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X-ray scattering experiments using Free Electron Lasers (XFELs) are a powerful tool to determine the molecular structure and function of unknown samples (such as COVID-19 viral proteins). XFEL experiments are a challenge to computing in two ways: i) due to the high cost of running XFELs, a fast turnaround time from data acquisition to data analysis is essential to make informed decisions on experimental protocols; ii) data collection rates are growing exponentially, requiring new scalable algorithms. Here we report our experiences analyzing data from two experiments at the Linac Coherent Light Source (LCLS) during September 2020. Raw data were analyzed on NERSC's Cori XC40 system, using the Superfacility paradigm: our workflow automatically moves raw data between LCLS and NERSC, where it is analyzed using the software package CCTBX. We achieved real time data analysis with a turnaround time from data acquisition to full molecular reconstruction in as little as 10 min -- sufficient time for the experiment's operators to make informed decisions. By hosting the data analysis on Cori, and by automating LCLS-NERSC interoperability, we achieved a data analysis rate which matches the data acquisition rate. Completing data analysis with 10 mins is a first for XFEL experiments and an important milestone if we are to keep up with data collection trends.

The P450 enzyme CYP121 from Mycobacterium tuberculosis catalyzes a carbon-carbon (C-C) bond coupling cyclization of the dityrosine substrate containing a diketopiperazine ring, cyclo(l-tyrosine-l-tyrosine) (cYY). An unusual high-spin (S = 5/2) ferric intermediate maximizes its population in less than 5 ms in the rapid freeze-quenching study of CYP121 during the shunt reaction with peracetic acid or hydrogen peroxide in acetic acid solution. We show that this intermediate can also be observed in the crystalline state by EPR spectroscopy. By developing an on-demand-rapid-mixing method for time-resolved serial femtosecond crystallography with X-ray free-electron laser (tr-SFX-XFEL) technology covering the millisecond time domain and without freezing, we structurally monitored the reaction in situ at room temperature. After a 200 ms peracetic acid reaction with the cocrystallized enzyme-substrate microcrystal slurry, a ferric-hydroperoxo intermediate is observed, and its structure is determined at 1.85 Å resolution. The structure shows a hydroperoxyl ligand between the heme and the native substrate, cYY. The oxygen atoms of the hydroperoxo are 2.5 and 3.2 Å from the iron ion. The end-on binding ligand adopts a near-side-on geometry and is weakly associated with the iron ion, causing the unusual high-spin state. This compound 0 intermediate, spectroscopically and structurally observed during the catalytic shunt pathway, reveals a unique binding mode that deviates from the end-on compound 0 intermediates in other heme enzymes. The hydroperoxyl ligand is only 2.9 Å from the bound cYY, suggesting an active oxidant role of the intermediate for direct substrate oxidation in the nonhydroxylation C-C bond coupling chemistry.

In natural photosynthesis, the light-driven splitting of water into electrons, protons and molecular oxygen forms the first step of the solar-to-chemical energy conversion process. The reaction takes place in photosystem II, where the Mn4CaO5 cluster first stores four oxidizing equivalents, the S0 to S4 intermediate states in the Kok cycle, sequentially generated by photochemical charge separations in the reaction center and then catalyzes the O-O bond formation chemistry1-3. Here, we report room temperature snapshots by serial femtosecond X-ray crystallography to provide structural insights into the final reaction step of Kok's photosynthetic water oxidation cycle, the S3→[S4]→S0 transition where O2 is formed and Kok's water oxidation clock is reset. Our data reveal a complex sequence of events, which occur over micro- to milliseconds, comprising changes at the Mn4CaO5 cluster, its ligands and water pathways as well as controlled proton release through the hydrogen-bonding network of the Cl1 channel. Importantly, the extra O atom Ox, which was introduced as a bridging ligand between Ca and Mn1 during the S2→S3 transition4-6, disappears or relocates in parallel with Yz reduction starting at approximately 700 μs after the third flash. The onset of O2 evolution, as indicated by the shortening of the Mn1-Mn4 distance, occurs at around 1,200 μs, signifying the presence of a reduced intermediate, possibly a bound peroxide.

