Advanced applications of X-ray Absorption Spectroscopy to the study of protein metal sites.

We present a study of the metal sites of different proteins through X-ray Absorption Fine Structure (XAFS) spectroscopy. First of all, the capabilities of XAFS analysis have been improved by ab initio simulation of the near-edge region of the spectra, and an original analysis method has been proposed. The method subsequently served ad a tool to treat diverse biophysical problems, like the inhibition of proton-translocating proteins by metal ions and the matrix effect exerted on photosynthetic proteins (the bacterial Reaction Center, RC) by strongly dehydrate sugar matrices. A time-resolved study of Fe site of RC with μs resolution has been as well attempted. Finally, a further step aimed to improve the reliability of XAFS analysis has been performed by calculating the dynamical parameters of the metal binding cluster by means of DFT methods, and the theoretical result obtained for MbCO has been successfully compared with experimental data.

Background minimization issues for next generation hard X-ray focusing telescopes

The hard X-ray band (10 - 100 keV) has been only observed so far by collimated and coded aperture mask instruments, with a sensitivity and an angular resolution lower than two orders of magnitude as respects the current X-ray focusing telescopes operating below 10 - 15 keV. The technological advance in X-ray mirrors and detection systems is now able to extend the X-ray focusing technique to the hard X-ray domain, filling the gap in terms of observational performances and providing a totally new deep view on some of the most energetic phenomena of the Universe. In order to reach a sensitivity of 1 muCrab in the 10 - 40 keV energy range, a great care in the background minimization is required, a common issue for all the hard X-ray focusing telescopes. In the present PhD thesis, a comprehensive analysis of the space radiation environment, the payload design and the resulting prompt X-ray background level is presented, with the aim of driving the feasibility study of the shielding system and assessing the scientific requirements of the future hard X-ray missions. A Geant4 based multi-mission background simulator, BoGEMMS, is developed to be applied to any high energy mission for which the shielding and instruments performances are required. It allows to interactively create a virtual model of the telescope and expose it to the space radiation environment, tracking the particles along their path and filtering the simulated background counts as a real observation in space. Its flexibility is exploited to evaluate the background spectra of the Simbol-X and NHXM mission, as well as the soft proton scattering by the X-ray optics and the selection of the best shielding configuration. Altough the Simbol-X and NHXM missions are the case studies of the background analysis, the obtained results can be generalized to any future hard X-ray telescope. For this reason, a simplified, ideal payload model is also used to select the major sources of background in LEO. All the results are original contributions to the assessment studies of the cited missions, as part of the background groups activities.

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.

Progress in x-ray spectroscopies for the study of advanced materials

This thesis work is focused on the use of selected core-level x-ray spectroscopies to study semiconductor materials of great technological interest and on the development of a new implementation of appearance potential spectroscopy. Core-level spectroscopies can be exploited to study these materials with a local approach since they are sensitive to the electronic structure localized on a chemical species present in the sample examined. This approach, in fact, provides important micro-structural information that is difficult to obtain with techniques sensitive to the average properties of materials. In this thesis work we present a novel approach to the study of semiconductors with core-level spectroscopies based on an original analysis procedure that leads to an insightful understanding of the correlation between the local micro-structure and the spectral features observed. In particular, we studied the micro-structure of Hydrogen induced defects in nitride semiconductors, since the analysed materials show substantial variations of optical and electronic properties as a consequence of H incorporation. Finally, we present a novel implementation of soft x-ray appearance potential spectroscopy, a core-level spectroscopy that uses electrons as a source of excitation and has the great advantage of being an in-house technique. The original set-up illustrated was designed to reach a high signal-to-noise ratio for the acquisition of good quality spectra that can then be analyzed in the framework of the real space full multiple scattering theory. This technique has never been coupled with this analysis approach and therefore our work unite a novel implementation with an original data analysis method, enlarging the field of application of this technique.

