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At least 451 records · Page 25

Anionic Oxygen Redox in the High-Lithium Material Li 8 SnO 6

Lithiated transition metal oxide cathode materials that combine oxygen-anion redox [O 2 – /(O 2 ) n– ] with cation redox offer substantial capacities and higher voltage than cathodes without oxygen redox, but oxygen-anion redox is usually accompanied by the formation of peroxo or superoxo species that may cause oxygen release. To clarify the relationship between the oxygen release and peroxide and superoxide dimers without the complication of transition-metal redox, we performed density functional theory calculations to study the layered Li 8 SnO 6 cathode because it has only oxygen-anion redox during delithiation. Features with O–O distances of ~1.5 Å (corresponding to the formation of a peroxide) were observed at 75% lithium concentration, and further delithiation to 62.5% lithium concentration shortened the O–O bond distance to ~1.3 Å (corresponding to the formation of superoxide). The solely anionic oxygen redox stabilizes the delithiated structure of Li 8–x SnO 6 , and it does not cause structural disorder or release oxygen gas. Ab initio molecular dynamics calculations in the supercell at 300 K indicate that oxygen dimerization may occur at 75% lithium concentration. On the (0001) surface with a high lithium concentration (98%), oxygen dimerization is unfavorable. The calculations by HSE06 show that oxygen redox in Li 8 SnO 6 offers an initial voltage (vs Li/Li + ) greater than 4.2 V. The GGA+U calculations indicate that the Li + -polaron in Li 95 Sn 12 O 72 migrates with a migration barrier of only 0.43 eV. Here, this work also quantifies a solely anionic oxygen redox mechanism in Li 8 SnO 6 , and it provides a deeper understanding of anionic oxygen redox in Li-excess oxide cathode materials.

25 ENERGY STORAGE↗

Impact of Chiral Symmetry Breaking on Spin-Texture and Lone Pair Expression in Chiral Crystals of Hybrid Antimony and Bismuth Halides

Chiral organic building blocks can be incorporated into hybrid organic-inorganic metal-halide crystalline semiconductors so as to control and impact the interconversion between light, charge, and spin. Here, we report a series of hybrid antimony and bismuth halide materials of the general formula MBA 4 B 2 X 10 (B = Sb 3+ , Bi 3+ ; X = Br - , I - ) and study how chiral symmetry breaking imposed by the templating organic chiral methylbenzylammonium (MBA) cations induces symmetry breaking within the inorganic sublattice and leads to a unique spin-texture. The chiral MBA cations introduce two structural modifications to the metal-halide sublattice that consists of isolated edge-sharing dimers of B 2 X 10 octahedra: (1) the dimers have a chiral spatial arrangement with respect to one another and (2) there is an asymmetric distortion of the two subunits within the individual dimers with a higher distortion caused by strong stereochemical activity of the Sb 5s 2 lone pair electrons. The structural distortions and chiral arrangement result in circular dichroism (CD) at the band edge of the inorganic framework with dissymmetry factors in the range of 10 -4 . Chiral spin-splitting of the inorganic states, caused by breaking of the inversion symmetry and large spin-orbit coupling, is studied via density functional theory (DFT), and a multiband effective mass theory was developed that links the DFT-derived spin-splitting of helical character (i.e., spin expectation value not perpendicular to the crystal momentum) to the observed CD. Furthermore, we also find broad red photoluminescence from the MBA 4 Sb 2 Br 10 compounds, which we attribute to self-trapped excitonic emission driven by the large distortion due to the lone pair expression.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Optimal Orbital Selection for Full Configuration Interaction (OptOrbFCI): Pursuing the Basis Set Limit under a Budget

