5 Naturwissenschaften und Mathematik
Iron spin crossovers at high pressures and temperatures and their effects on materials relevant tot he Earth’s lower mantle and core
- Iron is the most abundant element by mass in the Earth. The iron content and its spin or oxidation state have a major influence on the physical properties of the main phases in the Earth’s interior. Therefore it is of vast importance to understand the behavior of iron in mineral phases at the temperature and pressure conditions of the Earth’s interior. This cumulative thesis investigates Fe spin crossovers in iron-containing magnesium aluminum silicates, iron-bearing silicate glasses, the iron carbide Fe3C and the effect of Fe spin crossovers on the Fe/Mg partitioning between perovskite and ferropericlase in pyrolitic model system of the Earth’s lower mantle. The goal is first to understand the nature of the Fe spin crossover in respect to its oxidation state and second to estimate the consequences of their occurrence to processes and the structure in the Earth. Central tools in these studies are laser heated diamond anvil cells, to reach the pressure and temperature conditions of the Earth’s interior, Mössbauer spectroscopy, which is a sensitive probe for detecting structural and spin changes in Fe-bearing materials, and analytical transmission electron microscopy, as a probe of chemistry and oxidation state on the nm-scale. In this cumulative thesis I present the results of five research articles. For the analysis of conventional and recently developed synchrotron energy domain Mössbauer spectra the computer program MossA is introduced, which builds the basis for the analysis and interpretation of the results for the other studies. Based on synchrotron Mössbauer spectroscopy and electrical conductivity measurements of Fe-bearing silicate aluminum perovskite it is shown that Fe3+ occupies the dodecahedral A-site of the perovskite structure and remains in the high-spin state throughout the pressure and temperature conditions of the Earth’s lower mantle. Furthermore, a study on the electronic behavior of Fe in a Fe2+-rich aluminous silicate glass and a Fe3+-rich sodium silicate glass infers that no sharp high spin to low spin crossover occurs in silicate melts in the Earth’s lower mantle. This result excludes the possibility of negatively buoyant melts in the lower mantle in an early magma ocean solely due to strong preferential partitioning of iron into the melt phase, which would be induced by a Fe low-spin bearing melt. New insights into to decoupled partitioning behavior of Fe2+ and Fe3+ between the two dominant phases of the Earth’s lower mantle, perovskite and ferropericlase, are presented. The intermediate spin to low spin crossover of Fe2+ in perovskite at about 110 GPa seems to have a strong effect on partitioning and oxidation state of Fe. It leads to a change of the partitioning behavior of Fe between perovskite and ferropericlase and induces a reduction of Fe3+ to Fe2+ in perovskite. Finally, a Mössbauer spectroscopic and single-crystal x-ray diffraction study of Fe3C reveals a two-stage loss of magnetism in Fe3C at high pressures at room temperature: a ferro- to paramagnetic transition around 8-10 GPa and a para- to nonmagnetic transition at about 22 GPa.
High-Resolution Modelling of Surface-Atmosphere Interactions and Convection Development at Nam Co Lake, Tibetan Plateau
- The Tibetan Plateau has recently become an area of increased interest for the atmospheric and environmental sciences. Surface-atmosphere interactions and specifically the exchange of momentum, turbulent energy and water vapour as well as the development of convection are not only important for the surface energy balance and local water resources, but also have influence on the evolution of the monsoon system and climate. High-resolution, numerical atmospheric models with a fully coupled surface model are a valuable tool for the systematic investigation of surface-atmosphere interactions. Nam Co Lake, located at the northern extent of the monsoon's influence, was selected as a complex system in order to study the interaction of the land and the lake in the generation of mesoscale circulations and the development from boundary-layer clouds to moist convection.
Turbulent fluxes estimated by eddy-covariance and atmospheric profiles measured by radiosondes are used in this work in conjunction with the ATHAM (Active Tracer High-resolution Atmospheric Model) and Hybrid models. Substantial model development is undertaken for both ATHAM and Hybrid. This means a more consistent formulation of tracer and heat transport in ATHAM and improved model stability. Hybrid has been modified with an extrapolated surface temperature, to be used for the calculation of turbulent fluxes. A quadratic temperature profile based on the layer mean and surface model base temperature is assumed in each layer and extended to the surface. Compared to eddy-covariance measurements and a Surface-Vegetation-Atmosphere Transport (SVAT) Model there is an overall reasonable model performance, when tested on four days for two sites with variable environmental conditions during the 2009 summer monsoon season. At the same time, errors are reduced by 40-60% compared to the unmodified Hybrid.
