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The synthesis of Fe/Mn complexes able to model enzymes possessing related cofactors are still a challenge. Herein, we discuss the stepwise synthesis and characterization of a Fe( ii )/Mn( ii ) species and related Fe( ii )/Fe( ii ) complexes.
(PhPN H P)Ru(H)(Cl)(CO) serves as a precatalyst to a variety of important catalytic transformations but most improvements have been restricted to the replacement of the CO ligand cis to the hydride or changing the Ph groups of the pincer for other aryl or alkyl groups. The ligand trans to the hydride is often another hydride and studies that utilize other trans ligands in catalysis are limited. Here, in this work, we synthesized a series of [(PhPN H P)Ru(H)(CO)(L)][BPh 4 ] complexes bearing isonitrile, PMe 3 , or a N-heterocyclic ligand trans to the Ru–H. We compared the new complexes abilities to catalyze the transfer hydrogenation of ketones. We found that all the trans ligands improved the chemoselectivity and stability of the catalysts; and strong π-accepting ligands resulted in poor catalytic activities whereas strong σ-donating ligands accelerated the catalysis.
The first complexes containing a 2,3,4,5-tetraiodopyrrolyl anion as a ligand were isolated. The ligands' tendency to foster intermolecular σ-hole interactions was probed and compared to rare earth metal complexes bearing a 2,5-dimethylpyrrolyl anion.
Rare earth tris(alkyl) complexes such as M(CH 2 SiMe 3 ) 3 (sol) n are widely used as precursors for many compounds and as homogeneous catalysts for alkene polymerization and alkane functionalization. However, the thermal instability of those most conveniently made from the commercially available lithium salt of the neosilyl anion, LiCH 2 SiMe 3 , Li(r), restricts their utility. We present a new range of synthetically useful, more kinetically stable rare earth neosilyl solvates, derived from a full kinetic study of the various possible decomposition mechanisms of 7 known and 12 new solvated rare earth neosilyl complexes M(CH 2 SiMe 3 ) 3 (sol) n M = Sc(III), Y(III), Lu(III), Sm(III), and sol = THF; TMEDA; DMPE; diglyme ((CH 3 ) 2 (OCH 2 CH 2 ) 2 O, G 2 ), triglyme ((CH 3 ) 2 (OCH 2 CH 2 ) 3 O, G 3 ). Surprisingly, simply using higher-denticity donors to sterically disfavor neosilyl γ-H elimination is not effective. While Sc(r) 3 ((CH 3 ) 2 (OCH 2 CH 2 ) 2 O) has a half-life, t 1/2 , of 258.1 h, six times longer than for Sc(r) 3 (C 4 H 8 O) 2 (t 1/2 = 43 h), Lu(r) 3 ((CH 3 ) 2 (OCH 2 CH 2 ) 2 O) and Y(r) 3 ((CH 3 ) 2 (OCH 2 CH 2 ) 2 O) do not show the expected, analogous increased t 1/2 . This is because new decomposition pathways appear for poorly fitting donors. Finally, kinetic studies demonstrate the impact of small, and increasing amounts of LiCl on the kinetics of the reactivity of the smaller alkyls Y(r) 3 (THF) 2 and Lu(r) 3 (THF) 2 ; molecules used in hydrocarbon chemistry and catalysis for fifty years. A new route to pure Y(r) 3 (THF) 2 , which avoids the traditional use of Li(r), is presented.
