Chemical crystallography by serial femtosecond X-ray diffraction

Crystal structure via fluctuation scattering

Crystallography is a quintessential method for determining the atomic structure of crystals. The most common implementation of crystallography uses single crystals that must be of sufficient size, typically tens of micrometres or larger, depending on the complexity of the crystal structure. The emergence of serial data-collection methods in crystallography, particularly for time-resolved experiments, opens up opportunities to develop new routes to structure determination for nanocrystals and ensembles of crystals. Fluctuation X-ray scattering is a correlation-based approach for single-particle imaging from ensembles of identical particles, but has yet to be applied to crystal structure determination. Here, an iterative algorithm is presented that recovers crystal structure-factor intensities from fluctuation X-ray scattering correlations. The capabilities of this algorithm are demonstrated by recovering the structure of three small-molecule crystals and a protein crystal from simulated fluctuation X-ray scattering correlations. This method could facilitate the recovery of structure-factor intensities from crystals in serial crystallography experiments and relax sample requirements for crystallography experiments.

Real-time observation of a metal complex-driven reaction intermediate using a porous protein crystal and serial femtosecond crystallography

Determining short-lived intermediate structures in chemical reactions is challenging. Although ultrafast spectroscopic methods can detect the formation of transient intermediates, real-space structures cannot be determined directly from such studies. Time-resolved serial femtosecond crystallography (TR-SFX) has recently proven to be a powerful method for capturing molecular changes in proteins on femtosecond timescales. However, the methodology has been mostly applied to natural proteins/enzymes and limited to reactions promoted by synthetic molecules due to structure determination challenges. This work demonstrates the applicability of TR-SFX for investigations of chemical reaction mechanisms of synthetic metal complexes. We fix a light-induced CO-releasing Mn(CO)3 reaction center in porous hen egg white lysozyme (HEWL) microcrystals. By controlling light exposure and time, we capture the real-time formation of Mn-carbonyl intermediates during the CO release reaction. The asymmetric protein environment is found to influence the order of CO release. The experimentally-observed reaction path agrees with quantum mechanical calculations. Therefore, our demonstration offers a new approach to visualize atomic-level reactions of small molecules using TR-SFX with real-space structure determination. This advance holds the potential to facilitate design of artificial metalloenzymes with precise mechanisms, empowering design, control and development of innovative reactions.

3D Nanocrystallography and the Imperfect Molecular Lattice

Crystallographic analysis relies on the scattering of quanta from arrays of atoms that populate a repeating lattice. While large crystals built of lattices that appear ideal are sought after by crystallographers, imperfections are the norm for molecular crystals. Additionally, advanced X-ray and electron diffraction techniques, used for crystallography, have opened the possibility of interrogating micro- and nanoscale crystals, with edges only millions or even thousands of molecules long. These crystals exist in a size regime that approximates the lower bounds for traditional models of crystal nonuniformity and imperfection. Accordingly, data generated by diffraction from both X-rays and electrons show increased complexity and are more challenging to conventionally model. New approaches in serial crystallography and spatially resolved electron diffraction mapping are changing this paradigm by better accounting for variability within and between crystals. The intersection of these methods presents an opportunity for a more comprehensive understanding of the structure and properties of nanocrystalline materials.

Dynamic three-dimensional structures of a metal-organic framework captured with femtosecond serial crystallography

Crystalline systems consisting of small-molecule building blocks have emerged as promising materials with diverse applications. It is of great importance to characterize not only their static structures but also the conversion of their structures in response to external stimuli. Femtosecond time-resolved crystallography has the potential to probe the real-time dynamics of structural transitions, but, thus far, this has not been realized for chemical reactions in non-biological crystals. In this study, we applied time-resolved serial femtosecond crystallography (TR-SFX), a powerful technique for visualizing protein structural dynamics, to a metal-organic framework, consisting of Fe porphyrins and hexazirconium nodes, and elucidated its structural dynamics. The time-resolved electron density maps derived from the TR-SFX data unveil trifurcating structural pathways: coherent oscillatory movements of Zr and Fe atoms, a transient structure with the Fe porphyrins and Zr6 nodes undergoing doming and disordering movements, respectively, and a vibrationally hot structure with isotropic structural disorder. These findings demonstrate the feasibility of using TR-SFX to study chemical systems.