Subsequently, the coupled modelling system is used for 2-dimensional cross-sections through the Nam Co Lake basin with horizontal resolutions of
200 m and at least 150 vertical layers between the surface and the model top located in the lower stratosphere. The 2-dimensional modelling approach has a
tendency to overestimate convective strength due to the underestimation of dry air entrainment and cannot reproduce fully realistic flow fields. Nevertheless,
it provides a valuable tool for systematic investigations of environmental factors, where 3D simulations are prohibitively expensive.
In simulations with several background wind speeds it is found that the model adequately simulates the mesoscale circulation system between the lake and the surrounding mountain chains. Dependent on the geostrophic wind direction there are two different mechanisms for the triggering of convection: Convective triggering, when overflowing topography, and triggering due to convergence between the lake-breeze front and the background wind. It is concluded that coupled modelling setup is capable of reproducing the system's most important dynamics, such as realistic turbulent surface fluxes, mesoscale circulations and cloud evolution.
Thereafter, the influence of the atmospheric profiles of temperature and relative humidity and the uncertainty that arises from them is discussed.
Simulations are initialised with profiles based on direct measurements (radiosondes), NCEP-I and ERA-INT reanalysis and GFS-FNL analysis data on two
days during the summer of 2012. The simulated convection from radiosondes compares reasonably well with weather observations for the first day, but
less well for the second day, when large-scale synoptic effects, which are not included in the model, gain importance. The choice of vertical profile information leads to strongly differing convection development, causing modifications of the surface energy balance and thus of the energy and water
cycle for Nam Co Lake.
With respect to precipitation it is found that a large fraction of the precipitation that is generated in the simulations is deposited within the basin
and on the slopes of the surrounding mountain chains and thus locally recycled. This also means that a weather station in the centre of the basin is not representative of the system. Furthermore, Nam Co Lake may be of importance as a water supply for the region. Additionally, the choice of profile and the initial water vapour contents determine the amount of precipitation so that there are strong differences spanning one order of magnitude in the generated precipitation between the model simulations driven by different vertical profiles.
The findings from the thesis provide an example of the impacts of surface-atmosphere interactions, mesoscale circulations and convective evolution on
the Tibetan Plateau. Scaled to the entire plateau these processes are highly relevant to ecosystems, climate and the water cycle.
Effect of Dopants on the Local Atomic Structure and Sintering Behavior of Bismuth Sodium Titanate
- The most commonly used piezoceramic is lead zirconate titanate Pb(ZrxTi(1-x))O (PZT). It possesses outstanding piezoelectric properties which can be modified for numerous applications by the addition of dopants. However, because of environmental and health concerns regarding lead, lead-free alternatives are demanded by politics.
One of the two most promising lead-free replacement materials is the ferroelectric bismuth sodium titanate (Bi0.5Na0.5)TiO3 (BNT). Like PZT, it crystallizes in the perovskite structure.
Since the dielectric and piezoelectric properties of pure BNT ceramics are insufficient for application, BNT is often modified by the addition of dopants. These influence a great variety of material properties to different degrees, e.g. the sintering behavior, the dielectric and piezoelectric properties and their respective temperature stabilities. Doping of BNT aims to decrease the sintering temperature in order to avoid Bi vaporization, to increase the depolarization temperature and to enhance the piezoelectric coefficient.
The effects of numerous dopants on the resulting performance of BNT were studied extensively in the literature. However, so far little attention has been payed to the way in which dopants interact with the piezomaterial. Nevertheless, it is the understanding of these relationships that would make targeted modifications and improvements of BNT possible.
The primary goal of this study was to investigate and explain the effects of a model dopant -cobalt- on the phase formation, sintering behavior and microstructure of BNT as well as on the resulting dielectric and piezoelectric properties. In this regard, a core issue was to determine the preferred lattice site of Co in BNT.
