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At least 343 records · Page 19

Bridging the Transuranics with Uranium(IV) Sulfate Aqueous Species and Solid Phases

Isolating isomorphic compounds of tetravalent actinides (i.e., Th IV , U IV , Np IV , and Pu IV ) improve our understanding of the bonding behavior across the series, in addition to their relationship with tetravalent transition metals (Zr and Hf) and lanthanides (Ce). Similarities between these tetravalent metals are particularly illuminated in their hydrolysis and condensation behavior in aqueous systems, leading to polynuclear clusters typified by the hexamer [M IV 6 O 4 (OH) 4 ] 12+ building block. Prior studies have shown the predominance and coexistence of smaller species for Th IV (monomers, dimers, and hexamers) and larger species for U IV , Np IV , and Pu IV (including 38-mers and 70-mers). We show here that aqueous uranium(IV) sulfate also displays behavior similar to that of Th IV (and Zr IV ) in its isolated solidphase and solution speciation. Two single-crystal X-ray structures are described: a dihydroxide-bridged dimer (U 2 ) formulated as U 2 (OH) 2 (SO 4 ) 3 (H 2 O) 4 and a monomer-linked hexamer framework (U-U 6 ) as (U(H 2 O) 3.5 ) 2 U 6 O 4 (OH) 4 (SO 4 ) 10 (H 2 O) 9 . These structures are similar to those previously described for ThIV. Moreover, cocrystallization of monomer and dimer and of dimer and monomer–hexamer phases for both Th IV (prior) and U IV (current) indicates the coexistence of these species in solution. Because it was not possible to effectively study the sulfate-rich solutions via X-ray scattering from which U 2 and U-U 6 crystallized, we provide a parallel solution speciation study in low sulfate conditions, as a function of the pH. Raman spectroscopy, UV–vis spectroscopy, and small-angle X-ray scattering of these show decreasing sulfate binding, increased hydrolysis, increased species size, and increased complexity, with increasing pH. Furthermore, this study describes a bridge across the first half the actinide series, highlighting U IV similarities to Th IV , in addition to the previously known similarities to the transuranic elements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

On the Mechanism of Soot Nucleation. III. The Fate and Facility of the E-Bridge

Rotationally-excited dimerization of aromatic moieties is a mechanism proposed recently to explain the initial steps of soot particle inception in combustion and pyrolysis of hydrocarbons. The product of such dimerization, termed E-bridge, is an angled molecular structure composed of two aromatic rings sharing a common bond. The present study explores the immediate fate of the E-bridge. The performed theoretical analysis indicates that abstraction of a bridge H atom by a gaseous H leads to a rapid transformation of the angled to planar structure. The implications of this result is that the collisionally-activated E-bridge formation followed by its flattening effectively increases the size of “planar” aromatic precursors by combining two aromatic moieties with essentially collisional rates, instead of a slower “atom-by-atom” buildup. The faster growth speeds up PAH reaching a size when physical dimerization takes over. Furthermore, the dimerization can be further assisted by the biradicaloid valence structure of the flattened E-bridge.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Charged- and Multi-Exciton Dynamics in Colloidal Quantum Dot Molecules

Multicarrier states in quantum dots are confined to small volumes, resulting in increased nonradiative Auger recombination rates with implications for different optoelectronic applications. Recently, the fusion of two core-shell quantum dots into a dimer has provided a new physical landscape for multiexciton states, since the excitons may share a core (intradot, localized) or occupy different cores (interdot, segregated). Here, in this study, we employ transient absorption spectroscopy to investigate the multiexciton dynamics in coupled quantum dot dimers. We observe that multiexciton populations in the dimers live significantly longer in comparison to the parent monomers, in contrast to the single exciton regime. A kinetic model that accounts for the statistical differences between monomers and dimers reveals that, while intradot multiexcitons show Auger rates similar to the monomers, interdot states have reduced Auger rates. These results pave the way for the rational design of new quantum dot molecules with tailored multiexciton properties.