Full configuration interaction (FCI) solvers are limited to small basis sets due to their expensive computational costs. An optimal orbital selection for FCI (OptOrbFCI) is proposed to boost the power of existing FCI solvers to pursue the basis set limit under a computational budget. The optimization problem coincides with that of the complete active space SCF method (CASSCF), while OptOrbFCI is algorithmically quite different. OptOrbFCI effectively finds an optimal rotation matrix via solving a constrained optimization problem directly to compress the orbitals of large basis sets to one with a manageable size, conducts FCI calculations only on rotated orbital sets, and produces a variational ground-state energy and its wave function. Coupled with coordinate descent full configuration interaction (CDFCI), we demonstrate the efficiency and accuracy of the method on the carbon dimer and nitrogen dimer under basis sets up to cc-pV5Z. We also benchmark the binding curve of the nitrogen dimer under the cc-pVQZ basis set with 28 selected orbitals, which provide consistently lower ground-state energies than the FCI results under the cc-pVDZ basis set. Furthermore, the dissociation energy in this case is found to be of higher accuracy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Effective Fragment Molecular Orbital Method: Achieving High Scalability and Accuracy for Large Systems

The effective fragment molecular orbital (EFMO) method has been developed to predict the total energy of a very large molecular system accurately (with respect to the underlying quantum mechanical method) and efficiently by taking advantage of the locality of strong chemical interactions and employing a two-level hierarchical parallelism. The accuracy of the EFMO method is partly attributed to the accurate and robust intermolecular interaction prediction between distant fragments, in particular, the many-body polarization and dispersion effects, which require the generation of static and dynamic polarizability tensors by solving the coupled perturbed Hartree–Fock (CPHF) and time-dependent HF (TDHF) equations, respectively. Solving the CPHF and TDHF equations is the main EFMO computational bottleneck due to the inefficient (serial) and I/O-intensive implementation of the CPHF and TDHF solvers. In this work, the efficiency and scalability of the EFMO method are significantly improved with a new CPU memory-based implementation for solving the CPHF and TDHF equations that are parallelized by either message passing interface (MPI) or hybrid MPI/OpenMP. Here, the accuracy of the EFMO method is demonstrated for both covalently bonded systems and noncovalently bound molecular clusters by systematically examining the effects of basis sets and a key distance-related cutoff parameter, R cut . R cut determines whether a fragment pair (dimer) is treated by the chosen ab initio method or calculated using the effective fragment potential (EFP) method (separated dimers). Decreasing the value of Rcut increases the number of separated (EFP) dimers, thereby decreasing the computational effort. It is demonstrated that excellent accuracy (<1 kcal/mol error per fragment) can be achieved when using a sufficiently large basis set with diffuse functions coupled with a small R cut value. With the new parallel implementation, the total EFMO wall time is substantially reduced, especially with a high number of MPI ranks. Given a sufficient workload, nearly ideal strong scaling is achieved for the CPHF and TDHF parts of the calculation. For the first time, EFMO calculations with the inclusion of long-range polarization and dispersion interactions on a hydrated mesoporous silica nanoparticle with explicit water solvent molecules (more than 15k atoms) are achieved on a massively parallel supercomputer using nearly 1000 physical nodes. In addition, EFMO calculations on the carbinolamine formation step of an amine-catalyzed aldol reaction at the nanoscale with explicit solvent effects are presented.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effects of SARS-CoV-2 Main Protease Mutations at Positions L50, E166, and L167 Rendering Resistance to Covalent and Noncovalent Inhibitors

SARS-CoV-2 propagation under nirmatrelvir and ensitrelvir pressure selects for main protease (MPro) drug-resistant mutations E166V (DRM2), L50F/E166V (DRM3), E166A/L167F (DRM4), and L50F/E166A/L167F (DRM5). DRM2-DRM5 undergoes N-terminal autoprocessing to produce mature MPro with dimer dissociation constants (K dimer ) 2–3 times larger than that of the wildtype. Co-selection of L50F restores catalytic activity of DRM2 and DRM4 from ~10 to 30%, relative to that of the wild-type enzyme, without altering K dimer . Binding affinities and thermodynamic profiles that parallel the drug selection pressure, exhibiting significant decreases in affinity through entropy/enthalpy compensation, were compared with GC373. Reorganization of the active sites due to mutations observed in the inhibitor-free DRM3 and DRM4 structures as compared to MPro WT may account for the reduced binding affinities, although DRM2 and DRM3 complexes with ensitrelvir are almost identical to MPro WT -ensitrelvir. In conclusion, chemical reactivity changes of the mutant active sites due to differences in electrostatic and protein dynamics effects likely contribute to losses in binding affinities.

