Title: Theory and Applications of Optical Activity of Biomolecules Author: Monika Krupová Supervisor: prof. RNDr. Petr Bouř, DSc. Institutions: Faculty of Mathematics and Physics, Charles University, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic Abstract: This thesis describes how we used several chiroptical spectroscopic methods to study chiral molecules: vibrational circular dichroism (VCD), circularly polarized luminescence (CPL) and magnetic circular dichroism (MCD). VCD and induced lanthanide CPL were used to study the structure of amyloid protein fibrils. We found out that VCD is very sensitive to their structure and supramolecular chirality. It could be used to distinguish between various polymorphic fibrils. On the other hand, induced lanthanide CPL provided information on the local structure. VCD was also used to study the hydration polymorphism of nucleoside crystals. Due to the crystal packing, the VCD signal was strong and specific for different types of crystals. Finally, electronic structure of hydrated Ln3+ ions was studied by MCD. Molecular dynamics simulations together with crystal field theory (CFT) and multistate complete active space calculations with second order perturbation correction (MS-CASPT2) were used to interpret the spectra. CFT...

No description available.

Ever since the discovery of exotic phenomena like high temperature (Tc) superconductivity in the cuprates and colossal magnetoresistance in the manganites, strongly correlated electron systems have become the center of attention in the field of condensed matter physics research. This renewed interest has been further kindled by the rapid development of sophisticated experimental techniques and tremendous computational power. Computation plays a pivotal role in the theoretical investigation of these systems, because one cannot explain their complicated phase diagrams by simple, exactly solvable models. Among the plethora of experimental techniques, various kinds of high energy electron spectroscopies are fast gaining importance due to the multitude of physical properties and phenomena which they can access. However the physical processes involved and the interpretation of the spectra obtained from these spectroscopies are extremely complex and require extensive theoretical modelling. This thesis is concerned with the theoretical modelling of a certain class of high energy electron spectroscopies, viz. the core-level electron spectroscopies, for strongly correlated systems of various kinds. The spectroscopies covered are Auger electron spectroscopy (AES), core-level photoemission spectroscopy (core-level PES) and X-ray absorption spec- troscopy (XAS), which provide non-magnetic information, and also X-ray magnetic circular and linear dichroism (XMCD and XMLD), which provide magnetic information. .

No description available.

Das Schalten und das Auslesen der magnetischen Ausrichtung einzelner winziger magnetischer Informationsspeicher müssen zu wirklich nanoskopischer Dimension entwickelt werden, um mit der Miniaturisierung von modernen, nanoelektronischen Bauteilen Schritt zu halten. Daher sind neue Konzepte, den magnetischen Zustand von Nanostrukturen elektronisch gezielt zu beeinflussen, derzeitig im Mittelpunkt wissenschaftlicher Untersuchungen. Diese Arbeit befasst sich mit dem zuverlässigen Einstellen der Magnetisierung eines rein horizontal kontaktierten, nanoskopischen Magneten, in zwei stabile Zustände. Ein spinpolarisierter Strom wird bei Raumtemperatur in eine Leiterbahn unterhalb des magnetischen Nanopillars injiziert. Spindiffusion durch den Kontakt zwischen der Leiterbahn (Cu) und dem Pillar (CoFe) ruft eine Spin-Akkumulation im Nanopillar hervor, der durch den Spin Transfer Torque-Effekt (STT) vermittelt wird. Bei diesem Prozess verursachen die akkumulierten Elektronenspins ein auftretendes Netto-Moment, das senkrecht auf die Magnetisierungsorientierung des Nanopillars wirkt und so das Schalten ermöglicht. In den STT-induzierten Schaltexperimenten wird der magnetische Zustand des Nanopillars durch eine bildgebendes Messverfahren mittels Rasterröntgentransmissionsmikroskopie (STXM) erfasst. So konnte gezeigt werden, dass sich die Magnetisierung des Pillars auch gegen das Oersted-Feld des Schaltstroms reversibel schalten lässt. / “Changing and detecting the orientation of nanomagnetic structures, which can be used for durable information storage, needs to be developed towards true nanoscale dimensions for keeping up the miniaturization speed of modern nano electronic components. Therefore, new concepts for controlling the state of nano magnets are currently in the focus of research in the field of nanoelectronics. Here, we demonstrate reproducible switching of a purely metallic nanopillar placed on a lead that conducts a spin-polarized current at room temperature. Spin diffusion across the metal-metal (Cu to CoFe) interface between the pillar and the lead causes spin accumulation in the pillar, which may then be used to set the magnetic orientation of the pillar by means of Spin Transfer Torque (STT). In our experiments, the detection of the magnetic state of the nanopillar is performed by direct imaging via scanning transmission x-ray microscopy (STXM)” [1]. Therefore it could be demonstrated, to reversibly switch the nanopillar’s magnetic state even against the Oersted field which is induced by the switching current. Furthermore we could show, that magnetization switching is possible by a pure spin current that is diffusively transported beneath the nanopillar.