BNT was synthesized from oxide powders using the classic solid-state route and sintered at temperatures ranging from 1000 °C to 1150 °C. Cobalt was added in concentrations between 0.1 mol% and 2.6 mol% Co prior to the calcination as Co3O4.
About one third of the total cobalt amount was incorporated into the BNT lattice on the perovskite B-site, that is, it substituted for Ti. The cobalt in BNT appeared to be in equilibrium with the secondary phase Co2TiO4, which invariably formed at cobalt concentrations greater than 0.1 mol% Co. For charge balancing reasons, oxygen vacancies were created in the lattice of cobalt-doped BNT. These markedly enhanced the diffusivity. As a result, the sintering temperature of doped BNT decreased with increasing cobalt concentrations, and high final densities were achieved. However, in highly doped BNT sample swelling occurred at elevated temperatures of the sintering cycle. This phenomenon was attributed to evaporating oxygen caused by the valence transition of Co3+ to Co2+.
Up to 950 °C, BNT was found to densify via solid state sintering mechanisms. Above this temperature, a small amount of liquid phase was present, which probably formed from decomposing BNT because of a slight Ti-deficiency due to doping. Increased Bi vaporization from the melt above 1000 °C appeared to have stabilized sodium cobalt titanate, an additional secondary phase.
The rotation of the iso-lines in the kinetic field diagram of doped BNT was interpreted such that the activation energy for grain growth was higher than the activation energy for densification. Possible reasons are the solute-drag effect and the pinning of domain walls by secondary phase particles.
Both the depolarization temperature and the piezoelectric coefficient d33 decreased with increasing cobalt concentrations. The dielectric properties deteriorated as well. This was attributed to the high electrical conductivity of the doped samples, which prevented full poling.
Plasticity, Intraspecific Variability and Local Adaptation to Climatic Extreme Events of Ecotypes/Provenances of Key Plant Species
- Climate change, and especially an increase of magnitude and frequency of climatic extreme events such as drought periods or heatwaves, will alter growing conditions for plants in the future. Persistent ecosystems, with long-living organisms, such as forest or permanent grassland will be particularly impacted by this development. The velocity of these changes is likely to occur at a pace, which species may not be able to keep track with by natural dispersal or genetic adaptation. Agriculture, forestry and ecosystem management must develop counteracting practices to secure the persistence and functioning of these ecosystems and thus their provision of goods and services. Therefore it is important to develop a better understanding how species and ecosystems may respond to future climatic stressors. Impact assessments, e.g. via climatic envelope modelling are prone to misinterpretations of the adaptive capacity of species, as they do not incorporate the intraspecific genetic and phenotypic differences that exist within the populations accross the distribution range of a species.
Yet, intraspecific variation may exhibit potential tools for the development of climate change adaptation strategies. Here, I focus on key ecosystems in Central Europe. In particular the selective use of plant provenances or ecotypes may help to make ecosystems climate-resilient without a potentially more problematic introduction of exotic species. Especially provenances from warmer, drought-prone regions, with a current climate similar to the projected one for Central Europe recently came into focus as potential substitutes for local provenances, as they might have developed local adaptations to climate conditions at their location of origin. Insights about the response of these provenances to changing averages and extreme event regimes are crucial for a reasonable use of within-species diversity in climate change adaptation.
First, the concept of assisted colonization or migration of species or ecotypes and the role it can play as an adaptation strategy in agriculture, forestry or nature conservation is introduced (Manuscript1). It is suggested that a focus should be laid on keystone species that ensure ecosystem persistence and functioning as they govern the habitat structure and microclimate of a site. The assisted colonization of pre-adapted ecotypes of keystone species from climates similar to future projections for the target site is proposed.