Inorganic-Organic Hybrid Layered Semiconductor AgSePh: Quasi-Solution Synthesis, Optical Properties, and Thermolysis Behavior

Two-dimensional inorganic-organic hybrid layered semiconductors are actively studied because of their naturally formed multiquantum well (MQW) structures and associated optical, photoelectric, and quantum optics characteristics. Silver benzeneselenolate (AgSePh, Ph = C6H5) is a new member of such hybrid layered materials, but has not fully been exploited. Herein, we present a quasi-solution method to prepare high quality free-standing AgSePh flake-like microcrystals by reacting diphenyl diselenide (Ph2Se2) with silver nanoparticles. The resultant AgSePh microflakes exhibit room-temperature (RT) resolvable MQW-induced quasi-particle quantization and interesting optical properties, such as three distinct excitonic resonance absorptions X1 (2.67 eV), X2 (2.71 eV), and X3 (2.83 eV) in the visible region, strong narrow-line width blue photoluminescence at ∼2.64 eV (470 nm) from the radiative recombination of the X1 exciton state, and a large exciton binding energy (∼0.35 eV). Furthermore, AgSePh microcrystals show high stability under water, oxygen, and heat environments, while above 220 °C, they will thermally decompose to silver and Ph2Se2 as evidenced by a combination of thermogravimetry and differential scanning calorimetry and pyrolysis-coupled gas chromatography-mass spectrometry studies. Finally, a comparison is extended between AgSePh and other metal benzeneselenolates, benzenethiolates, and alkanethiolates to clarify differences in their solubility, decomposition/melting temperature, and pyrolytic products.

MOCHAs: An Emerging Class of Materials for Photocatalytic H2 Production

Production of green hydrogen (H2) is a sustainable process able to address the current energy crisis without contributing to long-term greenhouse gas emissions. Many Ag-based catalysts have shown promise for light-driven H2 generation, however, pure Ag-in its bulk or nanostructured forms-suffers from slow electron transfer kinetics and unfavorable Ag─H bond strength. It is demonstrated that the complexation of Ag with various chalcogenides can be used as a tool to optimize these parameters and reach improved photocatalytic performance. In this work, metal-organic-chalcogenolate assemblies (MOCHAs) are introduced as effective catalysts for light-driven hydrogen evolution reaction (HER) and investigate their performance and structural stability by examining a series of AgXPh (X = S, Se, and Te) compounds. Two catalyst-support sensitization strategies are explored: by designing MOCHA/TiO2 composites and by employing a common Ru-based photosensitizer. It is demonstrated that the heterogeneous approach yields stable HER performance but involves a catalyst transformation at the initial stage of the photocatalytic process. In contrast to this, the visible-light-driven MOCHA-dye dyad shows similar HER activity while also ensuring the structural integrity of the MOCHAs. The work shows the potential of MOCHAs in constructing photosystems for catalytic H2 production and provides a direct comparison between known AgXPh compounds.

Prediction of protein-ATP binding residues using multi-view feature learning via contextual-based co-attention network

Accurately predicting protein-ATP binding residues is critical for protein function annotation and drug discovery. Computational methods dedicated to the prediction of binding residues based on protein sequence information have exhibited notable advancements in predictive accuracy. Nevertheless, these methods continue to grapple with several formidable challenges, including limited means of extracting more discriminative features and inadequate algorithms for integrating protein and residue information. To address the problems, we propose ATP-Deep, a novel protein-ATP binding residues predictor. ATP-Deep harnesses the capabilities of unsupervised pre-trained language models and incorporates domain-specific evolutionary context information from homologous sequences. It further refines the embedding at the residue level through integration with corresponding protein-level information and employs a contextual-based co-attention mechanism to adeptly fuse multiple sources of features. The performance evaluation results on the benchmark datasets reveal that ATP-Deep achieves an AUC of 0.954 and 0.951, respectively, surpassing the performance of the state-of-the-art model. These findings underscore the effectiveness of assimilating protein-level information and deploying a contextual-based co-attention mechanism grounded in context to bolster the prediction performance of protein-ATP binding residues.

