TORO Indexer: a PyTorch-based indexing algorithm for kilohertz serial crystallography.

Serial crystallography (SX) involves combining observations from a very large number of diffraction patterns coming from crystals in random orientations. To compile a complete data set, these patterns must be indexed (i.e. their orientation determined), integrated and merged. Introduced here is TORO (Torch-powered robust optimization) Indexer, a robust and adaptable indexing algorithm developed using the PyTorch framework. TORO is capable of operating on graphics processing units (GPUs), central processing units (CPUs) and other hardware accelerators supported by PyTorch, ensuring compatibility with a wide variety of computational setups. In tests, TORO outpaces existing solutions, indexing thousands of frames per second when running on GPUs, which positions it as an attractive candidate to produce real-time indexing and user feedback. The algorithm streamlines some of the ideas introduced by previous indexers like DIALS real-space grid search [Gildea, Waterman, Parkhurst, Axford, Sutton, Stuart, Sauter, Evans & Winter (2014). Acta Cryst. D70, 2652-2666] and XGandalf [Gevorkov, Yefanov, Barty, White, Mariani, Brehm, Tolstikova, Grigat & Chapman (2019). Acta Cryst. A75, 694-704] and refines them using faster and principled robust optimization techniques which result in a concise code base consisting of less than 500 lines. On the basis of evaluations across four proteins, TORO consistently matches, and in certain instances outperforms, established algorithms such as XGandalf and MOSFLM [Powell (1999). Acta Cryst. D55, 1690-1695], occasionally amplifying the quality of the consolidated data while achieving superior indexing speed. The inherent modularity of TORO and the versatility of PyTorch code bases facilitate its deployment into a wide array of architectures, software platforms and bespoke applications, highlighting its prospective significance in SX.

X-ray absorption spectroscopy with time-tagged photon counting: application to study the structure of a Co(i) intermediate of H2 evolving photo-catalyst.

In order to probe the structure of reaction intermediates of photochemical reactions a new setup for laser-initiated time-resolved X-ray absorption (XAS) measurements has been developed. With this approach the arrival time of each photon in respect to the laser pulse is measured and therefore full kinetic information is obtained. All X-rays that reach the detector are used to measure this kinetic information and therefore the detection efficiency of this method is high. The newly developed setup is optimized for time-resolved experiments in the microsecond range for samples with relatively low metal concentration (∼1mM). This setup has been applied to study a multicomponent photocatalytic system with a Co(dmgBF(2))(2) catalyst (dmg(2-) = dimethylglyoximato dianion), [Ru(bpy)(3)](2+) chromophore (bpy = 2,2'-bipyridine) and methyl viologen as the electron relay. On the basis of the analysis of hundreds of Co K-edge XAS spectra corresponding to different delay times after the laser excitation of the chromophore, the presence of a Co(i) intermediate is confirmed. The calculated X-ray transient signal for a model of Co(i) state with a 0.14 Šdisplacement of Co out of the dmg ligand plane and with the closest solvent molecule at a distance of 2.06 Šgives reasonable agreement with the experimental data.

Bonding and charge transfer in nitrogen-donor uranyl complexes: insights from NEXAFS spectra.

We investigate the electronic structure of three newly synthesized nitrogen-donor uranyl complexes [(UO2)(H2bbp)Cl2], [(UO)2(Hbbp)(Py)Cl], and [(UO2)(bbp)(Py)2] using a combination of near-edge X-ray absorption fine structure (NEXAFS) spectroscopy experiments and simulations. The complexes studied feature derivatives of the tunable tridentate N-donor ligand 2,6-bis(2-benzimidazyl)pyridine (bbp) and exhibit discrete chemical differences in uranyl coordination. The sensitivity of the N K-edge X-ray absorption spectrum to local bonding and charge transfer is exploited to systematically investigate the evolution of structural as well as electronic properties across the three complexes. A thorough interpretation of the measured experimental spectra is achieved via ab initio NEXAFS simulations based on the eXcited electron and Core-Hole (XCH) approach and enables the assignment of spectral features to electronic transitions on specific absorbing sites. We find that ligand-uranyl bonding leads to a signature blue shift in the N K-edge absorption onset, resulting from charge displacement toward the uranyl, while changes in the equatorial coordination shell of the uranyl lead to more subtle modulations in the spectral features. Theoretical simulations show that the flexible local chemistry at the nonbinding imidazole-N sites of the bbp ligand is also reflected in the NEXAFS spectra and highlights potential synthesis strategies to improve selectivity. In particular, we find that interactions of the bbp ligand with solvent molecules can lead to changes in ligand-uranyl binding geometry while also modulating the K-edge absorption. Our results suggest that NEXAFS spectroscopy combined with first-principles interpretation can offer insights into the coordination chemistry of analogous functionalized conjugated ligands.