Furthermore, provenances of selected grassland and forest key-species were exposed to drought and warming in two experiments in Bayreuth and Landau, and their ecological responses were analysed. Results suggest that local adaptations to climatic stressors exist. However, the magnitude and direction of responses strongly depend on species and climatic variables. For grassland species, e.g. differences in drought sensitivity could be demonstrated in some cases (Manuscript 4). Fagus sylvatica exhibited differences between the provenances in response to drought conditions, as well (Manuscript 3). It seems that marginal provenances, from the dry margins of the distribution range, show less increment reduction due to the drought treatment. Yet, under more favourable conditions of water supply these provenances did not yield the same high increment rates than more central provenances, indicating a trade-off between stability under stress and yield under non-stress conditions. A pine species that is generally considered to be rather drought-resistant, Pinus nigra, which is a potential substitute for climate-threatened conifers on dry sites in Central Europe, did not show any differences in response to drought and warming (Manuscript 2), maybe due to a weak selective pressure as a result of high drought-resistance across the whole distribution range. The impacts of drought on increment became not visible before the second year after the treatment, stressing the need for more long-time experiments in climate impact research.
Even in a generally warmer environment, cold extremes in winter or spring are expected still to prevail in the future. Therefore, the provenances of the selected species were tested for their cold-hardiness and late frost resistance (Manuscripts 5-7). Growth of the grassland species and F. sylvatica were negatively impacted by a late frost event and differences in late-frost sensitivity between provenances or ecotypes were identified. The (sub-) mediterranean species P. nigra showed differences between provenances in their winter cold hardiness. Correlations between performance under cold stress and winter conditions or late frost proneness of the places of origin could be established for almost all species. However, preceding climate experience, such as the warming or drought treatment of the plants altered their reaction to cold extremes compared to the control treatment, indicating the complexity of the interactive impacts of climate factors on ecosystem and plant performance.
The uncertainty of climate projections and the multitude of changing climatic stressors, though, make the prospect of an easy and rapid success in the search for single “best-adapted” provenances very questionable. In economics the portfolio effect shows that a diversification of investments decreases the risk of a total loss of profits. Hence, in a modelling procedure based on the increment data from the above mentioned experiment it was tested if a “portfolio investment” in several provenances in one stand decreases the risk of yield losses (Manuscript 8). Results indicate that the higher the number of provenances the higher the chance for a “best-performer” to be included in the set. So the likelihood of higher yields, under different climatic conditions increases, yet the risk of low yields stays stable.
Generally, it seems that the selective use of plant species and ecotypes in climate change adaptation can be a feasible tool to maintain ecosystem functionality and productivity. However, the uncertain projections, the multitude of climatic stressors and their interplay with other environmental factors and the potential impacts of assisted colonization of ecotypes on the genetic diversity within species and populations require further research.
Soil erosion and conservation potential of row crop farming in mountainous landscapes of South Korea
- Soils play an essential role for mankind because they provide fundamental ecosystem services required for human life, primarily for the production of food by providing the environment for plant growth. However, soils worldwide became highly threatened by human induced degradation, especially as a consequence of accelerated erosion by water during recent decades. In consideration of climate change and an increasing food demand of a rising population, there is an urgent need to conserve the soil resources by implementing effective erosion control measures for agricultural production. The effective implementation of those measures strongly depends on the specific conditions of particular regions and requires the analysis of the existing farming systems and their capability for erosion control.
