Time-resolved Diffraction Research Articles

Scaling and merging time-resolved pink-beam diffraction with variational inference

Time-resolved x-ray crystallography (TR-X) at synchrotrons and free electron lasers is a promising technique for recording dynamics of molecules at atomic resolution. While experimental methods for TR-X have proliferated and matured, data analysis is often difficult. Extracting small, time-dependent changes in signal is frequently a bottleneck for practitioners. Recent work demonstrated this challenge can be addressed when merging redundant observations by a statistical technique known as variational inference (VI). However, the variational approach to time-resolved data analysis requires identification of successful hyperparameters in order to optimally extract signal. In this case study, we present a successful application of VI to time-resolved changes in an enzyme, DJ-1, upon mixing with a substrate molecule, methylglyoxal. We present a strategy to extract high signal-to-noise changes in electron density from these data. Furthermore, we conduct an ablation study, in which we systematically remove one hyperparameter at a time to demonstrate the impact of each hyperparameter choice on the success of our model. We expect this case study will serve as a practical example for how others may deploy VI in order to analyze their time-resolved diffraction data.

Nanosecond-Lived Excimer Observation in a Crystal of a Rhodium(I) Complex via Time-Resolved X-ray Laue Diffraction.

The rare observation of transient Rh···Rh excimer formation in a single crystal is reported. The estimated excited-state lifetime at 100 K is 2 ns, which makes it the shortest-lived small-molecule species caught experimentally using the laser-pump/X-ray-probe time-resolved Laue method. Upon excitation with 390 nm laser light, the intermolecular Rh···Rh distance decreases from 3.379(4) to 3.19(1) Å, and the metal-metal contact gains more bonding character. On the basis of the experimental results and theoretical modeling, the structural changes determined with 100 ps time resolution reflect principally the S0 → S1 electronic transition.

Scaling and Merging Time-Resolved Laue Data with Variational Inference.

Time-resolved X-ray crystallography (TR-X) at synchrotrons and free electron lasers is a promising technique for recording dynamics of molecules at atomic resolution. While experimental methods for TR-X have proliferated and matured, data analysis is often difficult. Extracting small, time-dependent changes in signal is frequently a bottleneck for practitioners. Recent work demonstrated this challenge can be addressed when merging redundant observations by a statistical technique known as variational inference (VI). However, the variational approach to time-resolved data analysis requires identification of successful hyperparameters in order to optimally extract signal. In this case study, we present a successful application of VI to time-resolved changes in an enzyme, DJ-1, upon mixing with a substrate molecule, methylglyoxal. We present a strategy to extract high signal-to-noise changes in electron density from these data. Furthermore, we conduct an ablation study, in which we systematically remove one hyperparameter at a time to demonstrate the impact of each hyperparameter choice on the success of our model. We expect this case study will serve as a practical example for how others may deploy VI in order to analyze their time-resolved diffraction data.

On the feasibility of time-resolved X-ray powder diffraction of macromolecules using laser-driven ultrafast X-ray sources.

With the emergence of ultrafast X-ray sources, interest in following fast processes in small molecules and macromolecules has increased. Most of the current research into ultrafast structural dynamics of macromolecules uses X-ray free-electron lasers. In parallel, small-scale laboratory-based laser-driven ultrafast X-ray sources are emerging. Continuous development of these sources is underway, and as a result many exciting applications are being reported. However, because of their low flux, such sources are not commonly used to study the structural dynamics of macromolecules. This article examines the feasibility of time-resolved powder diffraction of macromolecular microcrystals using a laboratory-scale laser-driven ultrafast X-ray source.

Resolving DJ-1 Glyoxalase Catalysis Using Mix-and-Inject Serial Crystallography at a Synchrotron.

DJ-1 (PARK7) is an intensively studied protein whose cytoprotective activities are dysregulated in multiple diseases. DJ-1 has been reported as having two distinct enzymatic activities in defense against reactive carbonyl species that are difficult to distinguish in conventional biochemical experiments. Here, we establish the mechanism of DJ-1 using a synchrotron-compatible version of mix-and-inject-serial crystallography (MISC), which was previously performed only at XFELs, to directly observe DJ-1 catalysis. We designed and used new diffusive mixers to collect time-resolved Laue diffraction data of DJ-1 catalysis at a pink beam synchrotron beamline. Analysis of structurally similar methylglyoxal-derived intermediates formed through the DJ-1 catalytic cycle shows that the enzyme catalyzes nearly two turnovers in the crystal and defines key aspects of its glyoxalase mechanism. In addition, DJ-1 shows allosteric communication between a distal site at the dimer interface and the active site that changes during catalysis. Our results rule out the widely cited deglycase mechanism for DJ-1 action and provide an explanation for how DJ-1 produces L-lactate with high chiral purity.