Auger recombination↗

Plasmonic Hybridization and Near-Field Localization in Gold “Dog Bone” Nanoparticles

Gold nanoparticles with complex anisotropic geometries offer unique opportunities for tailoring plasmonic near-fields beyond the limits of conventional nanorods. Here we combine photon-induced near-field electron microscopy (PINEM) and full-wave simulations to resolve plasmon hybridization and near-field localization in gold dog-bone nanoparticles and their dimers with and without conformal SiO 2 shells. We demonstrate that the dog-bone geometry drives unconventional polarization-dependent field confinement, including pronounced tip-localized near-fields under both longitudinal and transverse excitation. Conformal SiO 2 shells red-shift the plasmon resonances through dielectric screening and prevent charge-transfer coupling in adjacent dimers. Depending on the dimer orientation and excitation polarization, coupled structures exhibit distinct bonding- and antibonding-like hybridized modes as well as interparticle near-field channels. However, weakly interacting dimers retain largely independent particle responses with geometry-governed asymmetries. The close agreement between PINEM measurements and simulations establishes a direct picture of how shape, dielectric environment, and nanoscale coupling together define plasmonic modes in complex anisotropic nanoparticles. These findings provide design principles for engineering localized optical fields in plasmonic nanoscale structures.

hybridization↗

Rapid Electrochemical Methane Functionalization Involves Pd–Pd Bonded Intermediates

High-valent Pd complexes are potent agents for the oxidative functionalization of inert C-H bonds, and it was previously shown that rapid electrocatalytic methane monofunctionalization could be achieved by electro-oxidation of Pd II to a critical dinuclear Pd III intermediate in concentrated or fuming sulfuric acid. However, the structure of this highly reactive, unisolable intermediate, as well as the structural basis for its mechanism of electrochemical formation, remained elusive. Herein, we use X-ray absorption and Raman spectroscopies to assemble a structural model of the potent methane-activating intermediate as a Pd III dimer with a Pd-Pd bond and a 5-fold O atom coordination by H x SO 4 (x-2) ligands at each Pd center. We further use EPR spectroscopy to identify a mixed-valent M-M bonded Pd 2 II,III species as a key intermediate during the Pd II -to-Pd III 2 oxidation. Combining EPR and electrochemical data, we quantify the free energy of Pd dimerization as <-4.5 kcal/mol for Pd 2 II,III and <-9.1 kcal/mol for Pd III 2 . The structural and thermochemical data suggest that the aggregate effect of metal-metal and axial metal-ligand bond formation drives the critical Pd dimerization reaction in between electrochemical oxidation steps. This work establishes a structural basis for the facile electrochemical oxidation of Pd II to a M-M bonded Pd III dimer and provides a foundation for understanding its rapid methane functionalization reactivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mechanistic Insights into Molecular Copper Hydride Catalysis: the Kinetic Stability of CuH Monomers toward Aggregation is a Critical Parameter for Catalyst Performance

The activity of molecular copper hydride (CuH) complexes towards the selective insertion of unsaturated hydrocarbons under mild conditions has contributed significantly to versatile methodologies for upgrading these feedstocks. However, these catalysts are particularly susceptible to deleterious aggregation, leading to the depletion of active CuH species. Little is known about the mechanisms of CuH aggregation, how it influences overall catalyst performance, and how it can be controlled. We address these challenges with mechanistic studies on a model reaction of unactivated alkene hydroboration catalyzed by (IPr*CPh 3 )CuH (LCuH). Here, we report a comprehensive mechanistic investigation of this system, identifying an aggregation pathway that continuously depletes catalytically active LCuH to form inactive CuH clusters during turnover. Deactivation of LCuH is controlled primarily by the competition between the kinetics of the initial LCuH dimerization step and that of alkene insertion. We therefore propose that a more comprehensive understanding of CuH catalyst performance must account for the kinetics of the initial LCuH dimerization step, revising a previously explored thermodynamic understanding of CuH aggregation, where the concentration of active species is controlled by equilibria established between CuH dimers and monomers. With a series of (NHC)CuH congeners (NHC = N-heterocyclic carbene), we demonstrate that ostensibly minor structural modifications to the ligand peripheries can drastically affect the LCuH dimerization kinetics, while maintaining reactivity towards on–cycle alkene insertion. We employed a computational approach based on molecular dynamics simulations to provide an in-depth understanding of how specific structural ligand modifications can substantially increase the kinetic stability of monomeric CuH catalysts. Our combined experimental and computational studies suggest strategies for rational ligand design that can be broadly applied to molecular catalyst systems that are susceptible to deactivation via aggregation pathways.

