Ultrafast dynamics of fluorene initiated by highly intense laser fields.

We present an investigation of the ultrafast dynamics of the polycyclic aromatic hydrocarbon fluorene initiated by an intense femtosecond near-infrared laser pulse (810 nm) and probed by a weak visible pulse (405 nm). Using a multichannel detection scheme (mass spectra, electron and ion velocity-map imaging), we provide a full disentanglement of the complex dynamics of the vibronically excited parent molecule, its excited ionic states, and fragments. We observed various channels resulting from the strong-field ionization regime. In particular, we observed the formation of the unstable tetracation of fluorene, above-threshold ionization features in the photoelectron spectra, and evidence of ubiquitous secondary fragmentation. We produced a global fit of all observed time-dependent photoelectron and photoion channels. This global fit includes four parent ions extracted from the mass spectra, 15 kinetic-energy-resolved ionic fragments extracted from ion velocity map imaging, and five photoelectron channels obtained from electron velocity map imaging. The fit allowed for the extraction of 60 lifetimes of various metastable photoinduced intermediates.

Resolving Nonequilibrium Shape Variations among Millions of Gold Nanoparticles.

Nanoparticles, exhibiting functionally relevant structural heterogeneity, are at the forefront of cutting-edge research. Now, high-throughput single-particle imaging (SPI) with X-ray free-electron lasers (XFELs) creates opportunities for recovering the shape distributions of millions of particles that exhibit functionally relevant structural heterogeneity. To realize this potential, three challenges have to be overcome: (1) simultaneous parametrization of structural variability in real and reciprocal spaces; (2) efficiently inferring the latent parameters of each SPI measurement; (3) scaling up comparisons between 105 structural models and 106 XFEL-SPI measurements. Here, we describe how we overcame these three challenges to resolve the nonequilibrium shape distributions within millions of gold nanoparticles imaged at the European XFEL. These shape distributions allowed us to quantify the degree of asymmetry in these particles, discover a relatively stable "shape envelope" among nanoparticles, discern finite-size effects related to shape-controlling surfactants, and extrapolate nanoparticles' shapes to their idealized thermodynamic limit. Ultimately, these demonstrations show that XFEL SPI can help transform nanoparticle shape characterization from anecdotally interesting to statistically meaningful.

Water is a radiation protection agent for ionised pyrrole.

Radiation-induced damage of biological matter is an ubiquitous problem in nature. The influence of the hydration environment is widely discussed, but its exact role remains elusive. Utilising well defined solvated-molecule aggregates, we experimentally observed a hydrogen-bonded water molecule acting as a radiation protection agent for ionised pyrrole, a prototypical aromatic biomolecule. Pure samples of pyrrole and pyrrole(H2O) were outer-valence ionised and the subsequent damage and relaxation processes were studied. Bare pyrrole ions fragmented through the breaking of C-C or N-C covalent bonds. However, for pyrrole(H2O)+, we observed a strong protection of the pyrrole ring through the dissociative release of neutral water or by transferring an electron or proton across the hydrogen bond. Overall, a single water molecule strongly reduces the fragmentation probability and thus the persistent radiation damage of singly-ionised pyrrole.

Reaction Pathways of Water Dimer Following Single Ionization.

Water dimer (H2O)2─a vital component of the earth's atmosphere─is an important prototypical hydrogen-bonded system. It provides direct insights into fundamental chemical and biochemical processes, e.g., proton transfer and ionic supramolecular dynamics, occurring in astro- and atmospheric chemistry. Exploiting a purified molecular beam of water dimer and multimass ion imaging, we report the simultaneous detection of all generated ion products of (H2O)2+ fragmentation following single ionization. Detailed information about ion yields and reaction energetics of 13 ion-radical pathways, 6 of which are new, of (H2O)2+ are presented, including strong 18O-isotope effects.

Observation of a single protein by ultrafast X-ray diffraction.

The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory, the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier, and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes. This was first demonstrated on biological samples a decade ago on the giant mimivirus. Since then, a large collaboration has been pushing the limit of the smallest sample that can be imaged. The ability to capture snapshots on the timescale of atomic vibrations, while keeping the sample at room temperature, may allow probing the entire conformational phase space of macromolecules. Here we show the first observation of an X-ray diffraction pattern from a single protein, that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays, and demonstrate that the concept of diffraction before destruction extends to single proteins. From the pattern, it is possible to determine the approximate orientation of the protein. Our experiment demonstrates the feasibility of ultrafast imaging of single proteins, opening the way to single-molecule time-resolved studies on the femtosecond timescale.