Objective of this thesis is the analysis of the major agricultural practices applied for row crop cultivation in mountainous watersheds of South Korea with respect to water erosion and the identification of their conservation potential. Our first two studies analyze the subsurface flow processes, the runoff patterns, and the associated erosion rates of the widely applied plastic covered ridge-furrow system (plastic mulch), and our third study investigates the impact of herbicide applications on erosion associated with conventional and organic farming. To analyze the flow processes induced by the plastic mulch cultivation, we conducted four irrigation experiments on potato fields that represent a smooth surface, uncovered ridges, and plastic covered ridges with and without a developed crop canopy. With an automatic sprinkler, we irrigated small plots with a dye tracer solution of Brilliant Blue and potassium iodide, collected surface runoff, and excavated soil profiles to visualize the subsurface flow patterns, which were subsequently analyzed by image index functions. We found that the ridge-furrow system, especially when ridges are covered with plastic, decreased infiltration and generated high amounts of surface runoff, whereas a developed crop canopy increased infiltration due to interception and stem flow. The analyses of the subsurface flow patterns show that the plastic covered ridge-furrow system induces preferential infiltration in furrows and planting holes due to its topography and the impermeable covers, but that the impact on flow processes in the soils is relatively small compared to the impact on runoff generation. To identify the patterns of overland flow and the erosion rates associated with the plastic mulch system, we installed runoff collectors to monitor runoff and sediment transport of two potato fields with concave and convex topographies, and we applied the EROSION 3D model to compare the plastic covered ridge-furrow system to uncovered ridges and a smooth surface. We found that plastic mulch cultivation considerably increases soil erosion compared to uncovered ridges as a consequence of high amounts of surface runoff. Our results show that the ridge-furrow system concentrated overland flow on the concave field, resulting in severe gully erosion, but prevented flow accumulation and reduced erosion on the convex field, which demonstrates that the effect of this cultivation strategy is primarily controlled by the field topography and its orientation. To analyze the effects of conventional and organic farming on water erosion, we measured multiple vegetation parameters of crops and weeds of conventional and organic farms cultivating bean, potato, radish, and cabbage, and we simulated long-term soil loss rates with the Revised Universal Soil Loss Equation (RUSLE). We found that organic farming reduced erosion for radish, as a result of an increased weed biomass due to the absence of herbicides, but that it increased erosion for potato due to lower crop coverage, presumably as a consequence of crop-weed competition or herbivory associated with the absence of agricultural chemicals. Although we demonstrated that a developed weed cover in the furrows can potentially decrease the erosion risk for row crops, our results show that the average annual erosion rates of both farming systems exceed by far any tolerable soil loss.
In consideration of the generally high soil loss found in our studies, we conclude that the applied farming practices are not capable for effective erosion control and soil conservation in this region. However, based on our findings, we could identify possible modifications of those practices that can help to reduce the risk of erosion in the future. We recommend perforated plastic covers for ridges to reduce runoff generation, and the orientation of the ridge-furrow system along the contours or towards field edges to prevent flow accumulation and gully formation. Additionally, we suggest residue mulching of furrows to protect the soil surface from overland flow, and the cultivation of winter cover crops after harvest to maintain a better soil cover throughout the year.
Site-specific modelling of turbulent fluxes on the Tibetan Plateau
- The Tibetan Plateau attracts attention in recent decades due to its influence on the East-Asian Monsoon and regional hydrology. Therefore estimates of the regional energy and water balance have come into the focus, utilising remote sensing and regional model approaches, but such attempts require surface-specific flux data of high quality for validation. Eddy-covariance measurements are qualified for this task, but these are scarce on the Tibetan Plateau, incomplete due to quality filtering and potentially biased due to the well-known closure gap of the observed energy balance as well as small-scale heterogeneity. This thesis is related to the infrastructural EU project CEOP-AEGIS, aiming at a standardised processing of eddy-covariance data – including correction of the energy balance closure and gap-filling – on the Tibetan Plateau.
In a pre-analysis step, particular issues about data quality of turbulent fluxes (sensible heat flux and latent heat flux/evapotranspiration) at Tibetan Plateau sites have been addressed. One of them is the degradation of data quality due to the frequent occurrence of near-ground free convective conditions. Another issue arises from coordinate rotation for non-omnidirectional sonic anemometer, which requires a careful handling. In consequence, a sector-wise planar-fit is recommended, disregarding the sector influenced by the anemometer's mounting structure. This can reduce occurrences of invalid momentum flux data, whilst no effect on scalar fluxes can be seen.
As a main topic, this thesis investigates the application of process-based modelling to estimate turbulent flux exchange between the surface and the atmosphere for typical surface types on the Tibetan Plateau. Therefore a case study has been carried out at Nam Co, Tibetan Plateau. Turbulent flux measurements over dry and wet grassland as well as over a shallow lake have been conducted during the summer monsoon season of 2009, and modelled with the land surface scheme SEWAB and a hydrodynamic multilayer model for the lake. Adaptations were implemented to the land surface scheme with regard to the special conditions on the Tibetan Plateau, such as extreme diurnal variation of surface temperature and variation in soil moisture, further called TP version. The analysis includes a consequent model comparison with eddy-covariance data, using model parameters derived independently rather than applying optimisation strategies. Specific attention has been devoted to the impact of observed energy balance closure and its correction, establishing a new correction method according to the Buoyancy flux.
