Title: Magnetic circular dichroism and aromatic compounds Author: Petr Štěpánek Department/Institute: Institute of Organic Chemistry and Biochemistry AS CR, v.v.i. Supervisor: prof. RNDr. Petr Bouř, DSc., Institute of Organic Chemistry and Biochemistry AS CR, v.v.i. Abstract: The thesis presents a series of studies concerning magnetic circular dichroism (MCD), a spectroscopic method, which experienced an intense theo- retical development in the recent years. New computational codes opened possi- bilities to calculate MCD spectra of larger and more varied molecules than was possible in the past. In the presented studies, we took the advantage of the new computational codes to broaden the possible span of applications of the MCD technique. As an example, we present MCD as a method useful for obtaining information about the structure of fullerenes. We also studied the influence of the molecular conformation and the explicit and implicit solvent models on the MCD spectra of aromatic amino acids using the newly implemented alterna- tive computational protocol based on sum-over-states calculations. We have also theoretically predicted spectra of the nuclear spin circular dichroism (NSCD), a potential new high-resolution spectroscopy. Keywords: magnetic circular dichroism, quantum-chemical calculations, density...

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Die vorliegende Arbeit befasst sich mit der Untersuchung der mikromagnetischen Domänenstruktur und des gekoppelten magneto-strukturellen Phasenübergangs dünner epitaktischer MnAs-Filme auf GaAs. Im Besonderen wird der Einfluss der Substratorientierung, der Filmdicke und eines externen magnetischen Feldes auf die magnetischen und strukturellen Eigenschaften untersucht. Dabei kommen die komplementären Untersuchungsmethoden AFM (atomic force microscopy) / MFM (magnetic force microscopy) und LEEM (low energy electron microscopy) / XMCDPEEM (X-ray magnetic circular dichroism photoemission electron microscopy) zum Einsatz. Im Zuge des Phasenübergangs erster Ordnung zeigen MnAs Filme auf GaAs (001) und (311)A eine regelmäßige Anordnung ferromagnetischer alpha-MnAs und paramagnetischer beta-MnAs Streifen. Die Breite der Streifen ist eine Funktion der Temperatur, während die Periodizität eine lineare Funktion der Filmdicke ist. Die Domänenstruktur hängt stark von der Breite bzw. dem Abstand der ferromagnetischen Streifen ab, da diese direkt die Formanisotropie bzw. die magnetische Kopplung beeinflussen. Die Domänenstrukturen wird, abhängig von der Zahl der Subdomänen entlang der leichten Magnetisierungsrichtung, klassifiziert, wobei bis zu drei elementare Domänentypen beobachtet werden. Bei MnAs-Filmen die auf der GaAs (111)B Oberfläche gewachsen wurden, führt die Epitaxie zu einem geänderten Spannungszustands des Films, wobei eine erhöhte Phasenübergangstemperatur beobachtet wird. Durch temperaturabhängige XMCDPEEM-, AFM- und MFM-Messungen kann gezeigt werden, daß durch den lokalen Abbau der Verspannung in der Nähe eines Risses die Phasenübergangstemperatur lokal erhöht ist. Um Ummagnetisierungsprozesse auf einer mikroskopischen Skala untersuchen zu können und um den Einfluß eines magnetischen Feldes auf die Domänenstruktur sichtbar zu machen, wurde das temperaturvariable Rastersondenmikroskop um einen variablen Magnetfeldaufbau ergänzt. / This work presents the study of the micromagnetic domain structure and the coupled magneto-structural phase transition of epitaxial MnAs thin films on GaAs. In particular, the influence of substrate orientation, film thickness and external magnetic field on the magnetic and structural properties are investigated, employing the complementary measurement techniques atomic force microscopy (AFM) / magnetic force microscopy (MFM) and low energy electron microscopy (LEEM) / X-ray magnetic circular dichroism photoemission electron microscopy (XMCDPEEM. In the course of the first-order phase transition MnAs films on GaAs (001) and (311)A substrates show a regular array of ferromagnetic alpha- and paramagnetic beta-MnAs stripes. The width of the ferromagnetic stripes are a function of the temperature, whereas the periodicity of the stripe pattern is a function of the film thickness. The domain structure strongly depends on the width and the distance of the ferromagnetic stripes, as it directly affects the shape anisotropy and magnetic coupling, respectively. The domain patterns are classified depending on the number of subdomains along the easy axis direction. Up to three basic domain types can be distinguished. For MnAs films grown on GaAs (111)B, the epitaxy leads to a different strain state of the film, resulting in polygonal ferromagnetic structures embedded in a honeycomb-like paramagnetic network, and a higher phase transition temperature. Using temperature-dependent AFM, MFM and XMCDPEEM it is shown that the local strain relaxation in the vicinity of cracks in the MnAs film results in a locally increased phase transition temperature. In order to study magnetization reversal processes on a microscopic scale, as well as the influence of the magnetic field on the domain structure, a variable-magnetic field set-up is employed.