Ex situ X-­Ray absorption study of Li-­rich layered cathode material Li[Li0.2Mn0.56Ni0.16Co0.08]O2

The Li-rich layered transition metal oxides (LLOs) Li2MnO3-LiMO2 (M=Mn, Co, Ni, etc.) have drawn considerable attention as cathode materials for rechargeable lithium batteries. They generate large reversible capacities but the fundamental reaction mechanism and structural perturbations during cycling remain controversial. In the present thesis, ex situ X-ray absorption spectroscopy (XAS) measurements were performed on Li[Li0.2Mn0.56Ni0.16Co0.08]O2 at different stage of charge during electrochemical oxidation/reduction. K-edge spectra of Co, Mn and Ni were recorded through a voltage range of 3.7-4.8V vs. Li/Li+, which consist of X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS). Oxidation states during initial charge were discussed based on values from literature as well as XANES analysis. Information about bond distance, coordination number as well as corresponding Debye-Waller factor were extracted from Gnxas analysis of raw data in the EXAFS region. The possibility of oxygen participation in the initial charge was discussed. Co and Ni prove to take part in the oxidation/reduction process while Mn remain in the tetravalent state. The cathode material appears to retain good structural short-range order during charge-discharge. A resemblance of the pristine sample and sample 4 was discovered which was firstly reported for similar compounds.

Hard x-ray photoelectron spectroscopy of bulk and thin films of Heusler compounds

X-ray photoemission spectroscopy (XPS) is one of the most universal and powerful tools for investigation of chemical states and electronic structures of materials. The application of hard x-rays increases the inelastic mean free path of the emitted electrons within the solid and thus makes hard x-ray photoelectron spectroscopy (HAXPES) a bulk sensitive probe for solid state research and especially a very effective nondestructive technique to study buried layers.rnThis thesis focuses on the investigation of multilayer structures, used in magnetic tunnel junctions (MTJs), by a number of techniques applying HAXPES. MTJs are the most important components of novel nanoscale devices employed in spintronics. rnThe investigation and deep understanding of the mechanisms responsible for the high performance of such devices and properties of employed magnetic materials that are, in turn, defined by their electronic structure becomes feasible applying HAXPES. Thus the process of B diffusion in CoFeB-based MTJs was investigated with respect to the annealing temperature and its influence on the changes in the electronic structure of CoFeB electrodes that clarify the behaviour and huge TMR ratio values obtained in such devices. These results are presented in chapter 6. The results of investigation of the changes in the valence states of buried off-stoichiometric Co2MnSi electrodes were investigated with respect to the Mn content α and its influence on the observed TMR ratio are described in chapter 7.rnrnMagnetoelectronic properties such as exchange splitting in ferromagnetic materials as well as the macroscopic magnetic ordering can be studied by magnetic circular dichroism in photoemission (MCDAD). It is characterized by the appearance of an asymmetry in the photoemission spectra taken either from the magnetized sample with the reversal of the photon helicity or by reversal of magnetization direction of the sample when the photon helicity direction is fixed. Though recently it has been widely applied for the characterization of surfaces using low energy photons, the bulk properties have stayed inaccessible. Therefore in this work this method was integrated to HAXPES to provide an access to exploration of magnetic phenomena in the buried layers of the complex multilayer structures. Chapter 8 contains the results of the MCDAD measurements employing hard x-rays for exploration of magnetic properties of the common CoFe-based band-ferromagnets as well as half-metallic ferromagnet Co2FeAl-based MTJs.rnrnInasmuch as the magnetoresistive characteristics in spintronic devices are fully defined by the electron spins of ferromagnetic materials their direct measurements always attracted much attention but up to date have been limited by the surface sensitivity of the developed techniques. Chapter 9 presents the results on the successfully performed spin-resolved HAXPES experiment using a spin polarimeter of the SPLEED-type on a buried Co2FeAl0.5Si0.5 magnetic layer. The measurements prove that a spin polarization of about 50 % is retained during the transmission of the photoelectrons emitted from the Fe 2p3/2 state through a 3-nm-thick oxide capping layer.rn