Comprehensive Application of XFEL Microcrystallography for Challenging Targets in Various Organic Compounds

There is a growing demand for structure determination from small crystals, and the three-dimensional electron diffraction (3D ED) technique can be employed for this purpose. However, 3D ED has certain limitations related to the crystal thickness and data quality. We here present the application of serial X-ray crystallography (SX) with X-ray free electron lasers (XFELs) to small (a few μm or less) and thin (a few hundred nm or less) crystals of novel compounds dispersed on a substrate. For XFEL exposures, two-dimensional (2D) scanning of the substrate coupled with rotation enables highly efficient data collection. The recorded patterns can be successfully indexed using lattice parameters obtained through 3D ED. This approach is especially effective for challenging targets, including pharmaceuticals and organic materials that form preferentially oriented flat crystals in low-symmetry space groups. Some of these crystals have been difficult to solve or have yielded incomplete solutions using 3D ED. Our extensive analyses confirmed the superior quality of the SX data regardless of crystal orientations. Additionally, 2D scanning with XFEL pulses gives an overall distribution of the samples on the substrate, which can be useful for evaluating the properties of crystal grains and the quality of layered crystals. Therefore, this study demonstrates that XFEL crystallography has become a powerful tool for conducting structure studies of small crystals of organic compounds.

Kilohertz droplet-on-demand serial femtosecond crystallography at the European XFEL station FXE

X-ray Free Electron Lasers (XFELs) allow the collection of high-quality serial femtosecond crystallography data. The next generation of megahertz superconducting FELs promises to drastically reduce data collection times, enabling the capture of more structures with higher signal-to-noise ratios and facilitating more complex experiments. Currently, gas dynamic virtual nozzles (GDVNs) stand as the sole delivery method capable of best utilizing the repetition rate of megahertz sources for crystallography. However, their substantial sample consumption renders their use impractical for many protein targets in serial crystallography experiments. Here, we present a novel application of a droplet-on-demand injection method, which allowed operation at 47 kHz at the European XFEL (EuXFEL) by tailoring a multi-droplet injection scheme for each macro-pulse. We demonstrate a collection rate of 150 000 indexed patterns per hour. We show that the performance and effective data collection rate are comparable to GDVN, with a sample consumption reduction of two orders of magnitude. We present lysozyme crystallographic data using the Large Pixel Detector at the femtosecond x-ray experiment endstation. Significant improvement of the crystallographic statistics was made by correcting for a systematic drift of the photon energy in the EuXFEL macro-pulse train, which was characterized from indexing the individual frames in the pulse train. This is the highest resolution protein structure collected and reported at the EuXFEL at 1.38 Å resolution.

Applications and limitations of electron 3D crystallography

Three-dimensional electron diffraction (3D ED) is a measurement and analysis technique in transmission electron microscopy that is used for determining atomic structures from small crystals. Diverse targets such as proteins, polypeptides, and organic compounds, whose crystals exist in aqueous solutions and organic solvents, or as dried powders, can be studied with 3D ED. We have been involved in the development of this technique, which can now rapidly process a large number of data collected through AI control, enabling efficient structure determination. Here, we introduce this method and describe our recent results. These include the structures and pathogenic mechanisms of wild-type and mutant polypeptides associated with the debilitating disease amyotrophic lateral sclerosis (ALS), the double helical structure of nanographene promoting nanofiber formation, and the structural properties of an organic semiconductor containing disordered regions. We also discuss the limitations and prospects of 3D ED compared to microcrystallography with X-ray free electron lasers.