Sulfonated phthalocyanines were characterized using capillary electrophoresis and mass spectrometry. Derivatives investigated included the copper, cobalt, zinc and metal-free sulfonated phthalocyanines. The electropherograms of commercially available copper phthalocyanine-3,4',4'',4'''-tetrasulfonic acid and 4,4',4'',4'''-tetrasulfonic acid were very different, consistent with the latter compound having a structure that is not fully sulfonated. Matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) were used to characterize the sulfonated phthalocyanines. Mass spectral evidence was obtained for a pentasulfonated species of both the metal-free phthalocyanine and zinc phthalocyanine when these species were made by sulfonation of the metal-free phthalocyanine (followed by zinc insertion in the latter case). Many pathogenic bacteria require heme and obtain it from their environment. Heme transverses the cytoplasmic membrane via an ATP binding cassette (ABC) pathway. Although a number of heme ABC transport systems have been described in pathogenic bacteria, there is as yet little biophysical characterization of the proteins in these systems. The sia (hts) gene cluster encodes a heme ABC transporter in the Gram positive Streptococcus pyogenes. The heme binding protein (HBP) of this transporter is SiaA (HtsA). Several biophysical techniques were used to determine the coordination state, and spin state of both the ferric and ferrous forms of this protein. Identifiers from these techniques suggested that the heme is six-coordinate and low spin in both oxidation states of the protein, with methionine and histidine as axial ligands. The pKa of SiaA was determined, as were the reductive and oxidative midpoint potentials. Guanidinium titration studies of wild-type SiaA showed that the ferric state is less stable than the ferrous state. Free energy of unfolding values [ÄG(H2O)] for the oxidized and reduced proteins were 7.3 ± 0.8 and 16.0 ± 3.6 kcal mol−1, respectively. Denaturation of the histidine mutant H229A was not able to be followed via absorbance spectrometry, possibly due to the large amount of apoprotein present or to non-specific binding of the heme in the binding pocket. The biophysical characterization described herein will significantly advance our understanding of structure-function relationships in HBP.

