Structural transformations related to organic solid-state reactions: correlation studies of NMR and X-ray analysis

Eine zielgerichtete Steuerung und Durchführung von organischen Festkörperreaktionen wird unter anderem durch genaue Kenntnis von Packungseffekten ermöglicht. Im Rahmen dieser Arbeit konnte durch den kombinierten Einsatz von Einkristallröntgenanalyse und hochauf-lösender Festkörper-NMR an ausgewählten Beispielen ein tieferes Verständnis und Einblicke in die Reaktionsmechanismen von organischen Festkörperreaktionen auf molekularer Ebene gewonnen werden. So konnten bei der topotaktischen [2+2] Photodimerisierung von Zimt-säure Intermediate isoliert und strukturell charakterisiert werden. Insbesondere anhand statischer Deuteronen- und 13C-CPMAS NMR Spektren konnten eindeutig dynamische Wasserstoffbrücken nachgewiesen werden, die transient die Zentrosymmetrie des Reaktions-produkts aufheben. Ein weiterer Nachweis gelang daraufhin mittels Hochtemperatur-Röntgen-untersuchung, sodass der scheinbare Widerspruch von NMR- und Röntgenuntersuchungen gelöst werden konnte. Eine Veresterung der Zimtsäure entfernt diese Wasserstoffbrücken und erhält somit die Zentrosymmetrie des Photodimers. Weiterhin werden Ansätze zur Strukturkontrolle in Festkörpern basierend auf der molekularen Erkennung des Hydroxyl-Pyridin (OH-N) Heterosynthon in Co-Kristallen beschrieben, wobei vor allem die Stabilität des Synthons in Gegenwart funktioneller Gruppen mit Möglichkeit zu kompetetiver Wasserstoffbrückenbildung festgestellt wurde. Durch Erweiterung dieses Ansatzes wurde die molekulare Spezifität des Hydroxyl-Pyridin (OH-N) Heterosynthons bei gleichzeitiger Co-Kristallisation mit mehreren Komponenten erfolgreich aufgezeigt. Am Beispiel der Co-Kristallisation von trans--1,2-bis(4-pyridyl)ethylen (bpe) mit Resorcinol (res) in Gegenwart von trans-1,2-bis(4-pyridyl)ethan (bpet) konnten Zwischenprodukte der Fest-körperreaktionen und neuartige Polymorphe isoliert werden, wobei eine lückenlose Aufklärung des Reaktionswegs mittels Röntgenanalyse gelang. Dabei zeigte sich, dass das Templat Resorcinol aus den Zielverbindungen entfernbar ist. Ferner gelang die Durchführung einer seltenen, nicht-idealen Einkristall-Einkristall-Umlagerung von trans--1,2-bis(4-pyridyl)ethylen (bpe) mit Resorcinol (res). In allen Fällen konnten die Fragen zur Struktur und Dynamik der untersuchten Verbindungen nur durch gemeinsame Nutzung von Röntgenanalyse und NMR-Spektroskopie bei vergleichbaren Temperaturen eindeutig und umfassend geklärt werden.

Ab-initio determination of x-ray absorption near edge structure (xanes) spectra in an ultrasoft and norm conserving pseudopotentials scheme

X-ray absorption spectroscopy (XAS) is a powerful means of investigation of structural and electronic properties in condensed -matter physics. Analysis of the near edge part of the XAS spectrum, the so – called X-ray Absorption Near Edge Structure (XANES), can typically provide the following information on the photoexcited atom: - Oxidation state and coordination environment. - Speciation of transition metal compounds. - Conduction band DOS projected on the excited atomic species (PDOS). Analysis of XANES spectra is greatly aided by simulations; in the most common scheme the multiple scattering framework is used with the muffin tin approximation for the scattering potential and the spectral simulation is based on a hypothetical, reference structure. This approach has the advantage of requiring relatively little computing power but in many cases the assumed structure is quite different from the actual system measured and the muffin tin approximation is not adequate for low symmetry structures or highly directional bonds. It is therefore very interesting and justified to develop alternative methods. In one approach, the spectral simulation is based on atomic coordinates obtained from a DFT (Density Functional Theory) optimized structure. In another approach, which is the object of this thesis, the XANES spectrum is calculated directly based on an ab – initio DFT calculation of the atomic and electronic structure. This method takes full advantage of the real many-electron final wavefunction that can be computed with DFT algorithms that include a core-hole in the absorbing atom to compute the final cross section. To calculate the many-electron final wavefunction the Projector Augmented Wave method (PAW) is used. In this scheme, the absorption cross section is written in function of several contributions as the many-electrons function of the finale state; it is calculated starting from pseudo-wavefunction and performing a reconstruction of the real-wavefunction by using a transform operator which contains some parameters, called partial waves and projector waves. The aim of my thesis is to apply and test the PAW methodology to the calculation of the XANES cross section. I have focused on iron and silicon structures and on some biological molecules target (myoglobin and cytochrome c). Finally other inorganic and biological systems could be taken into account for future applications of this methodology, which could become an important improvement with respect to the multiscattering approach.