Large configurational disorder in compositionally complex ceramics can lead to unique functional properties that deviate from traditional rules of alloy mixing. In recent years, compositionally complex oxides (CCOs) have shown intriguing magnetic behavior including long-range order, enhanced magnetic exchange couplings, and mixed phase magnetic structures. This work focuses on how large local spin disorder affects magnetic ordering in a CCO. Specifically, we investigated the A-site alloyed perovskite, (Y 0.2 La 0.2 Pr 0.2 Nd 0.2 Tb 0.2 )MnO 3 , or (5A)MnO 3 , using a combination of bulk magnetometry, synchrotron X-ray diffraction, and temperature-dependent neutron diffraction. The five A-site ions have an average spin and ionic radius nearly equal to that of Nd 3+ ions, which minimizes structural distortions and allows for an understanding of the local spin disorder effects through a direct comparison with NdMnO 3 . Our magnetometry data show that (5A)MnO 3 exhibits two distinct phase transitions associated with the A-site and B-site sublattices, as seen in NdMnO 3 , as well as the presence of domain pinning and exchange bias at low temperature, suggesting a mixed phase magnetic ground state, as seen in other magnetic CCOs. Neutron powder diffraction shows clear long-range antiferromagnetic ordering below 67 K and refines to a Pn'ma' magnetic structure at low temperature, in excellent agreement with the well-studied behavior of NdMnO 3 . The two most notable differences in (5A)MnO 3 magnetism apparent from our data are a slight suppression of the B-site ordering temperature, which is explained by a smaller Mn–O–Mn bond angle in (5A)MnO 3 than NdMnO 3 , and the presence of a magnetic susceptibility transition above the B-site ordering, which could indicate the formation of a cluster glass but requires further study. Finally, this work demonstrates a general method of isolated investigation of size and spin disorder in CCOs and motivates future work using local structure probes to better understand the effects of nanoscale clustering and local spin disorder in magnetic CCOs.
Here, the utility of the sterically bulky terphenylthiolate ligand, (SAr iPr6 ) 1− in expanding uranium reductive chemistry has been explored. Reduction of U(SAr iPr6 ) 2 I forms the U(II) complex, U(SAr iPr6 ) 2 , in which the metal is protected by the flanking arene rings of the ligand, but they move out of the way to accommodate the four electron reduction of PhN=NPh to form the U(VI) bis(imido) product U(SAr iPr6 ) 2 (=NPh) 2 (THF) 2 . Here, the KC 8 reduction of U(SAr iPr6 ) 2 generates a more reduced complex, KU(μ-SAr iPr6 ) 2 , initially identified by a −2.55 V vs. Fc + /Fc electrochemical reduction event in THF.
Electrochemical transformations of metal ions in aqueous media are challenging to model accurately due to the dynamic solvation structure surrounding ions at different charge states. Predictive modeling at the atomistic scale is essential for understanding these solvation architectures but is often computationally prohibitive. In this contribution, we present a simple, fast, and accurate three-layer micro-solvation model to evaluate the redox potential of metal ions in aqueous solutions. Our model, developed and validated for Fe 3+ /Fe 2+ redox potentials, combines the DFT-based geometry optimizations of the octahedral Fe complex with two layers of explicit water molecules to capture solute–solvent interactions and an implicit solvation model to account for bulk solvent effects. This approach yields accurate predictions for Fe 3+ /Fe 2+ redox potentials in water, achieving errors of 0.02 V with ωB97X-V, 0.01 V with ωB97X-D3, 0.04 V with ωB97M-V, and 0.02 V with B3LYP-D3 functionals. We further demonstrate the generality of our model by applying it to additional metal complexes, including the challenging Fe(CN) 6 3−/4− system, where our model successfully achieves close agreement with experimental values, with an error of 0.07 V and an average error of 0.21 V for all five systems. In summary, the presented simple solvation model has broad applicability and potential for enhancing computational efficiency in redox potential predictions across various chemical and industrial processes of metal ions.
