Nucleophilic Displacement Reactions of Silver-Based Metal-Organic Chalcogenolates.

We report nucleophilic displacement reactions that can increase the dimensionality or coordination number of silver-based metal-organic chalcogenolates (MOChas). MOChas are crystalline ensembles containing one-dimensional (1D) or two-dimensional (2D) inorganic topologies with structures and properties defined by the choice of metal, chalcogen, and ligand. MOChas can be readily prepared from a variety of small-molecule ligands and metals or metal ions. Although MOChas offer ligand diversity, most reported examples use relatively small ligands, typically involving short alkyl chains, aryl rings, or molecular cages. This is because larger, more complex molecules often yield poor product morphologies with indeterminate structures. In this study, we overcame this limitation by employing a ligand exchange strategy whereby a 1D MOCha, silver(I) methyl 2-mercaptobenzoate (2MMB), is used as a silver source for preparing 2D examples. The reaction proceeds generally toward products composed of the stronger nucleophile. We show that the reaction prefers displacing 1D topologies to yield 2D ones and replacing thiolates with selenolates. We performed a study to characterize the mechanism by which organic chalcogenols and dichalcogenides exchange with MOChas. The collected data and product analysis support a proposed mechanism of nucleophilic substitution, explaining how both organic chalcogenols and dichalcogenides can displace ligands in MOChas. This work provides a new synthetic route that will enable the preparation of more elaborate MOChas and heterostructures thereof. This approach enabled the preparation of previously inaccessible oligophenyl MOChas, which were successfully solved via small-molecule serial femtosecond crystallography (smSFX) at the SPring-8 Ångström Compact Free Electron LAser (SACLA) facility.

Electron transport through supercrystals of atomically precise gold nanoclusters: a thermal bi-stability effect.

Nanoparticles (NPs) may behave like atoms or molecules in the self-assembly into artificial solids with stimuli-responsive properties. However, the functionality engineering of nanoparticle-assembled solids is still far behind the aesthetic approaches for molecules, with a major problem arising from the lack of atomic-precision in the NPs, which leads to incoherence in superlattices. Here we exploit coherent superlattices (or supercrystals) that are assembled from atomically precise Au103S2(SR)41 NPs (core dia. = 1.6 nm, SR = thiolate) for controlling the charge transport properties with atomic-level structural insights. The resolved interparticle ligand packing in Au103S2(SR)41-assembled solids reveals the mechanism behind the thermally-induced sharp transition in charge transport through the macroscopic crystal. Specifically, the response to temperature induces the conformational change to the R groups of surface ligands, as revealed by variable temperature X-ray crystallography with atomic resolution. Overall, this approach leads to an atomic-level correlation between the interparticle structure and a bi-stability functionality of self-assembled supercrystals, and the strategy may enable control over such materials with other novel functionalities.

In Situ Structural Observation of a Substrate- and Peroxide-Bound High-Spin Ferric-Hydroperoxo Intermediate in the P450 Enzyme CYP121.

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.

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 evidence for intermediates during O2 formation in photosystem II.

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.

High-Spin Superatom Stabilized by Dual Subshell Filling.

Quantum confinement in small symmetric clusters leads to the bunching of electronic states into closely packed shells, enabling the classification of clusters with well-defined valences as superatoms. Like atoms, superatomic clusters with filled shells exhibit enhanced electronic stability. Here, we show that octahedral transition-metal chalcogenide clusters can achieve filled shell electronic configurations when they have 100 valence electrons in 50 orbitals or 114 valence electrons in 57 orbitals. While these stable clusters are intrinsically diamagnetic, we use our understanding of their electronic structures to theoretically predict that a cluster with 107 valence electrons would uniquely combine high stability and high-spin magnetic moment, attained by filling a majority subshell of 57 electrons and a minority subshell of 50 electrons. We experimentally demonstrate this predicted stability, high-spin magnetic moment (S = 7/2), and fully delocalized electronic structure in a new cluster, [NEt4]5[Fe6S8(CN)6]. This work presents the first computational and experimental demonstration of the importance of dual subshell filling in transition-metal chalcogenide clusters.

XFEL serial crystallography reveals the room temperature structure of methyl-coenzyme M reductase.

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.

Chemical crystallography by serial femtosecond X-ray diffraction.

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.

Real-Time XFEL Data Analysis at SLAC and NERSC: a Trial Run of Nascent Exascale Experimental Data Analysis.

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.

Hybrid Perovskite at Full Tilt: Structure and Symmetry Relations of the Incommensurately Modulated Phase of Methylammonium Lead Bromide, MAPbBr3.

