Spectral monitoring at SwissFEL using a high-resolution on-line hard X-ray single-shot spectrometer.

The performance and parameters of the online photon single-shot spectrometer (PSSS) at the Aramis beamline of the SwissFEL free-electron laser are presented. The device operates between the photon energies 4 and 13 keV and uses diamond transmission gratings and bent Si crystals for spectral measurements on the first diffraction order of the beam. The device has an energy window of 0.7% of the median photon energy of the free-electron laser pulses and a spectral resolution (full width at half-maximum) ΔE/E on the order of 10-5. The device was characterized by comparing its performance with reference data from synchrotron sources, and a parametric study investigated other effects that could affect the reliability of the spectral information.

Experimental station Bernina at SwissFEL: condensed matter physics on femtosecond time scales investigated by X-ray diffraction and spectroscopic methods.

The Bernina instrument at the SwissFEL Aramis hard X-ray free-electron laser is designed for studying ultrafast phenomena in condensed matter and material science. Ultrashort pulses from an optical laser system covering a large wavelength range can be used to generate specific non-equilibrium states, whose subsequent temporal evolution can be probed by selective X-ray scattering techniques in the range 2-12 keV. For that purpose, the X-ray beamline is equipped with optical elements which tailor the X-ray beam size and energy, as well as with pulse-to-pulse diagnostics that monitor the X-ray pulse intensity, position, as well as its spectral and temporal properties. The experiments can be performed using multiple interchangeable endstations differing in specialization, diffractometer and X-ray analyser configuration and load capacity for specialized sample environment. After testing the instrument in a series of pilot experiments in 2018, regular user operation begins in 2019.

The SwissFEL soft X-ray free-electron laser beamline: Athos.

The SwissFEL soft X-ray free-electron laser (FEL) beamline Athos will be ready for user operation in 2021. Its design includes a novel layout of alternating magnetic chicanes and short undulator segments. Together with the APPLE X architecture of undulators, the Athos branch can be operated in different modes producing FEL beams with unique characteristics ranging from attosecond pulse length to high-power modes. Further space has been reserved for upgrades including modulators and an external seeding laser for better timing control. All of these schemes rely on state-of-the-art technologies described in this overview. The optical transport line distributing the FEL beam to the experimental stations was designed with the whole range of beam parameters in mind. Currently two experimental stations, one for condensed matter and quantum materials research and a second one for atomic, molecular and optical physics, chemical sciences and ultrafast single-particle imaging, are being laid out such that they can profit from the unique soft X-ray pulses produced in the Athos branch in an optimal way.

X-ray grating interferometer for in situ and at-wavelength wavefront metrology.

A wavefront metrology setup based on the X-ray grating interferometry technique for spatially resolved, quantitative, in situ and at-wavelength measurements of the wavefront at synchrotron radiation and hard X-ray free-electron laser beamlines is reported. Indeed, the ever-increasing demands on the optical components to preserve the wavefront shape and the coherence of the delivered X-ray beam call for more and more sensitive diagnostic instruments. Thanks to its angular sensitivity, X-ray grating interferometry has been established in recent years as an adequate wavefront-sensing technique for quantitatively assessing the quality of the X-ray wavefront under working conditions and hence for the in situ investigation of X-ray optical elements. In order to characterize the optical elements at any given beamline by measuring the aberrations introduced in the wavefront, a transportable X-ray grating interferometry setup was realised at the Swiss Light Source (SLS). The instrument, which is expected to be a valuable tool for investigating the quality of the X-ray beam delivered at an endstation, will be described hereafter in terms of the hardware setup and the related data analysis procedure. Several exemplary experiments performed at the X05DA Optics beamline of the SLS will be presented.

THz streak camera method for synchronous arrival time measurement of two-color hard X-ray FEL pulses.

The two-color operation of free electron laser (FEL) facilities allows the delivery of two FEL pulses with different energies, which opens new possibilities for user experiments. Measuring the arrival time of both FEL pulses relative to the external experimental laser and to each other improves the temporal resolution of the experiments using the two-color FEL beam and helps to monitor the performance of the machine itself. This work reports on the first simultaneous measurement of the arrival times of two hard X-ray FEL pulses with the THz streak camera. Measuring the arrival time of the two FEL pulses, the relative delay between them was calculated and compared to the set values. Furthermore, we present the first comparison of the THz streak camera method to the method of FEL induced transient transmission. The results indicate a good agreement between the two methods.