60 APPLIED LIFE SCIENCES↗

Supramolecular Interactions of Teixobactin Analogues in the Crystal State

This Note presents the X-ray crystallographic structure of the N-methylated teixobactin analogue N-Me- D -Gln 4 ,Lys 10 -teixobactin (1). Eight peptide molecules comprise the asymmetric unit, with each peptide molecule binding a chloride anion through hydrogen bonding with the amide NH group of residues 7, 8, 10, and 11. The peptide molecules form hydrogen-bonded antiparallel β-sheet dimers in the crystal lattice, with residues 1–3 comprising the dimerization interface. The dimers further assemble end-to-end in the crystal lattice.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantum Computing with Exciton Qubits in Colloidal Semiconductor Nanocrystals

The present work evaluates the feasibility of quantum computing with exciton qubits in coupled colloidal semiconductor nanocrystals (NCs). A strategy for manipulating two-qubit states of colloidal NC hetero-dimers is described. We show that a sequence of laser pulses with the same photon energy can bring excitonic states of a nanocrystal hetero-dimer into entanglement and perform arbitrary qubit rotations (quantum gates). Our simulations of a realistic two-particle assembly of CdSe/CdS core/shell NCs demonstrate that such two-qubit gate operations can be driven by optical parametric oscillators with a theoretical error of 0.1%. Furthermore, a strategy for upscaling two-qubit hetero-dimers to N-qubit exciton gates in semiconductor NC assemblies is discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Role of Axial Ligation in Gating the Reactivity of Dimethylplatinum(III) Diimine Radical Cations

Electrochemical methods are coupled with chemical oxidant-based analytical strategies to evaluate the oxidative reactivity of the platinum(II) diimine complex (bpy)Pt II (CH 3 ) 2 (bpy = 2,2'-bipyridine) in coordinating and non-coordinating media. Through this mechanistic analysis, we show that the one-electron oxidation of (bpy)Pt II (CH 3 ) 2 generates a highly reactive, 15-electron Pt III radical cation and identify three reaction pathways that can follow this oxidation: radical–substrate dimerization, radical-radical dimerization, and oxidative disproportionation. Axial ligation of the initially generated [(bpy)Pt III (CH 3 ) 2 ] •+ species is a critical driver of this reactivity, gating the available mechanistic pathways and tuning the competition between radical–radical dimerization and oxidative disproportionation.

14 SOLAR ENERGY↗

Steric Mapping, Ligand Dynamics, and Cycloisomerization Catalysis with Redox Robust Mn I/0/-I Dicarbenes

Manganese is perhaps the most electronically versatile element, yet the redox properties, reactivity, and catalytic applications of low-valent Mn 0 /Mn −I complexes remain underexplored due to the propensity for Mn 0 to dimerize, quenching highenergy metalloradicals. We report a series of redox-active monometallic Mn I , Mn 0 and Mn −I complexes containing a BH 2 - bridged dicarbene, characterized using a suite of experimental and cutting-edge computational (DFT) methods. Slow electron transfer kinetics at Mn I/0 are observed, with computations and electrochemical simulations in excellent agreement with experimental values. Despite the lack of steric bulk at the BH 2 -bridged Mn 0 , the t Bu groups at the dicarbene provide adequate steric protection to prevent dimerization, with percent buried volume (% V bur ) serving as a valuable steric ranking tool. We also show that a %V bur > 83% prevents dimerization for a diverse array of Mn 0 complexes from the literature. Ligand sterics of BPh 2 -and BH 2 -bridged complexes dictate reaction outcomes when Mn I and Mn −I are exposed to nucleophiles and electrophiles, respectively, while Mn0 facilitates the radical cycloisomerization catalysis of 6-iodo-1- hexene at room temperature. Furthermore, this work underscores the importance of ligand sterics in rationalizing reactivity patterns at Mn and provides valuable insights for designing chelating ligands that can selectively leverage Mn I/0/‑I states in redox-mediated catalytic reactions.