As energy-conversion materials, organic-inorganic hybrid perovskites remain a research- and finance-intensive topic. However, even for the arguably most iconic representatives, methylammonium and formamidinium lead halides, the crystal structures of several polymorphs have remained undetermined. Herein, we describe the incommensurately modulated structure of MAPbBr3 in (3+1)D superspace, as deduced from single-crystal X-ray diffractometry despite systematic twinning. Affirming the published average space group, we determined the superspace group Imma(00γ)s00 with cell parameters of a = 8.4657(9), b = 11.7303(12), c = 8.2388(8) Å, and q = 0.2022(8)c*. Via group-subgroup and mode analyses using irreducible representations, we establish symmetry relationships to the well-known cubic and orthorhombic polymorphs and break down distortions into the average tilt system a-b0a- and modulated contributions to tilt and deformation of the PbBr6 coordination polyhedra. Not only does our model fill a long-standing gap in structural knowledge, but it may also serve as a starting point for elucidating other modulated structures within this substance class.

Intermolecular Resonance Correlates Electron Pairs Down a Supermolecular Chain: Antiferromagnetism in K-Doped p-Terphenyl.

Recent interest in potassium-doped p-terphenyl has been fueled by reports of superconductivity at Tc values surprisingly high for organic compounds. Despite these interesting properties, studies of the structure-function relationships within these materials have been scarce. Here, we isolate a phase-pure crystal of potassium-doped p-terphenyl: [K(222)]2[p-terphenyl3]. Emerging antiferromagnetism in the anisotropic structure is studied in depth by magnetometry and electron spin resonance. Combining these experimental results with density functional theory calculations, we describe the antiferromagnetic coupling in this system that occurs in all 3 crystallographic directions. The strongest coupling was found along the ends of the terphenyls, where the additional electron on neighboring p-terphenyls antiferromagnetically couple. This delocalized bonding interaction is reminiscent of the doubly degenerate resonance structure depiction of polyacetylene. These findings hint toward magnetic fluctuation-induced superconductivity in potassium-doped p-terphenyl, which has a close analogy with high Tc cuprate superconductors. The new approach described here is very versatile as shown by the preparation of two additional salts through systematic changing of the building blocks.

Stepwise Assembly of an Electroactive Framework from a Co6 S8 Superatomic Metalloligand and Cuprous Iodide Building Units.

Invited for the cover of this issue is Christopher Bejger and co-workers at UNC Charlotte, Columbia University, and Donghua University. The image depicts a pair of star clusters in the constellation Perseus as the structure of two metal clusters in the reported framework. Read the full text of the article at 10.1002/chem.20201215.

Single-Electron Currents in Designer Single-Cluster Devices.

Atomically precise clusters can be used to create single-electron devices wherein a single redox-active cluster is connected to two macroscopic electrodes via anchoring ligands. Unlike single-electron devices comprising nanocrystals, these cluster-based devices can be fabricated with atomic precision. This affords an unprecedented level of control over the device properties. Herein, we design a series of cobalt chalcogenide clusters with varying ligand geometries and core nuclearities to control their current-voltage (I-V) characteristics in a scanning tunneling microscope-based break junction (STM-BJ) device. First, the device geometry is modified by precisely positioning junction-anchoring ligands on the surface of the cluster. We show that the I-V characteristics are independent of ligand placement, confirming a sequential, single-electron tunneling mechanism. Next, we chemically fuse two clusters to realize a larger cluster dimer that behaves as a single electronic unit, possessing a smaller reorganization energy and more accessible redox states than the monomeric analogues. As a result, dimer-based devices exhibit significantly higher currents and can even be pushed to current saturation at high bias. Owing to these controllable properties, single-cluster junctions serve as an excellent platform for exploring incoherent charge transport processes at the nanoscale. With this understanding, as well as properties such as nonlinear I-V characteristics and rectification, these molecular clusters may function as conductive inorganic nodes in new devices and materials.

Shape Matching in Superatom Chemistry and Assembly.

Creating structures with superatomic nanoclusters rather than atoms offers the possibility of new hierarchical solids with collective properties. The variability of chemical compositions, sizes, and shapes of these superatomic building blocks provides great opportunities to access unknown assemblies. Herein we explore this concept by using geometrically anisotropic superatomic nanoclusters as building blocks. We reveal a series of novel superatomic architectures that are built from rod-shaped Co12Se16(PEt3)10 and C140 nanoclusters. More importantly, these assemblies show nonclose packings that afford voids to accommodate solvent molecules as a result of the shape anisotropy of the constituent building blocks. These intercalated small molecules act as "crystal modulators" to modulate the solid-state structures and properties. As a result, we are able to tune the crystal packings and optical gaps of the solids and see the moment when electrical conduction is "turned on". Our results demonstrate the vast potential of using anisotropic superatomic nanoclusters to create solid-state materials and provide a novel approach to configure their assemblies and properties.