Experimental capabilities for liquid jet samples at sub-MHz rates at the FXE Instrument at European XFEL

The Femtosecond X-ray Experiments (FXE) instrument at the European X-ray Free-Electron Laser (EuXFEL) provides an optimized platform for investigations of ultrafast physical, chemical and biological processes. It operates in the energy range 4.7-20 keV accommodating flexible and versatile environments for a wide range of samples using diverse ultrafast X-ray spectroscopic, scattering and diffraction techniques. FXE is particularly suitable for experiments taking advantage of the sub-MHz repetition rates provided by the EuXFEL. In this paper a dedicated setup for studies on ultrafast biological and chemical dynamics in solution phase at sub-MHz rates at FXE is presented. Particular emphasis on the different liquid jet sample delivery options and their performance is given. Our portfolio of high-speed jets compatible with sub-MHz experiments includes cylindrical jets, gas dynamic virtual nozzles and flat jets. The capability to perform multi-color X-ray emission spectroscopy (XES) experiments is illustrated by a set of measurements using the dispersive X-ray spectrometer in von Hamos geometry. Static XES data collected using a multi-crystal scanning Johann-type spectrometer are also presented. A few examples of experimental results on ultrafast time-resolved X-ray emission spectroscopy and wide-angle X-ray scattering at sub-MHz pulse repetition rates are given.

Radiation damage to biological macromolecules∗

In this review, we describe recent research developments into radiation damage effects in macromolecular X-ray crystallography observed at synchrotrons and X-ray free electron lasers. Radiation damage in small molecule X-ray crystallography, small angle X-ray scattering experiments, microelectron diffraction, and single particle cryo-electron microscopy is briefly covered.

XFEL Microcrystallography of Self-Assembling Silver n-Alkanethiolates

New synthetic hybrid materials and their increasing complexity have placed growing demands on crystal growth for single-crystal X-ray diffraction analysis. Unfortunately, not all chemical systems are conducive to the isolation of single crystals for traditional characterization. Here, small-molecule serial femtosecond crystallography (smSFX) at atomic resolution (0.833 Å) is employed to characterize microcrystalline silver n-alkanethiolates with various alkyl chain lengths at X-ray free electron laser facilities, resolving long-standing controversies regarding the atomic connectivity and odd-even effects of layer stacking. smSFX provides high-quality crystal structures directly from the powder of the true unknowns, a capability that is particularly useful for systems having notoriously small or defective crystals. We present crystal structures of silver n-butanethiolate (C4), silver n-hexanethiolate (C6), and silver n-nonanethiolate (C9). We show that an odd-even effect originates from the orientation of the terminal methyl group and its role in packing efficiency. We also propose a secondary odd-even effect involving multiple mosaic blocks in the crystals containing even-numbered chains, identified by selected-area electron diffraction measurements. We conclude with a discussion of the merits of the synthetic preparation for the preparation of microdiffraction specimens and compare the long-range order in these crystals to that of self-assembled monolayers.

Structural resolution of a small organic molecule by serial X-ray free-electron laser and electron crystallography

Structure analysis of small crystals is important in areas ranging from synthetic organic chemistry to pharmaceutical and material sciences, as many compounds do not yield large crystals. Here we present the detailed characterization of the structure of an organic molecule, rhodamine-6G, determined at a resolution of 0.82 Å by an X-ray free-electron laser (XFEL). Direct comparison of this structure with that obtained by electron crystallography from the same sample batch of microcrystals shows that both methods can accurately distinguish the position of some of the hydrogen atoms, depending on the type of chemical bond in which they are involved. Variations in the distances measured by XFEL and electron diffraction reflect the expected differences in X-ray and electron scatterings. The reliability for atomic coordinates was found to be better with XFEL, but the electron beam showed a higher sensitivity to charges.