Investigating DNA Radiation Damage Using X-Ray Absorption Spectroscopy.

The biological influence of radiation on living matter has been studied for years; however, several questions about the detailed mechanism of radiation damage formation remain largely unanswered. Among all biomolecules exposed to radiation, DNA plays an important role because any damage to its molecular structure can affect the whole cell and may lead to chromosomal rearrangements resulting in genomic instability or cell death. To identify and characterize damage induced in the DNA sugar-phosphate backbone, in this work we performed x-ray absorption spectroscopy at the P K-edge on DNA irradiated with either UVA light or protons. By combining the experimental results with theoretical calculations, we were able to establish the types and relative ratio of lesions produced by both UVA and protons around the phosphorus atoms in DNA.

Probing the electronic and geometric structure of ferric and ferrous myoglobins in physiological solutions by Fe K-edge absorption spectroscopy.

We present an iron K-edge X-ray absorption study of carboxymyoglobin (MbCO), nitrosylmyoglobin (MbNO), oxymyoglobin (MbO2), cyanomyoglobin (MbCN), aquomet myoglobin (metMb) and unligated myoglobin (deoxyMb) in physiological media. The analysis of the XANES region is performed using the full-multiple scattering formalism, implemented within the MXAN package. This reveals trends within the heme structure, absent from previous crystallographic and X-ray absorption analysis. In particular, the iron-nitrogen bond lengths in the porphyrin ring converge to a common value of about 2 Å, except for deoxyMb whose bigger value is due to the doming of the heme. The trends of the Fe-Nε (His93) bond length is found to be consistent with the effect of ligand binding to the iron, with the exception of MbNO, which is explained in terms of the repulsive trans effect. We derive a high resolution description of the relative geometry of the ligands with respect to the heme and quantify the magnitude of the heme doming in the deoxyMb form. Finally, time-dependent density functional theory is used to simulate the pre-edge spectra and is found to be in good agreement with the experiment. The XAS spectra typically exhibit one pre-edge feature which arises from transitions into the unoccupied dσ and dπ - πligand* orbitals. 1s → dπ transitions contribute weakly for MbO2, metMb and deoxyMb. However, despite this strong Fe d contribution these transitions are found to be dominated by the dipole (1s → 4p) moment due to the low symmetry of the heme environment.

Science Opportunities at the SwissFEL X-ray Laser.

Next-generation X-ray sources, based on the X-ray Free Electron Laser (XFEL) concept, will provide highly coherent, ultrashort pulses of soft and hard X-rays with peak intensity many orders of magnitude higher than that of a synchrotron. These pulses will allow studies of femtosecond dynamics at nanometer resolution and with chemical selectivity. They will produce diffraction images of organic and inorganic nanostructures without deleterious effects of radiation damage.

Science opportunities at the SwissFEL X-ray Laser.

Next-generation X-ray sources, based on the X-ray Free Electron Laser (XFEL) concept, will provide highly coherent, ultrashort pulses of soft and hard X-rays with peak intensity many orders of magnitude higher than that of a synchrotron. These pulses will allow studies of femtosecond dynamics at nanometer resolution and with chemical selectivity. They will produce diffraction images of organic and inorganic nanostructures without deleterious effects of radiation damage.

Disentangling the evolution of electrons and holes in photoexcited ZnO nanoparticles.

The evolution of charge carriers in photoexcited room temperature ZnO nanoparticles in solution is investigated using ultrafast ultraviolet photoluminescence spectroscopy, ultrafast Zn K-edge absorption spectroscopy, and ab initio molecular dynamics (MD) simulations. The photoluminescence is excited at 4.66 eV, well above the band edge, and shows that electron cooling in the conduction band and exciton formation occur in <500 fs, in excellent agreement with theoretical predictions. The x-ray absorption measurements, obtained upon excitation close to the band edge at 3.49 eV, are sensitive to the migration and trapping of holes. They reveal that the 2 ps transient largely reproduces the previously reported transient obtained at 100 ps time delay in synchrotron studies. In addition, the x-ray absorption signal is found to rise in ∼1.4 ps, which we attribute to the diffusion of holes through the lattice prior to their trapping at singly charged oxygen vacancies. Indeed, the MD simulations show that impulsive trapping of holes induces an ultrafast expansion of the cage of Zn atoms in <200 fs, followed by an oscillatory response at a frequency of ∼100 cm-1, which corresponds to a phonon mode of the system involving the Zn sub-lattice.