Release of antimony from contaminated soil induced by redox changes.

Soil contamination by toxic antimony (Sb) released from corroding ammunition has become an issue of public concern in various countries. Many of these soils are at least occasionally subject to waterlogging; yet mechanisms controlling Sb mobility under anaerobic conditions are still poorly understood. We investigated Sb concentration and speciation dynamics in a calcareous shooting range soil in terms of changing redox conditions using microcosm experiments. The transition to reducing conditions invoked by indigenous microbial activity at first led to the immobilization of Sb, as Sb(V) was converted to Sb(III), which binds more extensively to iron (hydr)oxides. When reducing conditions continued, the previously sorbed Sb(III) was gradually released into solution due to reductive dissolution of the iron (hydr)oxides. Speciation measurements in the solid phase by Sb K-edge XANES spectroscopy and in the soil solution by liquid chromatography ICP-MS provided the first evidence that Sb(III) predominated at low redox conditions (Eh <0.05 V) in both phases. The results show that Sb(V) is less stable in reducing environments than commonly assumed. Given that Sb(III) is generally more toxic than Sb(V), the mobilization of Sb(III) under Fe-reducing conditions may significantly increase (eco)toxicological risks arising from Sb-contaminated soils that are prone to flooding or waterlogging.

Toward equatorial planarity about uranyl: synthesis and structure of tridentate nitrogen-donor {UO2}2+ complexes.

The reaction of UO2Cl2·3THF with the tridentate nitrogen donor ligand 2,6-bis(2-benzimidazolyl)pyridine (H2BBP) in pyridine leads to the formation of three different complexes: [(UO2)(H2BBP)Cl2] (1), [(UO)2(HBBP)(Py)Cl] (2), and [(UO2)(BBP)(Py)2] (3) after successive deprotonation of H2BBP with a strong base. Crystallographic determination of 1-3 reveals that increased charge through ligand deprotonation and displacement of chloride leads to equatorial planarity about uranyl as well as a more compact overall coordination geometry. Near-Edge X-ray Absorption Fine Structure (NEXAFS) spectra of 1-3 at the U-4d edges have been recorded using a soft X-ray Scanning Transmission X-ray Microscope (STXM) and reveal the uranium 4d5/2 and 4d3/2 transitions at energies associated with uranium in the hexavalent oxidation state. First-principles Density Functional Theory (DFT) electronic structure calculations for the complexes have been performed to determine and validate the coordination characteristics, which correspond well to the experimental results.

High energy resolution off-resonant spectroscopy at sub-second time resolution: (Pt(acac)2) decomposition.

We report on the decomposition of platinum acetylacetonate (Pt(acac)(2)) in hydrogen induced by flash heating. The changes in the local Pt structure were followed by high energy resolution off-resonant spectroscopy uniquely performed with sub-second time resolution. The decomposition consists of a two-step reduction process of the Pt(II) species.

The irreversible formation of palladium carbide during hydrogenation of 1-pentyne over silica-supported palladium nanoparticles: in situ Pd K and L3 edge XAS.