Unraveling the ultrafast dynamics of thermal-energy chemical reactions.

In this perspective, we discuss how one can initiate, image, and disentangle the ultrafast elementary steps of thermal-energy chemical dynamics, building upon advances in technology and scientific insight. We propose that combinations of ultrashort mid-infrared laser pulses, controlled molecular species in the gas phase, and forefront imaging techniques allow to unravel the elementary steps of general-chemistry reaction processes in real time. We detail, for prototypical first reaction systems, experimental methods enabling these investigations, how to sufficiently prepare and promote gas-phase samples to thermal-energy reactive states with contemporary ultrashort mid-infrared laser systems, and how to image the initiated ultrafast chemical dynamics. The results of such experiments will clearly further our understanding of general-chemistry reaction dynamics.

Specific versus Nonspecific Solvent Interactions of a Biomolecule in Water.

Solvent interactions, particularly hydration, are vital in chemical and biochemical systems. Model systems reveal microscopic details of such interactions. We uncover a specific hydrogen-bonding motif of the biomolecular building block indole (C8H7N), tryptophan's chromophore, in water: a strong localized N-H···OH2 hydrogen bond, alongside unstructured solvent interactions. This insight is revealed from a combined experimental and theoretical analysis of the electronic structure of indole in aqueous solution. We recorded the complete X-ray photoemission and Auger spectrum of aqueous-phase indole, quantitatively explaining all peaks through ab initio modeling. The efficient and accurate technique for modeling valence and core photoemission spectra involves the maximum-overlap method and the nonequilibrium polarizable-continuum model. A two-hole electron-population analysis quantitatively describes the Auger spectra. Core-electron binding energies for nitrogen and carbon highlight the specific interaction with a hydrogen-bonded water molecule at the N-H group and otherwise nonspecific solvent interactions.

Time-Resolved Single-Particle X-ray Scattering Reveals Electron-Density Gradients As Coherent Plasmonic-Nanoparticle-Oscillation Source.

Dynamics of optically excited plasmonic nanoparticles are presently understood as a series of scattering events involving the initiation of nanoparticle breathing oscillations. According to established models, these are caused by statistical heat transfer from thermalized electrons to the lattice. An additional contribution by hot-electron pressure accounts for phase mismatches between theory and experimental observations. However, direct experimental studies resolving the breathing-oscillation excitation are still missing. We used optical transient-absorption spectroscopy and time-resolved single-particle X-ray diffractive imaging to access the electron system and lattice. The time-resolved single-particle imaging data provided structural information directly on the onset of the breathing oscillation and confirmed the need for an additional excitation mechanism for thermal expansion. We developed a new model that reproduces all of our experimental observations. We identified optically induced electron density gradients as the initial driving source.

Conformational and state-specific effects in reactions of 2,3-dibromobutadiene with Coulomb-crystallized calcium ions.

Recent advances in experimental methodology enabled studies of the quantum-state- and conformational dependence of chemical reactions under precisely controlled conditions in the gas phase. Here, we generated samples of selected gauche and s-trans 2,3-dibromobutadiene (DBB) by electrostatic deflection in a molecular beam and studied their reaction with Coulomb crystals of laser-cooled Ca+ ions in an ion trap. The rate coefficients for the total reaction were found to strongly depend on both the conformation of DBB and the electronic state of Ca+. In the (4p)2P1/2 and (3d)2D3/2 excited states of Ca+, the reaction is capture-limited and faster for the gauche conformer due to long-range ion-dipole interactions. In the (4s)2S1/2 ground state of Ca+, the reaction rate for s-trans DBB still conforms with the capture limit, while that for gauche DBB is strongly suppressed. The experimental observations were analysed with the help of adiabatic capture theory, ab initio calculations and reactive molecular dynamics simulations on a machine-learned full-dimensional potential energy surface of the system. The theory yields near-quantitative agreement for s-trans-DBB, but overestimates the reactivity of the gauche-conformer compared to the experiment. The present study points to the important role of molecular geometry even in strongly reactive exothermic systems and illustrates striking differences in the reactivity of individual conformers in gas-phase ion-molecule reactions.

Ultrafast light-induced dynamics in the microsolvated biomolecular indole chromophore with water.