A trivalent plutonium–pyrazinyl–tetrazolate complex Na 2 [Pu(Hdtp)(dtp) 2 (H 2 O) 4 ]·9H 2 O (Pu_dtp, H 2 dtp = 2,3-di-1H-tetrazol-5-ylpyrazine) was synthesized through metathesis reaction of plutonium bromide and Na 2 (dtp)·2H 2 O in water. This structure is particularly notable among complexes formed by trivalent f-elements and the dtp 2− ligand in aqueous media. In contrast to other trivalent f-elements, including all Ln 3+ (with the exception of Pm 3+ ) and Cm 3+ , preferentially coordinated with eight water molecules rather than the nitrogen donors of the dtp 2− ligand, Pu 3+ exhibits a distinct affinity for nitrogen coordination. This observation provides strong evidence that the 5f electrons in Pu 3+ are more delocalized than other studied trivalent f-elements. In Pu_dtp, three distinct Pu(III)–N bonds are present: one Pu(III)–N5 from pyrazinyl, one Pu(III)–N4 from the least electronegative nitrogen in the tetrazolate, and three Pu(III)–N1/N2/N3 from the most electronegative nitrogens in the tetrazolate. Experimental Pu(III)–N bond lengths, Wiberg bond indices (WBI), natural localized molecular orbitals (NLMO), quantum theory of atoms in molecules (QTAIM), and energy decomposition analysis (EDA), reveal a covalency trend: Pu(III)–N from the most electronegative nitrogen in tetrazolate > Pu(III)–N from the least electronegative nitrogen in tetrazolate > Pu(III)–N from pyrazinyl. This trend arises from the increased negative charge on the most electronegative nitrogen atoms in the tetrazolate ring, enhancing electrostatic Pu–N1/N2/N3 interactions. These stronger electrostatic interactions lead to shorter bond lengths, thereby enhancing orbital overlap and greater covalency, compared to the less electronegative nitrogen in tetrazolate (Pu–N4) and the neutral pyrazinyl nitrogen (Pu–N5).
Gas-phase reactions of rhodium and platinum clusters with common ligand molecules in forming metal complexes, showing privileged cluster complexes with adaptive electron delocalization.
Protonated formic acid (PFA) is purported to be the active species in the catalytic activation of condensation reactions at the acidic interface of microdroplets. Here, we investigate the fundamental interaction between PFA and water with cryogenic ion vibrational spectroscopy of the binary PFA–H 2 O complexes generated via electrospray ionization followed by buffer gas cooling to about 20 K. The patterns displayed by the isomer-specific IR spectra of D 2 -tagged PFA–H 2 O indicate that two distinct, non-interconverting rotamers are present at low temperatures based on the cis and trans structures of the HCO 2 $H$$^{+}_{2}$ core ion. Both of these occur with the water molecule attached to the OH that is in a cis-configuration relative to the CH group (denoted E), but differ in the E vs Z (cis vs trans relative to the CH group) orientation of the spectator OH. This assignment scheme corrects a previous theoretical analysis that invoked a scenario in which structures with E- and Z-bound water molecules interconvert at low (20 K) temperatures. Isomer-specific bands arising from the OH stretches and water bending modes are deconvoluted using isotopomer-specific spectroscopy of the complexes with partial H/D exchange. The dependence of the nominal shared proton OH stretch frequency on the deuteration of the tethered water confirms strong coupling between this mode and the water bending fundamental.
In this work, we report on the experimental characterization of the second-order susceptibility in MoSe 2 /WS 2 heterobilayers, including their hidden complex phases. To this end, we developed a heterodyne-detection scheme for second-harmonic generation and applied it to macroscale heterobilayer samples prepared using the gold-tape exfoliation method. The heterodyne scheme enabled us to distinguish the relative orientation of the crystal domains, and furthermore, it allowed us to characterize the complex phases of the susceptibility relative to a reference quartz sample. By comparing the results from the monolayer regions and the heterobilayer region over several hundred microns of the sample area, we determined that the contribution of interlayer effects to second-harmonic generation is within the experimental uncertainty arising from the sample inhomogeneity. The results here provide fundamental quantitative information necessary for the precise design of nanophotonic systems based on stacking engineering.
Detecting viral infection is a key role of the innate immune system. The genomes of some RNA viruses have a high CpG dinucleotide content relative to most vertebrate cell RNAs, making CpGs a molecular marker of infection. The human zinc-finger antiviral protein (ZAP) recognizes CpG, mediates clearance of the foreign CpG-rich RNA, and causes attenuation of CpG-rich RNA viruses. While ZAP binds RNA, it lacks enzymatic activity that might be responsible for RNA degradation and thus requires interacting cofactors for its function. One of these cofactors, KHNYN, has a predicted nuclease domain. Using biochemical approaches, we found that the KHNYN NYN domain is a single-stranded RNA ribonuclease that does not have sequence specificity and digests RNA with or without CpG dinucleotides equivalently in vitro. We show that unlike most KH domains, the KHNYN KH domain does not bind RNA. Indeed, a crystal structure of the KH region revealed a double-KH domain with a negatively charged surface that accounts for the lack of RNA binding. Rather, the KHNYN C-terminal domain (CTD) interacts with the ZAP RNA-binding domain (RBD) to provide target RNA specificity. We define a minimal complex composed of the ZAP RBD and the KHNYN NYN-CTD and use a fluorescence polarization assay to propose a model for how this complex interacts with a CpG dinucleotide-containing RNA. In the context of the cell, this module would represent the minimum ZAP and KHNYN domains required for CpG-recognition and ribonuclease activity essential for attenuation of viruses with clusters of CpG dinucleotides.