A new double laser pulse pumping scheme for transient collisionally excited plasma soft X-ray lasers

Within this thesis a new double laser pulse pumping scheme for plasma-based, transient collisionally excited soft x-ray lasers (SXRL) was developed, characterized and utilized for applications. SXRL operations from ~50 up to ~200 electron volt were demonstrated applying this concept. As a central technical tool, a special Mach-Zehnder interferometer in the chirped pulse amplification (CPA) laser front-end was developed for the generation of fully controllable double-pulses to optimally pump SXRLs.rnThis Mach-Zehnder device is fully controllable and enables the creation of two CPA pulses of different pulse duration and variable energy balance with an adjustable time delay. Besides the SXRL pumping, the double-pulse configuration was applied to determine the B-integral in the CPA laser system by amplifying short pulse replica in the system, followed by an analysis in the time domain. The measurement of B-integral values in the 0.1 to 1.5 radian range, only limited by the reachable laser parameters, proved to be a promising tool to characterize nonlinear effects in the CPA laser systems.rnContributing to the issue of SXRL pumping, the double-pulse was configured to optimally produce the gain medium of the SXRL amplification. The focusing geometry of the two collinear pulses under the same grazing incidence angle on the target, significantly improved the generation of the active plasma medium. On one hand the effect was induced by the intrinsically guaranteed exact overlap of the two pulses on the target, and on the other hand by the grazing incidence pre-pulse plasma generation, which allows for a SXRL operation at higher electron densities, enabling higher gain in longer wavelength SXRLs and higher efficiency at shorter wavelength SXRLs. The observation of gain enhancement was confirmed by plasma hydrodynamic simulations.rnThe first introduction of double short-pulse single-beam grazing incidence pumping for SXRL pumping below 20 nanometer at the laser facility PHELIX in Darmstadt (Germany), resulted in a reliable operation of a nickel-like palladium SXRL at 14.7 nanometer with a pump energy threshold strongly reduced to less than 500 millijoule. With the adaptation of the concept, namely double-pulse single-beam grazing incidence pumping (DGRIP) and the transfer of this technology to the laser facility LASERIX in Palaiseau (France), improved efficiency and stability of table-top high-repetition soft x-ray lasers in the wavelength region below 20 nanometer was demonstrated. With a total pump laser energy below 1 joule the target, 2 mircojoule of nickel-like molybdenum soft x-ray laser emission at 18.9 nanometer was obtained at 10 hertz repetition rate, proving the attractiveness for high average power operation. An easy and rapid alignment procedure fulfilled the requirements for a sophisticated installation, and the highly stable output satisfied the need for a reliable strong SXRL source. The qualities of the DGRIP scheme were confirmed in an irradiation operation on user samples with over 50.000 shots corresponding to a deposited energy of ~ 50 millijoule.rnThe generation of double-pulses with high energies up to ~120 joule enabled the transfer to shorter wavelength SXRL operation at the laser facility PHELIX. The application of DGRIP proved to be a simple and efficient method for the generation of soft x-ray lasers below 10 nanometer. Nickel-like samarium soft x-ray lasing at 7.3 nanometer was achieved at a low total pump energy threshold of 36 joule, which confirmed the suitability of the applied pumping scheme. A reliable and stable SXRL operation was demonstrated, due to the single-beam pumping geometry despite the large optical apertures. The soft x-ray lasing of nickel-like samarium was an important milestone for the feasibility of applying the pumping scheme also for higher pumping pulse energies, which are necessary to obtain soft x-ray laser wavelengths in the water window. The reduction of the total pump energy below 40 joule for 7.3 nanometer short wavelength lasing now fulfilled the requirement for the installation at the high-repetition rate operation laser facility LASERIX.rn

Imaging and modeling of pore scale processes in porous media using X-ray computed tomography and lattice Boltzmann solver