The land surface model reasonably represented the dry and the wet grassland site by only setting the site-specific model parameters, and the TP version performed overall better than the original version, while laboratory measurements of soil parameters failed to improve model performance in comparison to standard parameter values. Soil temperature and moisture measurements as well as field based knowledge of the soil type have been identified as minimum requirements for model parameter acquisition. Lake surface fluxes have been modelled reliably, the lake depth has been taken into account. These results can be transferred to any lake on the Tibetan Plateau given the required forcing data including a representative lake surface temperature.
The choice of the surface model and the selection of the energy balance closure correction method are inter-related problems. The correction partitions the balance residual to the sensible and latent heat flux. This can be typically done according to the Bowen ratio, or according to the presented new method which attributes a larger fraction to the sensible heat flux. Testing both methods leads to partly ambiguous model performance, especially with respect to the used parameter sets. It clearly leads to shifts in model bias, while the R² metric suggests higher model compatibility to the Bowen ratio correction. The latter agrees with previous findings with respect to SEWAB modelling, but is in contradiction with recent experimental findings, attributing the closure gap to secondary circulations, driven by buoyancy. Future research on model structure should account for such processes.
As expected, the flux measurements showed distinct differences between the investigated land use types in magnitude and dynamics. The used models were able to resolve these differences in general with contrasts between surface types exceeding model errors. This must be considered when validating regional flux estimates with eddy-covariance data from the dry Nam Co station. The findings from this thesis provide the basis to process eddy-covariance data on the required level as described above.
Dynamic Self-Assembly of Magnetic Colloidal Particles
Dynamic self-assembly represent one of the most powerful tools in Nature to spontaneously organize a system on a hierarchy of different scales.
Most of the processes at the nano/micro scale occur at very low Reynold’s number where inertia can be neglected. Creeping flow magnetic systems can be characterized by the Mason number.
The Mason number measures the ratio between the viscous and the magnetic torque and is the main parameter governing the behavior of paramagnetic colloids investigated in this thesis.
The work presented in this thesis explores new dynamic regimes of colloidal dynamics which occur when suddenly switching to high Mason numbers.
In a static magnetic field the equilibrium structure of paramagnetic colloids are chains. At high Mason number in a rotating magnetic field the time averaged equilibrium conformation is a two dimensional cluster.
By switching from a static to a rotating magnetic external field, we cause a transient dynamics from a static to the dynamic equilibrium state.
The first question addressed in this thesis is: what is the physics that determines the transient folding pathway from one to the other equilibrium state?
Dynamic magnetic fields were used by others to propel top down DNA-linked chains of paramagnetic colloids in a liquid.
The second question asked is whether we can dynamically self-assemble swimmers taking a fully bottom up approach?
The third question is: is it possible to assemble more complex dynamic patterns that lead to motion of the swimmers governed by more collective coupled hydrodynamics that goes beyond slender body theory of the linked chains?
This thesis answers the three questions and contributes to the understanding of colloidal dynamics and self-assembly in dynamic magnetic fields in the regime of high Mason numbers.
We explore two aspects of the dynamic self-assembly i.e. the transient kinetics between two dynamic self-assembled equilibria and the dynamically self-assembled propulsion of magnetic swimmers beyond slender body hydrodynamics.
The thesis therefore aims at achieving magnetic control over the assembly of complex dynamic colloidal structures.
"The New Chemistry" - Sustainable Catalysis with Alcohols
- Subject of the thesis are new iridium complexes stabilized by anionic P,N- or P,N,P-ligands. These complexes were used in homogeneous catalysis. Furthermore, mechanistic studies were performed to provide an insight into the catalytic cycles. Synthesis protocols for a multitude of different product classes have been developed.
The iridium complex 1, stabilized by a neutral P,N-ligand, reacts under basic conditions with 2-aminopyridines. By elimination of dipyridylamine the new catalyst species 2a was formed, which is more stable than catalyst 1.
Based on this finding eight new anionic P,N-ligands and the resulting iridium complexes were synthesized.
