Resonant Auger decay of iodobenzene below the I 4d edge.

New data are presented on the resonant Auger decay of iodobenzene (C6H5I) in the region of the I 4d-1 ionization threshold. The excited molecules decay by participator and spectator processes to populate single-hole valence states and two-hole, one-particle excited states of the cation, providing new information on the structure of C6H5I+. Excitation of dissociative C6H5I (I 4d5/2,3/2-1)σ* resonances can, in principle, result in ultrafast dissociation to C6H5 + I** and the subsequent autoionization of I**, but no evidence for this process is observed. The results are compared with our recent study of the resonant Auger decay of methyl iodide (CH3I).

Resonant Auger decay of dissociating CH3I near the I 4d threshold.

Resonant Auger processes provide a unique perspective on electronic interactions and excited vibrational and electronic states of molecular ions. Here, new data are presented on the resonant Auger decay of excited CH3I in the region just below the I 4d-1 ionization threshold. The resonances include the Rydberg series converging to the five spin-orbit and ligand-field split CH3I (I 4d-1) thresholds, as well as resonances corresponding to excitation from the I 4d5/2,3/2 orbitals into the σ* lowest unoccupied molecular orbital. This study focuses on participator decay that populates the lowest lying states of CH3I+, in particular, the X̃2E3/2 and 2E1/2 states, and on spectator decay that populates the lowest-lying (CH3I2+)σ* states of CH3I+. The CH3I (I 4d-1)σ* resonances are broad, and dissociation to CH3 + I competes with the autoionization of the core-excited states. Auger decay as the molecule dissociates produces a photoelectron spectrum with a long progression (up to v3+ ∼ 25) in the C-I stretching mode of the X̃2E3/2 and 2E1/2 states, providing insights into the shape of the dissociative core-excited surface. The observed spectator decay processes indicate that CH3I+ is formed on the repulsive wall of the lower-lying (CH3I2+)σ* potentials, and the photon-energy dependence of the processes provides insights into the relative slopes of the (4d-1)σ* and (CH3I2+)σ* potential surfaces. Data are also presented for the spectator decay of higher lying CH3I (I 4d-1)nl Rydberg resonances. Photoelectron angular distributions for the resonant Auger processes provide additional information that helps distinguish these processes from the direct ionization signal.

A study of the valence photoelectron spectrum of uracil and mixed water-uracil clusters.

The valence ionization of uracil and mixed water-uracil clusters has been studied experimentally and by ab initio calculations. In both measurements, the spectrum onset shows a red shift with respect to the uracil molecule, with the mixed cluster characterized by peculiar features unexplained by the sum of independent contributions of the water or uracil aggregation. To interpret and assign all the contributions, we performed a series of multi-level calculations, starting from an exploration of several cluster structures using automated conformer-search algorithms based on a tight-binding approach. Ionization energies have been assessed on smaller clusters via a comparison between accurate wavefunction-based approaches and cost-effective DFT-based simulations, the latter of which were applied to clusters up to 12 uracil and 36 water molecules. The results confirm that (i) the bottom-up approach based on a multilevel method [Mattioli et al. Phys. Chem. Chem. Phys. 23, 1859 (2021)] to the structure of neutral clusters of unknown experimental composition converges to precise structure-property relationships and (ii) the coexistence of pure and mixed clusters in the water-uracil samples. A natural bond orbital (NBO) analysis performed on a subset of clusters highlighted the special role of H-bonds in the formation of the aggregates. The NBO analysis yields second-order perturbative energy between the H-bond donor and acceptor orbitals correlated with the calculated ionization energies. This sheds light on the role of the oxygen lone-pairs of the uracil CO group in the formation of strong H-bonds, with a stronger directionality in mixed clusters, giving a quantitative explanation for the formation of core-shell structures.

Dynamics of core-excited ammonia: disentangling fragmentation pathways by complementary spectroscopic methods.

Fragmentation dynamics of core-excited isolated ammonia molecules is studied by two different and complementary experimental methods, high-resolution resonant Auger spectroscopy and electron energy-selected Auger electron-photoion coincidence spectroscopy (AEPICO). The combined use of these two techniques allows obtaining information on different dissociation patterns, in particular fragmentation before relaxation, often called ultrafast dissociation (UFD), and fragmentation after relaxation. The resonant Auger spectra contain the spectral signature of both molecular and fragment final states, and therefore can provide information on all events occurring during the core-hole lifetime, in particular fragmentation before relaxation. Coincidence measurements allow correlating Auger electrons with ionic fragments from the same molecule, and relating the ionic fragments to specific Auger final electronic states, and yield additional information on which final states are dissociative, and which ionic fragments can be produced in timescales either corresponding to the core-hole lifetime or longer. Furthermore, we show that by the combined use of two complementary experimental techniques we are able to identify more electronic states of the NH2+ fragment with respect to the single one already reported in the literature.

