Accurate modeling of the X-ray absorption near-edge spectra (XANES) is required to unravel the local structure of metal sites in complex systems and their structural changes upon chemical or light ...stimuli. Two relevant examples are reported here concerning the following: (i) the effect of molecular adsorption on 3d metals hosted inside metal–organic frameworks and (ii) light induced dynamics of spin crossover in metal–organic complexes. In both cases, the amount of structural models for simulation can reach a hundred, depending on the number of structural parameters. Thus, the choice of an accurate but computationally demanding finite difference method for the ab initio X-ray absorption simulations severely restricts the range of molecular systems that can be analyzed by personal computers. Employing the FDMNES code Phys. Rev. B, 2001, 63, 125120 we show that this problem can be handled if a proper diagonalization scheme is applied. Due to the use of dedicated solvers for sparse matrices, the calculation time was reduced by more than 1 order of magnitude compared to the standard Gaussian method, while the amount of required RAM was halved. Ni K-edge XANES simulations performed by the accelerated version of the code allowed analyzing the coordination geometry of CO and NO on the Ni active sites in CPO-27-Ni MOF. The Ni–CO configuration was found to be linear, while Ni–NO was bent by almost 90°. Modeling of the Fe K-edge XANES of photoexcited aqueous Fe(bpy)32+ with a 100 ps delay we identified the Fe–N distance elongation and bipyridine rotation upon transition from the initial low-spin to the final high-spin state. Subsequently, the X-ray absorption spectrum for the intermediate triplet state with expected 100 fs lifetime was theoretically predicted.
European XFEL is a free-electron laser (FEL) user facility providing soft and hard X-ray FEL radiation to initially six scientific instruments. Starting user operation in fall 2017 European XFEL will ...provide new research opportunities to users from science domains as diverse as physics, chemistry, geo- and planetary sciences, materials sciences or biology. The unique feature of European XFEL is the provision of high average brilliance in the soft and hard X-ray regime, combined with the pulse properties of FEL radiation of extreme peak intensities, femtosecond pulse duration and high degree of coherence. The high average brilliance is achieved through acceleration of up to 27,000 electron bunches per second by the super-conducting electron accelerator. Enabling the usage of this high average brilliance in user experiments is one of the major instrumentation drivers for European XFEL. The radiation generated by three FEL sources is distributed via long beam transport systems to the experiment hall where the scientific instruments are located side-by-side. The X-ray beam transport systems have been optimized to maintain the unique features of the FEL radiation which will be monitored using build-in photon diagnostics. The six scientific instruments are optimized for specific applications using soft or hard X-ray techniques and include integrated lasers, dedicated sample environment, large area high frame rate detector(s) and computing systems capable of processing large quantities of data.
Reaction pathways of biochemical processes are influenced by the dissipative electrostatic interaction of the reagents with solvent water molecules. The simulation of these interactions requires a ...parametrization of the permanent and induced dipole moments. However, the underlying molecular polarizability of water and its dependence on ions are partially unknown. Here, we apply intense terahertz pulses to liquid water, whose oscillations match the timescale of orientational relaxation. Using a combination of terahertz pump / optical probe experiments, molecular dynamics simulations, and a Langevin dynamics model, we demonstrate a transient orientation of their dipole moments, not possible by optical excitation. The resulting birefringence reveals that the polarizability of water is lower along its dipole moment than the average value perpendicular to it. This anisotropy, also observed in heavy water and alcohols, increases with the concentration of sodium iodide dissolved in water. Our results enable a more accurate parametrization and a benchmarking of existing and future water models.
Disentangling the strong interplay between electronic and nuclear degrees of freedom is essential to achieve a full understanding of excited state processes during ultrafast nonadiabatic chemical ...reactions. However, the complexity of multi-dimensional potential energy surfaces means that this remains challenging. The energy flow during vibrational and electronic relaxation processes can be explored with structural sensitivity by probing a nuclear wavepacket using femtosecond time-resolved X-ray Absorption Near Edge Structure (TR-XANES). However, it remains unknown to what level of detail vibrational motions are observable in this X-ray technique. Herein we track the wavepacket dynamics of a prototypical Cu(2,9-dimethyl-1,10-phenanthroline)
complex using TR-XANES. We demonstrate that sensitivity to individual wavepacket components can be modulated by the probe energy and that the bond length change associated with molecular breathing mode can be tracked with a sub-Angstrom resolution beyond optical-domain observables. Importantly, our results reveal how state-of-the-art TR-XANES provides deeper insights of ultrafast nonadiabatic chemical reactions.