Sperm IZUMO1 binds to egg JUNO, and this interaction is essential for mammalian fertilization. Isolated from a female mouse immunized with syngeneic sperm, the antisperm antibody OBF13 recognizes IZUMO1 and inhibits murine fertilization. How OBF13 interferes with sperm–egg interactions was unknown. Here, we present the X-ray crystal structure of IZUMO1 in complex with OBF13. OBF13 binds to the apex of the four-helix domain of IZUMO1, distant from the JUNO-binding site. Our crystal structure of OBF13-bound IZUMO1 resembles apo-IZUMO1 and differs from the structure of IZUMO1 in complex with JUNO. We identify that OBF13 carries a low level of somatic hypermutation, and through deep mutational scanning, we engineer an affinity-enhanced OBF13 variant. This OBF13 variant single-chain fragment variable decreases the apparent affinity of IZUMO1 for membrane-bound murine JUNO and blocks the binding of acrosome-reacted sperm to eggs, thereby preventing fertilization. We propose allostery between the OBF13 epitope and the JUNO-binding site. OBF13 inhibits a conformational change in IZUMO1, preventing fusion-competent sperm from adhering to murine eggs during fertilization. Surprisingly, murine IZUMO1 binds to hamster JUNO with an affinity ~20-fold higher than to murine JUNO. The decreased affinity caused by OBF13 of murine IZUMO1 for hamster JUNO is sufficient for murine sperm to bind to and fuse with hamster eggs. Our studies provide a structural and mechanistic framework for species-specific, allosteric inhibition of IZUMO1 by a naturally occurring antisperm antibody and offer insights into the development of immunocontraceptives.
With the goal of accelerating the discovery of small molecule–protein complexes, we leverage fast, low-dose, event-based electron counting microcrystal electron diffraction (MicroED) data collection and native mass spectrometry. This approach, which we term electron diffraction with native mass spectrometry (ED-MS), allows assignment of protein target structures bound to ligands with data obtained from crystal slurries soaked with mixtures of known inhibitors and crude biosynthetic reactions. This extends to libraries of printed ligands dispensed directly onto TEM grids for later soaking with microcrystal slurries, and complexes with noncovalent ligands. ED-MS resolves structures of the natural product, epoxide-based cysteine protease inhibitor E-64, and its biosynthetic analogs bound to the model cysteine protease, papain. It further identifies papain binding to its preferred natural products, by showing that two analogs of E-64 outcompete others in binding to papain crystals, and by detecting papain bound to E-64 and an analog from crude biosynthetic reactions, without purification. ED-MS also resolves binding of the CTX-M-14 β-lactamase, a target of active drug development, to the non-β-lactam inhibitor, avibactam, alone or in a cocktail of unrelated compounds. These results illustrate the utility of ED-MS for natural product ligand discovery and for structure-based screening of small molecule binders to macromolecular targets, promising utility for drug discovery.
We present factorization and solution phases for a new linear complexity direct solver designed for concurrent batch operations on fine-grained parallel architectures, for matrices amenable to hierarchical representation. We focus on the strong-admissibility-based $\mathscr{H}^{2}$ format, where strong recursive skeletonization factorization compresses remote interactions. We build upon previous implementations of $\mathscr{H}^{2}$ matrix construction for efficient factorization and solution algorithm design, which are illustrated graphically in stepwise detail. The algorithms are ‘blackbox’ in the sense that the only inputs are the matrix and right-hand side, without analytical or geometrical information about the origin of the system. We demonstrate linear complexity scaling in both time and memory on four representative families of dense matrices up to one million in size. Parallel scaling up to 16 threads is enabled by a multi-level matrix graph coloring and avoidance of dynamic memory allocations thanks to prefix-sum memory management. An experimental backward error analysis is included. We break down the timings of different phases, identify phases that are memory-bandwidth limited, and discuss alternatives for phases that may be sensitive to the trend to employ lower precisions for performance.