Ryan, David E. [Pacific Northwest National Laborat↗

Understanding the structural basis of HIV-1 restriction by the full length double-domain APOBEC3G

APOBEC3G, a member of the double-domain cytidine deaminase (CD) APOBEC, binds RNA to package into virions and restrict HIV-1 through deamination-dependent or deamination-independent inhibition. Mainly due to lack of a full-length double-domain APOBEC structure, it is unknown how CD1/CD2 domains connect and how dimerization/multimerization is linked to RNA binding and virion packaging for HIV-1 restriction. We report rhesus macaque A3G structures that show different inter-domain packing through a short linker and refolding of CD2. The A3G dimer structure has a hydrophobic dimer-interface matching with that of the previously reported CD1 structure. A3G dimerization generates a surface with intensified positive electrostatic potentials (PEP) for RNA binding and dimer stabilization. Unexpectedly, mutating the PEP surface and the hydrophobic interface of A3G does not abolish virion packaging and HIV-1 restriction. The data support a model in which only one RNA-binding mode is critical for virion packaging and restriction of HIV-1 by A3G.

59 BASIC BIOLOGICAL SCIENCES↗

The intrinsically disordered protein TgIST from Toxoplasma gondii inhibits STAT1 signaling by blocking cofactor recruitment

Signal transducer and activator of transcription (STAT) proteins communicate from cell-surface receptors to drive transcription of immune response genes. The parasite Toxoplasma gondii blocks STAT1-mediated gene expression by secreting the intrinsically disordered protein TgIST that traffics to the host nucleus, binds phosphorylated STAT1 dimers, and occupies nascent transcription sites that unexpectedly remain silenced. Here we define a core region within internal repeats of TgIST that is necessary and sufficient to block STAT1-mediated gene expression. Cellular, biochemical, mutational, and structural data demonstrate that the repeat region of TgIST adopts a helical conformation upon binding to STAT1 dimers. The binding interface is defined by a groove formed from two loops in the STAT1 SH2 domains that reorient during dimerization. TgIST binding to this newly exposed site at the STAT1 dimer interface alters its conformation and prevents the recruitment of co-transcriptional activators, thus defining the mechanism of blocked transcription.

59 BASIC BIOLOGICAL SCIENCES↗

Hidden magnetism and split off flat bands in the insulator metal transition in VO 2

Transition metal d -electron oxides with an odd number of electrons per unit cell are expected to form metals with partially occupied energy bands, but exhibit in fact a range of behaviors, being either insulators, or metals, or having insulator-metal transitions. Traditional explanations involved predominantly electron-electron interactions in fixed structural symmetry. The present work focuses instead on the role of symmetry breaking local structural motifs. Viewing the previously observed V-V dimerization in VO 2 as a continuous knob, reveals in density functional calculations the splitting of an isolated flat band from the broad conduction band. This leads past a critical percent dimerization to the formation of the insulating phase while lowering the total energy. In VO 2 this transition is found to have a rather low energy barrier approaching the thermal energy at room temperature, suggesting energy-efficient switching in neuromorphic computing. Interestingly, sufficient V-V dimerization suppresses magnetism, leading to the nonmagnetic insulating state, whereas magnetism appears when dimerization is reduced, forming a metallic state. This study opens the way to design novel functional quantum materials with symmetry breaking-induced flat bands.