Alternative Pathway to Double-Core-Hole States.

Excited double-core-hole states of isolated water molecules resulting from the sequential absorption of two x-ray photons have been investigated. These states are formed through an alternative pathway, where the initial step of core ionization is accompanied by the shake-up of a valence electron, leading to the same final states as in the core-ionization followed by core-excitation pathway. The capability of the x-ray free-electron laser to deliver very intense, very short, and tunable light pulses is fully exploited to identify the two different pathways.

Electronic Structure and Solvation Effects from Core and Valence Photoelectron Spectroscopy of Serum Albumin.

X-ray photoelectron spectroscopy of bovine serum albumin (BSA) in a liquid jet is used to investigate the electronic structure of a solvated protein, yielding insight into charge transfer mechanisms in biological systems in their natural environment. No structural damage was observed in BSA following X-ray photoelectron spectroscopy in a liquid jet sample environment. Carbon and nitrogen atoms in different chemical environments were resolved in the X-ray photoelectron spectra of both solid and solvated BSA. The calculations of charge distributions demonstrate the difficulty of assigning chemical contributions in complex systems in an aqueous environment. The high-resolution X-ray core electron spectra recorded are unchanged upon solvation. A comparison of the valence bands of BSA in both phases is also presented. These bands display a higher sensitivity to solvation effects. The ionization energy of the solvated BSA is determined at 5.7 ± 0.3 eV. Experimental results are compared with theoretical calculations to distinguish the contributions of various molecular components to the electronic structure. This comparison points towards the role of water in hole delocalization in proteins.

Auger electron angular distributions following excitation or ionization from the Xe 3d and F 1s levels in xenon difluoride.

Linearly polarized synchrotron radiation has been used to record polarization dependent, non-resonant Auger electron spectra of XeF2, encompassing the bands due to the xenon M45N1N45, M45N23N45, M45N45N45 and M45N45V and fluorine KVV transitions. Resonantly excited Auger spectra have been measured at photon energies coinciding with the Xe 3d5/2 → σ* and the overlapped Xe 3d3/2/F 1s → σ* excitations in XeF2. The non-resonant and resonantly excited spectra have enabled the Auger electron angular distributions, as characterized by the ßA parameter, to be determined for the M45N45N45 transitions. In the photon energy range over which the Auger electron angular distributions were measured, theoretical results indicate that transitions into the εf continuum channel dominate the Xe 3d photoionization in XeF2. In this limit, the theoretical value of the atomic alignment parameter (A20) characterizing the core ionized state becomes constant. This theoretical value has been used to obtain the Auger electron intrinsic anisotropy parameters (α2) from the ßA parameters extracted from our non-resonant Auger spectra. For a particular Auger transition, the electron kinetic energy measured in the resonantly excited spectrum is higher than that in the directly ionized spectrum, due to the screening provided by the electron promoted into the σ* orbital. The interpretation of the F KVV Auger band in XeF2 has been discussed in relation to previously published one-site populations of the doubly charged ions (XeF22+). The experimental results show that the ionization energies of the doubly charged states predominantly populated in the decay of a vacancy in the F 1s orbital in XeF2 tend to be higher than those populated in the decay of a vacancy in the Xe 4d level in XeF2.

NEXAFS and MS-AES spectroscopy of the C 1s and Cl 2p excitation and ionization of chlorobenzene: Production of dicationic species.

We report on single- and double-charge photofragment formation by synchrotron radiation, following C 1s core excitation and ionization and Cl 2p inner excitation and ionization of chlorobenzene, C6H5Cl. From a comparison of experimental near-edge X-ray absorption fine structure spectra and theoretical ab initio calculations, the nature of various core and inner shell transitions of the molecule and pure atomic features were identified. To shed light on the normal Auger processes following excitation or ionization of the molecule at the Cl 2p or C 1s sites, we addressed the induced ionic species formation. With energy resolved electron spectra and ion time-of-flight spectra coincidence measurements, the ionic species were correlated with binding energy regions and initial states of vacancies. We explored the formation of the molecular dication C6H5Cl2+, the analogue benzene dication C6H42+, and the singly charged species produced by single loss of a carbon atom, C5HnCl+. The appearance and intensities of the spectral features associated with these ionic species are shown to be strongly site selective and dependent on the energy ranges of the Auger electron emission. Unexpected intensities for the analogue double charged benzene C6H42+ ion were observed with fast Auger electrons. The transitions leading to C6H5Cl2+ were identified from the binding energy representation of high resolution electron energy spectra. Most C6H5Cl2+ ions decay into two singly charged moieties, but intermediate channels are opened leading to other heavy dicationic species, C6H42+ and C6H4Cl2+, the channel leading to the first of these being much more favored than the other.

