A new route for enantio-sensitive structure determination by photoelectron scattering on molecules in the gas phase.

X-Ray as well as electron diffraction are powerful tools for structure determination of molecules. Studies on randomly oriented molecules in the gas phase address cases in which molecular crystals cannot be generated or the interaction-free molecular structure is to be addressed. Such studies usually yield partial geometrical information, such as interatomic distances. Here, we present a complementary approach, which allows obtaining insight into the structure, handedness, and even detailed geometrical features of molecules in the gas phase. Our approach combines Coulomb explosion imaging, the information that is encoded in the molecular-frame diffraction pattern of core-shell photoelectrons and ab initio computations. Using a loop-like analysis scheme, we are able to deduce specific molecular coordinates with sensitivity even to the handedness of chiral molecules and the positions of individual atoms, e.g., protons.

Crystallization kinetics of atomic crystals revealed by a single-shot and single-particle X-ray diffraction experiment.

Crystallization is a fundamental natural phenomenon and the ubiquitous physical process in materials science for the design of new materials. So far, experimental observations of the structural dynamics in crystallization have been mostly restricted to slow dynamics. We present here an exclusive way to explore the dynamics of crystallization in highly controlled conditions (i.e., in the absence of impurities acting as seeds of the crystallites) as it occurs in vacuum. We have measured the early formation stage of solid Xe nanoparticles nucleated in an expanding supercooled Xe jet by means of an X-ray diffraction experiment with 10-fs X-ray free-electron laser (XFEL) pulses. We found that the structure of Xe nanoparticles is not pure face-centered cubic (fcc), the expected stable phase, but a mixture of fcc and randomly stacked hexagonal close-packed (rhcp) structures. Furthermore, we identified the instantaneous coexistence of the comparably sized fcc and rhcp domains in single Xe nanoparticles. The observations are explained by the scenario of structural aging, in which the nanoparticles initially crystallize in the highly stacking-disordered rhcp phase and the structure later forms the stable fcc phase. The results are reminiscent of analogous observations in hard-sphere systems, indicating the universal role of the stacking-disordered phase in nucleation.

Photoelectron circular dichroism of O 1s-photoelectrons of uniaxially oriented trifluoromethyloxirane: energy dependence and sensitivity to molecular configuration.

The photoelectron circular dichroism (PECD) of the O 1s-photoelectrons of trifluoromethyloxirane (TFMOx) is studied experimentally and theoretically for different photoelectron kinetic energies. The experiments were performed employing circularly polarized synchrotron radiation and coincident electron and fragment ion detection using cold target recoil ion momentum spectroscopy. The corresponding calculations were performed by means of the single center method within the relaxed-core Hartree-Fock approximation. We concentrate on the energy dependence of the differential PECD of uniaxially oriented TFMOx molecules, which is accessible through the employed coincident detection. We also compare the results for the differential PECD of TFMOx to those obtained for the equivalent fragmentation channel and similar photoelectron kinetic energy of methyloxirane (MOx), studied in our previous work. Thereby, we investigate the influence of the substitution of the methyl group by the trifluoromethyl group at the chiral center on the molecular chiral response. Finally, the presently obtained angular distribution parameters are compared to those available in the literature.

Charge Trapping Process in Photoexcited Nitrogen-Doped Titanium Oxides.

We present a first-principles study on the structural changes induced by charge trapping that occurs after photoexcitation in nitrogen-doped titanium oxide (N-TiO2). The charge trapping site and the corresponding K edge EXAFS spectra of Ti atoms were predicted and compared with those obtained by an experiment under ultraviolet (UV) light excitation. The results indicate that charge trapping occurs in the neighborhood of the oxygen vacancy (O-vac) sites. Furthermore, our calculations show that the O-vac site significantly affects the EXAFS spectra, while substitutional nitrogen doping for an oxygen site in the vicinity of the O-vac site is insensitive in the EXAFS spectra. Based on this observation combined with the knowledge from previous experiments, we propose a charge trapping process where the UV light-excited electron migrates at the O-vac site in bulk (∼300 ps) while the visible light-excited electron (N 2p → Ti 3d) is immediately trapped at the O-vac site neighboring the N site (∼1 ps).

Characterizing crystalline defects in single nanoparticles from angular correlations of single-shot diffracted X-rays.