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Tyrosine Hydroxylase (TyrH) is a pterin-dependent mononuclear non-heme iron oxygenase. TyrH catalyzes the hydroxylation reaction of tyrosine to dihydroxyphenylalanine (DOPA). This reaction is the first and the rate-limiting step in the biosynthesis of the catecholamine neurotransmitters. The active site iron in TyrH is coordinated by the common facial triad motif, 2-His-1-Glu. A combination of kinetic and spectroscopic techniques was applied in order to obtain insight into the catalytic mechanism of this physiologically important enzyme. Analysis of the TyrH reaction by rapid freeze-quench Mossbauer spectroscopy allowed the first direct characterization of an Fe(IV) intermediate in a mononuclear nonheme enzyme catalyzing aromatic hydroxylation. Further rapid kinetic studies established the kinetic competency of this intermediate to be the long-postulated hydroxylating species, Fe(IV)O. Spectroscopic investigations of wild-type (WT) and mutant TyrH complexes using magnetic circular dichroism (MCD) and X-ray absorption spectroscopy (XAS) showed that the active site iron is 6-coordinate in the resting form of the enzyme and that binding of either tyrosine or 6MPH4 alone does not change the coordination. However, when both tyrosine and 6MPH4 are bound, the active site becomes 5-coordinate, creating an open site for reaction with O2. Investigation of the kinetics of oxygen reactivity of TyrH complexes in the absence and presence of tyrosine and/or 6MPH4 indicated that there is a significant enhancement in reactivity in the 5-coordinate complex in comparison to the 6-coordinate form. Similar investigations with E332A TyrH showed that Glu332 residue plays a role in directing the protonation of the bridged complex that forms prior to the formation of Fe(IV)O. Rapid chemical quench analyses of DOPA formation showed a burst of product formation, suggesting a slow product release step. Steady-state viscosity experiments established a diffusional step as being significantly rate-limiting. Further studies with stopped-flow spectroscopy indicated that the rate of TyrH reaction is determined by a combination of a number of physical and chemical steps. Investigation of the NO complexes of TyrH by means of optical absorption, electron paramagnetic resonance (EPR) and electron spin echo envelope modulation (ESEEM) techniques revealed the relative positions of the substrate and cofactor with respect to NO, an O2 mimic, and provided further insight into how the active site is tuned for catalytic reactivity upon substrate and cofactor binding.

Le but principal de cette thèse était de calculer les spectres de dichroïsme circulaire magnétique de rayons~X au seuil K afin de fournir un outil pour interpréter les spectres expérimentaux, jusqu'ici très déroutants. La détermination du dichroïsme circulaire nécessite le calcul précis des spectres d'absorption des rayons~X polarisés circulairement. Nous avons constaté que la théorie des perturbations semi-classique dépendante du temps, communément utilisée pour calculer les sections efficaces d'absorption et de diffusion, est incompatible à la fois, avec l'invariance de jauge et avec les descriptions semi-relativistes de la dynamique des électrons. Pour résoudre ces problèmes, on applique une transformation de Foldy-Wouthuysen aux sections efficaces relativistes données par l'électrodynamique quantique. Ainsi, un nouveau terme d'interaction lumière-matière émerge, que nous avons appelé "spin-position". Une approche performante a été développée pour calculer la section efficace d'absorption afin d'obtenir le dichroïsme circulaire magnétique de rayons~X (XMCD) et le dichroïsme circulaire naturel de rayons~X (XNCD). La méthode numérique repose sur la théorie de la fonctionnelle de la densité en ondes planes avec des pseudopotentiels. Nous constatons que le terme couplant l'opérateur dipolaire électrique avec l'opérateur spin-position contribue significativement au XMCD au seuil K du fer, du nickel et du cobalt ferromagnétiques et nous l'expliquons grâce aux règles de somme. Nous avons également appliqué la méthode aux calculs du XMCD dans FeH et CrO2. Dans les deux cas, la combinaison de l'expérience et de la théorie conduit à un enrichissement mutuel. / The main purpose of this thesis was to compute X-ray magnetic circular dichroism spectra at the K-edge in order to provide a tool to interpret the, so far very puzzling, experimental spectra. Computation of circular dichroism requires precise calculations of X-ray absorption spectra (XAS) for circularly polarized light. We have found that there is an incompatibility of the semi-classical time-dependent perturbation theory commonly used to calculate light absorption and scattering cross-sections with both gauge invariance and semi-relativistic descriptions of the electron dynamics. The problems are solved by applying a Foldy-Wouthuysen transformation to the fully relativistic cross-sections given by quantum electrodynamics. In the process, a new light-matter interaction term emerges, that we named the "spin-position" interaction. An efficient first-principles approach was developed to compute the absorption cross-section in order to obtain X-ray magnetic circular dichroism (XMCD) and X-ray natural circular dichroism (XNCD). The numerical method relies on density-functional theory with plane waves and pseudopotentials. We find that the term coupling the electric dipole operator with the spin-position operator contributes significantly to the XMCD at the K-edge of ferromagnetic iron, cobalt, and nickel. We obtain a sum rule relating this term to the spin magnetic moment of the p states. We also applied the method to calculations of K-edge XMCD in FeH and CrO2. In both cases, the combination of experiment and theory leads to mutual enrichment.

