above 32 ºC).rnFCS’s requirements, as a technique, match the limitations imposed by the system. Namely, the need to intimately probe a system in a solvent, which was also fragile and easy to alter. FCS, on the other hand, both requires a fluid environment to work, and is based on the observation of diffusion of fluorescents at nanomolar concentrations. FCS was applied to probe the hydrogels on the nanometer size with minimal invasivity.rnVariables in the gels were addressed in the project including crosslinking degree; structural changes during thermal collapse; behavior in different buffers; the possibility of decreasing the degree of inhomogeneity; behavior of differently sized probes; and the effectiveness of antibody functionalization upon thermal collapse.rnThe evidenced results included the heightening of structural inhomogeneities during thermal collapse and under different buffer conditions; the use of annealing to decrease the inhomogeneity degree; the use of differently sized probes to address different length scale of the gel; and the successful functionalization before and after collapse.rnThe thesis also addresses two side projects, also carried forward via FCS. One, diffusion in inverse opals, produced a predictive simulation model for diffusion of bodies in confined systems as dependent on the bodies’ size versus the characteristic sizes of the system. The other was the observation of interaction of bodies of opposite charge in a water solution, resulting in a phenomenological theory and an evaluation method for both the average residence time of the different bodies together, and their attachment likelihood.

Molecular dynamics simulations of sheared brush-like systems

Mit Hilfe von Molekulardynamik-Simulationen untersuchen wir bürstenartige Systeme unter guten Lösungsmittelbedingungen. Diese Systeme sind, dank ihren vielfältigen Beschaffenheiten, die von Molekularparametern und äußeren Bedingungen abhängig sind, wichtig für viele industrielle Anwendungen. Man vermutet, dass die Polymerbürsten eine entscheidende Rolle in der Natur wegen ihrer einzigartigen Gleiteigenschaften spielen. Ein vergröbertes Modell wird verwendet, um die strukturellen und dynamischen Eigenschaften zweier hochkomprimierter Polymerbürsten, die eine niedrige Reibung aufweisen, zu untersuchen. Allerdings sind die Lubrikationseigenschaften dieser Systeme, die in vielen biologischen Systemen vorhanden sind, beeinflußt. Wir untersuchen so-genannte "weiche Kolloide", die zwischen den beiden Polymerbürsten eingebettet sind, und wie diese Makroobjekte auf die Polymerbürsten wirken.rnrnNicht-Gleichgewichts-Molekulardynamik-Simulationen werden durchgeführt, in denen die hydrodynamischen Wechselwirkungen durch die Anwendung des DPD-Thermostaten mit expliziten Lösungsmittelmolekülen berücksichtigt werden. Wir zeigen, dass die Kenntnis der Gleichgewichtseigenschaften des Systems erlaubt, dynamische Nichtgleichgewichtsigenschaften der Doppelschicht vorherzusagen.rnrnWir untersuchen, wie die effektive Wechselwirkung zwischen kolloidalen Einschlüßen durch die Anwesenheit der Bürsten (in Abhängigkeit der Weichheit der Kolloide und der Pfropfdichte der Bürsten) beeinflußt wird. Als nächsten Schritt untersuchen wir die rheologische Antwort von solchen komplexen Doppelschichten auf Scherung. Wir entwickeln eine Skalen-Theorie, die die Abhängigkeit der makroskopischen Transporteigenschaften und der lateralen Ausdehnung der verankerten Ketten von der Weissenberg Zahl oberhalb des Bereichs, in dem die lineare Antwort-Theorie gilt, voraussagt. Die Vorhersagen der Theorie stimmen gut mit unseren und früheren numerischen Ergebnissen und neuen Experimenten überein. Unsere Theorie bietet die Möglichkeit, die Relaxationszeit der Doppelschicht zu berechnen. Wenn diese Zeit mit einer charakteristischen Längenskala kombiniert wird, kann auch das ''transiente'' (nicht-stationäre) Verhalten beschrieben werden.rnrnrnWir untersuchen die Antwort des Drucktensors und die Deformation der Bürsten während der Scherinvertierung für grosse Weissenberg Zahlen. Wir entwickeln eine Vorhersage für die charakteristische Zeit, nach der das System wieder den stationären Zustand erreicht.rnrnrnElektrostatik spielt eine bedeutende Rolle in vielen biologischen Prozessen. Die Lubrikationseigenschaften der Polymerbürsten werden durch die Anwesenheit langreichweitiger Wechselwirkungen stark beeinflusst. Für unterschiedliche Stärken der elektrostatischen Wechselwirkungen untersuchen wir rheologische Eigenschaften der Doppelschicht und vergleichen mit neutralen Systemen. Wir studieren den kontinuierlichen Übergang der Systemeigenschaften von neutralen zu stark geladenen Bürsten durch Variation der Bjerrumlänge und der Ladungsdichte.

