Mapping the emergence of molecular vibrations mediating bond formation

Photo-induced structural dynamics of o-nitrophenol by ultrafast electron diffraction

The photo-induced dynamics of o-nitrophenol, particularly its photolysis, has garnered significant scientific interest as a potential source of nitrous acid in the atmosphere. Although the photolysis products and preceding photo-induced electronic structure dynamics have been investigated extensively, the nuclear dynamics accompanying the non-radiative relaxation of o-nitrophenol on the ultrafast timescale, which include an intramolecular proton transfer step, have not been experimentally resolved. Herein, we present a direct observation of the ultrafast nuclear motions mediating photo-relaxation using ultrafast electron diffraction. This work spatiotemporally resolves the loss of planarity which enables access to a conical intersection between the first excited state and the ground state after the proton transfer step, on the femtosecond timescale and with sub-Angstrom resolution. Our observations, supported by ab initio multiple spawning simulations, provide new insights into the proton transfer mediated relaxation mechanism in o-nitrophenol.

A comparative review of time-resolved x-ray and electron scattering to probe structural dynamics

The structure of molecules, particularly the dynamic changes in structure, plays an essential role in understanding physical and chemical phenomena. Time-resolved (TR) scattering techniques serve as crucial experimental tools for studying structural dynamics, offering direct sensitivity to molecular structures through scattering signals. Over the past decade, the advent of x-ray free-electron lasers (XFELs) and mega-electron-volt ultrafast electron diffraction (MeV-UED) facilities has ushered TR scattering experiments into a new era, garnering significant attention. In this review, we delve into the basic principles of TR scattering experiments, especially focusing on those that employ x-rays and electrons. We highlight the variations in experimental conditions when employing x-rays vs electrons and discuss their complementarity. Additionally, cutting-edge XFELs and MeV-UED facilities for TR x-ray and electron scattering experiments and the experiments performed at those facilities are reviewed. As new facilities are constructed and existing ones undergo upgrades, the landscape for TR x-ray and electron scattering experiments is poised for further expansion. Through this review, we aim to facilitate the effective utilization of these emerging opportunities, assisting researchers in delving deeper into the intricate dynamics of molecular structures.

Capturing the generation and structural transformations of molecular ions

Molecular ions are ubiquitous and play pivotal roles1-3 in many reactions, particularly in the context of atmospheric and interstellar chemistry4-6. However, their structures and conformational transitions7,8, particularly in the gas phase, are less explored than those of neutral molecules owing to experimental difficulties. A case in point is the halonium ions9-11, whose highly reactive nature and ring strain make them short-lived intermediates that are readily attacked even by weak nucleophiles and thus challenging to isolate or capture before they undergo further reaction. Here we show that mega-electronvolt ultrafast electron diffraction (MeV-UED)12-14, used in conjunction with resonance-enhanced multiphoton ionization, can monitor the formation of 1,3-dibromopropane (DBP) cations and their subsequent structural dynamics forming a halonium ion. We find that the DBP+ cation remains for a substantial duration of 3.6 ps in aptly named 'dark states' that are structurally indistinguishable from the DBP electronic ground state. The structural data, supported by surface-hopping simulations15 and ab initio calculations16, reveal that the cation subsequently decays to iso-DBP+, an unusual intermediate with a four-membered ring containing a loosely bound17,18 bromine atom, and eventually loses the bromine atom and forms a bromonium ion with a three-membered-ring structure19. We anticipate that the approach used here can also be applied to examine the structural dynamics of other molecular ions and thereby deepen our understanding of ion chemistry.

Cerium Photocatalyst in Action: Structural Dynamics in the Presence of Substrate Visualized via Time-Resolved X-ray Liquidography

[Ce(III)Cl6]3-, with its earth-abundant metal element, is a promising photocatalyst facilitating carbon-halogen bond activation. Still, the structure of the reaction intermediate has yet to be explored. Here, we applied time-resolved X-ray liquidography (TRXL), which allows for direct observation of the structural details of reaction intermediates, to investigate the photocatalytic reaction of [Ce(III)Cl6]3-. Structural analysis of the TRXL data revealed that the excited state of [Ce(III)Cl6]3- has Ce-Cl bonds that are shorter than those of the ground state and that the Ce-Cl bond further contracts upon oxidation. In addition, this study represents the first application of TRXL to both photocatalyst-only and photocatalyst-and-substrate samples, providing insights into the substrate's influence on the photocatalyst's reaction dynamics. This study demonstrates the capability of TRXL in elucidating the reaction dynamics of photocatalysts under various conditions and highlights the importance of experimental determination of the structures of reaction intermediates to advance our understanding of photocatalytic mechanisms.

Spectral-brightness optimization of an X-ray free-electron laser by machine-learning-based tuning

A machine-learning-based beam optimizer has been implemented to maximize the spectral brightness of the X-ray free-electron laser (XFEL) pulses of SACLA. A new high-resolution single-shot inline spectrometer capable of resolving features of the order of a few electronvolts was employed to measure and evaluate XFEL pulse spectra. Compared with a simple pulse-energy-based optimization, the spectral width was narrowed by half and the spectral brightness was improved by a factor of 1.7. The optimizer significantly contributes to efficient machine tuning and improvement of XFEL performance at SACLA.