Comprendre les propriétés des interfaces molécules/métaux est d’une importance capitale pour la spintronique organique. La première partie porte sur l’étude des propriétés magnétiques de molécules de phtalocyanine de manganèse. Nous avons montré que les premières couches moléculaires forment des colonnes avec un arrangement antiferromagnétique sur la surface de Co(100). Ces dernières mènent à de l’anisotropie d’échange. La seconde partie porte sur l’étude d’une molécule à transition de spin, la Fe(phen)2(NCS)2, sublimée sur différentes surfaces. Nous avons identifié les états de spin d’une molécule unique sur du Cu(100). De plus, nous avons commuté l’état de spin d’une molécule unique pourvu qu’elle soit suffisamment découplée du substrat. / Understanding the properties of molecules at the interface with metals is a fundamental issue for organic spintronics. The first part is devoted to the study of magnetic properties of planar manganese-phthalocyanine molecules and Co films. We evidenced that the first molecular layers form vertical columns with antiferromagnetic ordering on the Co(100) surface. In turn, these molecular columns lead to exchange bias. The second part is focused on the study of a spin-crossover complex, Fe(phen)2(NCS)2 sublimed on different metallic surfaces. We identified the two spin states of a single molecules on Cu(100). By applying voltages pulses, we switched the spin state of a single molecule provided that it is sufficiently decoupled from the substrate.

Das Schalten und das Auslesen der magnetischen Ausrichtung einzelner winziger magnetischer Informationsspeicher müssen zu wirklich nanoskopischer Dimension entwickelt werden, um mit der Miniaturisierung von modernen, nanoelektronischen Bauteilen Schritt zu halten. Daher sind neue Konzepte, den magnetischen Zustand von Nanostrukturen elektronisch gezielt zu beeinflussen, derzeitig im Mittelpunkt wissenschaftlicher Untersuchungen. Diese Arbeit befasst sich mit dem zuverlässigen Einstellen der Magnetisierung eines rein horizontal kontaktierten, nanoskopischen Magneten, in zwei stabile Zustände. Ein spinpolarisierter Strom wird bei Raumtemperatur in eine Leiterbahn unterhalb des magnetischen Nanopillars injiziert. Spindiffusion durch den Kontakt zwischen der Leiterbahn (Cu) und dem Pillar (CoFe) ruft eine Spin-Akkumulation im Nanopillar hervor, der durch den Spin Transfer Torque-Effekt (STT) vermittelt wird. Bei diesem Prozess verursachen die akkumulierten Elektronenspins ein auftretendes Netto-Moment, das senkrecht auf die Magnetisierungsorientierung des Nanopillars wirkt und so das Schalten ermöglicht. In den STT-induzierten Schaltexperimenten wird der magnetische Zustand des Nanopillars durch eine bildgebendes Messverfahren mittels Rasterröntgentransmissionsmikroskopie (STXM) erfasst. So konnte gezeigt werden, dass sich die Magnetisierung des Pillars auch gegen das Oersted-Feld des Schaltstroms reversibel schalten lässt.:Kurzfassung v Abstract vi Danksagung xi 1 Einleitung 1 2 Grundlagen zu Spintronic 5 2.1 Elektronenspins als Grundlage für den Ferromagnetismus . . . . . . 6 2.2 Magnetowiderstandseffekte . . . . . . . . . . . . . . . . . . . . . . . 7 2.2.1 Anisotroper Magnetowiderstandseffekt (AMR) . . . . . . . . 8 2.2.2 Riesenmagnetowidersandseffekt (GMR) . . . . . . . . . . . . 10 2.2.3 Tunnelmagnetowiderstandeffekt (TMR) . . . . . . . . . . . 13 2.3 Spin–Transport . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 2.3.1 Spinpolarisation . . . . . . . . . . . . . . . . . . . . . . . . . 17 2.3.2 Spin-Injektion und Spin-Akkumulation . . . . . . . . . . . . 17 2.3.3 Spinpolarisierter elektrischer Transport . . . . . . . . . . . . 20 2.4 Spin Transfer Torque (STT) . . . . . . . . . . . . . . . . . . . . . . 25 2.5 Geometrien für Spintronic–Bauelemente . . . . . . . . . . . . . . . 30 3 Probenkonzept und Fabrikationsmethoden 35 3.1 Probenkonzept . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 3.1.1 Anforderungen an die CIP–STT-Struktur . . . . . . . . . . . 37 3.1.2 Anforderungen an die ferromagnetischer Materialien . . . . . 38 3.2 Techniken der Probenfabrikation . . . . . . . . . . . . . . . . . . . . 40 3.2.1 Elektronenstrahllithografie (EBL) . . . . . . . . . . . . . . . 41 3.2.2 Positiv- und Negtivlack Prozess . . . . . . . . . . . . . . . . 41 3.2.3 Physikalisches Ätzen . . . . . . . . . . . . . . . . . . . . . . 43 3.3 Probenfabrikation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 4 Experimentelle Methoden 49 4.1 Transmissionsröntgenmikroskopie . . . . . . . . . . . . . . . . . . . 49 4.1.1 Rastertransmissionsröntgenmikroskopie (STXM) . . . . . . . 51 4.1.2 Kontrastmechanismen . . . . . . . . . . . . . . . . . . . . . 53 4.1.3 Röntgenmagnetischer zirkularer Dichroismus (XMCD) . . . 54 4.2 Magneto-optische Kerr–Effekt Mikroskopie . . . . . . . . . . . . . . 57 4.2.1 Kerr–Mikroskop . . . . . . . . . . . . . . . . . . . . . . . . . 58 4.2.2 Longitudinale Kerr–Geometrie . . . . . . . . . . . . . . . . . 58 5 STT–Experimente und Diskussion 61 5.1 Experimenteller Aufbau . . . . . . . . . . . . . . . . . . . . . . . . 62 5.2 Eigenschaften der magnetischen Bauelemente . . . . . . . . . . . . . 64 5.2.1 MOKE-Mikroskopie . . . . . . . . . . . . . . . . . . . . . . . 65 5.2.2 Mikromagnetische Simulation . . . . . . . . . . . . . . . . . 67 5.2.3 Analytische Berechnung zum Nanopillar . . . . . . . . . . . 70 5.2.4 Röntgentransmissionsmikroskopie . . . . . . . . . . . . . . . 72 5.3 Spin Transfer Torque-Schalten . . . . . . . . . . . . . . . . . . . . 74 5.3.1 STT-Schalten mit unterstützendem Magnetfeld . . . . . . . 74 5.3.2 STT-Schalten ohne unterstützendes Magnetfeld . . . . . . . 79 5.3.3 Betrachtung besonderer experimenteller Aspekte . . . . . . . 81 5.3.4 STT-Schalten ohne direkten Ladungstransport . . . . . . . . 89 5.3.5 Magnetisierungsumkehr durch Oersted-Feld . . . . . . . . . 93 6 Zusammenfassung und Ausblick 97 A STXM-Hysteresemessungen der Polarisatoren und Nanopillar 101 Literaturverzeichnis 105 / “Changing and detecting the orientation of nanomagnetic structures, which can be used for durable information storage, needs to be developed towards true nanoscale dimensions for keeping up the miniaturization speed of modern nano electronic components. Therefore, new concepts for controlling the state of nano magnets are currently in the focus of research in the field of nanoelectronics. Here, we demonstrate reproducible switching of a purely metallic nanopillar placed on a lead that conducts a spin-polarized current at room temperature. Spin diffusion across the metal-metal (Cu to CoFe) interface between the pillar and the lead causes spin accumulation in the pillar, which may then be used to set the magnetic orientation of the pillar by means of Spin Transfer Torque (STT). In our experiments, the detection of the magnetic state of the nanopillar is performed by direct imaging via scanning transmission x-ray microscopy (STXM)” [1]. Therefore it could be demonstrated, to reversibly switch the nanopillar’s magnetic state even against the Oersted field which is induced by the switching current. Furthermore we could show, that magnetization switching is possible by a pure spin current that is diffusively transported beneath the nanopillar.:Kurzfassung v Abstract vi Danksagung xi 1 Einleitung 1 2 Grundlagen zu Spintronic 5 2.1 Elektronenspins als Grundlage für den Ferromagnetismus . . . . . . 6 2.2 Magnetowiderstandseffekte . . . . . . . . . . . . . . . . . . . . . . . 7 2.2.1 Anisotroper Magnetowiderstandseffekt (AMR) . . . . . . . . 8 2.2.2 Riesenmagnetowidersandseffekt (GMR) . . . . . . . . . . . . 10 2.2.3 Tunnelmagnetowiderstandeffekt (TMR) . . . . . . . . . . . 13 2.3 Spin–Transport . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 2.3.1 Spinpolarisation . . . . . . . . . . . . . . . . . . . . . . . . . 