In der Erdöl– und Gasindustrie sind bildgebende Verfahren und Simulationen auf der Porenskala im Begriff Routineanwendungen zu werden. Ihr weiteres Potential lässt sich im Umweltbereich anwenden, wie z.B. für den Transport und Verbleib von Schadstoffen im Untergrund, die Speicherung von Kohlendioxid und dem natürlichen Abbau von Schadstoffen in Böden. Mit der Röntgen-Computertomografie (XCT) steht ein zerstörungsfreies 3D bildgebendes Verfahren zur Verfügung, das auch häufig für die Untersuchung der internen Struktur geologischer Proben herangezogen wird. Das erste Ziel dieser Dissertation war die Implementierung einer Bildverarbeitungstechnik, die die Strahlenaufhärtung der Röntgen-Computertomografie beseitigt und den Segmentierungsprozess dessen Daten vereinfacht. Das zweite Ziel dieser Arbeit untersuchte die kombinierten Effekte von Porenraumcharakteristika, Porentortuosität, sowie die Strömungssimulation und Transportmodellierung in Porenräumen mit der Gitter-Boltzmann-Methode. In einer zylindrischen geologischen Probe war die Position jeder Phase auf Grundlage der Beobachtung durch das Vorhandensein der Strahlenaufhärtung in den rekonstruierten Bildern, das eine radiale Funktion vom Probenrand zum Zentrum darstellt, extrahierbar und die unterschiedlichen Phasen ließen sich automatisch segmentieren. Weiterhin wurden Strahlungsaufhärtungeffekte von beliebig geformten Objekten durch einen Oberflächenanpassungsalgorithmus korrigiert. Die Methode der „least square support vector machine” (LSSVM) ist durch einen modularen Aufbau charakterisiert und ist sehr gut für die Erkennung und Klassifizierung von Mustern geeignet. Aus diesem Grund wurde die Methode der LSSVM als pixelbasierte Klassifikationsmethode implementiert. Dieser Algorithmus ist in der Lage komplexe geologische Proben korrekt zu klassifizieren, benötigt für den Fall aber längere Rechenzeiten, so dass mehrdimensionale Trainingsdatensätze verwendet werden müssen. Die Dynamik von den unmischbaren Phasen Luft und Wasser wird durch eine Kombination von Porenmorphologie und Gitter Boltzmann Methode für Drainage und Imbibition Prozessen in 3D Datensätzen von Böden, die durch synchrotron-basierte XCT gewonnen wurden, untersucht. Obwohl die Porenmorphologie eine einfache Methode ist Kugeln in den verfügbaren Porenraum einzupassen, kann sie dennoch die komplexe kapillare Hysterese als eine Funktion der Wassersättigung erklären. Eine Hysterese ist für den Kapillardruck und die hydraulische Leitfähigkeit beobachtet worden, welche durch die hauptsächlich verbundenen Porennetzwerke und der verfügbaren Porenraumgrößenverteilung verursacht sind. Die hydraulische Konduktivität ist eine Funktion des Wassersättigungslevels und wird mit einer makroskopischen Berechnung empirischer Modelle verglichen. Die Daten stimmen vor allem für hohe Wassersättigungen gut überein. Um die Gegenwart von Krankheitserregern im Grundwasser und Abwässern vorhersagen zu können, wurde in einem Bodenaggregat der Einfluss von Korngröße, Porengeometrie und Fluidflussgeschwindigkeit z.B. mit dem Mikroorganismus Escherichia coli studiert. Die asymmetrischen und langschweifigen Durchbruchskurven, besonders bei höheren Wassersättigungen, wurden durch dispersiven Transport aufgrund des verbundenen Porennetzwerks und durch die Heterogenität des Strömungsfeldes verursacht. Es wurde beobachtet, dass die biokolloidale Verweilzeit eine Funktion des Druckgradienten als auch der Kolloidgröße ist. Unsere Modellierungsergebnisse stimmen sehr gut mit den bereits veröffentlichten Daten überein.

The relation between mass and concentration in x-ray galaxy clusters at high-redshift.

In this Thesis work we have studied the properties of high-redshift galaxy clusters through the X-ray emission from their intracluster gas. In particular, we have focused on the relation between concentration and mass that is related to the density of the universe at the formation time of the clusters and therefore, it is a powerful cosmological probe. Concentration is expected to be a decreasing function of mass but a complete characterization of this relation has not been reached yet. We have analysed 22 clusters observed withe the Chandra satellite at high redshift and we have investigated the concentration-mass relation.