Exploring fingerprints of ultrafast structural dynamics in molecular solutions with an X-ray laser

We apply ultrashort X-ray laser pulses to track optically excited structural dynamics of [Ir2(dimen)4]2+ molecules in solution. In our exploratory study we determine angular correlations in the scattered X-rays, which comprise a complex fingerprint of the ultrafast dynamics. Model-assisted analysis of the experimental correlation data allows us to elucidate various aspects of the photoinduced changes in the excited molecular ensembles. We unambiguously identify that in our experiment the photoinduced transition dipole moments in [Ir2(dimen)4]2+ molecules are oriented perpendicular to the Ir-Ir bond. The analysis also shows that the ground state conformer of [Ir2(dimen)4]2+ with a larger Ir-Ir distance is mostly responsible for the formation of the excited state. We also reveal that the ensemble of solute molecules can be characterized with a substantial structural heterogeneity due to solvent influence. The proposed X-ray correlation approach offers an alternative path for studies of ultrafast structural dynamics of molecular ensembles in the liquid and gas phases.

Mapping the photochemistry of cyclopentadiene: from theory to ultrafast X-ray scattering

The photoinduced ring-conversion reaction when cyclopentadiene (CP) is excited at 5.10 eV is simulated using surface-hopping semiclassical trajectories with XMS(3)-CASPT2(4,4)/cc-pVDZ electronic structure theory. In addition, PBE0/def2-SV(P) is employed for ground state propagation of the trajectories. The dynamics is propagated for 10 ps, mapping both the nonadiabatic short-time dynamics (<300 fs) and the increasingly statistical dynamics on the electronic ground state. The short-time dynamics yields a mixture of hot CP and bicyclo[2.1.0]pentene (BP), with the two products reached via different regions of the same conical intersection seam. On the ground state, we observe slow conversion from BP to CP which is modelled by RRKM theory with a transition state determined using PBE0/def2-TZVP. The CP products are furthermore associated with ground state hydrogen shifts and some H-atom dissociation. Finally, the prospects for detailed experimental mapping using novel ultrafast X-ray scattering experiments are discussed and observables for such experiments are predicted. In particular, we assess the possibility of retrieving electronic states and their populations alongside the structural dynamics.

Projection to extract the perpendicular component (PEPC) method for extracting kinetics from time-resolved data

Time-resolved x-ray liquidography (TRXL) is a potent method for investigating the structural dynamics of chemical and biological reactions in the liquid phase. It has enabled the extraction of detailed structural aspects of various dynamic processes, the molecular structures of intermediates, and kinetics of reactions across a wide range of systems, from small molecules to proteins and nanoparticles. Proper data analysis is key to extracting the information of the kinetics and structural dynamics of the studied system encrypted in the TRXL data. In typical TRXL data, the signals from solute scattering, solvent scattering, and solute-solvent cross scattering are mixed in the q-space, and the solute kinetics and solvent hydrodynamics are mixed in the time domain, thus complicating the data analysis. Various methods developed so far generally require prior knowledge of the molecular structures of candidate species involved in the reaction. Because such information is often unavailable, a typical data analysis often involves tedious trial and error. To remedy this situation, we have developed a method named projection to extract the perpendicular component (PEPC), capable of removing the contribution of solvent kinetics from TRXL data. The resulting data then contain only the solute kinetics, and, thus, the solute kinetics can be easily determined. Once the solute kinetics is determined, the subsequent data analysis to extract the structural information can be performed with drastically improved convenience. The application of the PEPC method is demonstrated with TRXL data from the photochemistry of two molecular systems: [Au(CN)₂^-]₃ in water and CHI₃ in cyclohexane.

Ultrafast X-Ray Probes of Elementary Molecular Events

Elementary events that determine photochemical outcomes and molecular functionalities happen on the femtosecond and subfemtosecond timescales. Among the most ubiquitous events are the nonadiabatic dynamics taking place at conical intersections. These facilitate ultrafast, nonradiative transitions between electronic states in molecules that can outcompete slower relaxation mechanisms such as fluorescence. The rise of ultrafast X-ray sources, which provide intense light pulses with ever-shorter durations and larger observation bandwidths, has fundamentally revolutionized our spectroscopic capabilities to detect conical intersections. Recent theoretical studies have demonstrated an entirely new signature emerging once a molecule traverses a conical intersection, giving detailed insights into the coupled nuclear and electronic motions that underlie, facilitate, and ultimately determine the ultrafast molecular dynamics. Following a summary of current sources and experiments, we survey these techniques and provide a unified overview of their capabilities. We discuss their potential to dramatically increase our understanding of ultrafast photochemistry.

Extracting Kinetics and Thermodynamics of Molecules without Heavy Atoms via Time-Resolved Solvent Scattering Signals

Time-resolved X-ray liquidography (TRXL) has emerged as a powerful technique for studying the structural dynamics of small molecules and macromolecules in liquid solutions. However, TRXL has limited sensitivity for small molecules containing light atoms only, whose signal has lower contrast compared with the signal from solvent molecules. Here, we present an alternative approach to bypass this limitation by detecting the change in solvent temperature resulting from a photoinduced reaction. Specifically, we analyzed the heat dynamics of TRXL data obtained from p-hydroxyphenacyl diethyl phosphate (HPDP). This analysis enabled us to experimentally determine the number of intermediates and their respective enthalpy changes, which can be compared to theoretical enthalpies to identify the intermediates. This work demonstrates that TRXL can be used to uncover the kinetics and reaction pathways for small molecules without heavy atoms even if the scattering signal from the solute molecules is buried under the strong solvent scattering signal.