Excited-state dynamics in donor-acceptor systems for energy conversion

In dieser Arbeit werden die Dynamiken angeregter Zustände in Donor-Akzeptorsystemen für Energieumwandlungsprozesse mit ultraschneller zeitaufgelöster optischer Spektroskopie behandelt. Der Hauptteil dieser Arbeit legt den Fokus auf die Erforschung der Photophysik organischer Solarzellen, deren aktive Schichten aus diketopyrrolopyrrole (DPP) basierten Polymeren mit kleiner Bandlücke als Elektronendonatoren und Fullerenen als Elektronenakzeptoren bestehen. rnEin zweiter Teil widmet sich der Erforschung von künstlichen primären Photosynthesereaktionszentren, basierend auf Porphyrinen, Quinonen und Ferrocenen, die jeweils als Lichtsammeleinheit, Elektronenakzeptor beziehungsweise als Elektronendonatoren eingesetzt werden, um langlebige ladungsgetrennte Zustände zu erzeugen.rnrnZeitaufgelöste Photolumineszenzspektroskopie und transiente Absorptionsspektroskopie haben gezeigt, dass Singulettexzitonenlebenszeiten in den Polymeren PTDPP-TT und PFDPP-TT Polymeren kurz sind (< 20 ps) und dass in Mischungen der Polymere mit PC71BM geminale Rekombination von gebundenen Ladungstransferzuständen ein Hauptverlustkanal ist. Zudem wurde in beiden Systemen schnelle nichtgeminale Rekombination freier Ladungen zu Triplettzuständen auf dem Polymer beobachtet. Für das Donor-Akzeptor System PDPP5T:PC71BM wurde nachgewiesen, dass die Zugabe eines Lösungsmittels mit hohem Siedepunkt, und zwar ortho-Dichlorbenzol, die Morphologie der aktiven Schicht stark beeinflusst und die Solarzelleneffizienz verbessert. Der Grund hierfür ist, dass die Donator- und Akzeptormaterialien besser durchmischt sind und sich Perkolationswege zu den Elektroden ausgebildet haben, was zu einer verbesserten Ladungsträgergeneration und Extraktion führt. Schnelle Bildung des Triplettzustands wurde in beiden PDPP5T:PC71BM Systemen beobachtet, da der Triplettzustand des Polymers über Laungstransferzustände mit Triplettcharakter populiert werden kann. "Multivariate curve resolution" (MCR) Analyse hat eine starke Intensitätsabhängigkeit gezeigt, was auf nichtgeminale Ladungsträgerrekombination in den Triplettzustand hinweist.rnrnIn den künstlichen primären Photosynthesereaktionszentren hat transiente Absorptionsspektroskopie bestätigt, dass photoinduzierter Ladungstransfer in Quinon-Porphyrin (Q-P) und Porphyrin-Ferrocen (P-Fc) Diaden sowie in Quinon-Porphyrin-Ferrocen (Q-P-Fc) Triaden effizient ist. Es wurde jedoch auch gezeigt, dass in den P-Fc unf Q-P-Fc Systemen die ladungsgetrennten Zustände in den Triplettzustand der jeweiligen Porphyrine rekombinieren. Der ladungsgetrennte Zustand konnte in der Q-P Diade durch Zugabe einer Lewissäure signifikant stabilisiert werden.

