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At least 379 records · Page 21

In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors

Sleeping sickness is a fatal disease caused by the protozoan parasite Trypanosoma brucei (Tb). Inosine-5’-monophosphate dehydrogenase (IMPDH) has been proposed as a potential drug target, since it maintains the balance between guanylate deoxynucleotide and ribonucleotide levels that is pivotal for the parasite. Here we report the structure of TbIMPDH at room temperature utilizing free-electron laser radiation on crystals grown in living insect cells. The 2.80 Å resolution structure reveals the presence of ATP and GMP at the canonical sites of the Bateman domains, the latter in a so far unknown coordination mode. Consistent with previously reported IMPDH complexes harboring guanosine nucleotides at the second canonical site, TbIMPDH forms a compact oligomer structure, supporting a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity. The oligomeric TbIMPDH structure we present here reveals the potential of in cellulo crystallization to identify genuine allosteric co-factors from a natural reservoir of specific compounds.

36 MATERIALS SCIENCE↗

Steric augmentation of three-coordinate Cu( I ) β-diketiminate isocyanide chromophores to achieve microsecond excited-state lifetime

Copper(I) complexes are promising alternatives to noble metal-based photosensitizers. A recently developed class of three-coordinate copper(I) charge-transfer chromophores, pairing β-diketiminate ligands with aryl isocyanides, exhibits excited-state lifetimes that are responsive to the steric profile of the isocyanide, reaching a value of nearly 300 nanoseconds when a substituted m-terphenyl isocyanide was used. In this work, we show that extreme steric augmentation of the β-diketiminate and m-terphenyl isocyanide ligands can lead to further improvements in excited-state lifetime, with one example surpassing 1 µs. This study includes a series of eight compounds of the general formula Cu(RNacNac)(CN-Ar X2 ), where RNacNac is the substituted β-diketiminate and CN-Ar X2 is the substituted m-terphenyl isocyanide. All eight compounds are crystallographically characterized, and their excited-state properties are thoroughly evaluated by a combination of steady-state and time-resolved photoluminescence studies. This combined structural/photophysical approach unveils a correlation between common steric parameters, derived from buried volume (%V bur ) and solid angle analysis, and the excited-state lifetime. Our investigation reveals that the steric profile of the β-diketiminate has a much larger impact on the steric profile and lifetime, whereas the m-terphenyl isocyanide substituents have an unsystematic and subtle influence on these two correlated parameters. Nevertheless, judicious pairing of the two ligands is critical for achieving long excited-state lifetimes.

Kumar, Ashish [University of Houston, TX (United S↗

Probing exciton diffusion dynamics in photosynthetic supercomplexes via exciton–exciton annihilation

Photosynthesis converts solar energy into chemical energy through coordinated energy transfer between light-harvesting complexes and reaction centers (RCs). Understanding exciton motion, particularly the exciton diffusion length, is essential for optimizing energy efficiency in photosystems. In this work, we combine intensity-cycling transient absorption spectroscopy with kinetic Monte Carlo (kMC) simulation to investigate exciton motion in the C2S2 photosystem II supercomplex of spinach. Using exciton–exciton annihilation, revealed in the fifth-order response, we experimentally estimate an exciton diffusion length of 10.9 nm based on a 3D normal diffusion model, suggesting the ability of excitons to traverse the supercomplex. However, kMC simulations reveal that exciton motion is sub-diffusive because of spatial constraints and the strong RC traps. An anomalous diffusion model analysis of the experimental data yields a diffusion length of 9.7 nm, while the simulated diffusion length is 7.4 nm. The variable exciton residence time across subunits, partly influenced by their connectivity to the trap, indicates inhomogeneous annihilation probability and suggests how plants balance efficient light harvesting with photoprotection. We also explore the influence of specific assumptions in the annihilation simulation, which are challenging to access in more complex environments, such as the thylakoid membrane. Our study provides a framework for studying exciton dynamics using exciton–exciton annihilation, which can be extended to understand the light-harvesting efficiencies of larger, more complex photosynthetic assemblies.