Chemistry↗

Hub stability in the calcium calmodulin-dependent protein kinase II

The calcium calmodulin protein kinase II (CaMKII) is a multi-subunit ring assembly with a central hub formed by the association domains. There is evidence for hub polymorphism between and within CaMKII isoforms, but the link between polymorphism and subunit exchange has not been resolved. Here, we present near-atomic resolution cryogenic electron microscopy (cryo-EM) structures revealing that hubs from the α and β isoforms, either standalone or within an β holoenzyme, coexist as 12 and 14 subunit assemblies. Single-molecule fluorescence microscopy of Venus-tagged holoenzymes detects intermediate assemblies and progressive dimer loss due to intrinsic holoenzyme lability, and holoenzyme disassembly into dimers upon mutagenesis of a conserved inter-domain contact. Molecular dynamics (MD) simulations show the flexibility of 4-subunit precursors, extracted in-silico from the β hub polymorphs, encompassing the curvature of both polymorphs. The MD explains how an open hub structure also obtained from the β holoenzyme sample could be created by dimer loss and analysis of its cryo-EM dataset reveals how the gap could open further. An assembly model, considering dimer concentration dependence and strain differences between polymorphs, proposes a mechanism for intrinsic hub lability to fine-tune the stoichiometry of αβ heterooligomers for their dynamic localization within synapses in neurons.

59 BASIC BIOLOGICAL SCIENCES↗

Characterization of an unusual SARS-CoV-2 main protease natural variant exhibiting resistance to nirmatrelvir and ensitrelvir

We investigate the effects of two naturally selected substitution and deletion (Δ) mutations, constituting part of the substrate binding subsites S2 and S4, on the structure, function, and inhibition of SARS CoV-2 main protease. Comparable to wild-type, MPro D48Y/ΔP168 undergoes N-terminal autoprocessing essential for stable dimer formation and mature-like catalytic activity. The structures are similar, but for an open active site conformation in MPro D48Y/ΔP168 and increased dynamics of the S2 helix, S5 loop, and the helical domain. Some dimer interface contacts exhibit shorter H bond distances corroborating the ~40-fold enhanced dimerization of the mutant although its thermal sensitivity to unfolding is 8 °C lower, relative to wild-type. ITC reveals a 3- and 5-fold decrease in binding affinity for nirmatrelvir and ensitrelvir, respectively, and similar GC373 affinity, to MPro D48Y/ΔP168 relative to wild-type. Structural differences in four inhibitor complexes of MPro D48Y/ΔP168 compared to wild-type are described. Consistent with enhanced dynamics, the S2 helix and S5 loop adopting a more open conformation appears to be a unique feature of MPro D48Y/ΔP168 both in the inhibitor-free and bound states. Our results suggest that mutational effects are compensated by changes in the conformational dynamics and thereby modulate N-terminal autoprocessing, K dimer , catalytic efficiency, and inhibitor binding.

60 APPLIED LIFE SCIENCES↗

Localization in the SCAN meta-generalized gradient approximation functional leading to broken symmetry ground states for graphene and benzene

Density functional theory calculations play a central role in understanding chemical and solid-state systems. Progress depends on density functionals that accurately reproduce both energies, for thermochemistry, and properly describe ground states and other properties that are of interest. The Cr dimer, benzene and graphene are especially important benchmark systems for quantum chemistry and condensed matter physics. The Strongly Constrained and Appropriately Normed (SCAN) functional, which is an advanced meta-generalized gradient approximation functional that significantly improves molecular energies is shown to perform poorly for the Cr dimer. This is connected with its poor performance for itinerant solid-state magnets and is a consequence of over localization of electrons, thus illustrating an analogy between the Cr dimer and itinerant magnets. The Cr dimer is a notoriously difficult system for density functionals. However, we additionally find that SCAN predicts an incorrect symmetry broken ground state for 2D graphene and for the benzene molecule, which is surprising considering that ground states of these are known to be well described even by the simplest local density approximation. We show that SCAN overly favors localized spin polarized states, which is a serious deficiency of this approach. Thus, the challenge of finding density functionals that accurately treat both localized and delocalized electronic systems remains.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electromagnetic control of spin ordered Mn 3 qubits: a density functional study