Methyl-Coenzyme M Reductase (MCR) catalyzes the biosynthesis of methane in methanogenic archaea, using a catalytic Ni-centered Cofactor F430 in its active site. It also catalyzes the reverse reaction, that is, the anaerobic activation and oxidation, including the cleavage of the CH bond in methane. Because methanogenesis is the major source of methane on earth, understanding the reaction mechanism of this enzyme can have massive implications in global energy balances. While recent publications have proposed a radical-based catalytic mechanism as well as novel sulfonate-based binding modes of MCR for its native substrates, the structure of the active state of MCR, as well as a complete characterization of the reaction, remain elusive. Previous attempts to structurally characterize the active MCR-Ni(I) state have been unsuccessful due to oxidation of the redox- sensitive catalytic Ni center. Further, while many cryo structures of the inactive Ni(II)-enzyme in various substrates-bound forms have been published, no room temperature structures have been reported, and the structure and mechanism of MCR under physiologically relevant conditions is not known. In this study, we report the first room temperature structure of the MCRred1-silent Ni(II) form using an X-ray Free-Electron Laser (XFEL), with simultaneous X-ray Emission Spectroscopy (XES) and X-ray Diffraction (XRD) data collection. In celebration of the seminal contributions of inorganic chemist Dick Holm to our understanding of nickel-based catalysis, we are honored to announce our findings in this special issue dedicated to this remarkable pioneer of bioinorganic chemistry.

Inorganic-organic hybrid materials represent a large share of newly reported structures, owing to their simple synthetic routes and customizable properties1. This proliferation has led to a characterization bottleneck: many hybrid materials are obligate microcrystals with low symmetry and severe radiation sensitivity, interfering with the standard techniques of single-crystal X-ray diffraction2,3 and electron microdiffraction4-11. Here we demonstrate small-molecule serial femtosecond X-ray crystallography (smSFX) for the determination of material crystal structures from microcrystals. We subjected microcrystalline suspensions to X-ray free-electron laser radiation12,13 and obtained thousands of randomly oriented diffraction patterns. We determined unit cells by aggregating spot-finding results into high-resolution powder diffractograms. After indexing the sparse serial patterns by a graph theory approach14, the resulting datasets can be solved and refined using standard tools for single-crystal diffraction data15-17. We describe the ab initio structure solutions of mithrene (AgSePh)18-20, thiorene (AgSPh) and tethrene (AgTePh), of which the latter two were previously unknown structures. In thiorene, we identify a geometric change in the silver-silver bonding network that is linked to its divergent optoelectronic properties20. We demonstrate that smSFX can be applied as a general technique for structure determination of beam-sensitive microcrystalline materials at near-ambient temperature and pressure.

X-ray scattering experiments using Free Electron Lasers (XFELs) are apowerful tool to determine the molecular structure and function of unknownsamples (such as COVID-19 viral proteins). XFEL experiments are a challenge tocomputing in two ways: i) due to the high cost of running XFELs, a fastturnaround time from data acquisition to data analysis is essential to makeinformed decisions on experimental protocols; ii) data collection rates aregrowing exponentially, requiring new scalable algorithms. Here we report ourexperiences analyzing data from two experiments at the Linac Coherent LightSource (LCLS) during September 2020. Raw data were analyzed on NERSC's CoriXC40 system, using the Superfacility paradigm: our workflow automatically movesraw data between LCLS and NERSC, where it is analyzed using the softwarepackage CCTBX. We achieved real time data analysis with a turnaround time fromdata acquisition to full molecular reconstruction in as little as 10 min --sufficient time for the experiment's operators to make informed decisions. Byhosting the data analysis on Cori, and by automating LCLS-NERSCinteroperability, we achieved a data analysis rate which matches the dataacquisition rate. Completing data analysis with 10 mins is a first for XFELexperiments and an important milestone if we are to keep up with datacollection trends.