The catalytically active phase of silica-supported palladium catalysts in the selective and non-selective hydrogenation of 1-pentyne was determined using in situ X-ray absorption spectroscopy at the Pd K and L(3) edges. Upon exposure to alkyne, a palladium carbide-like phase rapidly forms, which prevents hydrogen to diffuse into the bulk of the nano-sized particles. Both selective and non-selective hydrogenation occur over carbided particles. The palladium carbide-like phase is stable under reaction conditions and only partially decomposes under high hydrogen partial pressure. Non-selective hydrogenation to pentane is not indicative of hydride formation. The palladium carbide phase was detected in the EXAFS analysis and the K edge XANES showed representative features.

A high-repetition rate scheme for synchrotron-based picosecond laser pump/x-ray probe experiments on chemical and biological systems in solution.

We present the extension of time-resolved optical pump/x-ray absorption spectroscopy (XAS) probe experiments towards data collection at MHz repetition rates. The use of a high-power picosecond laser operating at an integer fraction of the repetition rate of the storage ring allows exploitation of up to two orders of magnitude more x-ray photons than in previous schemes based on the use of kHz lasers. Consequently, we demonstrate an order of magnitude increase in the signal-to-noise of time-resolved XAS of molecular systems in solution. This makes it possible to investigate highly dilute samples at concentrations approaching physiological conditions for biological systems. The simplicity and compactness of the scheme allows for straightforward implementation at any synchrotron beamline and for a wide range of x-ray probe techniques, such as time-resolved diffraction or x-ray emission studies.

Five-element Johann-type x-ray emission spectrometer with a single-photon-counting pixel detector.

A Johann-type spectrometer with five spherically bent crystals and a pixel detector was constructed for a range of hard x-ray photon-in photon-out synchrotron techniques, covering a Bragg-angle range of 60°-88°. The spectrometer provides a sub emission line width energy resolution from sub-eV to a few eV and precise energy calibration, better than 1.5 eV for the full range of Bragg angles. The use of a pixel detector allows fast and easy optimization of the signal-to-background ratio. A concentration detection limit below 0.4 wt% was reached at the Cu Kα(1) line. The spectrometer is designed as a modular mobile device for easy integration in a multi-purpose hard x-ray synchrotron beamline, such as the SuperXAS beamline at the Swiss Light Source.

In situ XAS and XRPD parametric rietveld refinement to understand dealumination of Y zeolite catalyst.

Dealumination of NH(4)-Y zeolite during steaming to 873 K was investigated with in situ, time-dependent, synchrotron radiation XRPD and in situ Al K-edge XAS. Water desorption is complete at 450 K, and ammonium decomposition occurs between 500 and 550 K. Only a small fraction of Al(3+) species (5%) leaves the framework during heating from 710 to 873 K; these species occupy site I' inside the sodalite cage. This fraction increases up to 8% in the first 50 min at 873 K and remains constant for the following 70 min isotherm and during the high-temperature part of the cooling experiment. During cooling from 500 to 450 K, the electron density at site I' increases suddenly, corresponding to a fraction of 30-35% of the total Al, confirmed by ex situ (27)Al MAS solid-state NMR. At that temperature, in situ Al K-edge XAS indicates a change in Al coordination of a large fraction of Al, and thermogravimetric (TG) data show the first water molecules start to repopulate the pores. Such molecules drive the dislodgment of most of the Al from the zeolitic framework. Our data indicate that considerable structural collapse caused by steaming does not occur at the highest temperature; however, defects form, which lead to significant migration of framework Al(3+) to extraframework positions, which occurs only as water is able to enter the pores again, that is, at much lower temperature. Contrary to general opinion, these results demonstrate that zeolite dealumination is not primarily a high-temperature process. The standard Rietveld refinement approach failed to identify extraframework Al species. These new results were obtained by adopting the innovative parametric refinement [J. Appl. Crystallogr. 2007, 40, 87]. Treating all of the XRPD patterns collected during the evolution of temperature as one unique data set significantly reduces the overall number of optimized variables and, thus, their relative correlation, and finally results in a more reliable estimate of the optimized parameters. Our results contribute to a better understanding of the phenomena involved on the atomic scale in the preparation of ultrastable Y zeolites (USY). USY are employed in fluid catalytic cracking (FCC), which is the most important conversion process in petroleum refineries to convert the high-boiling hydrocarbon fractions of petroleum crude oils to more valuable products like gasoline and olefinic gases.