Computer algebra for x-ray spectral reconstruction between 6 and 25 MV

A previously presented algorithm for the reconstruction of bremsstrahlung spectra from transmission data has been implemented into MATHEMATICA. Spectra vectorial algebra has been used to solve the matrix system A * F = T. The new implementation has been tested by reconstructing photon spectra from transmission data acquired in narrow beam conditions, for nominal energies of 6, 15, and 25 MV. The results were in excellent agreement with the original calculations. Our implementation has the advantage to be based on a well-tested mathematical kernel. Furthermore it offers a comfortable user interface.

In situ dehydration behavior of zeolite-like cavansite: A single-crystal X-ray study

To track dehydration behavior of cavansite, Ca(VO)(Si4O10)·4H2O space group Pnma, a = 9.6329(2), b = 13.6606(2), c = 9.7949(2) Å, V = 1288.92(4) Å3 single-crystal X-ray diffraction data on a crystal from Wagholi quarry, Poona district (India) were collected up to 400 °C in steps of 25 °C up to 250 °C and in steps of 50 °C between 250 and 400 °C. The structure of cavansite is characterized by layers of silicate tetrahedra connected by V4+O5 square pyramids. This way a porous framework structure is formed with Ca and H2O as extraframework occupants. At room temperature, the hydrogen bond system was analyzed. Ca is eightfold coordinated by four bonds to O of the framework structure and four bonds to H2O molecules. H2O linked to Ca is hydrogen bonded to the framework and also to adjacent H2O molecules. The dehydration in cavansite proceeds in four steps.At 75 °C, H2O at O9 was completely expelled leading to 3 H2O pfu with only minor impact on framework distortion and contraction V = 1282.73(3) Å3. The Ca coordination declined from originally eightfold to sevenfold and H2O at O7 displayed positional disorder.At 175 °C, the split O7 sites approached the former O9 position. In addition, the sum of the three split positions O7, O7a, and O7b decreased to 50% occupancy yielding 2 H2O pfu accompanied by a strong decrease in volume V = 1206.89(8) Å3. The Ca coordination was further reduced from sevenfold to sixfold.At 350 °C, H2O at O8 was released leading to a formula with 1 H2O pfu causing additional structural contraction (V = 1156(11) Å3). At this temperature, Ca adopted fivefold coordination and O7 rearranged to disordered positions closer to the original O9 H2O site.At 400 °C, cavansite lost crystallinity but the VO2+ characteristic blue color was preserved. Stepwise removal of water is discussed on the basis of literature data reporting differential thermal analyses, differential thermo-gravimetry experiments and temperature dependent IR spectra in the range of OH stretching vibrations.

Iron X-ray fluorescence (XRF) scannings of ODP Holes 165-1001A and 171-1050C

Abstract: Ocean Drilling Program Sites 1001A (Caribbean Sea) and 1050C (western North Atlantic) display obliquity and precession cycles throughout polarity zone C27 of the late Danian stage (earliest Cenozoic time). Sliding-window spectra analysis and direct cycle counting on downhole logs and high-resolution Fe variations at both sites yield the equivalent of 35-36 obliquity cycles. This cycle-tuned duration for polarity chron C27 of 1.45 Ma (applying a modern mean obliquity period of 40.4 ka) is consistent with trends from astronomical tuning of early Danian polarity chron C29 and 40Ar/39Ar age calibration of the Campanian-Maastrichtian magnetic polarity time scale. The cycle-tuned Danian stage (sensu Berggren et al. 1995, in SEPM Special Publications, 54, 129-212) spans 3.65 Ma (65.5-61.85 Ma). Spreading rates on a reference South Atlantic synthetic profile display progressive slowing during the Maastrichtian to Danian stages, then remained relatively constant through late Palaeocene and early Eocene time.