This thesis explores and expands upon theoretical means of quantifying a number of nonlinear spectroscopies, including two-photon absorption, resonant-inelastic x-ray scattering, Jones birefringence, and magnetic circular dichroism. On top of that, detailed information is given for the derivation and program implementation of damped cubic response functions. Complex-valued cubic response functions have been implemented in the quantum chemistry package DALTON, based on working equations formulated for an approximate-state wave function. An assessment of the implementation, such that for small frequencies the second-order hyperpolarizability should behave according to an analytic function that depends quadratically on the optical frequencies. It is demonstrated how two-photon absorption (TPA) can be described either through second-order transition moments or via the damped cubic response function. A few calculated TPA profiles are produced for a set of smaller molecules, in order to display the capability of the cubic response function in the x-ray frequency region. Resonance-inelastic x-ray scattering (RIXS) is explored in a similar manner as two-photon absorption. It is shown how the second-order hyperpolarizability can represent RIXS in the limit of intermediate-state and final-state resonances. Complications emerging from the complex dispersion of the hyperpolarizability are discussed. Moreover, linear birefringences, with focus on the Jones birefringence, are investigated for noble gases, monosubstituted benzenes, furan homologues, and a pure acetonitrile liquid. A linear relation between the Jones birefringence and the empirical para-Hammett constant as well as the permanent electric dipole moment is presented. Estimations of three linear birefringences --- Kerr, Cotton--Mouton, and Jones ---are obtained by averaging over a set of liquid snapshots. The Jones effect for acetonitrile turns out to be unusually large inmparison to the other two investigated linear birefringences. The final chapter of the thesis investigates magnetically induced circular dichroism (MCD). A question regarding relative stability of the first set of excited states for DNA-related molecular systems is resolved through MCD by exploiting the signed nature of circular dichroisms. Furthermore, to what extent solvent contributions affect MCD spectra is explored. The effect on uracil MCD spectrum due to thionation is studied, for which the degree of redshifting for systems 2-thiouracil and 4-thiouracil can be seen to be addative as compared to the 2,4-dithiouracil system. / <p>QC 20171129</p>

Orientadores: Narcizo Marques de Souza Neto, Flávio Cesar Guimarães Gandra / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Física Gleb Wataghin / Made available in DSpace on 2018-08-27T10:57:14Z (GMT). No. of bitstreams: 1 Veiga_LarissaSayuriIshibe_D.pdf: 10330689 bytes, checksum: 72bdd1a8fad1f82f880bb2c86fcd6a9e (MD5) Previous issue date: 2015 / Resumo: Este trabalho teve como objetivo a investigação de diversos mecanismos físicos provenientes das estruturas eletrônicas, magnéticas e cristalinas de sistemas ternários de terras raras e metais de transição 3d-5d através do uso das técnicas de espectroscopia de absorção de raios X e difração de raios X sob altas pressões. Dentre os fenômenos físicos estudados em função da compressão da rede cristalina induzida pela aplicação da pressão estão o magnetismo proveniente dos orbitais 4f e 5d nos sistemas ternários RERh4B4 (com RE = Dy e Er), os efeitos do campo elétrico cristalino e as interações de troca magnéticas nas perovskitas duplas 3d-5d (AFeOsO6, com A = Ca e Sr) e o acoplamento spin-órbita nos metais de transição 5d. As propriedades eletrônicas e magnéticas dos orbitais 4f e 5d das terras raras nos compostos da família RERh4B4 (RE = Dy e Er) foram investigadas através de experimentos de XANES e XMCD sob altas pressões na borda L3 do Dy e Er . Os sinais magnéticos das contribuições quadrupolar (2p3/2-> 4f) e dipolar (2p3/2->5d) presentes nos