[Mn 3 O(O 2 CMe)(dpd 3/2 )] 2 is composed of two monomers each of which contain three Mn atoms at the vertices of an equilateral triangle. A full analysis of the electronic and magnetic structure of the dimer shows that each Mn atom carries a local spin of S = 2 while other spin states are energetically much higher. This result suggests application for conventional as well as quantum tasks. A detailed analysis of the electronic and magnetic structure of the monomer, on the other hand, suggests that there are three spin states of S = 1, S = 3/2 and S = 2 per monomer which are energetically competitive. Additionally, we found that while monomer–monomer interactions are very weak, the coupling of monomers via covalent linkers affects both the magnetization and electronic energy levels of monomers. In particular, the isolated monomers prefer a ground state with local spin of S = 1 on Mn atoms and an antiferromagnetically ordered structure while the dimers possess a ground state with local spin of S = 2 on Mn atoms and a ferromagnetically ordered structure. The investigation of the polarizability of both monomer and dimer is examined for antiferromagnetically ordered structures which induces a high dipole moment of 0.08 (a.u.) and 0.16 (a.u.) for monomer and dimer, respectively. The energy of the antiferromagnetic structure is also high compared to other spin-electric molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The controlling role of atmosphere in dawsonite versus gibbsite precipitation from tetrahedral aluminate species

In highly alkaline solution, aluminum speciates as the tetrahedrally coordinated aluminate monomer, Al(OH)4- and/or dimer Al2O(OH)62-, yet precipitates as octahedrally coordinated gibbsite (Al(OH)3). This tetrahedral to octahedral transformation governs Al precipitation, which is crucial to worldwide Al production, and to the processing of caustic high-level radioactive wastes. Despite its significance, the transformation pathway remains unknown. Here we explore the roles of atmospheric water and carbon dioxide in mediating the transformation of the tetrahedrally coordinated potassium aluminate dimer salt (K2Al2O(OH)6) to gibbsite versus potassium dawsonite (KAl(CO3)(OH)2). A combination of in-situ attenuated total reflection infrared spectroscopy, ex-situ micro X-ray diffraction, and multivariate curve resolution-alternating least squares chemometrics analysis reveals that humidity plays a key role in the transformation by limiting the amount of alkalinity neutralization by dissolved CO2. Lower humidity favors higher alkalinity and incorporation of carbonate species in the final Al product to form KAl(CO3)(OH)2. Higher humidity enables more acid generation that destabilizes dawsonite and favors gibbsite as the solubility limiting phase. Because the transformation was restricted to occur in thin water films, the results suggest that transition from tetra- to octahedrally coordinated Al does not have to occur in bulk solution, as has often been hypothesized, but may instead appear on the source mineral surface.

Dembowski, Mateusz↗

Elucidating the mechanism of photochemical CO 2 reduction to CO using a cyanide-bridged di-manganese complex

The complex, [{[Mn(bpy)(CO) 3 ] 2 }(μ-CN)] + (Mn 2 CN + ), has previously been shown to photochemically reduce CO 2 to CO. The detailed mechanism behind its reactivity was not elucidated. In this work, the photoevolution of this reaction is studied in acetonitrile (MeCN) using IR and UV-vis spectroscopy. Samples were excited into the Mn I → π* bpy metal-to-ligand charge transfer (MLCT) absorption band triggering CO loss, and rapid MeCN solvent ligation at the open coordination site. It is concluded that this process occurs selectively at the Mn axial ligation site that is trans to the C-end of the bridging cyanide. Upon further photolysis, the metal–metal bonded dimeric species, [(CO) 3 (bpy)Mn–Mn(bpy)(CO) 3 ] (Mn–Mn) is observed to form under anaerobic conditions. The presence of this dimeric species coincides with the observation of CO production. When oxygen is present, CO 2 photoreduction does not occur, which is attributed to the inability of Mn 2 CN + to convert to the metal–metal bonded dimer. Photolysis experiments, where the Mn–Mn dimer is formed photochemically under argon first and then exposed to CO 2 , reveal that it is the radical species, [Mn(bpy)(CO) 3 ˙] (Mn˙), that interacts with the CO 2 . Since the presence of Mn–Mn and light is required for CO production, [Mn(bpy)(CO) 3 ˙] is proposed to be a photochemical reagent for the transformation of CO 2 to CO.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Prediction of the structures and heats of formation of MO 2 , MO 3 , and M 2 O 5 for M = V, Nb, Ta, Pa