Atomic-scale observation of solvent reorganization influencing photoinduced structural dynamics in a copper complex photosensitizer

Photochemical reactions in solution are governed by a complex interplay between transient intramolecular electronic and nuclear structural changes and accompanying solvent rearrangements. State-of-the-art time-resolved X-ray solution scattering has emerged in the last decade as a powerful technique to observe solute and solvent motions in real time. However, disentangling solute and solvent dynamics and how they mutually influence each other remains challenging. Here, we simultaneously measure femtosecond X-ray emission and scattering to track both the intramolecular and solvation structural dynamics following photoexcitation of a solvated copper photosensitizer. Quantitative analysis assisted by molecular dynamics simulations reveals a two-step ligand flattening strongly coupled to the solvent reorganization, which conventional optical methods could not discern. First, a ballistic flattening triggers coherent motions of surrounding acetonitrile molecules. In turn, the approach of acetonitrile molecules to the copper atom mediates the decay of intramolecular coherent vibrations and induces a further ligand flattening. These direct structural insights reveal that photoinduced solute and solvent motions can be intimately intertwined, explaining how the key initial steps of light harvesting are affected by the solvent on the atomic time and length scale. Ultimately, this work takes a step forward in understanding the microscopic mechanisms of the bidirectional influence between transient solvent reorganization and photoinduced solute structural dynamics.

Spectroscopic mapping of the gold complex oligomers (dimer, trimer, tetramer, and pentamer) by excited-state coherent nuclear wavepacket motion in aqueous solutions

We investigate the excited-state dynamics of the [Au(CN)₂^-] oligomers following photo-initiated intermolecular Au-Au bond formation by carrying out femtosecond time-resolved absorption and emission measurements at various concentrations (0.080-0.6 mol dm^-3) with different photoexcitation wavelengths (290-340 nm). The temporal profiles of the time-resolved absorption signals exhibit clear oscillations arising from the Au-Au stretch coherent wavepacket motion of the excited-state oligomers, which is initiated with the photo-induced Au-Au bond formation. The frequency of the observed oscillation is changed with the change of the concentration, excitation wavelength, and wavelength of the excited-state absorption monitored, reflecting the change in the size of the oligomers detected. Fourier transforms (FTs) of the oscillations provide 2D plots of the FT amplitude against the oscillation frequency versus the detected wavelengths. Because the FT amplitude exhibits a node at the peak wavelength of the absorption of the species that gives rise to the oscillation, the 2D plots enabled us to determine the peak wavelength of the excited-state absorption of the dimer, trimer, tetramer, and pentamer. We also performed femtosecond time-resolved absorption measurements for the 0.3 mol dm^-3 solution with 260 nm photoexcitation, which is the condition employed in previous time-resolved X-ray studies (e.g., K. H. Kim et al. Nature, 2015, 518 (7539), 385-389). It was found that various excited-state oligomers, including the dimer, were simultaneously generated under this condition, although the analysis of the previous time-resolved X-ray studies was made by assuming that only the excited-state trimer was generated. The obtained results show that the excited-state dynamics of the trimer claimed based on the time-resolved X-ray data is questionable and that re-analysis and re-examining of its data are necessary.

From a one-mode to a multi-mode understanding of conical intersection mediated ultrafast organic photochemical reactions

This review discusses how ultrafast organic photochemical reactions are controlled by conical intersections, highlighting that decay to the ground-state at multiple points of the intersection space results in their multi-mode character.

Expected resolution limits of x-ray free-electron laser single-particle imaging for realistic source and detector properties

The unprecedented intensity of x-ray free-electron laser sources has enabled single-particle x-ray diffraction imaging (SPI) of various biological specimens in both two-dimensional projection and three dimensions (3D). The potential of studying protein dynamics in their native conditions, without crystallization or chemical staining, has encouraged researchers to aim for increasingly higher resolutions with this technique. The currently achievable resolution of SPI is limited to the sub-10 nanometer range, mainly due to background effects, such as instrumental noise and parasitic scattering from the carrier gas used for sample delivery. Recent theoretical studies have quantified the effects of x-ray pulse parameters, as well as the required number of diffraction patterns to achieve a certain resolution, in a 3D reconstruction, although the effects of detector noise and the random particle orientation in each diffraction snapshot were not taken into account. In this work, we show these shortcomings and address limitations on achievable image resolution imposed by the adaptive gain integrating pixel detector noise.

Coherent Vibrational Spectrum via Time-Resolved Fluorescence for Molecular Dynamics and Identification of Emitting Species-Application to Excited-State Intramolecular Proton Transfer

Time-resolved fluorescence (TF) with high-enough resolution enables recording of a coherent vibrational spectrum (CVS). Because a CVS attained via TF (CVSF) is descended from the frequency modulation of the fluorescence spectrum, it gives the vibrational spectrum of the emitting state. Therefore, CVSF can be a powerful tool for the identification of an emitting state along with the investigation of molecular dynamics in excited states. Herein, we report CVSF of a Schiff base salicylaldehyde azine (SAA) that has two possible excited-state intramolecular proton transfer (ESIPT) sites. The ESIPT time of SAA in dichloromethane is determined to be 22 fs. Quantitative agreement between the experimental CVSF and calculated CVSF of the mono-keto isomer demonstrates that ESIPT indeed occurs in SAA only on one side. More importantly, we show that a CVSF can be utilized to identify an emitting species and its state with the help of quantum chemical calculations. Implications of the CVSF obtained by assuming impulsive excitation of vibrations are discussed in terms of the molecular mechanism of ESIPT and the generation of nuclear wave packets in the product state.