The Dynamics of a Small Model Glass Former as Viewed from Its Potential Energy Landscape

Despite intensive research during the last decades, thetheoreticalunderstanding of supercooled liquids and the glasstransition is stillfar from being complete. Besides analytical investigations,theso-called energy-landscape approach has turned out to beveryfruitful. In the literature, many numerical studies havedemonstratedthat, at sufficiently low temperatures, all thermodynamicquantities can be predicted with the help of the propertiesof localminima in the potential-energy-landscape (PEL). The main purpose of this thesis is to strive for anunderstanding ofdynamics in terms of the potential energy landscape. Incontrast to the study of static quantities, this requirestheknowledge of barriers separating the minima.Up to now, it has been the general viewpoint that thermallyactivatedprocesses ('hopping') determine the dynamics only belowTc(the critical temperature of mode-coupling theory), in thesense that relaxation rates follow from local energybarriers.As we show here, this viewpoint should be revisedsince the temperature dependence of dynamics is governed byhoppingprocesses already below 1.5Tc.At the example of a binary mixture of Lennard-Jonesparticles (BMLJ),we establish a quantitative link from the diffusioncoefficient,D(T), to the PEL topology. This is achieved in three steps:First, we show that it is essential to consider wholesuperstructuresof many PEL minima, called metabasins, rather than singleminima. Thisis a consequence of strong correlations within groups of PELminima.Second, we show that D(T) is inversely proportional to theaverageresidence time in these metabasins. Third, the temperaturedependenceof the residence times is related to the depths of themetabasins, asgiven by the surrounding energy barriers. We further discuss that the study of small (but not toosmall) systemsis essential, in that one deals with a less complex energylandscapethan in large systems. In a detailed analysis of differentsystemsizes, we show that the small BMLJ system consideredthroughout thethesis is free of major finite-size-related artifacts.

Simulation studies of correlation functions and relaxation in polymeric systems

We investigate the statics and dynamics of a glassy,non-entangled, short bead-spring polymer melt with moleculardynamics simulations. Temperature ranges from slightlyabove the mode-coupling critical temperature to the liquidregime where features of a glassy liquid are absent. Ouraim is to work out the polymer specific effects on therelaxation and particle correlation. We find the intra-chain static structure unaffected bytemperature, it depends only on the distance of monomersalong the backbone. In contrast, the distinct inter-chainstructure shows pronounced site-dependence effects at thelength-scales of the chain and the nearest neighbordistance. There, we also find the strongest temperaturedependence which drives the glass transition. Both the siteaveraged coupling of the monomer and center of mass (CM) andthe CM-CM coupling are weak and presumably not responsiblefor a peak in the coherent relaxation time at the chain'slength scale. Chains rather emerge as soft, easilyinterpenetrating objects. Three particle correlations arewell reproduced by the convolution approximation with theexception of model dependent deviations. In the spatially heterogeneous dynamics of our system weidentify highly mobile monomers which tend to follow eachother in one-dimensional paths forming ``strings''. Thesestrings have an exponential length distribution and aregenerally short compared to the chain length. Thus, arelaxation mechanism in which neighboring mobile monomersmove along the backbone of the chain seems unlikely.However, the correlation of bonded neighbors is enhanced. When liquids are confined between two surfaces in relativesliding motion kinetic friction is observed. We study ageneric model setup by molecular dynamics simulations for awide range of sliding speeds, temperatures, loads, andlubricant coverings for simple and molecular fluids. Instabilities in the particle trajectories are identified asthe origin of kinetic friction. They lead to high particlevelocities of fluid atoms which are gradually dissipatedresulting in a friction force. In commensurate systemsfluid atoms follow continuous trajectories for sub-monolayercoverings and consequently, friction vanishes at low slidingspeeds. For incommensurate systems the velocity probabilitydistribution exhibits approximately exponential tails. Weconnect this velocity distribution to the kinetic frictionforce which reaches a constant value at low sliding speeds. This approach agrees well with the friction obtaineddirectly from simulations and explains Amontons' law on themicroscopic level. Molecular bonds in commensurate systemslead to incommensurate behavior, but do not change thequalitative behavior of incommensurate systems. However,crossed chains form stable load bearing asperities whichstrongly increase friction.