Metal hydrides are important across diverse applications, such as hydrogen storage, batteries, gas sensors, nuclear reactions, and high-temperature superconductivity. Previous computational studies of metal hydrides under extreme pressures, e.g., 𝑂(10 2 ) GPa, usually treat them as stoichiometric compounds without considering interstitial lattice disorder. As pressures become more moderate in the 𝑂(10 0 ) GPa and below range, hydrogen disorder at interstitial lattice sites becomes prominent, e.g., in the N-doped Lu hydride that was recently claimed superconducting near 1 GPa. Further adding compositional complexity from alloying and/or multielement interstitial occupation makes elucidating pressure- and temperature-dependent observables intractable by first-principles calculations alone. We therefore propose a lattice graph neural-network surrogate modeling approach to predict configuration- and pressure-dependent equation-of-state properties. Their efficiency permits Monte Carlo simulations to calculate Gibbs energies and pressure-dependent phase diagrams, thereby revealing insights into the synthesis conditions required for achieving desired phase equilibria. We demonstrate this concept for the compositionally complex cubic Lu(H,N,Va) 3 system where three constituents (hydrogen, nitrogen and vacancy) have disordered multielement interstitial occupancies and insights into pressure-dependent phase equilibria are critically needed, e.g., N-doping levels can significantly lower dehydrogenation temperatures and provide a new strategy to optimize hydrogen-storage alloys. This work can improve the thermodynamic understanding of the Lu-H-N system and help rational synthesis of N-doped Lu hydrides, but more generally demonstrates an efficient approach to model pressure-dependent thermodynamics of multicomponent solid solutions.
Light sources worldwide have experienced rapid growth in the last decades, pushing toward higher brightness with lower emittance to meet growing demands from the user community. The quest for higher brightness motivates the development of low-emittance ring lattices. At this point, all fourth-generation storage ring light sources employ variations of the multibend achromat (MBA) lattice. In this paper, we discuss an extension of this approach, known as complex bend achromat lattice in relation to the future NSLS-II upgrade. A detailed approach for the lattice design will be described and the developed lattice will be presented. The advantages of using our complex bend approach are evident in reaching a natural emittance as low as 23 pm at a beam energy of 3 GeV, providing a straight section of 8.4 m for long insertion devices, and acquiring a ratio of about 50% of free space with respect to the ring circumference. The design includes the use of permanent magnets largely reducing the need for power supplies. Our new approach provides an extension to the MBA concept for the next-generation light source lattice design. Published by the American Physical Society 2024
Projected entangled pair states (PEPS) offer memory-efficient representations of some quantum many-body states that obey an entanglement area law and are the basis for classical simulations of ground states in two-dimensional (2d) condensed matter systems. However, rigorous results show that exactly computing observables from a 2d PEPS state is generically a computationally hard problem. Yet approximation schemes for computing properties of 2d PEPS are regularly used, and empirically seen to succeed, for a large subclass of (“not too entangled”) condensed matter ground states. Adopting the philosophy of random matrix theory, in this work, we analyze the complexity of approximately contracting a 2d random PEPS by exploiting an analytic mapping to an effective replicated statistical mechanics model that permits a controlled analysis at a large bond dimension. Through this statistical-mechanics lens, we argue that (i) although approximately sampling wave-function amplitudes of random PEPS faces a computational-complexity phase transition above a critical bond dimension, and (ii) one can generically efficiently estimate the norm and correlation functions for any finite bond dimension. Furthermore, these results are supported numerically for various bond-dimension regimes. It is an important open question whether the above results for random PEPS apply more generally also to PEPS representing physically relevant ground states.