1D Hybrid Semiconductor Silver 2,6-Difluorophenylselenolate

Organic-inorganic hybrid materials present new opportunities for creating low-dimensional structures with unique light-matter interaction. In this work, we report a chemically robust yellow emissive one-dimensional (1D) semiconductor, silver 2,6-difluorophenylselenolate─AgSePhF₂(2,6), a new member of the broader class of hybrid low-dimensional semiconductors, metal-organic chalcogenolates. While silver phenylselenolate (AgSePh) crystallizes as a two-dimensional (2D) van der Waals semiconductor, introduction of fluorine atoms at the (2,6) position of the phenyl ring induces a structural transition from 2D sheets to 1D chains. Density functional theory calculations reveal that AgSePhF₂ (2,6) has strongly dispersive conduction and valence bands along the 1D crystal axis. Visible photoluminescence centered around λ_p ≈ 570 nm at room temperature exhibits both prompt (110 ps) and delayed (36 ns) components. The absorption spectrum exhibits excitonic resonances characteristic of low-dimensional hybrid semiconductors, with an exciton binding energy of approximately 170 meV as determined by temperature-dependent photoluminescence. The discovery of an emissive 1D silver organoselenolate highlights the structural and compositional richness of the chalcogenolate material family and provides new insights for molecular engineering of low-dimensional hybrid organic-inorganic semiconductors.

Microwave-assisted synthesis of metal-organic chalcogenolate assemblies as electrocatalysts for syngas production

Today, many essential industrial processes depend on syngas. Due to a high energy demand and overall cost as well as a dependence on natural gas as its precursor, alternative routes to produce this valuable mixture of hydrogen and carbon monoxide are urgently needed. Electrochemical syngas production via two competing processes, namely carbon dioxide (CO₂) reduction and hydrogen (H₂) evolution, is a promising method. Often, noble metal catalysts such as gold or silver are used, but those metals are costly and have limited availability. Here, we show that metal-organic chalcogenolate assemblies (MOCHAs) combine several properties of successful electrocatalysts. We report a scalable microwave-assisted synthesis method for highly crystalline MOCHAs ([AgXPh] _∞: X = Se, S) with high yields. The morphology, crystallinity, chemical and structural stability are thoroughly studied. We investigate tuneable syngas production via electrocatalytic CO₂ reduction and find the MOCHAs show a maximum Faraday efficiency (FE) of 55 and 45% for the production of carbon monoxide and hydrogen, respectively.

Towards pump-probe single-crystal XFEL refinements for small-unit-cell systems

Serial femtosecond crystallography for small-unit-cell systems has so far seen very limited application despite obvious scientific possibilities. This is because reliable data reduction has not been available for these challenging systems. In particular, important intensity corrections such as the partiality correction critically rely on accurate determination of the crystal orientation, which is complicated by the low number of diffraction spots for small-unit-cell crystals. A data reduction pipeline capable of fully automated handling of all steps of data reduction from spot harvesting to merged structure factors has been developed. The pipeline utilizes sparse indexing based on known unit-cell parameters, seed-skewness integration, intensity corrections including an overlap-based combined Ewald sphere width and partiality correction, and a dynamically adjusted post-refinement routine. Using the pipeline, data measured on the compound K4[Pt2(P2O5H2)4]·2H2O have been successfully reduced and used to solve the structure to an R1 factor of ∼9.1%. It is expected that the pipeline will open up the field of small-unit-cell serial femtosecond crystallography experiments and allow investigations into, for example, excited states and reaction intermediate chemistry.

