Here, we describe recently developed upgrades to our experimental scheme for obtaining the photoelectron spectrum, the anisotropy parameter, and the photoelectron circular dichroism (PECD) of jet-cooled flexible molecules with conformer selectivity. The one-color resonance-enhanced multiphoton ionization process used allows ionizing selectively the different conformers present in the supersonic expansion by selecting their S-S transition. We first describe the experimental setup with emphasis on the data acquisition and processing. Then, we apply this ionization scheme to a flexible molecule, 1,2,3,4-tetrahydro-3-isoquinoline methanol (THIQM). This molecule shows two stereogenic centers, namely, an asymmetric carbon and a nitrogen atom. It exists in two conformers, THIQM and THIQM, which differ by the direction of the intramolecular hydrogen bond and the absolute configuration of the nitrogen atom. Therefore, these two conformers are also diastereomers, endowed with slightly different ionization energies. The ionization energy of THIQM, which shows an OH…N hydrogen bond, is slightly higher than that of THIQM. Their PECD spectra, although of identical signs, differ in shape and magnitude. Surprisingly, the anisotropy parameter is more sensitive than the PECD to the conformational isomerism at play in this system.

Interfacial thermal and acoustic phenomena have an important role in quantum science and technology, including in spintronic and spincaloritronic materials and devices. Simultaneous measurements of the low-temperature thermal and acoustic properties of a metal/insulator heterostructure reveal distinct dynamics in the characteristic phonon frequency ranges of acoustic and thermal transport. The measurements probed a heterostructure consisting of a thin film of Pt on the ferrimagnetic insulator gadolinium iron garnet (GdFeO, GdIG) grown epitaxially on a gadolinium gallium garnet substrate. Ultrafast structural dynamics within the Pt layer were tracked using time-resolved ultrafast x-ray diffraction and analyzed to probe interfacial acoustic and thermal properties. The rapid heating of the Pt layer by a 400 nm wavelength femtosecond-duration optical pulse produced transient structural changes that provided the stimulus for these measurements. Rapid heating produced a broadband acoustic pulse that was partially reflected by the Pt/GdIG interface. Temporal frequencies up to 740 GHz, corresponding to angular frequencies of several THz, were detected in a wavelet analysis of the acoustic oscillations of the strain in the Pt layer. The structural results were analyzed to determine (i) the acoustic damping coefficient and phonon mean free path in Pt at frequencies of hundreds of GHz and (ii) the Grüneisen anharmonicity parameter. The thermal conductance of the Pt/GdIG interface was tracked using the slower, tens-of-picosecond-scale, dynamics of the initial cooling of the heated Pt layer. Analysis using a model based on the Boltzmann transport equation shows that the phonon transmission is lower at the phonon frequencies relevant to thermal transport than for subterahertz regime acoustics.

Molybdenum oxides have attracted considerable attention in heterogeneous catalysis and energy storage applications owing to the unusual chemical flexibility of the Mo center. Unlike many transition metals, molybdenum can shift between several oxidation states without losing structural integrity, largely due to the stabilizing role of oxo-bridged linkages. This versatility gives rise to an extraordinary diversity of structural motifs that can be tailored for specific catalytic and electrochemical functions. In this study, we investigate the elusive structure and nuclear dynamics of the monohydrate (MoO HO) and dihydrate (MoO  2HO) phases of -MoO, an important family of precursors for molybdenum oxide-based hybrid materials. We employ a combined experimental and computational approach to explore the local environment and nuclear dynamics of protons in water confined within the interlamellar space of the -MoO layers. High-resolution neutron diffraction confirms the established structure of the dihydrate phase while revealing hydrogen-sublattice disorder in the metastable monohydrate. Complementary computational analysis, including harmonic lattice dynamics and Born-Oppenheimer molecular dynamics simulations, provides deeper insight into proton confinement in these systems, yielding plausible models of their local structure. These findings further validated through temperature-dependent inelastic neutron scattering and neutron Compton scattering, which probe the vibrational response and proton momentum distributions, respectively. The joint analysis of experimental data and molecular dynamics simulations identifies rotationally bound, orientationally disordered water molecules as the mechanism underlying proton disorder in -MoO HO. Overall, the results reveal pronounced differences in water ordering and proton dynamics between the mono- and dihydrate forms, offering a detailed quantum-mechanical description of the hydrogen behavior in hydrated molybdenum trioxides and highlighting the interplay between the thermal effect and the confinement-induced local proton dynamics.