High-temperature induced dehydration, phase transition and exsolution in amicite: A single-crystal X-ray study

Temperature dependent single-crystal X-ray data were collected on amicite K4Na4(Al8Si8O32)·11H2O from Kola Peninsula (Russia) in steps of 25 °C from room temperature to 175 °C and of 50 °C up to 425 °C. At room temperature amicite has space group I2 with a = 10.2112(1), b = 10.4154(1), c = 9.8802(1) Å, β = 88.458(1)°, V = 1050.416(18) Å3. Its crystal structure is based on a Si–Al ordered tetrahedral framework of the GIS type with two systems of eight-membered channels running along the a and c axes. Extraframework K and Na cations are ordered at two fully occupied sites. Above 75 °C amicite was found to partly dehydrate into two separate but coherently intergrown phases, both of space group I2/a, one K-rich ∼K8(Al8Si8O32) ·4H2O (at 75 °C: a = 10.038(2), b = 9.6805(19), c = 9.843(2) Å, β = 89.93(3)°, V = 956.5(3) Å3) and the other Na-rich ∼Na8(Al8Si8O32)·2H2O (at 75 °C: a = 9.759(2), b = 8.9078(18), c = 9.5270(19) Å, β = 89.98(3)°, V = 828.2(3) Å3). Upon further heating above 75 °C the Na- and K-phases lost remaining H2O with only minor influence on the framework structure and became anhydrous at 175 °C and 375 °C, respectively. The two anhydrous phases persisted up to 425 °C. Backscattered electron images of a heated crystal displayed lamellar intergrowth of the K- and Na-rich phases. Exposed to ambient humid conditions K- and Na-rich phases rehydrated and conjoined to the original one phase I2 structure.

Hohlraum Target for Overcoming Refractive Losses in Plasma X-ray Lasers

Refractive losses in laser-produced plasmas used as gain media are caused by electron density gradients, and limit the energy transport range. The pump pulse is thus deflected from the high-gain region and the short wavelength laser signal also steers away, causing loss of collimation. A Hohlraum used as a target makes the plasma homogeneous and can mitigate refractive losses by means of wave-guiding. A computational study combining a hydrodynamics code and an atomic physics code is presented, which includes a ray-tracing modeling based on the eikonal theory of the trajectory equation. This study presents gain calculations based on population inversion produced by free-electron collisions exciting bound electrons into metastable levels in the 3d94d1(J = 0) → 3d94p1(J = 1) transition of Ni-like Sn. Further, the Hohlraum suggests a dramatic enhancement of the conversion efficiency of collisionally excited x-ray lasing for Ni-like Sn.

Combining Monte Carlo methods with coherent wave optics for the simulation of phase-sensitive X-ray imaging

Phase-sensitive X-ray imaging shows a high sensitivity towards electron density variations, making it well suited for imaging of soft tissue matter. However, there are still open questions about the details of the image formation process. Here, a framework for numerical simulations of phase-sensitive X-ray imaging is presented, which takes both particle- and wave-like properties of X-rays into consideration. A split approach is presented where we combine a Monte Carlo method (MC) based sample part with a wave optics simulation based propagation part, leading to a framework that takes both particle- and wave-like properties into account. The framework can be adapted to different phase-sensitive imaging methods and has been validated through comparisons with experiments for grating interferometry and propagation-based imaging. The validation of the framework shows that the combination of wave optics and MC has been successfully implemented and yields good agreement between measurements and simulations. This demonstrates that the physical processes relevant for developing a deeper understanding of scattering in the context of phase-sensitive imaging are modelled in a sufficiently accurate manner. The framework can be used for the simulation of phase-sensitive X-ray imaging, for instance for the simulation of grating interferometry or propagation-based imaging.

Liquid–Vapor Interface of Formic Acid Solutions in Salt Water: A Comparison of Macroscopic Surface Tension and Microscopic in Situ X-ray Photoelectron Spectroscopy Measurements

The liquid–vapor interface is difficult to access experimentally but is of interest from a theoretical and applied point of view and has particular importance in atmospheric aerosol chemistry. Here we examine the liquid–vapor interface for mixtures of water, sodium chloride, and formic acid, an abundant chemical in the atmosphere. We compare the results of surface tension and X-ray photoelectron spectroscopy (XPS) measurements over a wide range of formic acid concentrations. Surface tension measurements provide a macroscopic characterization of solutions ranging from 0 to 3 M sodium chloride and from 0 to over 0.5 mole fraction formic acid. Sodium chloride was found to be a weak salting out agent for formic acid with surface excess depending only slightly on salt concentration. In situ XPS provides a complementary molecular level description about the liquid–vapor interface. XPS measurements over an experimental probe depth of 51 Å gave the C 1s to O 1s ratio for both total oxygen and oxygen from water. XPS also provides detailed electronic structure information that is inaccessible by surface tension. Density functional theory calculations were performed to understand the observed shift in C 1s binding energies to lower values with increasing formic acid concentration. Part of the experimental −0.2 eV shift can be assigned to the solution composition changing from predominantly monomers of formic acid to a combination of monomers and dimers; however, the lack of an appropriate reference to calibrate the absolute BE scale at high formic acid mole fraction complicates the interpretation. Our data are consistent with surface tension measurements yielding a significantly more surface sensitive measurement than XPS due to the relatively weak propensity of formic acid for the interface. A simple model allowed us to replicate the XPS results under the assumption that the surface excess was contained in the top four angstroms of solution.