Water-biomolecule clusters studied by photoemission spectroscopy and multilevel atomistic simulations: hydration or solvation?

The properties of mixed water-uracil nanoaggregates have been probed by core electron-photoemission measurements to investigate supramolecular assembly in the gas phase driven by weak interactions. The interpretation of the measurements has been assisted by multilevel atomistic simulations, based on semi-empirical tight-binding and DFT-based methods. Our protocol established a positive-feedback loop between experimental and computational techniques, which has enabled a sound and detailed atomistic description of such complex heterogeneous molecular aggregates. Among biomolecules, uracil offers interesting and generalized skeletal features; its structure encompasses an alternation of hydrophilic H-bond donor and acceptor sites and hydrophobic moieties, typical in biomolecular systems, that induces a supramolecular core-shell-like organization of the mixed clusters with a water core and an uracil shell. This structure is far from typical models of both solid-state hydration, with water molecules in defined positions, or liquid solvation, where disconnected uracil molecules are completely surrounded by water.

Unravelling molecular interactions in uracil clusters by XPS measurements assisted by ab initio and tight-binding simulations.

The C, N and O 1s XPS spectra of uracil clusters in the gas phase have been measured. A new bottom-up approach, which relies on computational simulations starting from the crystallographic structure of uracil, has been adopted to interpret the measured spectra. This approach sheds light on the different molecular interactions (H-bond, π-stacking, dispersion interactions) at work in the cluster and provides a good understanding of the observed XPS chemical shifts with respect to the isolated molecule in terms of intramolecular and intermolecular screening occurring after the core-hole ionization. The proposed bottom-up approach, reasonably expensive in terms of computational resources, has been validated by finite-temperature molecular dynamics simulations of clusters composed of up to fifty molecules.

Full-dimensional theoretical description of vibrationally resolved valence-shell photoionization of H2O.

We have performed a full-dimensional theoretical study of vibrationally resolved photoelectron emission from the valence shell of the water molecule by using an extension of the static-exchange density functional theory that accounts for ionization as well as for vibrational motion in the symmetric stretching, antisymmetric stretching, and bending modes. At variance with previous studies performed in centrosymmetric molecules, where vibrationally resolved spectra are mostly dominated by the symmetric stretching mode, in the present case, all three modes contribute to the calculated spectra, including intermode couplings. We have found that diffraction of the ejected electron by the various atomic centers is barely visible in the ratios between vibrationally resolved photoelectron spectra corresponding to different vibrational states of the remaining H2O+ cation (the so-called v-ratios), in contrast to the prominent oscillations observed in K-shell ionization of centrosymmetric molecules, including those that only contain hydrogen atoms around the central atoms, e.g., CH4. To validate the conclusions of our work, we have carried out synchrotron radiation experiments at the SOLEIL synchrotron and determined photoelectron spectra and v-ratios for H2O in a wide range of photon energies, from threshold up to 150 eV. The agreement with the theoretical predictions is good.

Resonant Photoelectron Confinement in the SF6 Molecule.

Recent thorough experimental activity aiming to generate high harmonics in the SF6 molecules requires the knowledge of, on one hand, accurate valence-shell photoionization cross sections and phases, from a threshold up to a few tens of eV, where resonances are likely to appear, and, on the other hand, the effect of the nuclear vibrational dynamics on the process. In this work, we have experimentally determined and theoretically evaluated vibrationally resolved photoionization cross sections of SF6 up to 80 eV photon energies, with an emphasis on the E2T1u channel, for which vibrational progressions are fully resolved in the experiment. Our results reveal the presence of shape resonances due to excitation to SF6 virtual states lying just above the ionization threshold, in agreement with previous synchrotron radiation work and theoretical calculations. More interestingly, our calculations also disclose resonance features at photoelectron energies as high as 40-50 eV, which are due to the transient confinement of the ejected electron in the octahedral cage formed by the peripheral F atoms. In the vicinity of all resonances, including those due to confinement, the calculated ionization phases experience an excursion of about π or π/2 and significantly depend on the final vibrational state of the remaining cation. Both effects should be taken into account to correctly interpret ongoing high-harmonic generation work in SF6. A similar behavior is expected for other symmetric molecules containing a central atom, such as BF3, CF4, and the like.