About 100 years ago, the field of structural biology was born, led by James B. Sumner who recognized that enzymes were molecules with specific functions. In its contemporary form structural biology is used to interpret and understand molecular and cellular function, to design drugs, and to advance biotechnology in general.

Given proteins' fundamental importance in human health and catalysis, the relationships between protein sequence, structure, dynamics, and function have become a topic of great interest. One way to extract information from proteins is to compute the local energetic frustration of their native state. Traditionally, energetic frustration calculations require protein structures as a starting point. However, using a single protein structure to evaluate the energetic frustration for a given amino acid sequence does not always fully represent the protein's structural ensemble. Therefore, we have developed a sequence-based method to evaluate energetic frustration in proteins using direct coupling analysis and statistical potentials. Our approach exhibits significant agreement with established structure-based frustration methods in terms of their mutual agreement with crystallographic B-factor. Moreover, our sequence-based method shows elevated precision in classifying high B-factor residues, suggesting that it has some robustness to unstructured regions of proteins.

The correct description of quantum scattering places the observed scattering contributions on the Ewald's sphere and its Friedel mate copy. In electron microscopy, due to the large radius of the Ewald's sphere, these scattering contributions are typically merged during data analysis. We present an approach that separates and factorizes those contributions into real and imaginary components of the image. When an inverted solution is calculated, the map derived from the real component of the image generates an inverted solution, while the map derived from the imaginary component of the image generates an inverted and sign-flipped solution. Therefore, the sign of correlation between reconstructions derived from the real and imaginary components provides the automatic determination of handedness and additional validation for the quality of 3D reconstructions. The factorization and its implementation are robust enough to be routinely used in single-particle reconstructions, even at resolutions below the limit where the curvature of the Ewald's sphere affects the overall signal-to-noise ratio.

A program for serial handling of crystallographic data is presented within Olex2. Especially for small molecule electron and x-ray diffraction, the handling of several datasets of the same structure can be tedious and prone to errors, which can affect comparability. The program SISYPHOS allows for the individual refinement of a starting model against several recorded datasets (in ".hkl" format) with adaptation to changes in the unit cell, wavelength, among other parameters. The program was tested for resonant diffraction (also known as anomalous dispersion), investigations on radiation damage, the benchmarking of different configurations for quantum crystallographic modeling, electron diffraction data, and for testing several datasets from the same measurement using various settings to identify the most suitable dataset.

The high-temperature phase of the hexagonal halide perovskite KNiCl is investigated using time-of-flight single crystal neutron diffraction at 633 K (360 °C). Phonons are captured through thermal diffuse scattering, integrated in energy but resolved in momentum. Harmonic phonon calculations based on density functional theory yield imaginary phonon frequencies for this phase, indicating the presence of structural instabilities at this level of theory. It is shown that the inclusion of anharmonic phonon-phonon interactions removes these instabilities, leading to good qualitative agreement with the experimental diffuse scattering. These results demonstrate that the high-temperature phase of KNiCl is stabilized by anharmonic phonon-phonon interactions.

Time-resolved serial femtosecond crystallography (TR-SFX) is a technique designed to reveal the molecular dynamics underlying chemical reactions, thereby providing insights into the relationship between structure and function. By capturing a series of conformational changes in intermediate states, TR-SFX enables the visualization of dynamic structural transitions. In this study, we have presented a new approach for modeling reaction state conformations using molecular dynamics (MD) simulations. In this approach, MD simulations were first performed to generate a large number of conformational samples, which were then used as initial models for refinement against diffraction data from the triggered states, thereby facilitating the construction of accurate dynamic structure models. The derived models were evaluated using tools such as Edstats and MolProbity to identify models with high-quality geometries and local electron density metrics. This procedure provides a semi-automated approach for building dynamic structural models from TR-SFX data, ensuring their robustness for further exploration and understanding of macromolecular dynamics.

This study systematically investigates the influence of various parameters of the wavefunction calculation during Hirshfeld atom refinement (HAR). We aim to address the lack of consensus in the literature and conflicting information on a generally recommended procedure. A set of amino acid test structures, known for their immense biochemical importance and unimpeachable experimental data quality, was employed to ensure reliable results, unbiased by the question of insufficient diffraction data quality. A comprehensive permutation of refinement parameters was conducted to avoid overlooking potential influences, resulting in 2496 structure refinements per amino acid. Applying a solvent model systematically improved refinement results compared to gas-phase calculations. Additionally, it was observed that the pure Hartree-Fock method outperforms all tested density functional theory methods across all structures in this test set of polar-organic molecules. These findings underscore the importance of carefully considering the level of theory applied in HAR and offer an overview of the performance of various methods and parameters.