After optimization of the reaction conditions (solvent, base, temperature and catalyst loading) these catalysts were used in BH (borrowing hydrogen)/HA (hydrogen autotransfer) reactions. The selective monoalkylation of anilines with primary alcohols was investigated. In comparative experiments the superiority of the new class of catalysts versus the original catalyst 1 was clearly shown. Under mild reaction conditions (70 °C) the selectivity profile with respect to the monoalkylation has been preserved.
The catalytic protocol was subsequently extended to the alkylation of aromatic diamines. Therefore various diaminobenzenes were used as substrates. Also Dapsone®, an important drug in treatment of leprosy could be used as starting material. We succeeded in both symmetric and unsymmetric monoalkylations of diamines. Due to the selectivity profile of the catalyst regarding aromatic amines, also unprotected amino alcohols could be used as alkylating reagents.
By the use of tridentate P,N,P-ligands, a novel class of more stable catalysts compared to complexes 2a-9a, could be developed. Due to sealing the synthesis reactor with a semipermeable membrane, the retransfer of the “borrowed” hydrogen could be prevented and H2 is released. Dehydrogenation and condensation steps are now possible instead of BH/HA. By reacting secondary alcohols with β-amino alcohols, pyrroles were accessible.
After adapting the synthesis protocol to this new class of products the tolerance of functional groups was tested. Diversely functionalized alcohols were used. Under mild reaction conditions (90 °C) and very low catalyst loadings (down to 0.03 mol% iridium), a large number of novel pyrroles was accessible. Using this protocol 21 differently substituted α,α-pyrroles, 12 bicyclic pyrroles, symmetrically as well as non-symmetrically substituted oligopyrroles and three β-aminopyrroles were synthesized. The catalyst resting state was identified by NMR experiments and X-ray structure analysis to be an iridium trihydride. This trihydride is formed under catalytic conditions, by treatment of the pre-catalyst with alcohols or in hydrogen atmosphere.
In the final part of the work, a catalytic pyridine synthesis was developed. In this so far unknown heterocycle synthesis up to four different substituents could be introduced within a single reaction step. 2,6-, 2,5-, 2,4- and 2,3-substituted pyridines were synthesized selectively by using variously substituted primary or secondary alcohols and γ-amino alcohols. Furthermore, both the synthesis of bicyclic pyridines as well as the synthesis of pyridines that bear chiral substituents is possible.
Coarse-grained Modeling of Protein Dynamics using Elastic Network Models
- Dynamics is crucial for the functioning of biological macromolecules. Because of severe limitations in studying protein dynamics experimentally or with all-atom simulations, coarse-grained methods, especially elastic network models (ENMs), are frequently employed. In the last years, studies on various proteins showed that ENMs reliably reproduce experimental data, despite the simplified protein representation and the purely harmonic potential function. This work on two proteins with very different dynamical properties highlights the remarkable success of ENMs and shows which kind of questions can be answered using coarse-grained methods.
The allosteric enzyme aminoglycoside phosphotransferase(3')-IIIa (APH), which confers resistance against a broad range of aminoglycoside antibiotics to pathogenic bacteria, drastically changes its flexibility upon binding of substrates, but without changing its average conformation. In contrast, the homotrimeric vesicular stomatitis virus glycoprotein G (VSV-G), which triggers the pH-dependent fusion of viral and host membrane, undergoes a large structural rearrangement. A striking difference between the two proteins is their shape. VSV-G contains weakly constrained protein segments, the fusion loops, which can undergo large-scale motions at low energetic cost, whereas APH is not obviously arranged into different protein segments. Nevertheless, ENM calculations show that also APH consists of independently moving segments with correlated internal motion, so-called dynamic domains. The concept of dynamic domains can explain the differential effects of ligand binding on the dynamics of APH.