Characterizing and controlling the uniformity of nanoparticles is crucial for their application in science and technology because crystalline defects in the nanoparticles strongly affect their unique properties. Recently, ultra-short and ultra-bright X-ray pulses provided by X-ray free-electron lasers (XFELs) opened up the possibility of structure determination of nanometre-scale matter with Å spatial resolution. However, it is often difficult to reconstruct the 3D structural information from single-shot X-ray diffraction patterns owing to the random orientation of the particles. This report proposes an analysis approach for characterizing defects in nanoparticles using wide-angle X-ray scattering (WAXS) data from free-flying single nanoparticles. The analysis method is based on the concept of correlated X-ray scattering, in which correlations of scattered X-ray are used to recover detailed structural information. WAXS experiments of xenon nanoparticles, or clusters, were conducted at an XFEL facility in Japan by using the SPring-8 Ångstrom compact free-electron laser (SACLA). Bragg spots in the recorded single-shot X-ray diffraction patterns showed clear angular correlations, which offered significant structural information on the nanoparticles. The experimental angular correlations were reproduced by numerical simulation in which kinematical theory of diffraction was combined with geometric calculations. We also explain the diffuse scattering intensity as being due to the stacking faults in the xenon clusters.

Refinement for single-nanoparticle structure determination from low-quality single-shot coherent diffraction data.

With the emergence of X-ray free-electron lasers, it is possible to investigate the structure of nanoscale samples by employing coherent diffractive imaging in the X-ray spectral regime. In this work, we developed a refinement method for structure reconstruction applicable to low-quality coherent diffraction data. The method is based on the gradient search method and considers the missing region of a diffraction pattern and the small number of detected photons. We introduced an initial estimate of the structure in the method to improve the convergence. The present method is applied to an experimental diffraction pattern of an Xe cluster obtained in an X-ray scattering experiment at the SPring-8 Angstrom Compact free-electron LAser (SACLA) facility. It is found that the electron density is successfully reconstructed from the diffraction pattern with a large missing region, with a good initial estimate of the structure. The diffraction pattern calculated from the reconstructed electron density reproduced the observed diffraction pattern well, including the characteristic intensity modulation in each ring. Our refinement method enables structure reconstruction from diffraction patterns under difficulties such as missing areas and low diffraction intensity, and it is potentially applicable to the structure determination of samples that have low scattering power.

Multi-particle momentum correlations extracted using covariance methods on multiple-ionization of diiodomethane molecules by soft-X-ray free-electron laser pulses.

Momenta of ions from diiodomethane molecules after multiple ionization by soft-X-ray free-electron-laser pulses are measured. Correlations between the ion momenta are extracted by covariance methods formulated for the use in multiparticle momentum-resolved ion time-of-flight spectroscopy. Femtosecond dynamics of the dissociating multiply charged diiodomethane cations is discussed and interpreted by using simulations based on a classical Coulomb explosion model including charge evolution.

Electron spectroscopic study of nanoplasma formation triggered by intense soft x-ray pulses.

Using electron spectroscopy, we investigated the nanoplasma formation process generated in xenon clusters by intense soft x-ray free electron laser (FEL) pulses. We found clear FEL intensity dependence of electron spectra. Multistep ionization and subsequent ionization frustration features are evident for the low FEL-intensity region, and the thermal electron emission emerges at the high FEL intensity. The present FEL intensity dependence of the electron spectra is well addressed by the frustration parameter introduced by Arbeiter and Fennel [New J. Phys. 13, 053022 (2011)].

Ultrafast Structural Dynamics of Nanoparticles in Intense Laser Fields.

Femtosecond laser pulses have opened new frontiers for the study of ultrafast phase transitions and nonequilibrium states of matter. In this Letter, we report on structural dynamics in atomic clusters pumped with intense near-infrared (NIR) pulses into a nanoplasma state. Employing wide-angle scattering with intense femtosecond x-ray pulses from a free-electron laser source, we find that highly excited xenon nanoparticles retain their crystalline bulk structure and density in the inner core long after the driving NIR pulse. The observed emergence of structural disorder in the nanoplasma is consistent with a propagation from the surface to the inner core of the clusters.

Photo-ionization and fragmentation of Sc3N@C80 following excitation above the Sc K-edge.

We have investigated the ionization and fragmentation of a metallo-endohedral fullerene, Sc3N@C80, using ultrashort (10 fs) x-ray pulses. Following selective ionization of a Sc (1s) electron (hν = 4.55 keV), an Auger cascade leads predominantly to either a vibrationally cold multiply charged parent molecule or multifragmentation of the carbon cage following a phase transition. In contrast to previous studies, no intermediate regime of C2 evaporation from the carbon cage is observed. A time-delayed, hard x-ray pulse (hν = 5.0 keV) was used to attempt to probe the electron transfer dynamics between the encapsulated Sc species and the carbon cage. A small but significant change in the intensity of Sc-containing fragment ions and coincidence counts for a delay of 100 fs compared to 0 fs, as well as an increase in the yield of small carbon fragment ions, may be indicative of incomplete charge transfer from the carbon cage on the sub-100 fs time scale.

Probing gaseous molecular structure by molecular-frame photoelectron angular distributions.