17 2.3.2 Spin-Injektion und Spin-Akkumulation . . . . . . . . . . . . 17 2.3.3 Spinpolarisierter elektrischer Transport . . . . . . . . . . . . 20 2.4 Spin Transfer Torque (STT) . . . . . . . . . . . . . . . . . . . . . . 25 2.5 Geometrien für Spintronic–Bauelemente . . . . . . . . . . . . . . . 30 3 Probenkonzept und Fabrikationsmethoden 35 3.1 Probenkonzept . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 3.1.1 Anforderungen an die CIP–STT-Struktur . . . . . . . . . . . 37 3.1.2 Anforderungen an die ferromagnetischer Materialien . . . . . 38 3.2 Techniken der Probenfabrikation . . . . . . . . . . . . . . . . . . . . 40 3.2.1 Elektronenstrahllithografie (EBL) . . . . . . . . . . . . . . . 41 3.2.2 Positiv- und Negtivlack Prozess . . . . . . . . . . . . . . . . 41 3.2.3 Physikalisches Ätzen . . . . . . . . . . . . . . . . . . . . . . 43 3.3 Probenfabrikation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 4 Experimentelle Methoden 49 4.1 Transmissionsröntgenmikroskopie . . . . . . . . . . . . . . . . . . . 49 4.1.1 Rastertransmissionsröntgenmikroskopie (STXM) . . . . . . . 51 4.1.2 Kontrastmechanismen . . . . . . . . . . . . . . . . . . . . . 53 4.1.3 Röntgenmagnetischer zirkularer Dichroismus (XMCD) . . . 54 4.2 Magneto-optische Kerr–Effekt Mikroskopie . . . . . . . . . . . . . . 57 4.2.1 Kerr–Mikroskop . . . . . . . . . . . . . . . . . . . . . . . . . 58 4.2.2 Longitudinale Kerr–Geometrie . . . . . . . . . . . . . . . . . 58 5 STT–Experimente und Diskussion 61 5.1 Experimenteller Aufbau . . . . . . . . . . . . . . . . . . . . . . . . 62 5.2 Eigenschaften der magnetischen Bauelemente . . . . . . . . . . . . . 64 5.2.1 MOKE-Mikroskopie . . . . . . . . . . . . . . . . . . . . . . . 65 5.2.2 Mikromagnetische Simulation . . . . . . . . . . . . . . . . . 67 5.2.3 Analytische Berechnung zum Nanopillar . . . . . . . . . . . 70 5.2.4 Röntgentransmissionsmikroskopie . . . . . . . . . . . . . . . 72 5.3 Spin Transfer Torque-Schalten . . . . . . . . . . . . . . . . . . . . 74 5.3.1 STT-Schalten mit unterstützendem Magnetfeld . . . . . . . 74 5.3.2 STT-Schalten ohne unterstützendes Magnetfeld . . . . . . . 79 5.3.3 Betrachtung besonderer experimenteller Aspekte . . . . . . . 81 5.3.4 STT-Schalten ohne direkten Ladungstransport . . . . . . . . 89 5.3.5 Magnetisierungsumkehr durch Oersted-Feld . . . . . . . . . 93 6 Zusammenfassung und Ausblick 97 A STXM-Hysteresemessungen der Polarisatoren und Nanopillar 101 Literaturverzeichnis 105

"Laser flash spectroscopy of photosystem II" Photosystem II (PS II) of plants and cyanobacteria oxidizes water in a light-powered reaction. Thereby, this protein is the ultimate source of the atmospheric oxygen. The capacity to oxidize water is owed to two properties of PS II: (i) The midpoint potential of the oxidizing chlorophyll moiety is increased by 0.6 V compared to photosystem I or photochemical reaction centers of anoxygenic bacteria, and (ii) the energy requirements of the four steps needed for the tetravalent oxidation of water are adapted to the energy of red light quanta. This thesis deals with two particular aspects, namely: 1. The coupling of the electron transfer from tyrosine Z (YZ) to the primary donor (P680+) to proton transfer, and an inquiry on the role of a positive charge on YZox (plus base cluster) in increasing the oxidizing potential at the catalytic site. 2. The localization of the electron hole, P680+, among the excitonically coupled four inner chlorophyll a molecules, and an estimation of the midpoint potential differences between them. Electron-proton-coupling by YZ This study was carried out with PS II core complexes from spinach or pea with a deactivated (removed) manganese cluster. The reduction of P680+ was investigated as a function of pH by detecting the laser flash induced absorption changes with nanosecond