Photoactivation of triosmium dodecacarbonyl at 400 nm probed with time-resolved X-ray liquidography

The photoactivation mechanism of Os₃(CO)₁₂ at 400 nm is examined with time-resolved X-ray liquidography. The data reveal two pathways: the vibrational relaxation following an internal conversion to the electronic ground state and the ligand dissociation to form Os₃(CO)₁₁ with a ligand vacancy at the axial position.

Light-induced protein structural dynamics in bacteriophytochrome revealed by time-resolved x-ray solution scattering

Bacteriophytochromes (BphPs) are photoreceptors that regulate a wide range of biological mechanisms via red light-absorbing (Pr)-to-far-red light-absorbing (Pfr) reversible photoconversion. The structural dynamics underlying Pfr-to-Pr photoconversion in a liquid solution phase are not well understood. We used time-resolved x-ray solution scattering (TRXSS) to capture light-induced structural transitions in the bathy BphP photosensory module of Pseudomonas aeruginosa. Kinetic analysis of the TRXSS data identifies three distinct structural species, which are attributed to lumi-F, meta-F, and Pr, connected by time constants of 95 μs and 21 ms. Structural analysis based on molecular dynamics simulations shows that the light activation of PaBphP accompanies quaternary structural rearrangements from an "II"-framed close form of the Pfr state to an "O"-framed open form of the Pr state in terms of the helical backbones. This study provides mechanistic insights into how modular signaling proteins such as BphPs transmit structural signals over long distances and regulate their downstream biological responses.

Determining the charge distribution and the direction of bond cleavage with femtosecond anisotropic x-ray liquidography

Energy, structure, and charge are fundamental quantities characterizing a molecule. Whereas the energy flow and structure change in chemical reactions are experimentally characterized, determining the atomic charges of a molecule in solution has been elusive, even for a triatomic molecule such as triiodide ion, I3-. Moreover, it remains to be answered how the charge distribution is coupled to the molecular geometry; which I-I bond, if two I-I bonds are unequal, dissociates depending on the electronic state. Here, femtosecond anisotropic x-ray solution scattering allows us to provide the following answers in addition to the overall rich structural dynamics. The analysis unravels that the negative charge of I3- is highly localized on the terminal iodine atom forming the longer bond with the central iodine atom, and the shorter I-I bond dissociates in the excited state, whereas the longer one in the ground state. We anticipate that this work may open a new avenue for studying the atomic charge distribution of molecules in solution and taking advantage of orientational information in anisotropic scattering data for solution-phase structural dynamics.

Recent Progress of the PAL-XFEL

The X-ray free-electron laser of the Pohang Accelerator Laboratory (PAL-XFEL) was opened to users in 2017. Since then, significant progress has been made in PAL-XFEL operation and beamline experiments. This includes increasing the FEL pulse energy, increasing the FEL photon energy, generating self-seeding FEL, and trials of two-color operation. In the beamline, new instruments or endstations have been added or are being prepared. Overall, beamline operation has been stabilized since its initiation, which has enabled excellent scientific results through efficient user experiments. In this paper, we describe details of the recent progress of the PAL-XFEL.

Capturing Atom-Specific Electronic Structural Dynamics of Transition-Metal Complexes with Ultrafast Soft X-Ray Spectroscopy

The atomic specificity of X-ray spectroscopies provides a distinct perspective on molecular electronic structure. For 3 d metal coordination and organometallic complexes, the combination of metal- and ligand-specific X-ray spectroscopies directly interrogates metal–ligand covalency—the hybridization of metal and ligand electronic states. Resonant inelastic X-ray scattering (RIXS), the X-ray analog of resonance Raman scattering, provides access to all classes of valence excited states in transition-metal complexes, making it a particularly powerful means of characterizing the valence electronic structure of 3 d metal complexes. Recent advances in X-ray free-electron laser sources have enabled RIXS to be extended to the ultrafast time domain. We review RIXS studies of two archetypical photochemical processes: charge-transfer excitation in ferricyanide and ligand photodissociation in iron pentacarbonyl. These studies demonstrate femtosecond-resolution RIXS can directly characterize the time-evolving electronic structure, including the evolution of the metal–ligand covalency.

Expected final online publication date for the Annual Review of Physical Chemistry, Volume 73 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Reaction dynamics studied via femtosecond X-ray liquidography at X-ray free-electron lasers

X-ray free-electron lasers (XFELs) provide femtosecond X-ray pulses suitable for pump–probe time-resolved studies with a femtosecond time resolution. Since the advent of the first XFEL in 2009, recent years have witnessed a great number of applications with various pump–probe techniques at XFELs. Among these, time-resolved X-ray liquidography (TRXL) is a powerful method for visualizing structural dynamics in the liquid solution phase. Here, we classify various chemical and biological molecular systems studied via femtosecond TRXL (fs-TRXL) at XFELs, depending on the focus of the studied process, into (i) bond cleavage and formation, (ii) charge distribution and electron transfer, (iii) orientational dynamics, (iv) solvation dynamics, (v) coherent nuclear wavepacket dynamics, and (vi) protein structural dynamics, and provide a brief review on each category. We also lay out a plausible roadmap for future fs-TRXL studies for areas that have not been explored yet.

Femtosecond X-ray liquidography using X-ray free-electron lasers (XFELs) visualizes various aspects of reaction dynamics.