X-ray free electron lasers (XFELs) deliver short (<100 fs) and intense (∼1012 photons) pulses of hard X-rays, making them excellent sources for time-resolved studies. Here we show that, despite the ...inherent instabilities of current (SASE based) XFELs, they can be used for measuring high-quality X-ray absorption data and we report femtosecond time-resolved X-ray absorption near-edge spectroscopy (XANES) measurements of a spin-crossover system, iron(II) tris(2,2′-bipyridine) in water. The data indicate that the low-spin to high-spin transition can be modeled by single-exponential kinetics convoluted with the overall time resolution. The resulting time constant is ∼160 fs.
X-ray free-electron laser sources enable time-resolved X-ray studies with unmatched temporal resolution. To fully exploit ultrashort X-ray pulses, timing tools are essential. However, new high ...repetition rate X-ray facilities present challenges for currently used timing tool schemes. Here we address this issue by demonstrating a sensitive timing tool scheme to enhance experimental time resolution in pump-probe experiments at very high pulse repetition rates. Our method employs a self-referenced detection scheme using a time-sheared chirped optical pulse traversing an X-ray stimulated diamond plate. By formulating an effective medium theory, we confirm subtle refractive index changes, induced by sub-milli-Joule intense X-ray pulses, that are measured in our experiment. The system utilizes a Common-Path-Interferometer to detect X-ray-induced phase shifts of the optical probe pulse transmitted through the diamond sample. Owing to the thermal stability of diamond, our approach is well-suited for MHz pulse repetition rates in superconducting linear accelerator-based free-electron lasers.
Spin cascade and doming in ferric hemes Bacellar, Camila; Kinschel, Dominik; Mancini, Giulia F. ...
Proceedings of the National Academy of Sciences,
09/2020, Letnik:
117, Številka:
36
Journal Article
Recenzirano
Odprti dostop
The structure–function relationship is at the heart of biology, and major protein deformations are correlated to specific functions. For ferrous heme proteins, doming is associated with the ...respiratory function in hemoglobin and myoglobins. Cytochrome c (Cyt c) has evolved to become an important electron-transfer protein in humans. In its ferrous form, it undergoes ligand release and doming upon photoexcitation, but its ferric form does not release the distal ligand, while the return to the ground state has been attributed to thermal relaxation. Here, by combining femtosecond Fe Kα and Kβ X-ray emission spectroscopy (XES) with Fe K-edge X-ray absorption near-edge structure (XANES), we demonstrate that the photocycle of ferric Cyt c is entirely due to a cascade among excited spin states of the iron ion, causing the ferric heme to undergo doming, which we identify. We also argue that this pattern is common to a wide diversity of ferric heme proteins, raising the question of the biological relevance of doming in such proteins.
Structural changes of the iron(II)-tris-bipyridine (Fe(II)(bpy)(3)(2+)) complex induced by ultrashort pulse excitation and population of its short-lived (< or =0.6 ns) quintet high spin state have ...been detected by picosecond x-ray absorption spectroscopy. The structural relaxation from the high spin to the low spin state was followed over the entire lifetime of the excited state. A combined analysis of the x-ray-absorption near-edge structure and extended x-ray-absorption fine structure spectroscopy features delivers an Fe-N bond elongation of 0.2 A in the quintet state compared to the singlet ground state.
We present a novel, highly versatile, and self-referenced arrival time monitor for measuring the femtosecond time delay between a hard X-ray pulse from a free-electron laser and an optical laser ...pulse, measured directly on the same sample used for pump-probe experiments. Two chirped and picosecond long optical supercontinuum pulses traverse the sample with a mutually fixed time delay of 970 fs, while a femtosecond X-ray pulse arrives at an instant in between both pulses. Behind the sample the supercontinuum pulses are temporally overlapped to yield near-perfect destructive interference in the absence of the X-ray pulse. Stimulation of the sample with an X-ray pulse delivers non-zero contributions at certain optical wavelengths, which serve as a measure of the relative arrival time of the X-ray pulse with an accuracy of better than 25 fs. We find an excellent agreement of our monitor with the existing timing diagnostics at the SACLA XFEL with a Pearson correlation value of 0.98. We demonstrate a high sensitivity to measure X-ray pulses with pulse energies as low as 30 Formula: see textJ. Using a free-flowing liquid jet as interaction sample ensures the full replacement of the sample volume for each X-ray/optical event, thus enabling its utility even at MHz repetition rate XFEL sources.
Ultrafast spin probe: A short‐lived transient species of light‐excited Fe(bpy)32+ (bpy=2,2′‐bipyridine) shows geometry variations that correspond to excitation to a high‐spin state, in which the spin ...momentum of FeII has now been directly determined to be S=2 by spin‐sensitive ultrafast X‐ray emission spectroscopy.
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