Carbon 1s photoelectron angular distributions of an iodomethane molecule were measured relative to the recoil-frame determined by the momentum correlation between I+ and CH3 + at photoelectron energies of 3, 6.1, and 12 eV. The energy dependent behavior of the recoil-frame photoelectron angular distributions is reproduced reasonably well by the time-dependent density functional theory with B-spline methods. We discuss potential applications of the fully differential photoelectron angular distribution measurements in the molecular frame to three-dimensional molecular structural determinations identifying the directions and lengths of the bonds.

xcalib: a focal spot calibrator for intense X-ray free-electron laser pulses based on the charge state distributions of light atoms.

The xcalib toolkit has been developed to calibrate the beam profile of an X-ray free-electron laser (XFEL) at the focal spot based on the experimental charge state distributions (CSDs) of light atoms. Characterization of the fluence distribution at the focal spot is essential to perform the volume integrations of physical quantities for a quantitative comparison between theoretical and experimental results, especially for fluence-dependent quantities. The use of the CSDs of light atoms is advantageous because CSDs directly reflect experimental conditions at the focal spot, and the properties of light atoms have been well established in both theory and experiment. Theoretical CSDs are obtained using xatom, a toolkit to calculate atomic electronic structure and to simulate ionization dynamics of atoms exposed to intense XFEL pulses, which involves highly excited multiple core-hole states. Employing a simple function with a few parameters, the spatial profile of an XFEL beam is determined by minimizing the difference between theoretical and experimental results. The optimization procedure employing the reinforcement learning technique can automatize and organize calibration procedures which, before, had been performed manually. xcalib has high flexibility, simultaneously combining different optimization methods, sets of charge states, and a wide range of parameter space. Hence, in combination with xatom, xcalib serves as a comprehensive tool to calibrate the fluence profile of a tightly focused XFEL beam in the interaction region.

Probing molecular bond-length using molecular-frame photoelectron angular distributions.

The molecular-frame photoelectron angular distributions (MFPADs) in O 1s photoemission from CO2 molecule were measured. Patterns due to photoelectron diffractions were observed in the MFPADs. The polarization-averaged MFPADs were compared with theoretical calculation and were found to be useful in determining the molecular bond-length, which is a component to determine molecular structures.

Real-time observation of X-ray-induced intramolecular and interatomic electronic decay in CH2I2.

The increasing availability of X-ray free-electron lasers (XFELs) has catalyzed the development of single-object structural determination and of structural dynamics tracking in real-time. Disentangling the molecular-level reactions triggered by the interaction with an XFEL pulse is a fundamental step towards developing such applications. Here we report real-time observations of XFEL-induced electronic decay via short-lived transient electronic states in the diiodomethane molecule, using a femtosecond near-infrared probe laser. We determine the lifetimes of the transient states populated during the XFEL-induced Auger cascades and find that multiply charged iodine ions are issued from short-lived (∼20 fs) transient states, whereas the singly charged ones originate from significantly longer-lived states (∼100 fs). We identify the mechanisms behind these different time scales: contrary to the short-lived transient states which relax by molecular Auger decay, the long-lived ones decay by an interatomic Coulombic decay between two iodine atoms, during the molecular fragmentation.

Radiation-Induced Chemical Dynamics in Ar Clusters Exposed to Strong X-Ray Pulses.

We show that electron and ion spectroscopy reveals the details of the oligomer formation in Ar clusters exposed to an x-ray free electron laser (XFEL) pulse, i.e., chemical dynamics triggered by x rays. With guidance from a dedicated molecular dynamics simulation tool, we find that van der Waals bonding, the oligomer formation mechanism, and charge transfer among the cluster constituents significantly affect ionization dynamics induced by an XFEL pulse of moderate fluence. Our results clearly demonstrate that XFEL pulses can be used not only to "damage and destroy" molecular assemblies but also to modify and transform their molecular structure. The accuracy of the predictions obtained makes it possible to apply the cluster spectroscopy, in connection with the respective simulations, for estimation of the XFEL pulse fluence in the fluence regime below single-atom multiple-photon absorption, which is hardly accessible with other diagnostic tools.

Two-colour serial femtosecond crystallography dataset from gadoteridol-derivatized lysozyme for MAD phasing.

We provide a detailed description of a gadoteridol-derivatized lysozyme (gadolinium lysozyme) two-colour serial femtosecond crystallography (SFX) dataset for multiple wavelength anomalous dispersion (MAD) structure determination. The data was collected at the Spring-8 Angstrom Compact free-electron LAser (SACLA) facility using a two-colour double-pulse beam to record two diffraction patterns simultaneously in one diffraction image. Gadolinium lysozyme was chosen as a well-established model system that has a very strong anomalous signal. Diffraction patterns from gadolinium lysozyme microcrystals were recorded to a resolution of 1.9 Å in both colours. This dataset is publicly available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development.