Capturing Catalyst Strain Dynamics during Operando CO Oxidation.

Understanding the strain dynamic behavior of catalysts is crucial for the development of cost-effective, efficient, stable, and long-lasting catalysts. Using time-resolved Bragg coherent diffraction imaging at the fourth generation Extremely Brilliant Source of the European Synchrotron (ESRF-EBS), we achieved subsecond time resolution during operando chemical reactions. Upon investigation of Pt nanoparticles during CO oxidation, the three-dimensional strain profile highlights significant changes in the surface and subsurface regions, where localized strain is probed along the [111] direction. Notably, a rapid increase in tensile strain was observed at the top and bottom Pt {111} facets during CO adsorption. Moreover, we detected oscillatory strain changes (6.4 s period) linked to CO adsorption during oxidation, where a time resolution of 0.25 s was achieved. This approach allows for the study of adsorption dynamics of catalytic nanomaterials at the single-particle level under operando conditions, which provides insight into nanoscale catalytic mechanisms.

Impacts of hot electron diffusion, electron–phonon coupling, and surface atoms on metal surface dynamics revealed by reflection ultrafast electron diffraction

Metals exhibit nonequilibrium electron and lattice subsystems at transient times following femtosecond laser excitation. In the past four decades, various optical spectroscopy and time-resolved diffraction methods have been used to study electron–phonon coupling and the effects of underlying dynamical processes. Here, we take advantage of the surface specificity of reflection ultrafast electron diffraction (UED) to examine the structural dynamics of photoexcited metal surfaces, which are apparently slower in recovery than predicted by thermal diffusion from the profile of absorbed energy. Fast diffusion of hot electrons is found to critically reduce surface excitation and affect the temporal dependence of the increased atomic motions on not only the ultrashort but also sub-nanosecond times. Whereas the two-temperature model with the accepted physical constants of platinum can reproduce the observed surface lattice dynamics, gold is found to exhibit appreciably larger-than-expected dynamic vibrational amplitudes of surface atoms while keeping the commonly used electron–phonon coupling constant. Such surface behavioral difference at transient times can be understood in the context of the different strengths of binding to surface atoms for the two metals. In addition, with the quantitative agreements between diffraction and theoretical results, we provide convincing evidence that surface structural dynamics can be reliably obtained by reflection UED even in the presence of laser-induced transient electric fields.

Photoinduced dynamics during electronic transfer from narrow to wide bandgap layers in one-dimensional heterostructured materials

Electron transfer is a fundamental energy conversion process widely present in synthetic, industrial, and natural systems. Understanding the electron transfer process is important to exploit the uniqueness of the low-dimensional van der Waals (vdW) heterostructures because interlayer electron transfer produces the function of this class of material. Here, we show the occurrence of an electron transfer process in one-dimensional layer-stacking of carbon nanotubes (CNTs) and boron nitride nanotubes (BNNTs). This observation makes use of femtosecond broadband optical spectroscopy, ultrafast time-resolved electron diffraction, and first-principles theoretical calculations. These results reveal that near-ultraviolet photoexcitation induces an electron transfer from the conduction bands of CNT to BNNT layers via electronic decay channels. This physical process subsequently generates radial phonons in the one-dimensional vdW heterostructure material. The gathered insights unveil the fundamentals physics of interfacial interactions in low dimensional vdW heterostructures and their photoinduced dynamics, pushing their limits for photoactive multifunctional applications.

Flash melting amorphous ice.