Ligands↗

Coupling of Flavonoid Initiation Sites with Monolignols Studied by Density Functional Theory

Lignin recalcitrance presents a challenge for the development of a bioeconomy that employs lignocellulosic feedstocks. The efficiency of lignin deconstruction is improved by a reduction of molecular weight, and given the discovery that flavones serve as initiation sites in lignin biosynthesis, these molecular weight reductions could potentially be achieved with plant metabolic engineering to over-express flavonoids. Upon increasing the flavonoid content in lignin, the bond strengths and properties of flavonoid-monolignol linkages become increasingly important. To that end, the current work applies density functional theory calculations to elucidate the bond dissociation enthalpies (BDEs) of flavonoid-monolignol linkages, including dimers with oxidized monolignols. Specifically, the dimer bond strengths and monomer hydrogen abstraction energies for the flavonoids tricin, chrysoeriol, luteolin, apigenin, catechin, epicatechin, epigallocatechin, and epigallocatechin gallate are calculated, when coupled to seven natural and engineered monolignols. Results indicate that 4'-O-ß linkage strengths between flavonoids and monolignols are of comparable strength to inter-monolignol ß-O-4 linkages, with average flavonoid-monolignol BDEs of 70.7 kcal/mol relative to ~69.3 kcal/mol in analogous canonical monolignols. Epigallocatechin yielded the lowest 4'-O-ß bond strength of 52.3 kcal/mol when coupled to an oxidized monolignol, while the flavones overall produced lower average BDEs, relative to the flavanols. Substituents at the 3'-C and 5'-C positions on flavonoids affected the dimer linkage strengths to a greater extent than glycosylation or substituents further from the linkage. Erythro and threo stereochemistry across the flavonoid-monolignol linkage library exhibited only small energetic differences and no pronounced correlations. Taken together, the predictions from this work support the concept that higher concentrations of flavonoid initiation sites in lignin may afford linkage properties conducive to more facile lignin depolymerization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Direct Observation of Modulated Radical Spin States in Metal–Organic Frameworks by Controlled Flexibility

Owing to their switchable spin states and dynamic electronic character, organic-based radical species have been invoked in phenomena unique to a variety of fields. When incorporated in solid state materials, generation of organic radicals proves challenging due to aggregation. Metal–organic frameworks (MOFs) are promising candidates for immobilization and stabilization of organic radicals because of the tunable spatial arrangement of organic linkers and metal nodes, which sequesters the reactive species. Herein, a flexible, redox-active tetracarboxylic acid linker bearing two imidazole units was chosen to construct a new Zr 6 -MOF, NU-910, with scu topology. By exploiting the structural flexibility of NU-910, we successfully modulate the dynamics between an isolated organic radical species and an organic radical π-dimer species in the MOF system. Single-crystal X-ray diffraction analysis reveals that through solvent exchange from N,N-diethylformamide to acetone, NU-910 undergoes a structural contraction with interlinker distances decreasing from 8.32 Å to 3.20 Å at 100 K. Organic radical species on the bridging linkers are generated via UV light irradiation. Direct observation of temperature-induced spin switches from an isolated radical species to a magnetically silent radical π-dimer in NU-910 after irradiation in the solid state was achieved via variable-temperature single-crystal X-ray diffraction and variable-temperature electron paramagnetic resonance spectroscopy. Ultraviolet–visible–near infrared spectroscopy and density functional theory calculations further substantiated the formation of a radical cation π-dimer upon irradiation. As a result, this work demonstrates the potential of using flexible MOFs as a platform to modulate radical spin states in the solid phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Direct Extraction of Sodium Hydroxide by Calix[4]pyrrole-Based Ion-Pair Receptors