Interactions between proteins and their solvent environment can be studied in a bottom-up approach using hydrogen-bonded chromophore-solvent clusters. The ultrafast dynamics following UV-light-induced electronic excitation of the chromophores, potential radiation damage, and their dependence on solvation are important open questions. The microsolvation effect is challenging to study due to the inherent mix of the produced gas-phase aggregates. We use the electrostatic deflector to spatially separate different molecular species in combination with pump-probe velocity-map-imaging experiments. We demonstrate that this powerful experimental approach reveals intimate details of the UV-induced dynamics in the near-UV-absorbing prototypical biomolecular indole-water system. We determine the time-dependent appearance of the different reaction products and disentangle the occurring ultrafast processes. This approach ensures that the reactants are well-known and that detailed characteristics of the specific reaction products are accessible - paving the way for the complete chemical-reactivity experiment.

The kinetic energy of PAH dication and trication dissociation determined by recoil-frame covariance map imaging.

We investigated the dissociation of dications and trications of three polycyclic aromatic hydrocarbons (PAHs), fluorene, phenanthrene, and pyrene. PAHs are a family of molecules ubiquitous in space and involved in much of the chemistry of the interstellar medium. In our experiments, ions are formed by interaction with 30.3 nm extreme ultraviolet (XUV) photons, and their velocity map images are recorded using a PImMS2 multi-mass imaging sensor. Application of recoil-frame covariance analysis allows the total kinetic energy release (TKER) associated with multiple fragmentation channels to be determined to high precision, ranging 1.94-2.60 eV and 2.95-5.29 eV for the dications and trications, respectively. Experimental measurements are supported by Born-Oppenheimer molecular dynamics (BOMD) simulations.

The nuclear-spin-forbidden rovibrational transitions of water from first principles.

The water molecule occurs in two nuclear-spin isomers that differ by the value of the total nuclear spin of the hydrogen atoms, i.e., I = 0 for para-H2O and I = 1 for ortho-H2O. Spectroscopic transitions between rovibrational states of ortho and para water are extremely weak due to the tiny hyperfine nuclear-spin-rotation interaction of only ∼30 kHz and, so far, have not been observed. We report the first comprehensive theoretical investigation of the hyperfine effects and ortho-para transitions in H2 16O due to nuclear-spin-rotation and spin-spin interactions. We also present the details of our newly developed general variational approach to the simulation of hyperfine effects in polyatomic molecules. Our results for water suggest that the strongest ortho-para transitions with room-temperature intensities on the order of 10-31 cm/molecule are about an order of magnitude larger than previously predicted values and should be detectable in the mid-infrared ν2 and near-infrared 2ν1 + ν2 and ν1 + ν2 + ν3 bands by current spectroscopy experiments.

Unsupervised learning approaches to characterizing heterogeneous samples using X-ray single-particle imaging.

One of the outstanding analytical problems in X-ray single-particle imaging (SPI) is the classification of structural heterogeneity, which is especially difficult given the low signal-to-noise ratios of individual patterns and the fact that even identical objects can yield patterns that vary greatly when orientation is taken into consideration. Proposed here are two methods which explicitly account for this orientation-induced variation and can robustly determine the structural landscape of a sample ensemble. The first, termed common-line principal component analysis (PCA), provides a rough classification which is essentially parameter free and can be run automatically on any SPI dataset. The second method, utilizing variation auto-encoders (VAEs), can generate 3D structures of the objects at any point in the structural landscape. Both these methods are implemented in combination with the noise-tolerant expand-maximize-compress (EMC) algorithm and its utility is demonstrated by applying it to an experimental dataset from gold nanoparticles with only a few thousand photons per pattern. Both discrete structural classes and continuous deformations are recovered. These developments diverge from previous approaches of extracting reproducible subsets of patterns from a dataset and open up the possibility of moving beyond the study of homogeneous sample sets to addressing open questions on topics such as nanocrystal growth and dynamics, as well as phase transitions which have not been externally triggered.

Picosecond pulse-shaping for strong three-dimensional field-free alignment of generic asymmetric-top molecules.

Fixing molecules in space is a crucial step for the imaging of molecular structure and dynamics. Here, we demonstrate three-dimensional (3D) field-free alignment of the prototypical asymmetric top molecule indole using elliptically polarized, shaped, off-resonant laser pulses. A truncated laser pulse is produced using a combination of extreme linear chirping and controlled phase and amplitude shaping using a spatial-light-modulator (SLM) based pulse shaper of a broadband laser pulse. The angular confinement is detected through velocity-map imaging of H+ and C2+ fragments resulting from strong-field ionization and Coulomb explosion of the aligned molecules by intense femtosecond laser pulses. The achieved three-dimensional alignment is characterized by comparing the result of ion-velocity-map measurements for different alignment directions and for different times during and after the alignment laser pulse to accurate computational results. The achieved strong three-dimensional field-free alignment of [Formula: see text] demonstrates the feasibility of both, strong three-dimensional alignment of generic complex molecules and its quantitative characterization.