Stepwise Assembly of an Electroactive Framework from a Co6 S8 Superatomic Metalloligand and Cuprous Iodide Building Units.

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 Co6 S8 (PTA)6 (PTA=1,3,5-triaza-7-phosphaadamantane) superatomic-metalloligand is assembled into a three-dimensional (3D) coordination polymer comprising Cu4 I4 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 Co6 S8 superatoms, which remain intact during framework synthesis.

The Structural Origins of Intense Circular Dichroism in a Waggling Helicene Nanoribbon.

We report the synthesis of a new perylene-diimide-based helical nanoribbon, which exhibits the largest molar electronic circular dichroism in the visible range of any molecule. This nanoribbon also displays a substantial increase in molar circular dichroism relative to a smaller helical analogue, even though they share a similar structure: both nanoribbons incorporate two conformationally dynamic double-[4]helicene termini and a rigid [6]helicene-based core within their helical superstructures. Using DFT and TDDFT calculations, we find that the double-[4]helicenes within both nanoribbons orient similarly in solution; as such, conformational differences do not account for the disparities in circular dichroism. Instead, our results implicate the configuration of the double-[6]helicene within the larger nanoribbon as the source of the observed chiroptical amplification.

Permethylation Introduces Destructive Quantum Interference in Saturated Silanes.

The single-molecule conductance of silanes is suppressed due to destructive quantum interference in conformations with cisoid dihedral angles along the molecular backbone. Yet, despite the structural similarity, σ-interference effects have not been observed in alkanes. Here we report that the methyl substituents used in silanes are a prerequisite for σ-interference in these systems. Through density functional theory calculations, we find that the destructive interference is not evident to the same extent in nonmethylated silanes. We find the same is true in alkanes as the transmission is significantly suppressed in permethylated cyclic and bicyclic alkanes. Using scanning tunneling microscope break-junction method we determine the single-molecule conductance of functionalized cyclohexane and bicyclo[2.2.2]octane that are found to be higher than that of equivalent permethylated silanes. Rather than the difference between carbon and silicon atoms in the molecular backbones, our calculations reveal that it is primarily the difference between hydrogen and methyl substituents that result in the different electron transport properties of nonmethylated alkanes and permethylated silanes. Chemical substituents play an important role in determining the single-molecule conductance of saturated molecules, and this must be considered when we improve and expand the chemical design of insulating organic molecules.

Nickel Phosphinidene Molecular Clusters from Organocyclophosphine Precursors.

We report a new family of nickel phosphinidene molecular clusters synthesized from the reaction of bis(1,5-cyclooctadiene)nickel(0) ([Ni(cod)2 ]) with organocyclophosphine and trialkylphosphine. We found that [Ni(cod)2 ] cleaves the organocyclophosphine P-P bonds to generate phosphinidene groups, establishing the cyclic molecules as valuable precursors for making charge-neutral molecular clusters passivated by two-electron donor capping ligands. The formation of the cluster core structure is controlled by the bulkiness of the precursor and of the capping ligand. As a demonstration of this new cluster-forming reaction, we describe three clusters with different core nuclearity and degree of ligation: Ni12 (PMe)10 (PEt3 )8 , Ni8 (PMe)6 (PMe3 )8 , and Ni8 (PiPr)6 (PMe3 )6 . In addition, we show that the larger cluster, Ni12 (PMe)10 (PEt3 )8 , can be used as a low temperature single-source molecular precursor to the catalytically active nickel phosphide phase Ni2 P.

Defying strain in the synthesis of an electroactive bilayer helicene.

We report the synthesis of a bilayer chiral nanographene incorporating a [7]helicene scaffold and two perylene-diimide (PDI) subunits. Twofold visible-light-induced oxidative cyclization of a phenanthrene framework selects for the desired PDI-helicene, despite the immense strain that distinguishes this helicene from two other accessible isomers. This strain arises from the extensive intramolecular overlap of the PDI subunits, which precludes racemization, even at elevated temperatures. Relative to a smaller homologue, this PDI-helicene exhibits amplified electronic circular dichroism. It also readily and reversibly accepts four electrons electrochemically. Modifications to the core phenanthrene subunit change the fluorescence and electrochemistry of the PDI-helicene without significantly impacting its electronic circular dichroism or UV-visible absorbance.