Zhang, Kunyan (ORCID:000000026830409X)↗

Deciphering the molecular components of the quorum sensing system in the fungus Ophiostoma piceae

Quorum sensing (QS) is a complex cell-cell communication mechanism that coordinates population-level behaviors in microbes. In eukaryotes, this phenomenon has been extensively described in the dimorphic yeast Candida albicans as its main QS molecule, the sesquiterpene alcohol farnesol, is responsible for various phenotypic (i.e., inhibition of yeast-to-hyphae transition, biofilm formation, and, hence, pathogenesis) and metabolic (i.e., induction of oxidative stress and apoptosis) changes. Ophiostoma piceae CECT 20416 is a dimorphic saprotrophic ascomycete with biotechnological interest that also produces farnesol as QS molecule, but in this case, the alcohol promotes the morphological transition to the mycelial form, biofilm formation, enzyme secretion, and melanin production. Here, we characterized the physiological response of Ophiostoma piceae to farnesol, the molecular components of the QS system of this fungus have been investigated using a “multiomics” approach that involved genomic, transcriptomic, and proteomic analyses. Some genes identified in this work are proposed as key factors in farnesol transport and signaling. We have also cataloged the genes undergoing major transcriptional changes triggered by the presence of the autoinducer, such as cell-wall remodeling, reactive oxygen species (ROS) protection, and melanin biosynthesis, using self-organizing maps. This analysis could be useful for applications in the forestry industry, for enzymes production, and for the valorization of residues. Furthermore, it might as well help to investigate the QS mechanisms of clinically relevant fungi phylogenetically related to Ophiostoma.

59 BASIC BIOLOGICAL SCIENCES↗

Rationalizing Calcium Electrodeposition Behavior by Quantifying Ethereal Solvation Effects on Ca 2+ Coordination in Well-Dissociated Electrolytes

Ca-ion electrochemical systems have been pushed to the forefront of recent multivalent energy storage advances due to their use of earth-abundant redox materials and their high theoretical specific densities in relation to monovalent or even other more widely explored multivalent-charge carriers. However, significant pitfalls in metal plating and stripping arise from electrolyte decomposition and can be related to the coordination environment around Ca 2+ with both the negatively charged anion and the organic–aprotic solvent. Here, we apply multiple spectroscopic techniques in conjunction with density functional theory to evaluate the coordination environment of Ca 2+ across a class of ethereal solvents. Through the combination of X-ray absorption fine structure and time-dependent density functional theory, descriptive measures of the local geometry, coordination, and electronic structure of Ca–ethereal complexes provide distinct structural trends depending on the extent of the Ca 2+ –solvent interaction. Finally, we correlate these findings with electrochemical measurements of calcium tetrakis(hexafluoroisopropoxy)borate (CaBHFIP 2 ) salts dissolved within this class of solvents to provide insight into the preferred structural configuration of Ca 2+ electrolytic solutions for optimized electrochemical plating and stripping.

25 ENERGY STORAGE↗

Methods of using multi-ligand metal complexes to perform oxidative catalytic pretreatment of lignocellulosic biomass

A homogeneous catalyst is provided comprising one or more metals; and at least two metal coordinating ligands wherein the homogeneous catalyst is a multi-ligand metal complex adapted for use with an oxidant in an oxidation reaction to catalytically pretreat lignocellulosic biomass. In one embodiment, the homogenous catalyst is copper (II) 2, 2′ bipyridine ethylenediamine (Cu(bpy)en). Related methods are also disclosed.

Hodge, David B.↗

$\mathrm{RADICAL}$-Pilot and $\mathrm{PMIx}$/$\mathrm{PRRTE}$: Executing Heterogeneous Workloads at Large Scale on Partitioned $\mathrm{HPC}$ Resources