Exciton delocalization length in chlorosomes investigated by lineshape dynamics of two-dimensional electronic spectra

A chlorosome, a photosynthetic light-harvesting complex found in green sulfur bacteria, is an aggregate of self-assembled pigments and is optimized for efficient light harvesting and energy transfer under dim-light conditions. In this highly-disordered aggregate, the absorption and transfer of photoexcitation energy are governed by the degree of disorder. To describe the disorder, the number of molecules forming excitons, which is termed exciton delocalization length (EDL), is a relevant parameter because the EDL sensitively changes with the disorder of the constituent molecules. In this work, we determined the EDL in chlorosomes using two-dimensional electronic spectroscopy (2D-ES). Since spectral features correlated with EDL are spread out in the two-dimensional (2D) electronic spectra, we were able to determine the EDL accurately without the effects of homogeneous and inhomogeneous line broadening. In particular, by taking advantage of the multi-dimensionality and the time evolution of 2D spectra, we not only determined the excitation frequency dependence of EDL but also monitored the temporal change of EDL. We found that the EDL is ∼7 at 77 K and ∼6 at 298 K and increases with the excitation frequency, with the maximum located well above the maximum of the absorption spectrum of chlorosomes. The spectral profile of EDL changes rapidly within 100 fs and becomes flat over time due to dephasing of initial exciton coherence. From the coherent oscillations superimposed on the decay of EDL, it was learned that high-frequency phonons are more activated at 298 K than at 77 K.

Structural Dynamics of C2F4I2 in Cyclohexane Studied via Time-Resolved X-ray Liquidography

The halogen elimination of 1,2-diiodoethane (C2H4I2) and 1,2-diiodotetrafluoroethane (C2F4I2) serves as a model reaction for investigating the influence of fluorination on reaction dynamics and solute-solvent interactions in solution-phase reactions. While the kinetics and reaction pathways of the halogen elimination reaction of C2H4I2 were reported to vary substantially depending on the solvent, the solvent effects on the photodissociation of C2F4I2 remain to be explored, as its reaction dynamics have only been studied in methanol. Here, to investigate the solvent dependence, we conducted a time-resolved X-ray liquidography (TRXL) experiment on C2F4I2 in cyclohexane. The data revealed that (ⅰ) the solvent dependence of the photoreaction of C2F4I2 is not as strong as that observed for C2H4I2, and (ⅱ) the nongeminate recombination leading to the formation of I2 is slower in cyclohexane than in methanol. We also show that the molecular structures of the relevant species determined from the structural analysis of TRXL data provide an excellent benchmark for DFT calculations, especially for investigating the relevance of exchange-correlation functionals used for the structural optimization of haloalkanes. This study demonstrates that TRXL is a powerful technique to study solvent dependence in the solution phase.

Optical Kerr Effect of Liquid Acetonitrile Probed by Femtosecond Time-Resolved X-ray Liquidography

Optical Kerr effect (OKE) spectroscopy is a method that measures the time-dependent change of the birefringence induced by an optical laser pulse using another optical laser pulse and has been used often to study the ultrafast dynamics of molecular liquids. Here we demonstrate an alternative method, femtosecond time-resolved X-ray liquidography (fs-TRXL), where the microscopic structural motions related to the OKE response can be monitored using a different type of probe, i.e., X-ray solution scattering. By applying fs-TRXL to acetonitrile and a dye solution in acetonitrile, we demonstrate that different types of molecular motions around photoaligned molecules can be resolved selectively, even without any theoretical modeling, based on the anisotropy of two-dimensional scattering patterns and extra structural information contained in the q-space scattering data. Specifically, the dynamics of reorientational (libration and orientational diffusion) and translational (interaction-induced motion) motions are captured separately by anisotropic and isotropic scattering signals, respectively. Furthermore, the two different types of reorientational motions are distinguished from each other by their own characteristic scattering patterns and time scales. The measured time-resolved scattering signals are in excellent agreement with the simulated scattering signals based on a molecular dynamics simulation for plausible molecular configurations, providing the detailed structural description of the OKE response in liquid acetonitrile.

Reversible molecular motional switch based on circular photoactive protein oligomers exhibits unexpected photo-induced contraction

Molecular switches alterable between two stable states by environmental stimuli, such as light and temperature, offer the potential for controlling biological functions. Here, we report a circular photoswitchable protein complex made of multiple protein molecules that can rapidly and reversibly switch with significant conformational changes. The structural and photochromic properties of photoactive yellow protein (PYP) are harnessed to construct circular oligomer PYPs (coPYPs) of desired sizes. Considering the light-induced N-terminal protrusion of monomer PYP, we expected coPYPs would expand upon irradiation, but time-resolved X-ray scattering data reveal that the late intermediate has a pronounced light-induced contraction motion. This work not only provides an approach to engineering a novel protein-based molecular switch based on circular oligomers of well-known protein units but also demonstrates the importance of characterizing the structural dynamics of designed molecular switches.

Filming ultrafast roaming-mediated isomerization of bismuth triiodide in solution

Roaming reaction, defined as a reaction yielding products via reorientational motion in the long-range region (3 - 8 Å) of the potential, is a relatively recently proposed reaction pathway and is now regarded as a universal mechanism that can explain the unimolecular dissociation and isomerization of various molecules. The structural movements of the partially dissociated fragments originating from the frustrated bond fission at the onset of roaming, however, have been explored mostly via theoretical simulations and rarely observed experimentally. Here, we report an investigation of the structural dynamics during a roaming-mediated isomerization reaction of bismuth triiodide (BiI₃) in acetonitrile solution using femtosecond time-resolved x-ray liquidography. Structural analysis of the data visualizes the atomic movements during the roaming-mediated isomerization process including the opening of the Bi-I_b-I_c angle and the closing of I_a-Bi-I_b-I_c dihedral angle, each by ~40°, as well as the shortening of the I_b···I_c distance, following the frustrated bond fission.