A comparison of 4f vs 5f metal-metal bonds in (CpSiMe3)3M-ECp* (M = Nd, U; E = Al, Ga; Cp* = C5Me5): synthesis, thermodynamics, magnetism, and electronic structure.

Reaction of (CpSiMe(3))(3)U or (CpSiMe(3))(3)Nd with (Cp*Al)(4) or Cp*Ga (Cp* = C(5)Me(5)) afforded the isostructural complexes (CpSiMe(3))(3)M-ECp* (M = U, E = Al (1); M = U, E = Ga (2); M = Nd, E = Al (3); M = Nd, E = Ga (4)). In the case of 1 and 2 the complexes were isolated in 39 and 90% yields, respectively, as crystalline solids and were characterized by single-crystal X-ray diffraction, variable-temperature (1)H NMR spectroscopy, elemental analysis, variable-temperature magnetic susceptibility, and UV-visible-NIR spectroscopy. In the case of 3 and 4, the complexes were observed by variable-temperature (1)H NMR spectroscopy but were not isolated as pure materials. Comparison of the equilibrium constants and thermodynamic parameters DeltaH and DeltaS obtained by (1)H NMR titration methods revealed a much stronger U-Ga interaction in 2 than the Nd-Ga interaction in 4. Competition reactions between (CpSiMe(3))(3)U and (CpSiMe(3))(3)Nd indicate that Cp*Ga selectively binds U over Nd in a 93:7 ratio at 19 degrees C and 96:4 at -33 degrees C. For 1 and 3, comparison of (1)H NMR peak intensities suggests that Cp*Al also achieves excellent U(III)/Nd(III) selectivity at 21 degrees C. The solution electronic spectra and solid-state temperature-dependent magnetic susceptibilities of 1 and 2, in addition to X-ray absorption near-edge structure (XANES) measurements from scanning transmission X-ray microscopy (STXM) of 1, are consistent with those observed for other U(III) coordination complexes. DFT calculations using five different functionals were performed on the model complexes Cp(3)M-ECp (M = Nd, U; E = Al, Ga), and empirical fitting of the values for Cp(3)M-ECp allowed the prediction of binding energy estimates for Cp*Al compounds 1 and 3. NBO/NLMO bonding analyses on Cp(3)U-ECp indicate that the bonding consists predominantly of a E-->U sigma-interaction arising from favorable overlap between the diffuse ligand lone pair and the primarily 7s/6d acceptor orbitals on U(III), with negligible U-->E pi-donation. The overall experimental and computational bonding analysis suggests that Cp*Al and Cp*Ga behave as good sigma-donors in these systems.

Influence of crystallographic orientation of biogenic calcite on in situ Mg XANES analyses.

Micro X-ray absorption near-edge spectroscopy at the Mg K-edge is a useful technique for acquiring information about the environment of Mg(2+) in biogenic calcite. These analyses can be applied to shell powders or intact shell structures. The advantage of the latter is that the XANES analyses can be applied to specific areas, at high (e.g. micrometre) spatial resolution, to determine the environment of Mg(2+) in a biomineral context. Such in situ synchrotron analysis has to take into account the potential effect of crystallographic orientation given the anisotropy of calcite crystals and the polarized nature of X-rays. Brachiopod shells of species with different crystallographic orientations are used to assess this crystallographic effect on in situ synchrotron measurements at the Mg K-edge. Results show that, owing to the anisotropy of calcite, in situ X-ray absorption spectra (XAS) are influenced by the crystallographic orientation of calcite crystals with a subsequent potentially erroneous interpretation of Mg(2+) data. Thus, this study demonstrates the importance of crystallography for XAS analyses and, therefore, the necessity to obtain crystallographic information at high spatial resolution prior to spectroscopic analysis.