Multi-wavelength anomalous diffraction de novo phasing using a two-colour X-ray free-electron laser with wide tunability.

Serial femtosecond crystallography at X-ray free-electron lasers (XFELs) offers unprecedented possibilities for macromolecular structure determination of systems prone to radiation damage. However, de novo structure determination, i.e., without prior structural knowledge, is complicated by the inherent inaccuracy of serial femtosecond crystallography data. By its very nature, serial femtosecond crystallography data collection entails shot-to-shot fluctuations in X-ray wavelength and intensity as well as variations in crystal size and quality that must be averaged out. Hence, to obtain accurate diffraction intensities for de novo phasing, large numbers of diffraction patterns are required, and, concomitantly large volumes of sample and long X-ray free-electron laser beamtimes. Here we show that serial femtosecond crystallography data collected using simultaneous two-colour X-ray free-electron laser pulses can be used for multiple wavelength anomalous dispersion phasing. The phase angle determination is significantly more accurate than for single-colour phasing. We anticipate that two-colour multiple wavelength anomalous dispersion phasing will enhance structure determination of difficult-to-phase proteins at X-ray free-electron lasers.

Observation of Enhanced Chiral Asymmetries in the Inner-Shell Photoionization of Uniaxially Oriented Methyloxirane Enantiomers.

Most large molecules are chiral in their structure: they exist as two enantiomers, which are mirror images of each other. Whereas the rovibronic sublevels of two enantiomers are almost identical (neglecting a minuscular effect of the weak interaction), it turns out that the photoelectric effect is sensitive to the absolute configuration of the ionized enantiomer. Indeed, photoionization of randomly oriented enantiomers by left or right circularly polarized light results in a slightly different electron flux parallel or antiparallel with respect to the photon propagation direction-an effect termed photoelectron circular dichroism (PECD). Our comprehensive study demonstrates that the origin of PECD can be found in the molecular frame electron emission pattern connecting PECD to other fundamental photophysical effects such as the circular dichroism in angular distributions (CDAD). Accordingly, distinct spatial orientations of a chiral molecule enhance the PECD by a factor of about 10.

Ultrafast Coulomb explosion of a diiodomethane molecule induced by an X-ray free-electron laser pulse.

Coulomb explosion of diiodomethane CH2I2 molecules irradiated by ultrashort and intense X-ray pulses from SACLA, the Japanese X-ray free electron laser facility, was investigated by multi-ion coincidence measurements and self-consistent charge density-functional-based tight-binding (SCC-DFTB) simulations. The diiodomethane molecule, containing two heavy-atom X-ray absorbing sites, exhibits a rather different charge generation and nuclear motion dynamics compared to iodomethane CH3I with only a single heavy atom, as studied earlier. We focus on charge creation and distribution in CH2I2 in comparison to CH3I. The release of kinetic energy into atomic ion fragments is also studied by comparing SCC-DFTB simulations with the experiment. Compared to earlier simulations, several key enhancements are made, such as the introduction of a bond axis recoil model, where vibrational energy generated during charge creation processes induces only bond stretching or shrinking. We also propose an analytical Coulomb energy partition model to extract the essential mechanism of Coulomb explosion of molecules from the computed and the experimentally measured kinetic energies of fragment atomic ions by partitioning each pair Coulomb interaction energy into two ions of the pair under the constraint of momentum conservation. Effective internuclear distances assigned to individual fragment ions at the critical moment of the Coulomb explosion are then estimated from the average kinetic energies of the ions. We demonstrate, with good agreement between the experiment and the SCC-DFTB simulation, how the more heavily charged iodine fragments and their interplay define the characteristic features of the Coulomb explosion of CH2I2. The present study also confirms earlier findings concerning the magnitude of bond elongation in the ultrashort X-ray pulse duration, showing that structural damage to all but C-H bonds does not develop to a noticeable degree in the pulse length of ∼10 fs.

Transient lattice contraction in the solid-to-plasma transition.

In condensed matter systems, strong optical excitations can induce phonon-driven processes that alter their mechanical properties. We report on a new phenomenon where a massive electronic excitation induces a collective change in the bond character that leads to transient lattice contraction. Single large van der Waals clusters were isochorically heated to a nanoplasma state with an intense 10-fs x-ray (pump) pulse. The structural evolution of the nanoplasma was probed with a second intense x-ray (probe) pulse, showing systematic contraction stemming from electron delocalization during the solid-to-plasma transition. These findings are relevant for any material in extreme conditions ranging from the time evolution of warm or hot dense matter to ultrafast imaging with intense x-ray pulses or, more generally, any situation that involves a condensed matter-to-plasma transition.