Execution of heterogeneous workflows on high-performance computing (HPC) platforms present unprecedented resource management and execution coordination challenges for runtime systems. Task heterogeneity increases the complexity of resource and execution management, limiting the scalability and efficiency of workflow execution. Re-source partitioning and distribution of tasks execution over portioned re-sources promises to address those problems but we lack an experimental evaluation of its performance at scale. Here this paper provides a performance evaluation of the Process Management Interface for Exascale (PMIx) and its reference implementation PRRTE on the leadership-class HPC plat-form Summit, when integrated into a pilot-based runtime system called RADICAL-Pilot. We partition resources across multiple PRRTE Distributed Virtual Machine (DVM) environments, responsible for launching tasks via the PMIx interface. We experimentally measure the work-load execution performance in terms of task scheduling/launching rate and distribution of DVM task placement times, DVM startup and termination overheads on the Summit leadership-class HPC platform. Integrated solution with PMIx/PRRTE enables using an abstracted, standardized set of interfaces for orchestrating the launch process, dynamic process management and monitoring capabilities. It extends scaling capabilities allowing to overcome a limitation of other launching mechanisms (e.g., JSM/LSF). Explored different DVM setup configurations provide insights on DVM performance and a layout to leverage it. Our experimental results show that heterogeneous workload of 65,500 tasks on 2048 nodes, and partitioned across 32 DVMs, runs steady with resource utilization not lower than 52%. While having less concurrently executed tasks resource utilization is able to reach up to 85%, based on results of heterogeneous workload of 8200 tasks on 256 nodes and 2 DVMs.

97 MATHEMATICS AND COMPUTING↗

Isolation of Inner-Sphere Aquo Complexes of Samarium(II)

The cis-anti-cis and cis-syn-cis isomers of [Sm(dicyclohexano-18-crown-6)(H 2 O) 2 ]I 2 exhibiting trans water molecules bound to the Sm 2+ ion have been isolated and characterized. Sm 2+ possesses an electrochemical potential sufficient for water reduction, and thus these complexes add to the recent body of evidence that the oxidation of Sm 2+ by water can operate by a mechanism that is not straightforward. These complexes are obtained by the direct addition of stoichiometric amounts of water to solutions of the respective Sm(dicyclohexano-18-crown-6)I 2 isomers under an inert atmosphere. The parent complex, Sm(dicyclohexano-18-crown-6)I 2 , lacking coordinating water molecules can be obtained through rigorous exclusion of water. It was determined that the bulky cyclohexano-substituents deter intramolecular interactions between [Sm(dicyclohexano-18-crown-6)(H 2 O) 2 ]I 2 complexes and slow the oxidization of the metal centers. The extent of the stability of these complexes to the presence of water has been further probed through cyclic voltammetry, where it was found that the redox potential of both isomers of [Sm(dicyclohexano-18-crown-6)(H 2 O) 2 ]I 2 maintains quasi-reversible behavior with a 50,000-fold excess of water to Sm 2+ in solution with the cis-syn-cis complex being quasi-reversible at even higher concentrations of water. Solution-phase spectroscopy of these complexes in acetonitrile shows a corresponding hypsochromic shift of the Sm 2+ 4f → 5d transition typically observed in the visible region from Sm 2+ complexes. Here, the crystalline compounds obtained in this study support solid-state spectroscopic trends observed from other Sm 2+ crown-ether complexes containing iodide counterions, wherein the proximity of the iodide ions to the metal center determines whether the complex can exhibit 4f → 4f photoluminescence.

Crystals↗

Determining the Effects of Zero-Field Splitting and Magnetic Exchange in Dimeric Europium(II) Complexes

Related BAP [BAP = bis(acyl)phosphide] and Acac (Acac = β-diketonate) molecules perform as robust supports for both lanthanide and actinide metals. Here, a molecular bimetallic Eu 2+ complex was successfully targeted and isolated by employing sodium bis(mesitoyl)phosphide [Na( mes BAP)] in a salt metathesis with EuI 2 , producing [Eu( mes BAP) 2 (et 2 o)] 2 (et 2 o = metal-coordinated diethyl ether). The corresponding Acac-Eu 2+ complex was targeted using mes Acac– (1,3-dimesityl-1,3-propanedione), generating [Eu( mes Acac) 2 (et 2 o)] 2 . Both complexes were characterized by single-crystal X-ray diffraction, UV–vis, IR, and NMR spectroscopies, and variable-temperature magnetic susceptibility. [Eu( mes BAP) 2 (et 2 o)] 2 was persistent under anaerobic, anhydrous conditions, whereas the analogous [Eu( mes Acac) 2 (et 2 o)] 2 showed evidence of decomposition under identical conditions. Finally, variable-temperature magnetic susceptibility and magnetization studies of [Eu( mes BAP) 2 (et 2 o)] 2 and [Eu( mes Acac) 2 (et 2 o)] 2 were performed, resulting in similar magnetic exchange coupling values of J ex = –0.018 and –0.023 cm –1 and axial zero-field-splitting D values of –0.38 and –0.51 cm –1 , respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Optimization of the generator coordinate method with machine-learning techniques for nuclear spectra and neutrinoless double- β decay: Ridge regression for nuclei with axial deformation