Sulfur K-edge x-ray absorption spectroscopy: A spectroscopic tool to examine the redox state of S-containing metabolites in vivo

The sulfur K-edge x-ray absorption spectra for the amino acids cysteine and methionine and their corresponding oxidized forms cystine and methionine sulfoxide are presented. Distinct differences in the shape of the edge and the inflection point energy for cysteine and cystine are observed. For methionine sulfoxide the inflection point energy is 2.8 eV higher compared with methionine. Glutathione, the most abundant thiol in animal cells, also has been investigated. The x-ray absorption near-edge structure spectrum of reduced glutathione resembles that of cysteine, whereas the spectrum of oxidized glutathione resembles that of cystine. The characteristic differences between the thiol and disulfide spectra enable one to determine the redox status (thiol to disulfide ratio) in intact biological systems, such as unbroken cells, where glutathione and cyst(e)ine are the two major sulfur-containing components. The sulfur K-edge spectra for whole human blood, plasma, and erythrocytes are shown. The erythrocyte sulfur K-edge spectrum is similar to that of fully reduced glutathione. Simulation of the plasma spectrum indicated 32% thiol and 68% disulfide sulfur. The whole blood spectrum can be simulated by a combination of 46% disulfide and 54% thiol sulfur.

Identification, retinoid binding, and x-ray analysis of a human retinol-binding protein

Two cellular retinol-binding proteins (CRBP I and II) with distinct tissue distributions and retinoid-binding properties have been recognized thus far in mammals. Here, we report the identification of a human retinol-binding protein resembling type I (55.6% identity) and type II (49.6% identity) CRBPs, but with a unique H residue in the retinoid-binding site and a distinctively different tissue distribution. Additionally, this binding protein (CRBP III) exhibits a remarkable sequence identity (62.2%) with the recently identified ι-crystallin/CRBP of the diurnal gecko Lygodactylus picturatus [Werten, P. J. L., Röll, B., van Alten, D. M. F. & de Jong, W. W. (2000) Proc. Natl. Acad. Sci. USA 97, 3282–3287 (First Published March 21, 2000; 10.1073/pnas.050500597)]. CRBP III and all-trans-retinol form a complex (Kd ≈ 60 nM), the absorption spectrum of which is characterized by the peculiar fine structure typical of the spectra of holo-CRBP I and II. As revealed by a 2.3-Å x-ray molecular model of apo-CRBP III, the amino acid residues that line the retinol-binding site in CRBP I and II are positioned nearly identically in the structure of CRBP III. At variance with the human CRBP I and II mRNAs, which are most abundant in ovary and intestine, respectively, the CRBP III mRNA is expressed at the highest levels in kidney and liver thus suggesting a prominent role for human CRBP III as an intracellular mediator of retinol metabolism in these tissues.

The masses of the neutron and donor star in the high-mass X-ray binary IGR J18027-2016

Aims. We report near-infrared observations of the supergiant donor to the eclipsing high mass X-ray binary pulsar IGR J18027-2016. We aim to determine its spectral type and measure its radial velocity curve and hence determine the stellar masses of the components. Methods. ESO/VLT observations of the donor utilising the NIR spectrograph ISAAC were obtained in the H and K bands. The multi-epoch H band spectra were cross-correlated with RV templates in order to determine a radial solution for the system. Results. The spectral type of the donor was confirmed as B0-1 I. The radial velocity curve constructed has a semi-amplitude of 23.8 ± 3.1 km s-1. Combined with other measured system parameters, a dynamically determined neutron star mass of 1.4  ±  0.2–1.6  ±  0.3 M⊙ is found. The mass range of the B0-B1 I donor was 18.6  ±  0.8–21.8  ±  2.4 M⊙. These lower and upper limits were obtained under the assumption that the system is viewed edge-on (i = 90° with β = 0.89) for the lower limit and the donor fills its Roche lobe (β = 1 with i = 73.1°) for the upper limit respectively.