Light Emission in 2D Silver Phenylchalcogenolates

Silver phenylselenolate (AgSePh, also known as "mithrene") and silver phenyltellurolate (AgTePh, also known as "tethrene") are two-dimensional (2D) van der Waals semiconductors belonging to an emerging class of hybrid organic-inorganic materials called metal-organic chalcogenolates. Despite having the same crystal structure, AgSePh and AgTePh exhibit a strikingly different excitonic behavior. Whereas AgSePh exhibits narrow, fast luminescence with a minimal Stokes shift, AgTePh exhibits comparatively slow luminescence that is significantly broadened and red-shifted from its absorption minimum. Using time-resolved and temperature-dependent absorption and emission microspectroscopy, combined with subgap photoexcitation studies, we show that exciton dynamics in AgTePh films are dominated by an intrinsic self-trapping behavior, whereas dynamics in AgSePh films are dominated by the interaction of band-edge excitons with a finite number of extrinsic defect/trap states. Density functional theory calculations reveal that AgSePh has simple parabolic band edges with a direct gap at Γ, whereas AgTePh has a saddle point at Γ with a horizontal splitting along the Γ-N₁ direction. The correlation between the unique band structure of AgTePh and exciton self-trapping behavior is unclear, prompting further exploration of excitonic phenomena in this emerging class of hybrid 2D semiconductors.

Wall-free droplet microfluidics for probing biological processes by high-brilliance X-ray scattering techniques

Here we review probing biological processes initiated by the deposition of droplets on surfaces by micro- and nanobeam X-ray scattering techniques using synchrotron radiation and X-ray free-electron laser sources. We review probing droplet evaporation on superhydrophobic surfaces and reactions with substrates, basics of droplets deposition and flow simulations, droplet deposition techniques and practical experience at a synchrotron beamline. Selected applications with biological relevance will be reviewed and perspectives for the latest generation of high-brilliance X-ray sources discussed.

Acoustic Focusing of Protein Crystals for In-Line Monitoring and Up-Concentration during Serial Crystallography

Serial femtosecond crystallography (SFX) has become one of the standard techniques at X-ray free-electron lasers (XFELs) to obtain high-resolution structural information from microcrystals of proteins. Nevertheless, reliable sample delivery is still often limiting data collection, as microcrystals can clog both field- and flow-focusing nozzles despite in-line filters. In this study, we developed acoustic 2D focusing of protein microcrystals in capillaries that enables real-time online characterization of crystal size and shape in the sample delivery line after the in-line filter. We used a piezoelectric actuator to create a standing wave perpendicular to the crystal flow, which focused lysozyme microcrystals into a single line inside a silica capillary so that they can be imaged using a high-speed camera. We characterized the acoustic contrast factor, focus size, and the coaxial flow lines and developed a splitting union that enables up-concentration to at least a factor of five. The focus size, flow rates, and geometry may enable an upper limit of up-concentration as high as 200 fold. The novel feedback and concentration control could be implemented for serial crystallography at synchrotrons with minor modifications. It will also aid the development of improved sample delivery systems that will increase SFX data collection rates at XFELs, with potential applications to many proteins that can only be purified and crystallized in small amounts.

Layered Organic Metal Chalcogenides (OMCs): From Bulk to Two-Dimensional Materials

The modification of inorganic two-dimensional (2D) materials with organic functional motifs is in high demand for the optimization of their properties, but it is still a daunting challenge. Organic metal chalcogenides (OMCs) are a type of newly emerging 2D materials, with metal chalcogenide layers covalently anchored by long-range ordered organic functional motifs, these materials are extremely desirable but impossible to realize by traditional methods. Both the inorganic layer and organic functional motifs of OMCs are highly designable and thus provide this type of 2D materials with enormous variety in terms of their structure and properties. This Minireview aims to review the latest developments in OMCs and their bulk precursors. Firstly, the structure types of the bulk precursors for OMCs are introduced. Second, the synthesis and applications of OMC 2D materials in photoelectricity, catalysis, sensors, and energy transfer are explored. Finally, the challenges and perspectives for future research on OMCs are discussed.

SDPD-SX: Combining a single crystal X-ray diffraction setup with advanced powder data structure determination for use in early stage drug discovery

We report a method for routine crystal structure determination on very small (typically 0.1 mg or less) amounts of crystalline material using powder X-ray diffraction data from a laboratory-based single-crystal...