Water can be vitrified if it is cooled at high rates, which makes it possible to outrun crystallization in so-called no man's land, a range of deeply supercooled temperatures where water crystallizes rapidly. Here, we study the reverse process in pure water samples by flash melting amorphous ice with microsecond laser pulses. Time-resolved electron diffraction reveals that the sample transiently crystallizes despite a heating rate of more than 5 × 106 K/s, even though under the same conditions, vitrification can be achieved with a similar cooling rate of 107 K/s. Moreover, we observe different crystallization kinetics for amorphous solid water and hyperquenched glassy water. These experiments open up new avenues for elucidating the crystallization mechanism of water and studying its dynamics in no man's land. They also add important insights into the laser melting and revitrification processes that are integral to the emerging field of microsecond time-resolved cryo-electron microscopy.

Ultrafast Optically Induced Perturbation of Oxygen Octahedral Rotations in Multiferroic BiFeO3 Thin Films.

The functional properties of complex oxides, including magnetism and ferroelectricity, are closely linked to subtle structural distortions. Ultrafast optical excitations provide the means to manipulate structural features and ultimately to affect the functional properties of complex oxides with picosecond-scale precision. We report that the lattice expansion of multiferroic BiFeO3 following above-bandgap optical excitation leads to distortion of the oxygen octahedral rotation (OOR) pattern. The continuous coupling between OOR and strain was probed using time-resolved X-ray free-electron laser diffraction with femtosecond time resolution. Density functional theory calculations predict a relationship between the OOR and the elastic strain consistent with the experiment, demonstrating a route to employing this approach in a wider range of systems. Ultrafast control of the functional properties of BiFeO3 thin films is enabled by this approach because the OOR phenomena are related to ferroelectricity, and via the Fe-O-Fe bond angles, the superexchange interaction between Fe atoms.

Shaped Laser Pulses for Microsecond Time-Resolved Cryo-EM: Outrunning Crystallization during Flash Melting.

Water vitrifies if cooled at rates above 3 × 105 K/s. In contrast, when the resulting amorphous ice is flash heated, crystallization occurs even at a more than 10 times higher heating rate, as we have recently shown. This may present an issue for microsecond time-resolved cryo-electron microscopy experiments, in which vitreous ice samples are briefly melted with a laser pulse because transient crystallization could potentially alter the dynamics of the embedded proteins. Here, we demonstrate how shaped microsecond laser pulses can be used to increase the heating rate and outrun crystallization. Time-resolved electron diffraction experiments reveal that the critical heating rate for amorphous solid water (ASW) is about 108 K/s. Our experiments add to the toolbox of the emerging field of microsecond time-resolved cryo-electron microscopy by demonstrating a straightforward approach for avoiding crystallization during laser melting and for achieving significantly higher heating rates, which paves the way for nanosecond time-resolved experiments.

Predicting the photodynamics of cyclobutanone triggered by a laser pulse at 200nm and its MeV-UED signals-A trajectory surface hopping and XMS-CASPT2 perspective.

This work is part of a prediction challenge that invited theoretical/computational chemists to predict the photochemistry of cyclobutanone in the gas phase, excited at 200nm by a laser pulse, and the expected signal that will be recorded during a time-resolved megaelectronvolt ultrafast electron diffraction (MeV-UED). We present here our theoretical predictions based on a combination of trajectory surface hopping with XMS-CASPT2 (for the nonadiabatic molecular dynamics) and Born-Oppenheimer molecular dynamics with MP2 (for the athermal ground-state dynamics following internal conversion), coined (NA+BO)MD. The initial conditions were sampled from Born-Oppenheimer molecular dynamics coupled to a quantum thermostat. Our simulations indicate that the main photoproducts after 2ps of dynamics are CO + cyclopropane (50%), CO + propene (10%), and ethene and ketene (34%). The photoexcited cyclobutanone in its second excited electronic state S2 can follow two pathways for its nonradiative decay: (i) a ring-opening in S2 and a subsequent rapid decay to the ground electronic state, where the photoproducts are formed, or (ii) a transfer through a closed-ring conical intersection to S1, where cyclobutanone ring opens and then funnels to the ground state. Lifetimes for the photoproduct and electronic populations were determined. We calculated a stationary MeV-UED signal [difference pair distribution function-ΔPDF(r)] for each (interpolated) pathway as well as a time-resolved signal [ΔPDF(r,t) and ΔI/I(s,t)] for the full swarm of (NA+BO)MD trajectories. Furthermore, our analysis provides time-independent basis functions that can be used to fit the time-dependent experimental UED signals [both ΔPDF(r,t) and ΔI/I(s,t)] and potentially recover the population of photoproducts. We also offer a detailed analysis of the limitations of our model and their potential impact on the predicted experimental signals.