Here, described in this work, are calix[4]pyrrole-based ion-pair receptors, cis/trans-1 and cis/trans-2, designed for the extraction of sodium hydroxide. An X-ray diffraction analysis of a single crystal of the cis-1·NaOH isomer isolated from a mixture of cis/trans-1 revealed a unique dimeric supramolecular structure. An average dimer in toluene-d 8 solution was inferred on the basis of diffusion-ordered spectroscopy (DOSY). Support for the proposed stoichiometry came from density functional theory (DFT) calculations. The structural stability of the dimeric cis-1·NaOH complex in toluene solution was further confirmed by ab initio molecular dynamics (AIMD) simulation with explicit representation of solvent. Under conditions of liquid–liquid extraction (LLE), purified receptors cis- and trans-2 were both found to remove NaOH from a pH 11.01 aqueous source phase into toluene with extraction efficiencies (E%) of 50–60% when used equimolar to NaOH. However, in all cases, precipitation was observed. Complexities associated with precipitation could be avoided by immobilization of the receptors onto a chemically inert poly(styrene) resin by means of solvent impregnation. The use of solvent-impregnated resins (SIRs) eliminated precipitation in solution while retaining the extraction efficiency toward NaOH. This allowed both the pH and salinity of the alkaline source phase to be lowered.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Cationic Cobalt(II) Bisphosphine Hydroformylation Catalysis: In Situ Spectroscopic and Reaction Studies

[HCo(CO) x (bisphosphine)](BF 4 ), x = 1–3, is a highly active hydroformylation catalyst system, especially for internal branched alkenes. In situ infrared spectroscopy (IR), electron paramagnetic resonance (EPR), and nuclear magnetic resonance studies support the proposed catalyst formulation. IR studies reveal the formation of a dicationic Co(I) paramagnetic CO-bridged dimer, [Co 2 (μ-CO) 2 (CO)(bisphosphine) 2 ] 2+ , at lower temperatures formed from the reaction of two catalyst complexes via the elimination of H 2 . Here, DFT studies indicate a dimer structure with square-pyramidal and tetrahedral cobalt centers. This monomer–dimer equilibrium is analogous to that seen for HCo(CO) 4 , reacting to eliminate H 2 and form Co 2 (CO) 8 . EPR studies on the catalyst show a high-spin (S = 3/2) Co(II) complex. Reaction studies are presented that support the cationic Co(II) bisphosphine catalyst as the catalyst species present in this system and minimize the possible role of neutral Co(I) species, HCo(CO) 4 or HCo(CO) 3 (phosphine), as catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural Evidence of Interanionic Hydrogen Bonding in Phosphoric Acid Solutions

Interanionic hydrogen bonding (IAHB) is a noncovalent interaction between like-charged ions that challenges conventional electrostatic understanding. This study provides direct structural evidence of IAHB in concentrated aqueous phosphoric acid (PA) solutions, which exhibit >60% dissociation under these conditions. Oxygen K-edge X-ray absorption fine structure spectroscopy, combined with electron affinity time-dependent density functional theory calculations, reveals the formation of stable, cyclic phosphate-phosphate IAHB dimers at PA concentrations ≥7 M. Extended X-ray absorption fine structure data show distinct long-range ordering consistent with these dimers, and near-edge X-ray absorption fine structure spectra confirm a concentration-dependent transition from monomeric to dimeric species. Energy decomposition analysis through density functional theory shows that the formation of solution-phase IAHB is energetically favored and is attributed to polarization of and the charge transfer between the two fragments driven by the surrounding solvent molecules, in addition to the permanent electrostatics. These findings offers crucial structural insights into the H-bonded networks in concentrated PA, highlighting the critical role of solvent in facilitating anion–anion association.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Conformational rearrangement of the NMDA receptor amino-terminal domain during activation and allosteric modulation

N-Methyl-D-aspartate receptors (NMDARs) are ionotropic glutamate receptors essential for synaptic plasticity and memory. Receptor activation involves glycine- and glutamate-stabilized closure of the GluN1 and GluN2 subunit ligand binding domains that is allosterically regulated by the amino-terminal domain (ATD). Using single molecule fluorescence resonance energy transfer (smFRET) to monitor subunit rearrangements in real-time, we observe a stable ATD inter-dimer distance in the Apo state and test the effects of agonists and antagonists. We find that GluN1 and GluN2 have distinct gating functions. Glutamate binding to GluN2 subunits elicits two identical, sequential steps of ATD dimer separation. Glycine binding to GluN1 has no detectable effect, but unlocks the receptor for activation so that glycine and glutamate together drive an altered activation trajectory that is consistent with ATD dimer separation and rotation. We find that protons exert allosteric inhibition by suppressing the glutamate-driven ATD separation steps, and that greater ATD separation translates into greater rotation and higher open probability.