Simulations of X-ray absorption spectra: the effect of the solvent.

We perform quantum mechanics/molecular mechanics molecular dynamics simulations on the [Pt(2)(P(2)O(5)H(2))(4)](4-) (abbreviated PtPOP) complex; in water, dimethylformamide and ethanol. These are used to calculate the ground state X-ray absorption spectrum of the complex. The structural parameters from X-ray spectra are usually extracted using a fit of the experimental data. In such simulations the solvent is neglected meaning that any effect of the local environment will be compensated for by structural changes of the solute, leading to possible discrepancies in the extracted structural parameters. Our simulations show a significant solvent effect on the spectra, which has important implications for the structural analysis of molecules in solution.

Probing the transition from hydrophilic to hydrophobic solvation with atomic scale resolution.

Picosecond and femtosecond X-ray absorption spectroscopy is used to probe the changes of the solvent shell structure upon electron abstraction of aqueous iodide using an ultrashort laser pulse. The transient L(1,3) edge EXAFS at 50 ps time delay points to the formation of an expanded water cavity around the iodine atom, in good agreement with classical and quantum mechanical/molecular mechanics (QM/MM) molecular dynamics (MD) simulations. These also show that while the hydrogen atoms pointed toward iodide, they predominantly point toward the bulk solvent in the case of iodine, suggesting a hydrophobic behavior. This is further confirmed by quantum chemical (QC) calculations of I(-)/I(0)(H(2)O)(n=1-4) clusters. The L(1) edge sub-picosecond spectra point to the existence of a transient species that is not present at 50 ps. The QC calculations and the QM/MM MD simulations identify this transient species as an I(0)(OH(2)) complex inside the cavity. The simulations show that upon electron abstraction most of the water molecules move away from iodine, while one comes closer to form the complex that lives for 3-4 ps. This time is governed by the reorganization of the main solvation shell, basically the time it takes for the water molecules to reform an H-bond network. Only then is the interaction with the solvation shell strong enough to pull the water molecule of the complex toward the bulk solvent. Overall, much of the behavior at early times is determined by the reorientational dynamics of water molecules and the formation of a complete network of hydrogen bonded molecules in the first solvation shell.

Iodide accumulation provides kelp with an inorganic antioxidant impacting atmospheric chemistry.

Brown algae of the Laminariales (kelps) are the strongest accumulators of iodine among living organisms. They represent a major pump in the global biogeochemical cycle of iodine and, in particular, the major source of iodocarbons in the coastal atmosphere. Nevertheless, the chemical state and biological significance of accumulated iodine have remained unknown to this date. Using x-ray absorption spectroscopy, we show that the accumulated form is iodide, which readily scavenges a variety of reactive oxygen species (ROS). We propose here that its biological role is that of an inorganic antioxidant, the first to be described in a living system. Upon oxidative stress, iodide is effluxed. On the thallus surface and in the apoplast, iodide detoxifies both aqueous oxidants and ozone, the latter resulting in the release of high levels of molecular iodine and the consequent formation of hygroscopic iodine oxides leading to particles, which are precursors to cloud condensation nuclei. In a complementary set of experiments using a heterologous system, iodide was found to effectively scavenge ROS in human blood cells.

Can energetic terahertz pulses initiate surface catalytic reactions on the picosecond time scale?

In preparation for picosecond pump-probe experiments at the SwissFEL X-ray laser facility, the feasibility of collectively initiating surface chemical reactions using energetic pulses of terahertz radiation is being tested.

L-edge XANES analysis of photoexcited metal complexes in solution.

Ultrafast X-ray absorption spectroscopy is a powerful tool to observe electronic and geometric structures of short-lived reaction intermediates. The ab initio FEFF9 code is applied to simulate the Pt L(3)-edge XANES spectrum of the photocatalytic diplatinum molecule [Pt(2)(P(2)O(5)H(2))(4)](4-) and the photo-induced changes that occur therein. The spectra are interpreted within a XAFS-like scattering theoretical framework (bound-continuum transitions) or in terms of a final-state local l-projected density of states (LDOS) (bound-bound transitions). By using a novel Bayesian fitting procedure, we show that the ground-state structures obtained independently from the XANES and EXAFS regions of the spectrum are in good agreement with each other. The semi-quantitative result obtained for the Pt-Pt contraction in the excited state is in line with recently published values. The improved theoretical treatment of inelastic losses has shown to result in more accurate peak positions in the above-continuum region of the spectrum which is an important prerequisite for obtaining quantitative structural information from (time-resolved) XANES spectra.