Structure and dynamics of supramolecular assemblies studied by advanced solid-state NMR spectroscopy

Ziel der vorliegenden Arbeit ist die Aufklärung von Struktur und Dynamik komplexer supramolekularer Systeme mittels Festkörper NMR Spektroskopie. Die Untersuchung von pi-pi Wechselwirkungen, welche einen entscheidenden Einfluss auf die strukturellen und dynamischen Eigenschaften supra- molekularer Systeme haben, hilft dabei, die Selbst- organisationsprozesse dieser komplexen Materialien besser zu verstehen. Mit dipolaren 1H-1H and 1H-13C Wiedereinkopplungs NMR Methoden unter schnellem MAS können sowohl 1H chemische Verschiebungen als auch dipolare 1H-1H und 1H-13C Kopplungen untersucht werden, ohne dass eine Isotopenmarkierung erforderlich ist. So erhält man detaillierte Informationen über die Struktur und die Beweglichkeit einzelner Molekül- segmente. In Verbindung mit sogenannten nucleus independent chemical shift (NICS) maps (berechnet mit ab-initio Methoden) lassen sich Abstände von Protonen relativ zu pi-Elektronensystemen bestimmen und so Strukturvorschläge ableiten. Mit Hilfe von homo- und heteronuklearen dipolaren Rotationsseitenbandenmustern könnenaußerdem Ordnungs- parameter für verschiedene Molekülsegmente bestimmt werden. Die auf diese Weise gewonnenen Informationen über die strukturellen und dynamischen Eigenschaften supramolekularer Systeme tragen dazu bei, strukturbestimmende Molekül- einheiten und Hauptordnungsphänomene zu identifizieren sowie lokale Wechselwirkungen zu quantifizieren, um so den Vorgang der Selbstorganisation besser zu verstehen.

Mechanics and dynamics of liposomes and cells studied by QCM and ECIS

The present thesis introduces a novel sensitive technique based on TSM resonators that provides quantitative information about the dynamic properties of biological cells and artificial lipid systems. In order to support and complement results obtained by this method supplementary measurements based on ECIS technique were carried out. The first part (chapters 3 and 4) deals with artificial lipid systems. In chapter 3 ECIS measurements were used to monitor the adsorption of giant unilamellar vesicles as well as their thermal fluctuations. From dynamic Monte Carlo Simulations the rate constant of vesicle adsorption was determined. Furthermore, analysis of fluctuation measurements reveals Brownian motion reflecting membrane undulations of the adherent liposomes. In chapter 4 QCM-based fluctuation measurements were applied to quantify nanoscopically small deformations of giant unilamellar vesicles with an external electrical field applied simultaneously. The response of liposomes to an external voltage with shape changes was monitored as a function of cholesterol content and adhesion force. In the second part (chapters 5 - 8) attention was given to cell motility. It was shown for the first time, that QCM can be applied to monitor the dynamics of living adherent cells in real time. QCM turned out to be a highly sensitive tool to detect the vertical motility of adherent cells with a time resolution in the millisecond regime. The response of cells to environmental changes such as temperature or osmotic stress could be quantified. Furthermore, the impact of cytochalasin D (inhibits actin polymerization) and taxol (facilitate polymerization of microtubules) as well as nocodazole (depolymerizes microtubules) on the dynamic properties of cells was scrutinized. Each drug provoked a significant reduction of the monitored cell shape fluctuations as expected from their biochemical potential. However, not only the abolition of fluctuations was observed but also an increase of motility due to integrin-induced transmembrane signals. These signals were activated by peptides containing the RGD sequence, which is known to be an integrin recognition motif. Ultimately, two pancreatic carcinoma cell lines, derived from the same original tumor, but known to possess different metastatic potential were studied. Different dynamic behavior of the two cell lines was observed which was attributed to cell-cell as well as cell-substrate interactions rather than motility. Thus one may envision that it might be possible to characterize the motility of different cell types as a function of many variables by this new highly sensitive technique based on TSM resonators. Finally the origin of the broad cell resonance was investigated. Improvement of the time resolution reveals the "real" frequency of cell shape fluctuations. Several broad resonances around 3-5 Hz, 15-17 Hz and 25-29 Hz were observed and that could unequivocally be assigned to biological activity of living cells. However, the kind of biological process that provokes this synchronized collective and periodic behavior of the cells remains to be elucidated.