Direct observation of ultrafast hydrogen bond strengthening in liquid water

Water is one of the most important, yet least understood, liquids in nature. Many anomalous properties of liquid water originate from its well-connected hydrogen bond network¹, including unusually efficient vibrational energy redistribution and relaxation². An accurate description of the ultrafast vibrational motion of water molecules is essential for understanding the nature of hydrogen bonds and many solution-phase chemical reactions. Most existing knowledge of vibrational relaxation in water is built upon ultrafast spectroscopy experiments^2-7. However, these experiments cannot directly resolve the motion of the atomic positions and require difficult translation of spectral dynamics into hydrogen bond dynamics. Here, we measure the ultrafast structural response to the excitation of the OH stretching vibration in liquid water with femtosecond temporal and atomic spatial resolution using liquid ultrafast electron scattering. We observed a transient hydrogen bond contraction of roughly 0.04 Å on a timescale of 80 femtoseconds, followed by a thermalization on a timescale of approximately 1 picosecond. Molecular dynamics simulations reveal the need to treat the distribution of the shared proton in the hydrogen bond quantum mechanically to capture the structural dynamics on femtosecond timescales. Our experiment and simulations unveil the intermolecular character of the water vibration preceding the relaxation of the OH stretch.

Revealing the Chemical Bonding in Adatom Arrays via Machine Learning of Hyperspectral Scanning Tunneling Spectroscopy Data

The adatom arrays on surfaces offer an ideal playground to explore the mechanisms of chemical bonding via changes in the local electronic tunneling spectra. While this information is readily available in hyperspectral scanning tunneling spectroscopy data, its analysis has been considerably impeded by a lack of suitable analytical tools. Here we develop a machine learning based workflow combining supervised feature identification in the spatial domain and unsupervised clustering in the energy domain to reveal the details of structure-dependent changes of the electronic structure in adatom arrays on the Co₃Sn₂S₂ cleaved surface. This approach, in combination with first-principles calculations, provides insight for using artificial neural networks to detect adatoms and classifies each based on their local neighborhood comprised of other adatoms. These structurally classified adatoms are further spectrally deconvolved. The unexpected inhomogeneity of electronic structures among adatoms in similar configurations is unveiled using this method, suggesting there is not a single atomic species of adatoms, but rather multiple types of adatoms on the Co₃Sn₂S₂ surface. This is further supported by a slight contrast difference in the images (or slight size variation) of the topography of the adatoms.

Laser-Driven Anharmonic Oscillator: Ground-State Dissociation of the Helium Hydride Molecular Ion by Midinfrared Pulses

The vibrational motion of molecules represents a fundamental example of an anharmonic oscillator. Using a prototype molecular system, HeH^{+}, we demonstrate that appropriate laser pulses make it possible to drive the nuclear motion in the anharmonic potential of the electronic ground state, increasing its energy above the potential barrier and facilitating dissociation by purely vibrational excitation. We find excellent agreement between the frequency-dependent response of the helium hydride molecular cation to both classical and quantum mechanical simulations, thus removing any ambiguities through electronic excitation. Our results provide access to the rich dynamics of anharmonic quantum oscillator systems and pave the way to state-selective control schemes in ground-state chemistry by the adequate choice of the laser parameters.

Ultrafast coherent motion and helix rearrangement of homodimeric hemoglobin visualized with femtosecond X-ray solution scattering

Ultrafast motion of molecules, particularly the coherent motion, has been intensively investigated as a key factor guiding the reaction pathways. Recently, X-ray free-electron lasers (XFELs) have been utilized to elucidate the ultrafast motion of molecules. However, the studies on proteins using XFELs have been typically limited to the crystalline phase, and proteins in solution have rarely been investigated. Here we applied femtosecond time-resolved X-ray solution scattering (fs-TRXSS) and a structure refinement method to visualize the ultrafast motion of a protein. We succeeded in revealing detailed ultrafast structural changes of homodimeric hemoglobin involving the coherent motion. In addition to the motion of the protein itself, the time-dependent change of electron density of the hydration shell was tracked. Besides, the analysis on the fs-TRXSS data of myoglobin allows for observing the effect of the oligomeric state on the ultrafast coherent motion.

Femtosecond time-resolved X-ray solution scattering (fs-TRXSS) measurements provide information on the structural dynamics of proteins in solution. Here, the authors present a structure refinement method for the analysis of fs-TRXSS data and use it to characterise the ultrafast structural changes of homodimeric haemoglobin.

Surface adhesion of viruses and bacteria: Defend only and/or vibrationally extinguish also?! A perspective

Coronaviruses COVID-19, SARS-CoV and NL63 use spikes in their corona to bind to angiotensin converting enzyme 2 (ACE2) sites on cytoskeletal membranes of host cells to deliver their viral payload. While groups such as disulfides in ACE2's zinc metallopeptidase, and also in COVID-19's spikes, facilitate such binding, it is worth exploring how similar complementary sites on materials such as polymers, metals, ceramics, fabrics, and biomaterials promote binding of viruses and bacteria and how they could be further engineered to prevent bioactivity, or to act as agents to collect viral payloads in filters or similar devices. In that vein, this article offers a perspective on novel tools and approaches for chemically and topologically modifying most utilitarian surfaces via defensive topological vibrational engineering to either prevent such adhesion or to enhance adhesion and elicit vibrational characteristics/'musical signatures' from the surfaces so that the structure of the binding sites of viruses and bacteria is permanently altered and/or their cellular machinery is permanently disabled by targeted chemical transformations.