Minerals, geochemistry and x-ray power characteristics at DSDP Sites 54-424, 60-458 and 60-459

Secondary minerals filling veins and vesicles in volcanic basement at Deep Sea Drilling Project Sites 458 and 459 indicate that there were two stages of alteration at each site: an early oxidative, probably hydrothermal, stage and a later, low-temperature, less oxidative stage, probably contemporaneous with faulting in the tectonically active Mariana forearc region. The initial stage is most evident in Hole 459B, where low-Al, high Fe smectites and iron hydroxides formed in vesicles in pillow basalts and low-Al palygorskite formed in fractures. Iron hydroxides and celadonite formed in massive basalts next to quartz-oligoclase micrographic intergrowths. Palygorskite was found in only one sample near the top of basement in Hole 458, but it too is associated with iron hydroxides. Palygorskite has previously been reported only in marine sediments in DSDP and other occurrences. It evidently formed here as a precipitate from fluids in which Si, Mg, Fe, and even some Al were concentrated. Experimental data suggest that the solutions probably had high pH and somewhat elevated temperatures. The compositions of associated smectites resemble those in hydrothermal sediments and in basalts at the Galapagos mounds geothermal field. The second stage of alteration was large-scale replacement of basalt by dioctahedral, trioctahedral, or mixed-layer clays and phillipsite along zones of intense fracturing, especially near the bottom of Holes 458 and 459B. The basalts are commonly slickensided, and there are recemented microfault offsets in overlying sediments. Native copper occurs in one core of Hole 458, but associated smectites are dominantly dioctahedral, unlike Hole 459B, where they are mainly trioctahedral, indicating nonoxidative alteration. The alteration in both holes is more intense than at most DSDP ocean crust sites and may have been augmented by water derived from subducting ocean crust beneath the fore-arc region.

A proposal for multi-tens of GW fully coherent femtosecond soft X-ray lasers

X-ray free-electron lasers1,2 delivering up to 131013 coherent photons in femtosecond pulses are bringing about a revolution in X-ray science3?5. However, some plasma-based soft X-ray lasers6 are attractive because they spontaneously emit an even higher number of photons (131015), but these are emitted in incoherent and long (hundreds of picoseconds) pulses7 as a consequence of the amplification of stochastic incoherent self-emission. Previous experimental attempts to seed such amplifiers with coherent femtosecond soft X-rays resulted in as yet unexplained weak amplification of the seed and strong amplification of incoherent spontaneous emission8. Using a time-dependent Maxwell?Bloch model describing the amplification of both coherent and incoherent soft X-rays in plasma, we explain the observed inefficiency and propose a new amplification scheme based on the seeding of stretched high harmonics using a transposition of chirped pulse amplification to soft X-rays. This scheme is able to deliver 531014 fully coherent soft X-ray photons in 200 fs pulses and with a peak power of 20 GW.

Structural features of the γ subunit of the Escherichia coli F1 ATPase revealed by a 4.4-Å resolution map obtained by x-ray crystallography

The F1 part of the F1FO ATP synthase from Escherichia coli has been crystallized and its structure determined to 4.4-Å resolution by using molecular replacement based on the structure of the beef-heart mitochondrial enzyme. The bacterial F1 consists of five subunits with stoichiometry α3, β3, γ, δ, and ɛ. δ was removed before crystallization. In agreement with the structure of the beef-heart mitochondrial enzyme, although not that from rat liver, the present study suggests that the α and β subunits are arranged in a hexagonal barrel but depart from exact 3-fold symmetry. In the structures of both beef heart and rat-liver mitochondrial F1, less than half of the structure of the γ subunit was seen because of presumed disorder in the crystals. The present electron-density map includes a number of rod-shaped features which appear to correspond to additional α-helical regions within the γ subunit. These suggest that the γ subunit traverses the full length of the stalk that links the F1 and FO parts and makes significant contacts with the c subunit ring of FO.