Understanding how chemical modifications alter the atomic‐scale organization of materials is of fundamental importance in materials engineering and the target of considerable efforts in computational prediction. Incorporating covalent and noncovalent interactions in designing crystals while "piggybacking" on the driving force of molecular self‐assembly has augmented efforts to understand the emergence of complex structures using directed synthesis. In this work, microcrystalline powders of the silver 2‐, 3‐, and 4‐fluorobenzenethiolates are prepared and their structures are resolved by small‐molecule serial femtosecond X‐ray crystallography. These three compounds enable the emergence and role of supramolecular synthons in the crystal structures of 3D metal‐organic chalcogenolates to be examined. The unique divergence in their optoelectronic, morphological, and structural behaviors is assessed. The extent of CHF interactions and their influence on the structure and the observed trends in the thermal stability of the crystals are quantified through theoretical calculations and thermogravimetric analysis. [ABSTRACT FROM AUTHOR]

The tunnelling of electrons through molecules (and through any nanoscale insulating and dielectric material.sup.1) shows exponential attenuation with increasing length.sup.2, a length dependence that is reflected in the ability of the electrons to carry an electrical current. It was recently demonstrated.sup.3-5 that coherent tunnelling through a molecular junction can also be suppressed by destructive quantum interference.sup.6, a mechanism that is not length-dependent. For the carbon-based molecules studied previously, cancelling all transmission channels would involve the suppression of contributions to the current from both the [pi]-orbital and [sigma]-orbital systems. Previous reports of destructive interference have demonstrated a decrease in transmission only through the [pi]-channel. Here we report a saturated silicon-based molecule with a functionalized bicyclo[2.2.2]octasilane moiety that exhibits destructive quantum interference in its [sigma]-system. Although molecular silicon typically forms conducting wires.sup.7, we use a combination of conductance measurements and ab initio calculations to show that destructive [sigma]-interference, achieved here by locking the silicon-silicon bonds into eclipsed conformations within a bicyclic molecular framework, can yield extremely insulating molecules less than a nanometre in length. Our molecules also exhibit an unusually high thermopower (0.97 millivolts per kelvin), which is a further experimental signature of the suppression of all tunnelling paths by destructive interference: calculations indicate that the central bicyclo[2.2.2]octasilane unit is rendered less conductive than the empty space it occupies. The molecular design presented here provides a proof-of-concept for a quantum-interference-based approach to single-molecule insulators.Highly insulating silicon-based molecules, engineered so that conduction is fully suppressed by [sigma] quantum interference even for molecules less than a nanometre long, could prove useful in molecular-scale electronic circuitry., Author(s): Marc H. Garner [sup.1] , Haixing Li [sup.2] [sup.6] , Yan Chen [sup.3] , Timothy A. Su [sup.4] [sup.7] , Zhichun Shangguan [sup.3] [sup.8] , Daniel W. Paley [sup.4] [...]

The design of metal–organic frameworks (MOFs) that incorporate more than one metal cluster constituent is a challenging task. Conventional one‐pot reaction protocols require judicious selection of ligand and metal ion precursors, yet remain unpredictable. Stable, preformed nanoclusters, with ligand shells that can undergo additional coordination‐driven reactions, provide a platform for assembling multi‐cluster solids with precision. Herein, a discrete Co6S8(PTA)6 (PTA=1,3,5‐triaza‐7‐phosphaadamantane) superatomic‐metalloligand is assembled into a three‐dimensional (3D) coordination polymer comprising Cu4I4 secondary building units (SBUs). The resulting heterobimetallic framework (1) contains two distinct cluster constituents and bifunctional PTA linkers. Solid‐state diffuse reflectance studies reveal that 1 is an optical semiconductor with a band‐gap of 1.59 eV. Framework‐modified electrodes exhibit reversible redox behavior in the solid state arising from the Co6S8 superatoms, which remain intact during framework synthesis. [ABSTRACT FROM AUTHOR]