The first chapter of this thesis describes how experimental evidence for the importance of dynamics successively replaced the former idea of static proteins, and explains the dynamic basis of ligand binding, allostery and conformational changes. In the second chapter, theoretical methods for the analysis of protein dynamics are introduced, with emphasis on the ENM-based methods used in my studies. The studies are summarized in the third chapter. In the study on APH, I employ the Gaussian network model to analyze the ligand-dependent dynamics, the broad substrate specificity and the perturbation-sensitivity of the ligand binding sites. In a second study, ENM-based as well as all-atom molecular dynamics simulations are used to analyze the conformational change of VSV-G. Both approaches detect the fusion loops of VSV-G as most flexible parts of the protein, and thus as most likely starting point for the structural rearrangement, but only the all-atom model can generate deviations from the average structure at low pH. The last study describes the implementation and application of a dynamic domain assignment method, called CovarDom, which is based on covariances of residue fluctuations. Calculation of dynamic domains for a large protein set demonstrates the general applicability of CovarDom.
Direct Force Measurements on the Colloidal Scale: From Modified Electrodes to Particle Manipulation
- In this thesis the interfacial surface forces and mechanical properties of thin films have been studied by the colloidal probe technique. One central point is the combination of direct force measurements with an electrochemical setup in order to tune interfacial properties of an electrode modified with an organic layer. In particular the adhesion and ion adsorption have been studied, which are ubiquitous phenomena in the colloid science, electrochemistry, and biology. Moreover, a novel technique has been developed to fabricate chemically and mechanically stable colloidal probes for atomic force microscopy (AFM). Additionally, the elastic properties of polyelectrolyte multilayer films were locally resolved under controlled humidity.
The adhesive behaviour of colloidal particles on modified electrodes has been studied by direct force measurements with a micrometre-sized silica probe attached to an AFM-cantilever. By controlling the external potential applied to the modified electrode by means of a potentiostat, separate adhesion contributions at the modification layers in electrolyte solution were quantified. In particular, to determine the influence of the terminating functional groups, gold electrodes modified with self-assembled monolayers (SAMs) terminated in non-ionizable groups were used. It has been demonstrated that electrostatic double-layer forces dominate the adhesion of colloidal particles on hydrophobic and hydrophilic interfaces. In contrast to hydrophilic interface, for hydrophobic one forces due to the solvent exclusion play a significant role and leads to an offset in the adhesive force, which otherwise can be compensated by the external potential. However, the electrocapillarity is of minor importance and can be neglected.
To quantify the ion adsorption at organic interfaces a novel approach was followed, which is based on direct force measurements with silica colloidal probes on SAM-modified electrodes in electrolyte solutions. By variation of applied potential and concentration of specifically adsorbed ions, given by the solution’s pH, the charging behaviour of hydrophilic SAM-OH and hydrophobic SAM-CH3 has been determined. In difference to electrokinetic techniques, direct force measurements allow to probe the full range of the diffuse layer. The analysis of the diffuse layer potential as a function of externally applied potential provides important information. In particular, the shift of the potential of zero charge (pzc) indicates on the specific ion adsorption in the Stern layer as it alters the charging behaviour of the electrode’s interface. It has been demonstrated that hydronium and hydroxide ions adsorb on both the hydrophobic and hydrophilic interfaces. However, the presence of the background electrolyte (KCl) does not shift pzc and thus its ions have no specific affinity towards the interfacial adsorption. The adsorption of hydronium and hydroxide ions is stronger on hydrophobic, than on hydrophilic interface. This is in agreement with theoretical studies. The simple three-capacitor model based on a Langmuir-type adsorption isotherm provides semi-quantitative description of observed dependence of the diffuse double layer potential on applied potential.
A new technique for colloidal probe preparation was developed. A great challenge for the force measurements with the AFM is to ensure the cleanliness, chemical and mechanical stability of the used probes. The approach is based on high-temperature sintering of micrometer-sized silica particles to AFM cantilever with enhanced contact area. Due to a “neck” formed by nanometer-sized particles the increased mechanical stability of colloidal probes was achieved, which has been quantitatively determined by lateral force spectroscopy. The implementation of sintering procedure for silica colloids allowed the development of the highly stable colloidal probes, whose surface properties could be renewed by heating.
Finally, the mechanical properties of polyelectrolyte multilayer films have been determined by nanoindentation as a function of relative humidity. For these series of measurements again a colloidal probe has been used. It has been demonstrated that films containing polyglutamic acid have Young’s modulus, which depends on humidity. The change of stiffness with ambient humidity has reversible character.