Ultrafast Kapitza-Dirac effect.

Similar to the optical diffraction of light passing through a material grating, the Kapitza-Dirac effect occurs when an electron is diffracted by a standing light wave. In its original description, the effect is time independent. Here, we extended the Kapitza-Dirac effect to the time domain. By tracking the spatiotemporal evolution of a pulsed electron wave packet diffracted by a 60-femtosecond (where one femtosecond = 10-15 seconds) standing wave pulse in a pump-probe scheme, we observed time-dependent diffraction patterns. The fringe spacing in the observed pattern differs from that generated by the conventional Kapitza-Dirac effect. By exploiting this time-resolved diffraction scheme, we can access the time evolution of the phase properties of a free electron and potentially image ionic potentials and electronic decoherences.

Quantum tomography of molecules using ultrafast electron diffraction.

We propose a quantum tomography (QT) approach to retrieve the temporally evolving reduced density matrix in electronic state basis, where the populations and coherence between the ground state and excited state are reconstructed from the ultrafast electron diffraction signal. In order to showcase the capability of the proposed QT approach, we simulate the nuclear wavepacket dynamics and ultrafast electron diffraction of photoexcited pyrrole molecules using the abinitio quantum chemical CASSCF method. From the simulated time-resolved diffraction data, we retrieve the evolving density matrix in a crude diabatic representation basis and reveal the symmetry of the excited pyrrole wavepacket. Our QT approach opens the route to make a quantum version of "molecular movie" that covers the electronic degree of freedom and equips ultrafast electron diffraction with the power to reveal the coherence between electronic states, relaxation, and dynamics of population transfer.

High bunch charge low-energy electron streak diffraction

For time-resolved diffraction studies of irreversible structural dynamics upon photoexcitation, there are constraints on the number of perturbation cycles due to thermal effects and accumulated strain, which impact the degree of crystal order and spatial resolution. This problem is exasperated for surface studies that are more prone to disordering and defect formation. Ultrafast electron diffraction studies of these systems, with the conventional stroboscopic pump–probe protocol, require repetitive measurements on well-prepared diffraction samples to acquire and average signals above background in the dynamic range of interest from few tens to hundreds of picoseconds. Here, we present ultrafast streaked low-energy electron diffraction (LEED) that demands, in principle, only a single excitation per nominal data acquisition timeframe. By exploiting the space–time correlation characteristics of the streaking method and high-charge 2 keV electron bunches in the transmission geometry, we demonstrate about one order of magnitude reduction in the accumulated number of the excitation cycles and total electron dose, and 48% decrease in the root mean square error of the model fit residual compared to the conventional time-scanning measurement. We believe that our results demonstrate a viable alternative method with higher sensitivity to that of nanotip-based ultrafast LEED studies relying on a few electrons per a single excitation, to access to all classes of structural dynamics to provide an atomic level view of surface processes.

A modular table-top setup for ultrafast x-ray diffraction.

We present a table-top setup for femtosecond time-resolved x-ray diffraction based on a Cu Kα (8.05keV) laser driven plasma x-ray source. Due to its modular design, it provides high accessibility to its individual components (e.g., x-ray optics and sample environment). The Kα-yield of the source is optimized using a pre-pulse scheme. A magnifying multilayer x-ray mirror with Montel-Helios geometry is used to collect the emitted radiation, resulting in a quasi-collimated flux of more than 105 Cu Kα photons/pulse impinging on the sample under investigation at a repetition rate of 10Hz. A gas ionization chamber detector is placed right after the x-ray mirror and used for the normalization of the diffraction signals, enabling the measurement of relative signal changes of less than 1% even at the given low repetition rate. Time-resolved diffraction experiments on laser-excited epitaxial Bi films serve as an example to demonstrate the capabilities of the setup. The setup can also be used for Debye-Scherrer type measurements on poly-crystalline samples.

Aluminothermic reduction of CeO2: mechanism of an economical route to aluminum-cerium alloys.