Structures for the mono-, di-, and tri-bridge isomers of M 2 O 5 as well as those for the MO 2 and MO 3 fragments for M = V, Nb, Ta, and Pa were optimized at the density functional theory (DFT) level. Single point CCSD(T) calculations extrapolated to the complete basis set (CBS) limit at the DFT geometries were used to predict the energetics. Here, the lowest energy dimer isomer was the di-bridge for M = V and Nb and the tri-bridge for M = Ta and Pa. The di-bridge isomers were predicted to be composed of MO 2 + and MO 3 - fragments, whereas the mono- and tri-bridge are two MO 2 + fragments linked by an O 2 - . The heats of formation of M 2 O 5 dimers, as well as MO 2 and MO 3 neutral and ionic species were predicted using the Feller–Peterson–Dixon (FPD) approach. The heats of formation of the MF 5 species were calculated to provide additional benchmarks. Dimerization energies to form the M 2 O 5 dimers are predicted to become more negative going down group 5 and range from -29 to -45 kcal mol -1 . The ionization energies (IEs) for VO 2 and TaO 2 are essentially the same at 8.75 eV whereas the IEs for NbO 2 and PaO 2 are 8.10 and 6.25 eV, respectively. The predicted adiabatic electron affinities (AEAs) range from 3.75 eV to 4.45 eV for the MO 3 species and vertical detachment energies from 4.21 to 4.59 eV for MO 3 - . The calculated M[double bond, length as m-dash]O bond dissociation energies increase from 143 kcal mol -1 for M = V to ~170 kcal mol -1 for M = Nb and Ta to ~200 kcal mol -1 for M = Pa. The M–O bond dissociation energies are all similar ranging from 97 to 107 kcal mol -1 . Natural bond analysis provided insights into the types of chemical bonds in terms of their ionic character. Pa 2 O 5 is predicted to behave like an actinyl species dominated by the interactions of approximately linear PaO 2 + groups.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Influence of solution phase environmental heterogeneity and fluctuations on vibronic spectra: Perylene diimide molecular chromophore complexes in solution

Ensembles of ab initio parameterized Frenkel-exciton model Hamiltonians for different perylene diimide dimer systems are used, together with various dissipative quantum dynamics approaches, to study the influence of the solvation environment and fluctuations in chromophore relative orientation and packing on the vibronic spectra of two different dimer systems: a π-stacked dimer in aqueous solution in which the relative chromophore geometry is strongly confined by a phosphate bridge and a side-by-side dimer in dichloromethane involving a more flexible alkyne bridge that allows quasi-free rotation of the chromophores relative to one another. These entirely first-principles calculations are found to accurately reproduce the main features of the experimental absorption spectra, providing a detailed mechanistic understanding of how the structural fluctuations and environmental interactions influence the vibronic dynamics and spectroscopy of solutions of these multi-chromophore complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Comparing correlation components and approximations in Hartree–Fock and Kohn–Sham theories via an analytical test case study

The asymmetric Hubbard dimer is a model that allows for explicit expressions of the Hartree–Fock (HF) and Kohn–Sham (KS) states as analytical functions of the external potential, Δv, and of the interaction strength, U. We use this unique circumstance to establish a rigorous comparison between the individual contributions to the correlation energies stemming from the two theories in the {U, Δv} parameter space. Within this analysis of the Hubbard dimer, we observe a change in the sign of the HF kinetic correlation energy, compare the indirect repulsion energies, and derive an expression for the “traditional” correlation energy, i.e., the one that corrects the HF estimate, in a pure site-occupation function theory spirit [Eq. (45)]. Next, we test the performances of the Liu–Burke and the Seidl–Perdew–Levy functionals, which model the correlation energy based on its weak- and strong-interaction limit expansions and can be used for both the traditional and the KS correlation energies. Further, our results show that, in the Hubbard dimer setting, they typically work better for the HF reference, despite having been originally devised for KS. These conclusions are somewhat in line with prior assessments of these functionals on various chemical datasets. However, the Hubbard dimer model allows us to show the extent of the error that may occur in using the strong-interaction ingredient for the KS reference in place of the one for the HF reference, as has been carried out in most of the prior assessments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