Supramolecular order and dynamics of functional materials studied by solid state NMR

The goal of this thesis was the investigation of the structure, conformation, supramolecular order and molecular dynamics of different classes of functional materials (phthalocyanine, perylene and hexa-peri-hexabenzocoronene derivatives and mixtures of those), all having planar aromatic cores modified with various types of alkyl chains. The planar aromatic systems are known to stack in the solid and the liquid-crystalline state due to p-p interactions forming columnar superstructures with high one-dimensional charge carrier mobility and potential application in photovoltaic devices. The different functionalities attached to the aromatic cores significantly influence the behavior of these systems allowing the experimentalists to modify the structures to fine-tune the desired thermotropic properties or charge carrier mobility. The aim of the presented studies was to understand the interplay between the driving forces causing self-assembly by relating the structural and dynamic information about the investigated systems. The supramolecular organization is investigated by applying 1H solid state NMR recoupling techniques. The results are related with DSC and X-ray scattering data. Detailed information about the site-specific molecular dynamics is gained by recording spinning sideband patterns using 1H-1H and 13C-1H solid state NMR recoupling techniques. The determined dipole-dipole coupling constants are then related with the coupling constants of the respective rigid pairs, thus providing local dynamic order parameters for the respective moieties. The investigations presented reveal that in the crystalline state the preferred arrangement in the columnar stack of discotic molecules modified with alkyl chains is tilted. This leads to characteristic differences in the 1H chemical shifts of otherwise chemically equivalent protons. Introducing branches and increasing the length of the alkyl chains results in lower mesophase transitions and disordered columnar stacks. In the liquid-crystalline state some of the discs lose the tilted orientation, others do not, but all start a rapid rotation about the columnar axis.

Atomic force microscopy of biomimetic systems

This thesis was driven by the ambition to create suitable model systems that mimic complex processes in nature, like intramolecular transitions, such as unfolding and refolding of proteins, or intermolecular interactions between different cell compo-nents. Novel biophysical approaches were adopted by employing atomic force mi-croscopy (AFM) as the main measurement technique due to its broad diversity. Thus, high-resolution imaging, adhesion measurements, and single-molecule force distance experiments were performed on the verge of the instrumental capabilities. As first objective, the interaction between plasma membrane and cytoskeleton, me-diated by the linker protein ezrin, was pursued. Therefore, the adsorption process and the lateral organization of ezrin on PIP2 containing solid-supported membranes were characterized and quantified as a fundament for the establishment of a biomimetic model system. As second component of the model system, actin filaments were coated on functionalized colloidal probes attached on cantilevers, serving as sensor elements. The zealous endeavor of creating this complex biomimetic system was rewarded by successful investigation of the activation process of ezrin. As a result, it can be stated that ezrin is activated by solely binding to PIP2 without any further stimulating agents. Additional cofactors may stabilize and prolong the active conformation but are not essentially required for triggering ezrin’s transformation into an active conformation. In the second project, single-molecule force distance experiments were performed on bis-loop tetra-urea calix[4]arene-catenanes with different loading rates (increase in force per second). These macromolecules were specifically designed to investigate the rupture and rejoining mechanism of hydrogen bonds under external load. The entangled loops of capsule-like molecules locked the unbound state of intramolecular hydrogen bonds mechanically, rendering a rebinding observable on the experimental time scale. In conjunction with Molecular Dynamics simulations, a three-well potential of the bond rupture process was established and all kinetically relevant parameters of the experiments were determined by means of Monte Carlo simulations and stochastic modeling. In summary, it can be stated that atomic force microscopy is an invaluable tool to scrutinize relevant processes in nature, such as investigating activation mechanisms in proteins, as shown by analysis of the interaction between F-actin and ezrin, as well as exploring fundamental properties of single hydrogen bonds that are of paramount interest for the complete understanding of complex supramolecular structures.