Photoionization of the iodine 3d, 4s, and 4p orbitals in methyl iodide.

Ionization of the I 3d, 4s, and 4p orbitals in methyl iodide (CH3I) has been studied by using synchrotron radiation to measure the total ion yield and by recording photoelectron spectra with linearly polarized radiation in two polarization orientations. The complete photoelectron spectrum of CH3I has been recorded at several photon energies, and bands due to the C 1s, I 3d, 4s, 4p, and 4d atomic-like orbitals, as well as the molecular orbitals, have been observed and assigned. In the vicinity of the I 3d5/2 and 3d3/2 ionization thresholds at 626.8 and 638.3 eV, respectively, the ion yield displays weak structure in the pre-edge region due to transitions into valence or Rydberg states, and, at higher energies, a shoulder and a broad maximum attributed to the I 3d5/2 → εf and the I 3d3/2 → εf shape resonances, respectively. The absorption spectrum calculated using time-dependent density functional theory, within the Tamm-Dancoff approximation, has allowed assignments to be proposed for the valence and Rydberg states. The Stieltjes imaging technique has been used to simulate the absorption spectrum above the ionization threshold and indicates that transitions into the f(l = 3) continuum channel dominate. This conclusion has been corroborated by a Continuum Multiple Scattering-Xα (CMS-Xα) calculation. The asymmetric broadening of the photoelectron bands associated with the I 3d orbital, due to post collision interaction, is taken into account in our experimental analysis. Experimentally derived photoelectron anisotropy parameters for the I 3d orbital are in good agreement with the theoretical predictions obtained with the CMS-Xα approach. The I 3d shake-up/shake-off photoelectron spectrum has been recorded, and assignments have been proposed for several of the satellites. The M4N45N45 and M5N45N45 Auger electron yields have been measured, and that for the M5N45N45 decay exhibits a maximum due to interchannel coupling between the 3d5/2 and 3d3/2 continua. The photoelectron band associated with the I 4p orbital has an unusual appearance. Based upon previous theoretical work for the analogous Xe 4p orbital, it appears that the initial I 4p-1 hole state decays rapidly through Coster-Kronig and super-Coster-Kronig transitions. This leads to a redistribution of the spectral intensity associated with the I 4p orbital and results in a photoelectron spectrum containing a single structured band together with an extended continuum. Another continuum is observed on the high binding energy side of the peak due to the 4s orbital, and we assign this to super-Coster-Kronig transitions into the 4p-14d-1 continuum.

Auger electron angular distributions following excitation or ionization of the I 3d level in methyl iodide.

Auger electron spectra following excitation or ionization of the I 3d level in CH3I have been recorded with horizontally or vertically plane polarized synchrotron radiation. These spectra have enabled the Auger electron angular distributions, as characterized by the ß parameter, to be determined. The I 3d photoionization partial cross section of CH3I has been calculated with the continuum multiple scattering approach, and the results show that in the photon energy range over which Auger spectra were measured, the I 3d cross section exhibits an atomic-like behavior and is dominated by transitions into the εf continuum channel. In this limit, the theoretical value of the alignment parameter (A20) characterizing the core ionized state in an atom becomes constant, independent of photon energy. This theoretical value has been used to obtain the Auger electron intrinsic anisotropy parameters (α2) from the ß parameters extracted from our normal (non-resonant) molecular Auger spectra. The resulting anisotropy parameters for the M45N45N45 transitions in CH3I have been compared to those calculated for the corresponding transitions in xenon, and the experimental and theoretical results are in good agreement. Anisotropy parameters have also been measured for the M45N1N45, M45N23N45, and M45N45O23 transitions. For the M45N1N45 and M45N23N45 Auger decays in CH3I, the experimentally derived angular distributions do not exhibit the strong dependence on the final ionic state that is predicted for these transitions in xenon. Resonantly excited Auger spectra have been recorded at 620.4 and 632.0 eV, coinciding with the I 3d5/2 → σ* and 3d3/2 → σ* transitions, respectively. The resulting Auger electron angular distributions for the M4N45N45 and M5N45N45 decays were found to exhibit a higher anisotropy than those for the normal process. This is due to the larger photo-induced alignment in the neutral core excited state. For a particular Auger transition, the Auger electron kinetic energy measured in the resonantly excited spectrum is higher than that in the normal spectrum. This shift, due to the screening provided by the electron excited into the σ* orbital, has been rationalized by calculating orbital ionization energies of I 3d excited and I 3d ionized states in CH3I.