Optimizing the geometry of aerodynamic lens injectors for single-particle coherent diffractive imaging of gold nanoparticles.

Single-particle X-ray diffractive imaging (SPI) of small (bio-)nanoparticles (NPs) requires optimized injectors to collect sufficient diffraction patterns to allow for the reconstruction of the NP structure with high resolution. Typically, aerodynamic lens-stack injectors are used for NP injection. However, current injectors were developed for larger NPs (>100 nm), and their ability to generate high-density NP beams suffers with decreasing NP size. Here, an aerodynamic lens-stack injector with variable geometry and a geometry-optimization procedure are presented. The optimization for 50 nm gold-NP (AuNP) injection using a numerical-simulation infrastructure capable of calculating the carrier-gas flow and the particle trajectories through the injector is also introduced. The simulations were experimentally validated using spherical AuNPs and sucrose NPs. In addition, the optimized injector was compared with the standard-installation 'Uppsala injector' for AuNPs. Results for these heavy particles showed a shift in the particle-beam focus position rather than a change in beam size, which results in a lower gas background for the optimized injector. Optimized aerodynamic lens-stack injectors will allow one to increase NP beam density, reduce the gas background, discover the limits of current injectors and contribute to structure determination of small NPs using SPI.

Active learning of potential-energy surfaces of weakly bound complexes with regression-tree ensembles.

Several pool-based active learning (AL) algorithms were employed to model potential-energy surfaces (PESs) with a minimum number of electronic structure calculations. Theoretical and empirical results suggest that superior strategies can be obtained by sampling molecular structures corresponding to large uncertainties in their predictions while at the same time not deviating much from the true distribution of the data. To model PESs in an AL framework, we propose to use a regression version of stochastic query by forest, a hybrid method that samples points corresponding to large uncertainties while avoiding collecting too many points from sparse regions of space. The algorithm is implemented with decision trees that come with relatively small computational costs. We empirically show that this algorithm requires around half the data to converge to the same accuracy in comparison to the uncertainty-based query-by-committee algorithm. Moreover, the algorithm is fully automatic and does not require any prior knowledge of the PES. Simulations on a 6D PES of pyrrole(H2O) show that <15 000 configurations are enough to build a PES with a generalization error of 16 cm-1, whereas the final model with around 50 000 configurations has a generalization error of 11 cm-1.

Conformer-specific polar cycloaddition of dibromobutadiene with trapped propene ions.

Diels-Alder cycloadditions are efficient routes for the synthesis of cyclic organic compounds. There has been a long-standing discussion whether these reactions proceed via stepwise or concerted mechanisms. Here, we adopt an experimental approach to explore the mechanism of the model polar cycloaddition of 2,3-dibromo-1,3-butadiene with propene ions by probing its conformational specificities in the entrance channel under single-collision conditions in the gas phase. Combining a conformationally controlled molecular beam with trapped ions, we find that both conformers of the diene, gauche and s-trans, are reactive with capture-limited reaction rates. Aided by quantum-chemical and quantum-capture calculations, this finding is rationalised by a simultaneous competition of concerted and stepwise reaction pathways, revealing an interesting mechanistic borderline case.

Electric quadrupole transitions in carbon dioxide.

Recent advances in high sensitivity spectroscopy have made it possible, in combination with accurate theoretical predictions, to observe, for the first time, very weak electric quadrupole transitions in a polar polyatomic molecule of water. Here, we present accurate theoretical predictions of the complete quadrupole rovibrational spectrum of a non-polar molecule CO2, important in atmospheric and astrophysical applications. Our predictions are validated by recent cavity enhanced absorption spectroscopy measurements and are used to assign few weak features in the recent ExoMars Atmospheric Chemistry Suite mid-infrared spectroscopic observations of the Martian atmosphere. Predicted quadrupole transitions appear in some of the mid-infrared CO2 and water vapor transparency regions, making them important for detection and characterization of the minor absorbers in water- and CO2-rich environments, such as those present in the atmospheres of Earth, Venus, and Mars.