Graphic abstract

Supplementary Information

The online version contains supplementary material available at 10.1557/s43580-021-00079-0.

Capturing photochemical and photophysical transformations in iron complexes with ultrafast X-ray spectroscopy and scattering

Light-driven chemical transformations provide a compelling approach to understanding chemical reactivity with the potential to use this understanding to advance solar energy and catalysis applications. Capturing the non-equilibrium trajectories of electronic excited states with precision, particularly for transition metal complexes, would provide a foundation for advancing both of these objectives. Of particular importance for 3d metal compounds is characterizing the population dynamics of charge-transfer (CT) and metal-centered (MC) electronic excited states and understanding how the inner coordination sphere structural dynamics mediate the interaction between these states. Recent advances in ultrafast X-ray laser science has enabled the electronic excited state dynamics in 3d metal complexes to be followed with unprecedented detail. This review will focus on simultaneous X-ray emission spectroscopy (XES) and X-ray solution scattering (XSS) studies of iron coordination and organometallic complexes. These simultaneous XES-XSS studies have provided detailed insight into the mechanism of light-induced spin crossover in iron coordination compounds, the interaction of CT and MC excited states in iron carbene photosensitizers, and the mechanism of Fe-S bond dissociation in cytochrome c.

Spiers Memorial Lecture: Introduction to ultrafast spectroscopy and imaging of photochemical reactions

A brief overview is presented on ultrafast spectroscopy and imaging of photochemical reactions by highlighting several experimental studies reported in the last five years. A particular focus is placed on new experiments performed using high-order harmonic generation, X-ray free electron lasers, and relativistic electron beams. Exploration of fundamental chemical reaction dynamics using these advanced experimental methodologies is in an early stage, and exciting new research opportunities await in this rapidly expanding and advancing research field. At the same time, there is no experimental methodology that provides all aspects of the electronic and structural dynamics in a single experiment, and investigations using different methodologies with various perspectives need to be considered in a comprehensive manner.

Ultrafast X-ray scattering offers a structural view of excited-state charge transfer

Intramolecular charge transfer and the associated changes in molecular structure in N,N'-dimethylpiperazine are tracked using femtosecond gas-phase X-ray scattering. The molecules are optically excited to the 3p state at 200 nm. Following rapid relaxation to the 3s state, distinct charge-localized and charge-delocalized species related by charge transfer are observed. The experiment determines the molecular structure of the two species, with the redistribution of electron density accounted for by a scattering correction factor. The initially dominant charge-localized state has a weakened carbon-carbon bond and reorients one methyl group compared with the ground state. Subsequent charge transfer to the charge-delocalized state elongates the carbon-carbon bond further, creating an extended 1.634 Å bond, and also reorients the second methyl group. At the same time, the bond lengths between the nitrogen and the ring-carbon atoms contract from an average of 1.505 to 1.465 Å. The experiment determines the overall charge transfer time constant for approaching the equilibrium between charge-localized and charge-delocalized species to 3.0 ps.

Femtosecond X-ray Liquidography Visualizes Wavepacket Trajectories in Multidimensional Nuclear Coordinates for a Bimolecular Reaction

ConspectusVibrational wavepacket motions on potential energy surfaces are one of the critical factors that determine the reaction dynamics of photoinduced reactions. The motions of vibrational wavepackets are often discussed in the interpretation of observables measured with various time-resolved vibrational or electronic spectroscopies but mostly in terms of the frequencies of wavepacket motions, which are approximated by normal modes, rather than the actual positions of the wavepacket. Although the time-dependent positions (that is, the trajectory) of wavepackets are hypothesized or drawn in imagined or calculated potential energy surfaces, it is not trivial to experimentally determine the trajectory of wavepackets, especially in multidimensional nuclear coordinates for a polyatomic molecule. Recently, we performed a femtosecond X-ray liquidography (solution scattering) experiment on a gold trimer complex (GTC), [Au(CN)₂^-]₃, in water at X-ray free-electron lasers (XFELs) and elucidated the time-dependent positions of vibrational wavepackets from the Franck-Condon region to equilibrium structures on both excited and ground states in the course of the formation of covalent bonds between gold atoms.Bond making is an essential process in chemical reactions, but it is challenging to keep track of detailed atomic movements associated with bond making because of its bimolecular nature that requires slow diffusion of two reaction parties to meet each other. Bond formation in the solution phase has been elusive because the diffusion of the reactants limits the reaction rate of a bimolecular process, making it difficult to initiate and track the bond-making processes with an ultrafast time resolution. In principle, if the bimolecular encounter can be controlled to overcome the limitation caused by diffusion, the bond-making processes can be tracked in a time-resolved manner, providing valuable insight into the bimolecular reaction mechanism. In this regard, GTC offers a good model system for studying the dynamics of bond formation in solution. Au(I) atoms in GTC exhibit a noncovalent aurophilic interaction, making GTC an aggregate complex without any covalent bond. Upon photoexcitation of GTC, an electron is excited from an antibonding orbital to a bonding orbital, leading to the formation of covalent bonds among Au atoms. Since Au atoms in the ground state of GTC are located in close proximity within the same solvent cage, the formation of Au-Au covalent bonds occurs without its reaction rate being limited by diffusion through the solvent.Femtosecond time-resolved X-ray liquidography (fs-TRXL) data revealed that the ground state has an asymmetric bent structure. From the wavepacket trajectory determined in three-dimensional nuclear coordinates (two internuclear distances and one bond angle), we found that two covalent bonds are formed between three Au atoms of GTC asynchronously. Specifically, one covalent bond is formed first for the shorter Au-Au pair (of the asymmetric and bent ground-state structure) in 35 fs, and subsequently, the other covalent bond is formed for the longer Au-Au pair within 360 fs. The resultant trimer complex has a symmetric and linear geometry, implying the occurrence of bent-to-linear transformation concomitant with the formation of two equivalent covalent bonds, and exhibits vibrations that can be unambiguously assigned to specific normal modes based on the wavepacket trajectory, even without the vibrational frequencies provided by quantum calculation.