The generator coordinate method (GCM) is an important tool of choice for modeling large-amplitude collective motion in atomic nuclei. The computational complexity of the GCM increases rapidly with the number of collective coordinates. It imposes a strong restriction on the applicability of the method. In this work, we propose a subspace-reduction algorithm that employs optimal statistical ML models as surrogates for exact quantum-number projection calculations for norm and Hamiltonian kernels. The model space of the original GCM is reduced to a subspace relevant for nuclear low energy spectra and the NME of ground state to ground state 0νββ decay based on the orthogonality condition (OC) and the energy-transition-orthogonality procedure (ENTROP), respectively. For simplicity, the polynomial ridge regression (RR) algorithm is used to learn the norm and Hamiltonian kernels of axially deformed configurations. The efficiency and accuracy of this algorithm are illustrated for 76 Ge and 76 Se by comparing results obtained using the optimal RR models to direct GCM calculations. The low-lying energy spectra of 76 Ge and 76 Se, as well as the 0νββ-decay NME between their ground states, are computed. Furthermore, the results show that the performance of the GCM+OC/ENTROP+RR is more robust than that of the GCM+RR alone, and the former can reproduce the results of the original GCM calculation accurately with a significantly reduced computational cost.

59 ≤ A ≤ 89↗

Gating Single Molecules with Counterions

We report atomic-scale gating and visualization of local charge distribution within individual rare-earth-based molecular complexes on a metallic surface. The complexes are formed by a positively charged lanthanum ion coordinated to a (pcam)3 molecule and a negatively charged counterion trapped underneath via electrostatic interactions on a Au(111) surface. Local gating is performed by adding an additional negatively charged counterion to one side of the complex, which results in the redistribution of charges within the complex and a positive shift of the frontier orbitals. This is caused by the internal Stark effect induced by the added counterion. This effect is directly captured using tunneling spectroscopy and spectroscopic mapping at 5 K substrate temperature. The polarizability of the complex is corroborated by density functional theory and analytical calculations based on experimental findings. Furthermore, the influence of charge polarization on nearby complexes is investigated in a cluster purposely assembled using three complexes, which reveals maintaining the charge states as in single complexes. These findings will enable the design of robust charged rare-earth complexes to be tailored for potential solid-state applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Catalytic, Spectroscopic, and Theoretical Studies of Fe 4 S 4 -Based Coordination Polymers as Heterogenous Coupled Proton–Electron Transfer Mediators for Electrocatalysis

Iron–sulfur clusters play essential roles in biological systems, and thus synthetic [Fe 4 S 4 ] clusters have been an area of active research. Recent studies have demonstrated that soluble [Fe 4 S 4 ] clusters can serve as net H atom transfer mediators, improving the activity and selectivity of a homogeneous Mn CO 2 reduction catalyst. Here, in this work, we demonstrate that incorporating these [Fe 4 S 4 ] clusters into a coordination polymer enables heterogeneous H atom transfer from an electrode surface to a Mn complex dissolved in solution. A previously reported solution-processable Fe 4 S 4 -based coordination polymer was successfully deposited on the surfaces of different electrodes. The coated electrodes serve as H atom transfer mediators to a soluble Mn CO 2 reduction catalyst displaying good product selectivity for formic acid. Furthermore, these electrodes are recyclable with a minimal decrease in activity after multiple catalytic cycles. The heterogenization of the mediator also enables the characterization of solution-phase and electrode surface species separately. Surface enhanced infrared absorption spectroscopy (SEIRAS) reveals spectroscopic signatures for an in situ generated active Mn–H species, providing a more complete mechanistic picture for this system. The active species, reaction mechanism, and the protonation sites on the [Fe 4 S 4 ] clusters were further confirmed by density functional theory calculations. The observed H atom transfer reactivity of these coordination polymer-coated electrodes motivates additional applications of this composite material in reductive H atom transfer electrocatalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Impact of lanthanide ion complexation and temperature on the chemical reactivity of N , N , N ', N '-tetraoctyl diglycolamide (TODGA) with the dodecane radical cation

