Investigation of structural properties in biomolecular systems using synchrotron-based spectroscopies

Solid state approaches to structural properties like diffraction or microscopy techniques often cannot be applied to biomolecular systems, at least not without special postpreparation which often corrupts the desired properties of the pristine systems. In this work the capabilities of synchrotron-based, soft X-ray spectroscopies as an alternative way to unravel structural properties of such systems are tested. To this end, three exemplary systems were investigated each with the focus on another facet and characteristic length scale. The first example are DNA-alkanethiol self-assembled monolayers, also known as DNA microarrays or DNA chips, for which a way to monitor and controllably tune the structural composition on the mesoscopic scale of many thousands of molecules was sought for. The second example focuses on the single-molecule and submolecular scale in metalprotein hybrid compounds with the aim to identify the binding site of metal atoms or ions within protein molecules and the underlying interaction mechanisms. The most fundamental structural scale, the level of single bonds and molecular orbitals, is addressed in the last example where it was tried to elaborate an approach to map the topology of molecular orbitals based upon X-ray absorption properties. This approach was put to the practical test for the characteristic pi*peptide orbitals in protein backbones. For all three investigated examples, spectroscopies using soft X-ray synchrotron radiation were able to extract the desired information, thus confirming that they may grant alternative access to structural properties of soft-matter systems in cases where standard approaches fail.Klassische Festkörpertechniken zur Strukturuntersuchung, wie Streu- oder Mikroskopiemethoden, können häufig nicht auf Biomolekülsysteme angewandt werden, zumindest nicht ohne spezielle Postpräparation, die die ursprünglichen Eigenschaften dieser Systeme oft verfälscht. In dieser Arbeit soll untersucht werden, inwieweit Röntgenspektroskopien basierend auf Synchrotronstrahlung einen alternativen Zugang zu Struktureigenschaften solcher Systeme bieten. Dazu wurden drei Systeme exemplarisch untersucht, jeweils mit Schwerpunkt auf einen anderen Aspekt und charakteristischen Längenbereich. Für selbstorganisierende DNA-Alkanthiol-Schichten, sogenannte DNA-Chips, wurde nach eine Weg gesucht, ihre strukturelle Zusammensetzung auf der mesoskopischen Ebene vieler tausend Moleküle zu bestimmen und kontrolliert zu modifizieren. Metallisierte Proteinstrukturen wurden auf Einzelmolekül- bzw. submolekularer Ebene untersucht, mit dem Ziel, die Orte der Metallanlagerung innerhalb des Proteins und die zugrundeliegenden Wechselwirkungsmechanismen zu identifizieren. Die unterste strukturelle Ebene, der Bereich einzelne Bindungen und Molekülorbitale, wurde adressiert am Beispiel der pi*peptide Orbitale des Proteinrückrats. Dafür wurde eine Methode zur Kartographierung einzelner Orbitale anhand von Röntgenabsorptionseigentschaften herausgearbeitet und praktisch getestet. In allen drei Fällen konnten Röntgenspektroskopien die nötigen Informationen liefern und damit ihr Potential für Strukturuntersuchungen in weicher Materie unter Beweis stellen

Charge, lattice and magnetism across the valence crossover in EuIr2_2Si2_2 single crystals

We present a detailed study of the temperature evolution of the crystal structure, specific heat, magnetic susceptibility and resistivity of single crystals of the paradigmatic valence-fluctuating compound EuIr$_2$Si$_2$. A comparison to stable-valent isostructural compounds EuCo$_2$Si$_2$ (with Eu$^{3+}$), and EuRh$_2$Si$_2$, (with Eu$^{2+}$) reveals an anomalously large thermal expansion indicative of the lattice softening associated to valence fluctuations. A marked broad peak at temperatures around 65-75 K is observed in specific heat, susceptibility and the derivative of resistivity, as thermal energy becomes large enough to excite Eu into a divalent state, which localizes one f electron and increases scattering of conduction electrons. In addition, the intermediate valence at low temperatures manifests in a moderately renormalized electron mass, with enhanced values of the Sommerfeld coefficient in the specific heat and a Fermi-liquid-like dependence of resistivity at low temperatures. The high residual magnetic susceptibility is mainly ascribed to a Van Vleck contribution. Although the intermediate/fluctuating valence duality is to some extent represented in the interconfiguration fluctuation model commonly used to analyze data on valence-fluctuating systems, we show that this model cannot describe the different physical properties of EuIr$_2$Si$_2$ with a single set of parameters.Comment: 12 pages, 4 figures, 1 tabl

Using a dual plasma process to produce cobalt--polypyrrole catalysts for the oxygen reduction reaction in fuel cells -- part II: analysing the chemical structure of the films