Ultrafast excited state relaxation dynamics in a heteroleptic Ir(iii) complex, fac-Ir(ppy)2(ppz), revealed by femtosecond X-ray transient absorption spectroscopy

The experimental and calculation results demonstrate that the ³ML_ppzCT state generated by the spin-forbidden transition rapidly relaxes to ³ML_ppyCT through internal conversion process with a time constant of ∼450 fs.

Ultrafast structural dynamics of in-cage isomerization of diiodomethane in solution

Despite extensive studies on the isomer species formed by photodissociation of haloalkanes in solution, the molecular structure of the precursor of the isomer, which is often assumed to be a vibrationally hot isomer formed from the radical pair, and its in-cage isomerization mechanism remain elusive. Here, the structural dynamics of CH₂I₂ upon 267 nm photoexcitation in methanol were probed with femtosecond X-ray solution scattering at an X-ray free-electron laser. The determined molecular structure of the transiently formed species that converts to the CH₂I–I isomer has the I–I distance of 4.17 Å, which is longer than that of the isomer (3.15 Å) by more than 1.0 Å and the mean-squared displacement of 0.45 Ų, which is about 100 times larger than those of typical regular chemical bonds. These unusual structural characteristics are consistent with either a vibrationally hot form of the CH₂I–I isomer or the loosely-bound radical pair (CH₂I˙⋯I˙).

The structural dynamics of in-cage isomerization of CH₂I₂ and the unusual structure of the loosely-bound isomer precursor were unveiled with femtosecond X-ray liquidography (solution scattering).

Observing the Structural Evolution in the Photodissociation of Diiodomethane with Femtosecond Solution X-Ray Scattering

Resolving the structural dynamics of the initial steps of chemical reactions is challenging. We report the femtosecond time-resolved wide-angle x-ray scattering of the photodissociation of diiodomethane in cyclohexane. The data reveal with structural detail how the molecule dissociates into radicals, how the radicals collide with the solvent, and how they form the photoisomer. We extract how translational and rotational kinetic energy is dispersed into the solvent. We also find that 85% of the primary radical pairs are confined to their original solvent cage and discuss how this influences the downstream recombination reactions.

Femtosecond Optical Laser System with Spatiotemporal Stabilization for Pump-Probe Experiments at SACLA

We constructed a synchronized femtosecond optical laser system with spatiotemporal stabilization for pump-probe experiments at SPring-8 Angstrom Compact Free Electron Laser (SACLA). Stabilization of output power and pointing has been achieved with a small fluctuation level of a few percent by controlling conditions of temperature and air-flow in the optical paths. A feedback system using a balanced optical-microwave phase detector (BOMPD) has been successfully realized to reduce jitter down to 50 fs. We demonstrated the temporal stability with a time-resolved X-ray diffraction measurement and observed the coherent phonon oscillation of the photo-excited Bi without the post-processing using the timing monitor.

Demonstration of Transmission Mode Soft X-ray NEXAFS Using Third- and Fifth-Order Harmonics of FEL Radiation at SACLA BL1

We demonstrate the applicability of third- and fifth-order harmonics of free-electron laser (FEL) radiation for soft X-ray absorption spectroscopy in the transmission mode at SACLA BL1, which covers a photon energy range of 20 to 150 eV in the fundamental FEL radiation. By using the third- and fifth-order harmonics of the FEL radiation, we successfully recorded near-edge X-ray absorption fine structure (NEXAFS) spectra for Ar 2p core ionization and CO2 C 1s and O 1s core ionizations. Our results show that the utilization of third- and fifth-order harmonics can significantly extend the available photon energies for NEXAFS spectroscopy using an FEL and opens the door to femtosecond pump-probe NEXAFS using a soft X-ray FEL.

Gold Nanoparticle Formation via X-ray Radiolysis Investigated with Time-Resolved X-ray Liquidography

We report the generation of gold nanoparticles (AuNPs) from the aqueous solution of chloro(2,2',2″-terpyridine)gold(III) ion ([Au(tpy)Cl]²⁺) through X-ray radiolysis and optical excitation at a synchrotron. The original purpose of the experiment was to investigate the photoinduced structural changes of [Au(tpy)Cl]²⁺ upon 400 nm excitation using time-resolved X-ray liquidography (TRXL). Initially, the TRXL data did not show any signal that would suggest structural changes of the solute molecule, but after an induction time, the TRXL data started to show sharp peaks and valleys. In the early phase, AuNPs with two types of morphology, dendrites, and spheres, were formed by the reducing action of hydrated electrons generated by the X-ray radiolysis of water, thereby allowing the detection of TRXL data due to the laser-induced lattice expansion and relaxation of AuNPs. Along with the lattice expansion, the dendritic and spherical AuNPs were transformed into smaller, raspberry-shaped AuNPs of a relatively uniform size via ablation by the optical femtosecond laser pulse used for the TRXL experiment. Density functional theory calculations confirm that the reduction potential of the metal complex relative to the hydration potential of X-ray-generated electrons determines the facile AuNP formation observed for [Au(tpy)Cl]²⁺.