The impact of trivalent lanthanide ion complexation and temperature on the chemical reactivity of N,N,N',N'-tetraoctyl diglycolamide (TODGA) with the n-dodecane radical cation (RH˙+) has been measured by electron pulse radiolysis and evaluated by quantum mechanical calculations. Additionally, Arrhenius parameters were determined for the reaction of the non-complexed TODGA ligand with the RH˙ + from 10–40 °C, giving the activation energy (E a = 17.43 ± 1.64 kJ mol –1 ) and pre-exponential factor (A = (2.36 ± 0.05) × 10 13 M –1 s –1 ). The complexation of Nd(III), Gd(III), and Yb(III) ions by TODGA yielded [LnIII(TODGA)3(NO3)3] complexes that exhibited significantly increased reactivity (up to 9.3× faster) with the RH˙ + , relative to the non-complexed ligand: k([Ln III (TODGA) 3 (NO 3 ) 3 ] + RH˙ + ) = (8.99 ± 0.93) × 10 10 , (2.88 ± 0.40) × 10 10 , and (1.53 ± 0.34) × 10 10 M –1 s –1 , for Nd(III), Gd(III), and Yb(III) ions, respectively. The rate coefficient enhancement measured for these complexes exhibited a dependence on atomic number, decreasing as the lanthanide series was traversed. Preliminary reaction free energy calculations—based on a model [Ln III (TOGDA)] 3+ complex system—indicate that both electron/hole and proton transfer reactions are energetically unfavorable for complexed TODGA. Furthermore, complementary average local ionization energy calculations showed that the most reactive region of model N,N,N',N'-tetraethyl diglycolamide (TEDGA) complexes, [Ln III (TEGDA) 3 (NO 3 ) 3 ], toward electrophilic attack is for the coordinated nitrate (NO 3 – ) counter anions. Furthermore, it is possible that radical reactions with the complexed NO 3 – counter anions dominate the differences in rates seen for the [Ln III (TODGA) 3 (NO 3 ) 3 ] complexes, and are likely responsible for the reported radioprotection in the presence of TODGA complexes.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Noncoordinating Secondary Sphere Ion Modulates Supramolecular Clustering of Lanthanides

The role of counterions in molecular recognition of lanthanides is underexplored, especially when they exhibit weak interactions with the metal cations. Here, we report a complementary and comprehensive investigation integrating theoretical calculations with X-ray absorption fine structure spectroscopy, dynamic light scattering, and small-angle X-ray scattering to reveal atomic-scale structural features beyond the immediate coordination sphere of a system used for rare-earth element separations. Here, our results indicate the formation of an unusual T-shaped outer-sphere lanthanide complex, containing two ligands and two nitrate ions in the first coordination sphere, whereas the third nitrate is weakly coordinated and resides in the second shell. This unique structural arrangement causes inhomogeneous charge distribution, leading to self-assembly of the complexes into larger nanoclusters through sterically directed electrostatic interactions in the nonpolar medium. Our findings point to the importance of "noncoordinating" anions in defining the degree of supramolecular aggregation and ion cluster assembly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Lewis Acids and Electron-Withdrawing Ligands Accelerate CO Coordination to Dinuclear Cu I Compounds