Structure, organization and dynamics of functional supramolecular materials studied by solid-state NMR

Functional materials have great importance due to their many important applications. The characterization of supramolecular architectures which are held together by non-covalent interactions is of most importance to understand their properties. Solid-state NMR methods have recently been proven to be able to unravel such structure-property relations with the help of fast magic-angle spinning and advanced pulse sequences. The aim of the current work is to understand the structure and dynamics of functional supramolecular materials which are potentially important for fuel-cell (proton conducting membrane materials) and solar-cell or plastic-electronic applications (photo-reactive aromatic materials). In particular, hydrogen-bonding networks, local proton mobility, molecular packing arrangements, and local dynamics will be studied by the use of advanced solid-state NMR methods. The first class of materials studied in this work is proton conducting polymers which also form hydrogen-bonding network. Different materials, which are prepared for high 1H conduction by different approaches are studied: PAA-P4VP, PVPA-ABPBI, Tz5Si, and Triazole-functional systems. The materials are examples of the following major groups; - Homopolymers with specific functional groups (Triazole functional polysiloxanes). - Acid-base polymer blends approach (PAA-P4VP, PVPA-ABPBI). - Acid-base copolymer approach (Triazole-PVPA). - Acid doped polymers (Triazole functional polymer doped with H3PO4). Perylenebisimide (PBI) derivatives, a second type of important functional supramolecular materials with potent applications in plastic electronics, were also investigated by means of solid-state NMR. The preparation of conducting nanoscopic fibers based on the self-assembling functional units is an appealing aim as they may be incorporated in molecular electronic devices. In this category, perylene derivatives have attracted great attention due to their high charge carrier mobility. A detailed knowledge about their supramolecular structure and molecular dynamics is crucial for the understanding of their electronic properties. The aim is to understand the structure, dynamics and packing arrangements which lead to high electron conductivity in PBI derivatives.