Circumstellar emission in Be/X-ray binaries of the Magellanic Clouds and the Milky Way

Aims. We study the optical and near-infrared colour excesses produced by circumstellar emission in a sample of Be/X-ray binaries. Our main goals are exploring whether previously published relations, valid for isolated Be stars, are applicable to Be/X-ray binaries and computing the distance to these systems after correcting for the effects of the circumstellar contamination. Methods. Simultaneous UBVRI photometry and spectra in the 3500−7000 Å spectral range were obtained for 11 optical counterparts to Be/X-ray binaries in the LMC, 5 in the SMC and 12 in the Milky Way. As a measure of the amount of circumstellar emission we used the Hα equivalent width corrected for photospheric absorption. Results. We find a linear relationship between the strength of the Hα emission line and the component of E(B − V) originating from the circumstellar disk. This relationship is valid for stars with emission lines weaker than EW ≈ −15   Å. Beyond this point, the circumstellar contribution to E(B − V) saturates at a value ≈0.17   mag. A similar relationship is found for the (V − I) near infrared colour excess, albeit with a steeper slope and saturation level. The circumstellar excess in (B − V) is found to be about five times higher for Be/X-ray binaries than for isolated Be stars with the same equivalent width EW(Hα), implying significant differences in the physical properties of their circumstellar envelopes. The distance to Be/X-ray binaries (with non-shell Be star companions) can only be correctly estimated by taking into account the excess emission in the V band produced by free-free and free-bound transitions in the circumstellar envelope. We provide a simple method to determine the distances that includes this effect.

GRO J1008−57: an (almost) predictable transient X-ray binary

A study of archival RXTE, Swift, and Suzaku pointed observations of the transient high-mass X-ray binary GRO J1008−57 is presented. A new orbital ephemeris based on pulse arrival-timing shows the times of maximum luminosities during outbursts of GRO J1008−57 to be close to periastron at orbital phase − 0.03. This makes the source one of a few for which outburst dates can be predicted with very high precision. Spectra of the source in 2005, 2007, and 2011 can be well described by a simple power law with high-energy cutoff and an additional black body at lower energies. The photon index of the power law and the black-body flux only depend on the 15–50 keV source flux. No apparent hysteresis effects are seen. These correlations allow us to predict the evolution of the pulsar’s X-ray spectral shape over all outbursts as a function of just one parameter, the source’s flux. If modified by an additional soft component, this prediction even holds during GRO J1008−57’s 2012 type II outburst.

Accreting magnetars: a new type of high-mass X-ray binaries?

The discovery of very slow pulsations (Pspin =5560 s) has solved the long-standing question of the nature of the compact object in the high-mass X-ray binary 4U 2206+54 but has posed new ones. According to spin evolutionary models in close binary systems, such slow pulsations require a neutron star magnetic field strength larger than the quantum critical value of 4.4 × 1013 G, suggesting the presence of a magnetar. We present the first XMM–Newton observations of 4U 2206+54 and investigate its spin evolution. We find that the observed spin-down rate agrees with the magnetar scenario. We analyse Integral Spacecraft Gamma-Ray Imager (ISGRI)/INTErnational Gamma-RAy Laboratory (INTEGRAL) observations of 4U 2206+54 to search for the previously suggested cyclotron resonance scattering feature at ∼30 keV. We do not find a clear indication of the presence of the line, although certain spectra display shallow dips, not always at 30 keV. The association of these dips with a cyclotron line is very dubious because of its apparent transient nature. We also investigate the energy spectrum of 4U 2206+54 in the energy range 0.3–10 keV with unprecedented detail and report for the first time the detection of very weak 6.5 keV fluorescence iron lines. The photoelectric absorption is consistent with the interstellar value, indicating very small amount of local matter, which would explain the weakness of the florescence lines. The lack of matter locally to the source may be the consequence of the relatively large orbital separation of the two components of the binary. The wind would be too tenuous in the vicinity of the neutron star.