We compared ultrafast spin dynamics in laser-excited NiCo alloy and pure Ni thin films exhibiting magnetic weak stripe domains using x-ray resonant magnetic scattering. By relying on extreme ultraviolet pulses obtained via high-harmonic generation, we simultaneously probed our samples using four energies around the Co and Ni edges. Our results show a significant laser-induced reduction of the intensity of the magnetic scattering peaks on fs timescales and clearly highlight that this effect depends sensitively on the probing wavelength: different quenching amplitudes and characteristic timescales are found when changing the probing energy. More particularly, in our alloyed thin film, we observe a delay of about 17 fs in the scattered intensity dynamics between probing energies close to the Ni and Co edges, respectively. This delay is not observed in the pure Ni sample and is therefore most likely induced by the presence of Co in the thin film, reflecting the different ultrafast magnetic responses of the two 3 metals in these alloys.

Time-resolved x-ray liquidography (TRXL) is a powerful technique for directly tracking ultrafast structural dynamics in real space. However, resolving the motion of vibrational wavepackets generated by femtosecond laser pulses remains challenging due to the limited temporal resolution and signal-to-noise ratio (SNR) of experimental data. This study addresses these challenges by introducing singular spectrum analysis (SSA) as an efficient method for extracting oscillatory signals associated with vibrational wavepackets from TRXL data. To evaluate its performance, we conducted a comparative study using simulated TRXL data, demonstrating that SSA outperforms conventional analysis methods such as the Fourier transform of temporal profiles and singular value decomposition, particularly under low SNR conditions. We further applied SSA to experimental TRXL data on the photodissociation of triiodide ( ) in methanol, successfully isolating oscillatory signals arising from wavepacket dynamics in ground-state and excited-state , which had been challenging to resolve in previous TRXL studies. These results establish SSA as a highly effective tool for analyzing ultrafast structural dynamics in time-resolved experiments and open new opportunities for studying wavepacket dynamics in a wide range of photoinduced reactions.

The insulating chiral magnet CuOSeO exhibits a rich array of low-temperature magnetic phenomena, making it a prime candidate for the study of its spin dynamics. Using spin wave small-angle neutron scattering (SWSANS), we systematically investigated the temperature-dependent behavior of the helimagnon excitations in the field-polarized phase of CuOSeO. Our measurements, spanning 5-55 K, reveal the temperature evolution of spin-wave stiffness and damping constant with unprecedented resolution, facilitated by the insulating nature of CuOSeO. These findings align with theoretical predictions and resolve discrepancies observed in previous studies, emphasizing the enhanced sensitivity of the SWSANS method. The results provide deeper insights into the fundamental magnetic properties of CuOSeO, contributing to a broader understanding of chiral magnets.

The energetics and dynamics of ion assembly in solution has broad influence in nanomaterials and inorganic synthesis. To investigate the fundamental processes involved, we present a time-resolved x-ray solution scattering (TR-XSS) study of the trinuclear silver and thallium complexes of the diplatinum ion PtPOP [Pt(HPO) ] in aqueous solution. These complexes, their structural properties, and their electronic structure are not well understood and afford a unique opportunity to study the metal-metal bond formation that influences molecular and material assembly in solution. We present model-independent analysis of the observed dynamics as well as an analysis incorporating time-resolved structural refinements of key bond lengths with <100 fs time resolution. We find that upon photoexcitation, the Pt atoms contract 0.25 Å toward the center of both the Ag- and the Tl-PtPOP complexes, as previously observed for the PtPOP anion. For the AgPtPOP system, an ultrafast Ag-Pt bond expansion of 0.2 Å is observed, whereas in contrast, the TlPtPOP system exhibits a Tl-Pt bond contraction of 0.3 Å upon photoexcitation. For both complexes, the change in electronic state leads to coherent ("wave-packet") oscillations along the metal-Pt coordinates. Based on these structural dynamics, we propose an electronic structure model that describes the metal-metal bonding behavior in both the ground and excited state for both complexes.

In October 2024, the Challenges in Structural Biology Summit was held at the UCLA Lake Arrowhead Lodge. The meeting focused on new advancements and methods developments in structural biology. Here, we briefly summarize the 2024 Challenges in Structural Biology Summit.