resolution. Two kinetic components were found with different pH-dependence and activation energies. The alteration of kinetic parameters by H/D isotope substitutions or by addition of divalent cations implied two different types of YZ-oxidation: At acidic pH the electron transfer was coupled with proton transfer, whereas in the alkaline region it was more rapid and no longer controlled by proton transfer. The conversion between both mechanisms occured at pH 7.4. This value corresponds either to the apparent pK of YZ itself (i.e. of the hydroxy group of the phenol ring) or to the pK of an acid-base-cluster, which includes YZ. Independent measurements of pH-transients by following the absorption changes of hydrophilic proton indicators corroborated this notion. The data were interpreted as indicating that the phenolic proton of YZ was released into the medium at acidic, but not at alkaline pH. The electron transfer and proton release characteristics of intact, oxygen-evolving PS II resembled those in deactivated samples kept at alkaline pH. We concluded that the electron transfer from YZ to P680+ in the native system was not coupled with proton transfer into the bulk. This has shed doubt on a popular hypothesis on the role of YZ as 'hydrogen abstractor' from bound water. On the other hand, the energetic constraints of water oxidation could be eased by the positive upcharging during oxidation of YZox plus its base cluster. On the localization of the electron hole of P680+ Photooxidation of PS II oxidizes the set of four innermost chlorophyll a molecules giving rise to the only spectroscopically defined species P680+. The deconvolution of difference spectra into bands of pigments is ambiguous. By using photoselective excitation of antennae, i.e. chl a molecules with site specific energies at the long wavelength border of the mean Qy-band, and by polarized detection, it was possible to tag P680+QA-/P680QA and 3P680/P680 difference spectra with a further parameter, the (wavelength-dependent) anisotropy r. Results obtained at liquid nitrogen temperature (77 K) can be clearly interpreted in terms of two chl a monomer bands. The two main components of the P680+QA-/P680QA difference spectrum were marked by two distinct values of the anisotropy and could be interpreted in a straightforward manner: the bleaching of a band at 675 nm belonging to the charged species (chl a+) and an electrochromic blue-shift of a nearby chl a from 684 to 682 nm. The main bleaching band of the 3P680/P680 spectrum (at 77 K) can be apparently attributed to a third (or several) chl a component(s). The analysis of the P680+QA-/P680QA spectrum at cryogenic temperature is compatible with monomeric chl a bands. On the other hand, one could assume a system of excitonically coupled core pigments, as it was recently introduced in the literature on the basis of energy transfer studies ('multimer model'). However, in view of the clear indications for an electrochromic band shift and the location of the bleaching band, which absorbs in a wavelength region of monomeric chl a, one assumption of the 'multimer model' should be questioned. Presumably, the excitonic couplings are rather weak, in particular between each of the two central chl a-molecules (PA/PB) and its respective accessory chl a (BA/BB), because of (i) the distances and (ii) different site energies of the monomeric chromophores. At room temperature, the absorption difference and anisotropy spectra of P680+QA-/P680QA were clearly altered. The anisotropy data indicated that the changes could no longer exclusively be ascribed to thermal broadening of individual bands. The localization of the positive charge on one pigment, analogous to the situation at 77 K, was now unlikely. Hence, the midpoint potential differences between the inner four chlorophyll a molecules were small and were estimated as approximately 15 meV.