Advances in long-wavelength native phasing at X-ray free-electron lasers.

Long-wavelength pulses from the Swiss X-ray free-electron laser (XFEL) have been used for de novo protein structure determination by native single-wavelength anomalous diffraction (native-SAD) phasing of serial femtosecond crystallography (SFX) data. In this work, sensitive anomalous data-quality indicators and model proteins were used to quantify improvements in native-SAD at XFELs such as utilization of longer wavelengths, careful experimental geometry optimization, and better post-refinement and partiality correction. Compared with studies using shorter wavelengths at other XFELs and older software versions, up to one order of magnitude reduction in the required number of indexed images for native-SAD was achieved, hence lowering sample consumption and beam-time requirements significantly. Improved data quality and higher anomalous signal facilitate so-far underutilized de novo structure determination of challenging proteins at XFELs. Improvements presented in this work can be used in other types of SFX experiments that require accurate measurements of weak signals, for example time-resolved studies.

Structural determination of a photochemically active diplatinum molecule by time-resolved EXAFS spectroscopy.

Metallica: A large contraction of the Pt-Pt bond in the triplet excited state of the photoreactive [Pt(2)(P(2)O(5)H(2))(4)](4-) ion is determined by time-resolved X-ray absorption spectroscopy (see picture). The strengthening of the Pt-Pt interaction is accompanied by a weakening of the ligand coordination bonds, resulting in an elongation of the platinum-ligand bond that is determined for the first time.

Core-level nonlinear spectroscopy triggered by stochastic X-ray pulses.

Stochastic processes are highly relevant in research fields as different as neuroscience, economy, ecology, chemistry, and fundamental physics. However, due to their intrinsic unpredictability, stochastic mechanisms are very challenging for any kind of investigations and practical applications. Here we report the deliberate use of stochastic X-ray pulses in two-dimensional spectroscopy to the simultaneous mapping of unoccupied and occupied electronic states of atoms in a regime where the opacity and transparency properties of matter are subject to the incident intensity and photon energy. A readily transferable matrix formalism is presented to extract the electronic states from a dataset measured with the monitored input from a stochastic excitation source. The presented formalism enables investigations of the response of the electronic structure to irradiation with intense X-ray pulses while the time structure of the incident pulses is preserved.

Revealing hole trapping in zinc oxide nanoparticles by time-resolved X-ray spectroscopy.

Nanostructures of transition metal oxides, such as zinc oxide, have attracted considerable interest for solar-energy conversion and photocatalysis. Both applications are sensitive to the transport and trapping of photoexcited charge carriers. The probing of electron trapping has recently become possible using time-resolved element-sensitive methods, such as X-ray spectroscopy. However, valence-band-trapped holes have so far escaped observation. Herein we use X-ray absorption spectroscopy combined with a dispersive X-ray emission spectrometer to probe the charge carrier relaxation and trapping processes in zinc oxide nanoparticles after above band-gap photoexcitation. Our results, supported by simulations, demonstrate that within 80 ps, photoexcited holes are trapped at singly charged oxygen vacancies, which causes an outward displacement by ~15% of the four surrounding zinc atoms away from the doubly charged vacancy. This identification of the hole traps provides insight for future developments of transition metal oxide-based nanodevices.

X-ray free electron laser: opportunities for drug discovery.

Past decades have shown the impact of structural information derived from complexes of drug candidates with their protein targets to facilitate the discovery of safe and effective medicines. Despite recent developments in single particle cryo-electron microscopy, X-ray crystallography has been the main method to derive structural information. The unique properties of X-ray free electron laser (XFEL) with unmet peak brilliance and beam focus allow X-ray diffraction data recording and successful structure determination from smaller and weaker diffracting crystals shortening timelines in crystal optimization. To further capitalize on the XFEL advantage, innovations in crystal sample delivery for the X-ray experiment, data collection and processing methods are required. This development was a key contributor to serial crystallography allowing structure determination at room temperature yielding physiologically more relevant structures. Adding the time resolution provided by the femtosecond X-ray pulse will enable monitoring and capturing of dynamic processes of ligand binding and associated conformational changes with great impact to the design of candidate drug compounds.