Contrasting behavior of covalent and molecular carbon allotropes exposed to extreme ultraviolet and soft x-ray free-electron laser radiation

All carbon materials, e.g., amorphous carbon (a-C) coatings and C60 fullerene thin films, play an important role in short-wavelength free-electron laser (FEL) research motivated by FEL optics development and prospective nanotechnology applications. Responses of a-C and C60 layers to the extreme ultraviolet (SPring-8 Compact SASE Source in Japan) and soft x-ray (free-electron laser in Hamburg) free-electron laser radiation are investigated by Raman spectroscopy, differential interference contrast, and atomic force microscopy. A remarkable difference in the behavior of covalent (a-C) and molecular (C60) carbonaceous solids is demonstrated under these irradiation conditions. Low thresholds for ablation of a fullerene crystal (estimated to be around 0.15 eV/atom for C60 vs 0.9 eV/atom for a-C in terms of the absorbed dose) are caused by a low cohesive energy of fullerene crystals. An efficient mechanism of the removal of intact C60 molecules from the irradiated crystal due to Coulomb repulsion of fullerene-cage cation radicals formed by the ionizing radiation is revealed by a detailed modeling

Catalytic Cycle of Multicopper Oxidases Studied by Combined Quantum- and Molecular-Mechanical Free-Energy Perturbation Methods

We have used combined quantum mechanical and molecular mechanical free-energy perturbation methods in combination with explicit solvent simulations to study the reaction mechanism of the multicopper oxidases, in particular the regeneration of the reduced state from the native intermediate. For 52 putative states of the trinuclear copper cluster, differing in the oxidation states of the copper ions and the protonation states of water- and O2-derived ligands, we have studied redox potentials, acidity constants, isomerisation reactions, as well as water- and O2 binding reactions. Thereby, we can propose a full reaction mechanism of the multicopper oxidases with atomic detail. We also show that the two copper sites in the protein communicate so that redox potentials and acidity constants of one site are affected by up to 0.2 V or 3 pKa units by a change in the oxidation state of the other site

Reorganization Energy for Internal Electron Transfer in Multicopper Oxidases.

We have calculated the reorganization energy for the intramolecular electron transfer between the reduced type 1 copper site and the peroxy intermediate of the trinuclear cluster in the multicopper oxidase CueO. The calculations are performed at the combined quantum mechanics and molecular mechanics (QM/MM) level, based on molecular dynamics simulations with tailored potentials for the two copper sites. We obtain a reorganization energy of 91-133 kJ/mol, depending on the theoretical treatment. The two Cu sites contribute by 12 and 22 kJ/mol to this energy, whereas the solvent contribution is 34 kJ/mol. The rest comes from the protein, involving small contributions from many residues. We have also estimated the energy difference between the two electron-transfer states and show that the reduction of the peroxy intermediate is exergonic by 43-87 kJ/mol, depending on the theoretical method. Both the solvent and the protein contribute to this energy difference, especially charged residues close to the two Cu sites. We compare these estimates with energies obtained from QM/MM optimizations and QM calculations in a vacuum and discuss differences between the results obtained at various levels of theory

Vibrational structure in magnetic circular dichroism spectra of polycyclic aromatic hydrocarbons

Abstract Absorption and magnetic circular dichroism (MCD) spectroscopies are powerful and simple methods to discriminate among various compounds. Polycyclic aromatic hydrocarbons provide particularly strong signal, which, for example, facilitates their detection in the environment. However, interpretation of the spectra is often based on quantum-chemical simulations, providing a limited precision only. In the present work, we use time-dependent density functional theory and complete active space second-order perturbation theories to understand spectral features observed in a series of naphthalene, anthracene, phenanthrene, and three larger compounds. The electronic computations provided reasonable agreement with the experiment for the smaller molecules, while a large error persisted for the bigger ones. However, many discrepancies could be explained by vibrational splitting of the electronic transitions across the entire spectral range. Compared to plain absorption, MCD spectral bands and their vibrational splitting were more specific for each aromatic molecule. The computational tools allowing simulations of detailed vibrational features in the electronic spectra thus promise to open a qualitatively new chapter in the spectroscopy of aromatic compounds

In situ focus characterization by ablation technique to enable optics alignment at an XUV FEL source

In situ focus characterization is demonstrated by working at an extreme ultraviolet (XUV) freeelectronlaser source using ablation technique. Design of the instrument reported here allows reachinga few micrometres resolution along with keeping the ultrahigh vacuum conditions and ensureshigh-contrast visibility of ablative imprints on optically transparent samples, e.g., PMMA. This enableson-line monitoring of the beam profile changes and thus makes possible in situ alignment ofthe XUV focusing optics. A good agreement between focal characterizations retrieved from in situinspection of ablative imprints contours and from well-established accurate ex situ analysis with Nomarskimicroscope has been observed for a typical micro-focus experiment

Saturation of a Ce:Y3Al5O12\mathrm{Y}_{3}\mathrm{Al}_{5}\mathrm{O}_{12} scintillator response to ultra-short pulses of extreme ultraviolet soft X-ray and X-ray laser radiation

Investigations of radioluminescence saturation in monocrystalline cerium doped yttrium aluminum garnet (Ce:YAG) exposed to intense extreme ultraviolet (XUV), soft X-ray and X-ray radiation delivered from three free-electron lasers are described in this article. The measurements were performed with wavelengths of 98, 25.6, 13.5 and 0.15 nm. We have found that saturation of the photon yield occurs at an excitation level of 2.0 x 10$^{20}$ eV/cm$^3$ resulting in an emission of 1.5 x 10$^{18}$ visible photons per cubic centimeter. This number is much smaller than the concentration of Ce$^{3+}$ in the scintillator that was equal to 2 x 10$^{20}$ cm$^{-3}$. Because the internal radiance efficiency. does not depend strongly on the irradiating photon energy, i. e., $\eta \approx$ 0.035 $\pm$ 0.015 in the range 10 to 100 000 eV, the results presented here could be used to predict saturation effects in scintillator slabs placed in imaging systems of bright XUV, X-ray and particle beams. The saturation of the Ce$^{3+}$ emission is explained by mutual quenching of excitons created at high densities, preceding the stage of energy transfer to the Ce$^{3+}$ ions