Reconstruction of the time-dependent electronic wave packet arising from molecular autoionization.

Autoionizing resonances are paradigmatic examples of two-path wave interferences between direct photoionization, which takes a few attoseconds, and ionization via quasi-bound states, which takes much longer. Time-resolving the evolution of these interferences has been a long-standing goal, achieved recently in the helium atom owing to progress in attosecond technologies. However, already for the hydrogen molecule, similar time imaging has remained beyond reach due to the complex interplay between fast nuclear and electronic motions. We show how vibrationally resolved photoelectron spectra of H2 allow one to reconstruct the associated subfemtosecond autoionization dynamics by using the ultrafast nuclear dynamics as an internal clock, thus forgoing ultrashort pulses. Our procedure should be general for autoionization dynamics in molecules containing light nuclei, which are ubiquitous in chemistry and biology.

The LAMP instrument at the Linac Coherent Light Source free-electron laser.

The Laser Applications in Materials Processing (LAMP) instrument is a new end-station for soft X-ray imaging, high-field physics, and ultrafast X-ray science experiments that is available to users at the Linac Coherent Light Source (LCLS) free-electron laser. While the instrument resides in the Atomic, Molecular and Optical science hutch, its components can be used at any LCLS beamline. The end-station has a modular design that provides high flexibility in order to meet user-defined experimental requirements and specifications. The ultra-high-vacuum environment supports different sample delivery systems, including pulsed and continuous atomic, molecular, and cluster jets; liquid and aerosols jets; and effusive metal vapor beams. It also houses movable, large-format, high-speed pnCCD X-ray detectors for detecting scattered and fluorescent photons. Multiple charged-particle spectrometer options are compatible with the LAMP chamber, including a double-sided spectrometer for simultaneous and even coincident measurements of electrons, ions, and photons produced by the interaction of the high-intensity X-ray beam with the various samples. Here we describe the design and capabilities of the spectrometers along with some general aspects of the LAMP chamber and show some results from the initial instrument commissioning.

Open data set of live cyanobacterial cells imaged using an X-ray laser.

Structural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes with an ultra-short and extremely bright coherent X-ray pulse. Diffraction-before-destruction experiments provide high-resolution data from cells that are alive when the femtosecond X-ray pulse traverses the sample. This paper presents two data sets from micron-sized cyanobacteria obtained at the Linac Coherent Light Source, containing a total of 199,000 diffraction patterns. Utilizing this type of diffraction data will require the development of new analysis methods and algorithms for studying structure and structural variability in large populations of cells and to create abstract models. Such studies will allow us to understand living cells and populations of cells in new ways. New X-ray lasers, like the European XFEL, will produce billions of pulses per day, and could open new areas in structural sciences.

Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser.

Free-electron lasers (FEL) hold the potential to revolutionize structural biology by producing X-ray pules short enough to outrun radiation damage, thus allowing imaging of biological samples without the limitation from radiation damage. Thus, a major part of the scientific case for the first FELs was three-dimensional (3D) reconstruction of non-crystalline biological objects. In a recent publication we demonstrated the first 3D reconstruction of a biological object from an X-ray FEL using this technique. The sample was the giant Mimivirus, which is one of the largest known viruses with a diameter of 450 nm. Here we present the dataset used for this successful reconstruction. Data-analysis methods for single-particle imaging at FELs are undergoing heavy development but data collection relies on very limited time available through a highly competitive proposal process. This dataset provides experimental data to the entire community and could boost algorithm development and provide a benchmark dataset for new algorithms.

A data set from flash X-ray imaging of carboxysomes.

Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth's carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere.

Two mirror X-ray pulse split and delay instrument for femtosecond time resolved investigations at the LCLS free electron laser facility.

We built a two-mirror based X-ray split and delay (XRSD) device for soft X-rays at the Linac Coherent Light Source free electron laser facility. The instrument is based on an edge-polished mirror design covering an energy range of 250 eV-1800 eV and producing a delay between the two split pulses variable up to 400 femtoseconds with a sub-100 attosecond resolution. We present experimental and simulation results regarding molecular dissociation dynamics in CH3I and CO probed by the XRSD device. We observed ion kinetic energy and branching ratio dependence on the delay times which were reliably produced by the XRSD instrument.