Cerium oxide is a low-value byproduct of rare-earth mining yet constitutes the largest fraction of the rare earth elements. The reduction of cerium oxide by liquid aluminum is proposed as an energy- and cost-efficient route to produce high-strength Al-Ce alloys. This work investigated the mechanism of a multi-step reduction reaction to facilitate the industrial adaptation of the process. Differential scanning calorimetry in combination with time-resolved synchrotron diffraction data uncovered the rate-limiting reaction step as the origin of the reported temperature dependence of reduction efficiency. This is the first in situ study of a metallothermic reaction mechanism and will serve as guidance for cost- and energy efficient industrial process control.

Time-resolved photoelectron diffraction imaging of methanol photodissociation involving molecular hydrogen ejection.

Imaging ultrafast atomic and molecular hydrogen motion with femtosecond time resolution is a challenge for ultrafast spectroscopy due to the low mass and small scattering cross section of the moving neutral hydrogen atoms and molecules. Here, we propose time- and momentum-resolved photoelectron diffraction (TMR-PED) as a way to overcome limitations of existing methodologies and illustrate its performance using a prototype molecular dissociation process involving the sequential ejection of a neutral hydrogen molecule and a proton from the methanol dication. By combining state-of-the-art molecular dynamics and electron-scattering methods, we show that TMR-PED allows for direct imaging of hydrogen atoms in action. More specifically, the fingerprint of hydrogen dynamics reflects the time evolution of polarization-averaged molecular-frame photoelectron angular distributions (PA-MFPADs) as would be recorded in X-ray pump/X-ray probe experiments with few-femtosecond resolution. We present the results of two precursor experiments that support the feasibility of this approach.

Preparation of damage-free kerogen specimen for microscopy: Understanding the damage mechanisms induced by ion milling techniques

Focused ion beam (FIB) milling techniques have been used for more than a decade to prepare organic-rich shale samples for electron microscopy. Nano- and micro-scale imaging of organic pores is used to assess pore volumes and hence estimate gas-in-place. Ion milling natural composites is particularly challenging due to drastic extremes in the physical properties of individual phases such as minerals and organics. Damage to the organic-rich phases occurs due to the large differences in thermal conductivities of minerals and organics that could reach an order of magnitude and the resulting buildup of heat in the organics. Furthermore, radiation damage via ion implantation may also alter the structural characteristics of the shale.Herein, the damage associated with preparing electron-transparent kerogen specimen using low kV FIB, cryo-FIB, and cryomicrotome, a new technique for shale kerogen, is quantified using experimental and modeling techniques. The degree of gallium implantation is quantified using scanning transmission electron microscopy (STEM), selected area electron diffraction (SAED), and energy dispersive X-ray spectroscopy (EDX) along with the stopping range of ions in matter (SRIM) model. Interestingly, although the use of cryogenic temperature removes the thermal effect, Ga+ ion implantation is observed in the specimen prepared by cryo-FIB.Furthermore, the magnitude of the thermal damage at a highly localized level was determined using nano-beam electron diffraction (NBED) performed at −196 °C. Time-resolved diffraction patterns indicate that despite the fact kerogen is among the most stable geopolymers, the aromatic components still degraded due to the local temperature increases. On the other hand, the cryomicrotome technique operating at liquid nitrogen temperature is demonstrated as a suitable method to prepare thin kerogen specimen while minimizing structural damage and preserving its native porosity and chemical composition.

Ultrafast dynamics of a photoinduced phase transition in single-crystal trititanium pentoxide

We investigate photoinduced phase transition of Ti3O5 using the pump-probe method in an ultrafast electron microscope. We measured time-resolved electron diffraction patterns of single-crystal lamellae of Ti3O5 excited by the femtosecond laser at the wavelength of 800 and 400 nm. Under 800 nm laser excitation, the photoinduced phase transition from the β-phase to the λ-phase with a similar timescale to previous measurements conducted using nanocrystals was observed. This indicates that the photoinduced phase transition is not a phenomenon influenced by the material surface, size, or boundary, but an intrinsic property in a bulk crystal of Ti3O5. The photoinduced phase transition was not detected, when excited by the laser at the wavelength of 400 nm. The results are discussed based on the electronic states of β-Ti3O5 and λ-Ti3O5. The density of the dissociated interatomic bonds between Ti at the specific site should be an important factor for triggering the photoinduced phase transition.