59 BASIC BIOLOGICAL SCIENCES↗

Structures of the DarR transcription regulator reveal unique modes of second messenger and DNA binding

The mycobacterial repressor, DarR, a TetR family regulator (TFR), was the first transcription regulator shown to bind c-di-AMP. However, the molecular basis for this interaction and the mechanism involved in DNA binding by DarR remain unknown. Here we describe DarR-c-di-AMP and DarR-DNA structures and complementary biochemical assays. The DarR-c-di-AMP structure reveals a unique effector binding site for a TFR, located between DarR dimer subunits. Strikingly, we show this motif also binds cAMP. The location of the adenine nucleotide binding site between subunits suggests this interaction may facilitate dimerization and hence DNA binding. Indeed, biochemical assays show cAMP enhances DarR DNA binding. Finally, DarR-DNA structures reveal a distinct TFR DNA-binding mechanism involving two interacting dimers on the DNA. Thus, the combined data unveil a newly described second messenger binding motif and DNA binding mode for this important family of regulators.

59 BASIC BIOLOGICAL SCIENCES↗

The critical role of hot carrier cooling in optically excited structural transitions

The hot carrier cooling occurs in most photoexcitation-induced phase transitions (PIPTs), but its role has often been neglected in many theoretical simulations as well as in proposed mechanisms. Here, by including the previously ignored hot carrier cooling in real-time time-dependent density functional theory (rt-TDDFT) simulations, we investigated the role of hot carrier cooling in PIPTs. Taking IrTe2 as an example, we reveal that the cooling of hot electrons from the higher energy levels of spatially extended states to the lower energy levels of the localized Ir–Ir dimer antibonding states strengthens remarkably the atomic driving forces and enhances atomic kinetic energy. These two factors combine to dissolute the Ir–Ir dimers on a timescale near the limit of atomic motions, thus initiating a deterministic kinetic phase transition. We further demonstrate that the subsequent cooling induces nonradiative recombination of photoexcited electrons and holes, leading to the ultrafast recovery of the Ir–Ir dimers observed experimentally. These findings provide a complete picture of the atomic dynamics in optically excited structural phase transitions.

36 MATERIALS SCIENCE↗

Structural basis for SHOC2 modulation of RAS signalling

The RAS–RAF pathway is one of the most commonly dysregulated in human cancers. Despite decades of study, understanding of the molecular mechanisms underlying dimerization and activation of the kinase RAF remains limited. Recent structures of inactive RAF monomer and active RAF dimer bound to 14-3-3 have revealed the mechanisms by which 14-3-3 stabilizes both RAF conformations via specific phosphoserine residues. Prior to RAF dimerization, the protein phosphatase 1 catalytic subunit (PP1C) must dephosphorylate the N-terminal phosphoserine (NTpS) of RAF to relieve inhibition by 14-3-3, although PP1C in isolation lacks intrinsic substrate selectivity. SHOC2 is as an essential scaffolding protein that engages both PP1C and RAS to dephosphorylate RAF NTpS, but the structure of SHOC2 and the architecture of the presumptive SHOC2–PP1C–RAS complex remain unknown. Here we present a cryo-electron microscopy structure of the SHOC2–PP1C–MRAS complex to an overall resolution of 3Å, revealing a tripartite molecular architecture in which a crescent-shaped SHOC2 acts as a cradle and brings together PP1C and MRAS. Our work demonstrates the GTP dependence of multiple RAS isoforms for complex formation, delineates the RAS-isoform preference for complex assembly, and uncovers how the SHOC2 scaffold and RAS collectively drive specificity of PP1C for RAF NTpS. Our data indicate that disease-relevant mutations affect complex assembly, reveal the simultaneous requirement of two RAS molecules for RAF activation, and establish rational avenues for discovery of new classes of inhibitors to target this pathway.

59 BASIC BIOLOGICAL SCIENCES↗