A series of dinuclear molecular copper complexes were prepared and used to model the binding and Lewis acid stabilization of CO in heterogeneous copper CO 2 reduction electrocatalysts. Experimental studies (including measurement of rate and equilibrium constants) and electronic structure calculations suggest that the key kinetic barrier for CO binding may be a σ-interaction between CuI and the incoming CO ligand. The rate of CO coordination can be increased upon the addition of Lewis acids or electron-withdrawing substituents on the ligand backbone. Conversely, K eq for CO coordination can be increased by adding electron density to the metal centers of the compound, consistent with stronger π-backbonding. Lastly, the electrochemically measured kinetic results were mapped onto an electrochemical zone diagram to illustrate how these system changes enabled access to each zone.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Size matters: altering the metal-surface coordination in micropores via structural confinement effects

Solid-state NMR experiments were used to investigate the dynamics of supported complexes grafted to a series of silica gel materials of varied pore sizes. Through dipolar recoupling measurements, we found that ligand dynamics were impeded in the more confined environments, as would be expected. A new form of motion involving the complex as a whole, however, appeared in the most restricted environment consisting of 22 Å diameter pores. These motions persisted down to –100 °C at which point the ligands were frozen on the NMR timescale. The newly observed dynamics could only result from the breaking of secondary dative metal–siloxane interactions that otherwise lock the complex in a preferred orientation on the surface. Crucially, these results show that confinement effects alone can be sufficient to reduce a grafted metal's effective coordination number in direct analogy to the synthesis of undercoordinated complexes using bulky ligands. Finally, this finding could have important implications in the synthesis of more active heterogeneous catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Local Coordination Environment of Lanthanides Adsorbed onto Cr- and Zr-based Metal–Organic Frameworks

Separating individual lanthanide (Ln) elements in aqueous mixtures is challenging. Ion-selective capture by porous materials, such as metal–organic frameworks (MOFs), is a promising approach. To design ion-selective MOFs, molecular details of the Ln adsorption complexes within the MOFs must be understood. We determine the local coordination environment of lanthanides Nd(III), Gd(III), and Lu(III) adsorbed onto Cr(III)-based terephthalate MOF (Cr-MIL-101) and Zr(IV)-based Universitet in Oslo MOFs (UiO-66 and UiO-68) and their derivatives. In the Cr(III)- and Zr(IV)-based MOFs, Ln adsorb as inner-sphere complexes at the metal oxo clusters, regardless of whether the organic linkers are decorated with amino groups. Missing linkers result in favorable Ln binding sites at oxo clusters; however, Ln can coordinate to metal sites even with linkers in place. Further, MOF functionalization with phosphonate groups led to Ln chemisorption onto these groups, which out-compete metal cluster sites. Ln form monodentate and bidentate and mononuclear and binuclear surface complexes. We conclude that MOFs for ion-selective Ln capture can be designed by a combination of (1) maximizing metal-lanthanide interactions via shared O atoms at the metal oxo cluster sites, where mixed oxo clusters can lead to ion-selective Ln adsorption, and (2) functionalizing MOFs with Ln-selective groups capable of out-completing the metal oxo cluster sites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The high-valent vanadium chemistry of isoindoline chelates

Isoindoline-based chelates, in particular bis(arylimino)isoindolines, have shown extensive metal binding chemistry. Although this chemistry has been explored for the middle and late transition metal ions, little work has been carried out on early transition metal complexes. In this article, we present the first examples of vanadium coordinated using four bis(arylimino)isoindolines, in which the aryl groups are pyrazole, indazole, benzimidazole, and pyridine (ligands 1–4 , respectively). We isolated five complexes using vanadyl sulfate or vanadyl acetylacetonate as the vanadium source. In all cases, the ligands bound in a meridional mode, and for four of the complexes, the vanadium ion was observed in the V(v) oxidation state. Three of the ligands ( 1–3 ) formed VO 2 complexes with vanadyl sulfate and vanadyl acetylacetonate, but the bis(pyridylimino)isoindoline (ligand 4 ) formed a V(v) oxosulfonato complex with the former starting material and a vanadyl V(iv) acetylacetonate with the latter starting material. All metal compounds were structurally elucidated by X-ray crystallographic methods, and we probed their electronic structures using DFT methods.

Bore, Joan C. [Univ. of Akron, OH (United States)]↗