Structural dynamics research requires robust computational methods, reliable software, accessible data, and scalable infrastructure. Managing these components is complex and directly affects reproducibility and efficiency. The SBGrid Consortium addresses these challenges through a three-pillar approach that encompasses Software, Data, and Infrastructure, designed to foster a consistent and rigorous computational environment. At the core is the SBGrid software collection (>620 curated applications), supported by the Capsules Software Execution Environment, which ensures conflict-free, version-controlled execution. The SBGrid Data Bank supports open science by enabling the publication of primary experimental data. SBCloud, a fully managed cloud computing platform, provides scalable, on-demand infrastructure optimized for structural biology workloads. Together, they reduce computational friction, enabling researchers to focus on interpreting time-resolved data, modeling structural transitions, and managing large simulation datasets for advancing structural dynamics. This integrated platform delivers a reliable and accessible foundation for computationally intensive research across diverse scientific fields sharing common computational methods.

High-intensity femtosecond-duration x-rays from free electron lasers have enabled innovative imaging techniques that employ smaller crystal sizes than conventional crystallography. Developments aimed at increasing x-ray pulse intensities bring opportunities and constraints due to ultra-fast changes to atomic scattering form factors from electron dynamics. Experiments on silicon by Inoue [Inoue , Phys. Rev. Lett. , 163201 (2023)] illustrate this by measuring diffraction efficiencies with increasing x-ray pulse intensities. Results at the highest experimental x-ray pulse intensity have been theoretically studied [Inoue , Phys. Rev. Lett. , 163201 (2023); Ziaja , Atoms , 154 (2023)] but not fully reproduced, which raises questions about the mechanisms behind these changes. Using collisional radiative simulations and relativistic configuration-averaged atomic data, we compute the ionization dynamics and diffraction efficiency of silicon and find good agreement within the experimental uncertainty. We incorporate the effects of ionization potential depression by removing energy levels close to the ionization threshold over selected charge states. We identify the main electron impact mechanisms present in our simulations. We bridge the gap between high and low intensity and find regimes where electronic damage affects the efficiency of high- and low-momentum transfer. We computationally examine the effects of free electron degeneracy and find that it does not influence ionization dynamics. Finally, we consider how a non-thermal electron distribution may modify our results. This investigation gives insight into the mechanisms and helps guide future experiments that utilize intense x-ray pulses to achieve high-resolution structural determination.

Estimates show that up to 85% of the human therapeutic proteomes are undruggable by traditional small molecules. Macrocycles, a class of molecular leads, often extend beyond the traditional drug space and offer the potential to modulate challenging targets within this 85%. These modalities exhibit significant conformational flexibility and often function as molecular chameleons, enabling them to adapt to environments with varying polarities while ensuring good oral bioavailability. In this study, we explore the conformational adaptability in target binding of the three known molecular chameleons, paritaprevir, grazoprevir, and simeprevir, by docking their experimental crystal structures, solution conformations, and target-bound structures into multiple protein targets, including human drug transporters associated with drug-drug interactions and COVID-19 related proteins. Our findings reveal that the macrocyclic core conformational class, or "chameleonic group," determines the overall pharmacophore conformations and influences the conformational changes required for binding to various proteins. These insights provide a pathway toward rationalizing drug optimizations for molecular chameleons as well as offering specific guidance for improving Hepatitis C virus nonstructural protein 3/4A inhibitors, including providing a starting point for their COVID-19 repurposing and cancer therapy.

Cryo-electron tomography (cryo-ET) is a powerful modality for resolving cellular structures in their native state. While single-particle cryo-electron microscopy excels in determining protein structures purified from recombinant or endogenous sources due to an abundance of particles, weak contrast issues are accentuated in cryo-ET by low copy numbers in crowded cellular milieux. Continuous laser phase plates offer improved contrast in cryo-ET; however, their implementation demands exceptionally high-peak optical intensities. Instead, a novel experimental approach to enhance contrast in cryo-ET is to manipulate the phase of scattered pulsed electrons using ultrafast pulsed photons. Here, we outline the experimental design of a proof-of-concept electron microscope and demonstrate synchronization between electron packets and laser pulses. Furthermore, we show ultrabright photoemission of electrons from an alloy field emission tip using femtosecond ultraviolet pulses. These experiments pave the way toward exploring the utility of the ponderomotive effect using pulsed radiation to increase phase contrast in cryo-ET of subcellular protein complexes , thus advancing the field of cell biology.