Dynamics, rheology and critical properties of colloidal fluid mixtures

Liquids under the influence of external fields exhibit a wide range of intriguing phenomena that can be markedly different from the behaviour of a quiescent system. This work considers two different systems — a glassforming Yukawa system and a colloid-polymer mixture — by Molecular Dynamics (MD) computer simulations coupled to dissipative particle dynamics. The former consists of a 50-50 binary mixture of differently-sized, like-charged colloids interacting via a screened Coulomb (Yukawa) potential. Near the glass transition the influence of an external shear field is studied. In particular, the transition from elastic response to plastic flow is of interest. At first, this model is characterised in equilibrium. Upon decreasing temperature it exhibits the typical dynamics of glassforming liquids, i.e. the structural relaxation time τα grows strongly in a rather small temperature range. This is discussed with respect to the mode-coupling theory of the glass transition (MCT). For the simulation of bulk systems under shear, Lees-Edwards boundary conditions are applied. At constant shear rates γ˙ ≫ 1/τα the relevant time scale is given by 1/γ˙ and the system shows shear thinning behaviour. In order to understand the pronounced differences between a quiescent system and a system under shear, the response to a suddenly commencing or terminating shear flow is studied. After the switch-on of the shear field the shear stress shows an overshoot, marking the transition from elastic to plastic deformation, which is connected to a super-diffusive increase of the mean squared displacement. Since the average static structure only depends on the value of the shear stress, it does not discriminate between those two regimes. The distribution of local stresses, in contrast, becomes broader as soon as the system starts flowing. After a switch-off of the shear field, these additional fluctuations are responsible for the fast decay of stresses, which occurs on a time scale 1/γ˙ . The stress decay after a switch-off in the elastic regime, on the other hand, happens on the much larger time scale of structural relaxation τα. While stresses decrease to zero after a switch-off for temperatures above the glass transition, they decay to a finite value for lower temperatures. The obtained results are important for advancing new theoretical approaches in the framework of mode-coupling theory. Furthermore, they suggest new experimental investigations on colloidal systems. The colloid-polymer mixture is studied in the context of the behaviour near the critical point of phase separation. For the MD simulations a new effective model with soft interaction potentials is introduced and its phase diagram is presented. Here, mainly the equilibrium properties of this model are characterised. While the self-diffusion constants of colloids and polymers do not change strongly when the critical point is approached, critical slowing down of interdiffusion is observed. The order parameter fluctuations can be determined through the long-wavelength limit of static structure factors. For this strongly asymmetric mixture it is shown how the relevant structure factor can be extracted by a diagonalisation of a matrix that contains the partial static structure factors. By presenting first results of this model under shear it is demonstrated that it is suitable for non-equilibrium simulations as well.

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.

Crystal phases and glassy dynamics in monodisperse hard ellipsoids

We have performed Monte Carlo and molecular dynamics simulations of suspensions of monodisperse, hard ellipsoids of revolution. Hard-particle models play a key role in statistical mechanics. They are conceptually and computationally simple, and they offer insight into systems in which particle shape is important, including atomic, molecular, colloidal, and granular systems. In the high density phase diagram of prolate hard ellipsoids we have found a new crystal, which is more stable than the stretched FCC structure proposed previously . The new phase, SM2, has a simple monoclinic unit cell containing a basis of two ellipsoids with unequal orientations. The angle of inclination is very soft for length-to-width (aspect) ratio l/w=3, while the other angles are not. A symmetric state of the unit cell exists, related to the densest-known packings of ellipsoids; it is not always the stable one. Our results remove the stretched FCC structure for aspect ratio l/w=3 from the phase diagram of hard, uni-axial ellipsoids. We provide evidence that this holds between aspect ratios 3 and 6, and possibly beyond. Finally, ellipsoids in SM2 at l/w=1.55 exhibit end-over-end flipping, warranting studies of the cross-over to where this dynamics is not possible. Secondly, we studied the dynamics of nearly spherical ellipsoids. In equilibrium, they show a first-order transition from an isotropic phase to a rotator phase, where positions are crystalline but orientations are free. When over-compressing the isotropic phase into the rotator regime, we observed super-Arrhenius slowing down of diffusion and relaxation, and signatures of the cage effect. These features of glassy dynamics are sufficiently strong that asymptotic scaling laws of the Mode-Coupling Theory of the glass transition (MCT) could be tested, and were found to apply. We found strong coupling of positional and orientational degrees of freedom, leading to a common value for the MCT glass-transition volume fraction. Flipping modes were not slowed down significantly. We demonstrated that the results are independent of simulation method, as predicted by MCT. Further, we determined that even intra-cage motion is cooperative. We confirmed the presence of dynamical heterogeneities associated with the cage effect. The transit between cages was seen to occur on short time scales, compared to the time spent in cages; but the transit was shown not to involve displacements distinguishable in character from intra-cage motion. The presence of glassy dynamics was predicted by molecular MCT (MMCT). However, as MMCT disregards crystallization, a test by simulation was required. Glassy dynamics is unusual in monodisperse systems. Crystallization typically intervenes unless polydispersity, network-forming bonds or other asymmetries are introduced. We argue that particle anisometry acts as a sufficient source of disorder to prevent crystallization. This sheds new light on the question of which ingredients are required for glass formation.