The chemical structure of cobalt--polypyrrole -- produced by a dual plasma process -- is analysed by means of X-ray photoelectron spectroscopy (XPS), near edge X-ray absorption spectroscopy (NEXAFS), X-ray diffraction (XRD), energy-dispersive X-Ray spectroscopy (EDX) and extended x-ray absorption spectroscopy (EXAFS).It is shown that only nanoparticles of a size of 3\,nm with the low temperature crystal structure of cobalt are present within the compound. Besides that, cobalt--nitrogen and carbon--oxygen structures are observed. Furthermore, more and more cobalt--nitrogen structures are produced when increasing the magnetron power. Linking the information on the chemical structure to the results about the catalytic activity of the films -- which are presented in part I of this contribution -- it is concluded that the cobalt--nitrogen structures are the probable catalytically active sites. The cobalt--nitrogen bond length is calculated as 2.09\,\AA\ and the carbon--nitrogen bond length as 1.38\,\AA

Dynamics of graphene growth on a metal surface: A time-dependent photoemission study

Applying time-dependent photoemission we unravel the graphene growth process on a metallic surface by chemical vapor deposition (CVD). Graphene CVD growth is in stark contrast to the standard growth process of two-dimensional films because it is self-limiting and stops as soon as a monolayer of graphene has been synthesized. Most importantly, a novel phase of metastable graphene was discovered that is characterized by permanent and simultaneous construction and deconstruction. The high quality and large area graphene flakes are characterized by angle-resolved photoemission, proving that they are indeed monolayer and cover the whole 1×1 cm Ni(111) substrate. These findings are of high relevance to the intensive search for reliable synthesis methods for large graphene flakes of controlled layer number

Dynamics of graphene growth on a metal surface: a time-dependent photoemission study

Applying time-dependent photoemission we unravel the graphene growth process on a metallic surface by chemical vapor deposition (CVD). Graphene CVD growth is in stark contrast to the standard growth process of two--dimensional films because it is self-limiting and stops as soon as a monolayer graphene has been synthesized. Most importantly, a novel phase of metastable graphene was discovered that is characterized by permanent and simultaneous construction and deconstruction. The high quality and large area graphene flakes are characterized by angle-resolved photoemission proofing that they are indeed monolayer and cover the whole 1$\times$1 cm Nickel substrate. These findings are of high relevance to the intensive search for reliable synthesis methods for large graphene flakes of controlled layer number

Experimental Determination of Momentum-Resolved Electron-Phonon Coupling

We provide a novel experimental method to quantitatively estimate the electron-phonon coupling and its momentum dependence from resonant inelastic x-ray scattering (RIXS) spectra based on the detuning of the incident photon energy away from an absorption resonance. We apply it to the cuprate parent compound NdBa$_2$Cu$_3$O$_6$ and find that the electronic coupling to the oxygen half-breathing phonon mode is strongest at the Brillouin zone boundary, where it amounts to $\sim 0.17$ eV, in agreement with previous studies. In principle, this method is applicable to any absorption resonance suitable for RIXS measurements and will help to define the contribution of lattice vibrations to the peculiar properties of quantum materials.Comment: 6 pages, 3 figure

Fractional Spin Excitations in the Infinite-Layer Cuprate CaCuO2

We use resonant inelastic x-ray scattering (RIXS) to investigate the magnetic dynamics of the infinite-layer cuprate CaCuO2. We find that close to the (1/2,0) point, the single magnon decays into a broad continuum of excitations accounting for about 80% of the total magnetic spectral weight. Polarization-resolved RIXS spectra reveal the overwhelming dominance of the spin-flip (Delta S = 1) character of this continuum with respect to the Delta S = 0 multimagnon contributions. Moreover, its incident-energy dependence is identical to that of the magnon, supporting a common physical origin. We propose that the continuum originates from the decay of the magnon into spinon pairs, and we relate it to the exceptionally high ring exchange J(c) similar to J(1) of CaCuO2. In the infinite-layer cuprates, long-range and multisite hopping integrals are very important, and they amplify the 2D quantum magnetism effects in spite of the 3D antiferromagnetic Neel order

Structure and magnetism of Tm atoms and monolayers on W(110)

We investigated the growth and magnetic properties of Tm atoms and monolayers deposited on a W(110) surface using scanning tunneling microscopy and x-ray magnetic circular and linear dichroism. The equilibrium structure of Tm monolayer films is found to be a strongly distorted hexagonal lattice with a Moiré pattern due to the overlap with the rectangular W(110) substrate. Monolayer as well as isolated Tm adatoms on W present a trivalent ground-state electronic configuration, contrary to divalent gas phase Tm and weakly coordinated atoms in quench-condensed Tm films. Ligand field multiplet simulations of the x-ray absorption spectra further show that Tm has a $j =6,Jz=±4 and$j =6,Jz=±5 electronic ground state separated by a few meV from the next lowest substates $j =6,Jz=±6. Accordingly, both the Tm atoms and monolayer films exhibit large spin and orbital moments with out-of-plane uniaxial magnetic anisotropy. X-ray magnetic dichroism measurements as a function of temperature show that the Tm monolayers develop antiferromagnetic correlations at about 50 K. The triangular structure of the Tm lattice suggests the presence of significant magnetic frustration in this system, which may lead to either a noncollinear staggered spin structure or intrinsic disorder