espectros de XMCD, em ambos os compostos, diminuem progressivamente em função da pressão. Este comportamento foi explicado em termos das interações de troca magnéticas entre os íons de terras raras, que são enfraquecidas pelas alterações locais da estrutura atômica induzidas pela compressão da rede cristalina. Já no sistema de perovskitas duplas, foi demonstrado que a compressão da estrutura Sr2FeOsO6, com um arranjo cristalino ordenado dos íons de Fe (3d) e Os (5d), permite o controle contínuo e reversível da coercividade e magnetização de saturação. Este efeito foi explicado em termos do aumento do campo elétrico cristalino em função da pressão, que altera as interações de troca magnéticas Fe-O-Os e transforma o material com magnetização remanente e coercividade praticamente nulas a pressão ambiente em outro com uma coercividade robusta (~0.5 T) e magnetização de saturação expressiva a pressões acima de ~10 GPa. Por fim, a última parte desta tese de doutorado foi dedicada ao uso da seletividade química e orbital da técnica de XANES na investigação do acoplamento spin-órbita nos elementos Pt (Pt0, 5d9) e Hf (Hf0, 5d2) sob altas pressões. Ao contrário do observado para a Pt, o cálculo do branching ratio a partir dos espectros de absorção nas bordas L2,3 do Hf revelaram que o acoplamento spin-órbita aumenta monotonicamente em função da pressão aplicada. Esse comportamento foi relacionado às propriedades supercondutoras e estruturais presentes nesse elemento sob altas pressões / Abstract: The scientific goal of this work has been the investigation of several physical mechanisms derived from the electronic, magnetic and structural properties of ternary rare earth and transition metal systems by means of X-ray absorption spectroscopy and X-ray diffraction techniques in a diamond anvil cell. Among the physical properties studied as a function of lattice compression induced by applied pressure are the magnetism of the 4f and 5d orbitals in tetragonal rare earth rhodium borides RERh4B4 (with RE = Dy e Er), the crystal electric field effects and magnetic exchange interactions in 3d-5d double perovskite systems (A2FeOsO6, with A = Ca e Sr) and the spin-orbit coupling in 5d transition metals. The electronic and magnetic properties of the rare earth 4f and 5d orbitals in the RERh4B4 (RE = Dy e Er) systems were investigated through high pressure XANES and XMCD experiments at Dy and Er L3 edges. For both compounds, the magnetic signals of the quadrupole (2p3/2->4f) and dipole (2p3/2->5d) contributions to the XMCD spectra progressively decrease as a function of pressure. This behavior was explained in terms of the magnetic exchange interactions between the rare earth ions, which are weakened by changes in the local atomic structure induced by compression of the crystal lattice. In the double perovskite system, it has been shown that compression of Sr2FeOsO6 structure with an ordered crystalline arrangement of iron (3d) and osmium (5d) transition metal ions, allows for continuous and reversible control of magnetic coercivity and saturation magnetization. This effect was explained in terms of enhanced crystal electric fields under high pressure, which alter the Fe-O-Os magnetic exchange interactions and transform the material with an otherwise mute response to magnetic fields into one with a strong coercivity (~0.5 T) and substantial saturation magnetization at pressures above ~10 GPa. Finally, the last part of this thesis is dedicated to the use of chemical and orbital selectivity of XANES technique as a tool to investigate the spin-orbit coupling in Pt (Pt0, 5d9) and Hf (Hf0, 5d2) elements under high pressures. Unlike observed for Pt, the calculated branching ratio determined from the integrated intensities of the Hf L2,3 white lines shows that the spin-orbit coupling increases monotonically as a function of applied pressure. This behavior was related to the superconducting and structural properties displayed by this element at high pressures / Doutorado / Física / Doutora em Ciências