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Elucidating Structural Transition Dynamics in the Magnesium Cathode MgCr 2 O 4
Multivalent batteries, e.g., those based on magnesium (Mg), are promising candidates for next-generation energy storage due to their high volumetric energy densities and low cost. However, the corresponding ion migration and structural transition mechanisms are often linked and difficult to observe directly. Here, in this paper, we report the direct investigation of atomic transport pathways of cations in spinel magnesium chromate (MgCr 2 O 4 ) by using aberration-corrected scanning transmission electron microscopy (STEM). Cr atoms are directly observed to reversibly occupy the otherwise vacant octahedrally coordinated interstitial sites, passing through tetrahedral sites normally occupied by Mg. Furthermore, imaging and electron energy loss spectroscopy show that electron irradiation induces the formation of Mg and O vacancies, facilitating the migration of Cr and leading to an irreversible phase transition. These results demonstrate the ability of STEM to capture the pathway of deleterious point defects that can result in undesirable phase transitions.
Structural Elucidation of Ivermectin Binding to α7nAChR and the Induced Channel Desensitization
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Structural Elucidation of a Polypeptoid Chain in a Crystalline Lattice Reveals Key Morphology-Directing Role of the N-Terminus
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Structural elucidation of full-length Pfs48/45 in complex with potent monoclonal antibodies isolated from a naturally exposed individual
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A framework for automated structure elucidation from routine NMR spectra
A machine learning model and graph generator were able to accurately predict for the presence of nearly 1000 substructures and the connectivity of small organic molecules from experimental 1D NMR data.
The isolation and structural elucidation of voacristine hydroxyindolenine
Isolation and characterization of voacristine hydroxyindolenine
Atmospheric-pressure ionization and fragmentation of molecules for structural elucidation
A solution-cathode glow discharge (SCGD) spectrometry apparatus may comprise an SCGD source and a mass or ion mobility spectrometer. A method for ionizing a molecular analyte may comprise contacting the molecular analyte with a plasma discharge to form ions and separating the ions in a mass spectrometer or ion mobility spectrometer. The contacting step may occur under atmospheric pressure and/or ambient conditions. The molecular analyte may be fragmented by the plasma discharge.
Atmospheric-pressure ionization and fragmentation of molecules for structural elucidation
A solution-cathode glow discharge mass spectrometry (SCGD-MS) apparatus comprises a SCGD source and a mass spectrometer. The SCGD source may comprise conductive rods, a power source, and a capillary. A method for ionizing an analyte comprises flowing an electrically conductive liquid onto a conductive rod, applying an electric potential to a second conductive rod such that a plasma discharge forms between the first conductive rod and the electrically conductive liquid to produce ions, and separating the ions in a mass spectrometer. The analyte may be a polypeptide that may be contacted with trypsin. The analyte may be a solid, liquid, gas, chemical complex, or ion in solution. The method may comprise sequencing the polypeptide.
Molecular structural dataset of lignin macromolecule elucidating experimental structural compositions
Abstract Lignin is one of the most abundant biopolymers in nature and has great potential to be transformed into high-value chemicals. However, the limited availability of molecular structure data hinders its potential industrial applications. Herein, we present the Lignin Structural (LGS) Dataset that includes the molecular structure of milled wood lignin focusing on two major monomeric units (coniferyl and syringyl), and the six most common interunit linkages (phenylpropane β-aryl ether, resinol, phenylcoumaran, biphenyl, dibenzodioxocin, and diaryl ether). The dataset constitutes a unique resource that covers a part of lignin’s chemical space characterized by polymer chains with lengths in the range of 3 to 25 monomer units. Structural data were generated using a sequence-controlled polymer generation approach that was calibrated to match experimental lignin properties. The LGS dataset includes 60 K newly generated lignin structures that match with high accuracy (~90%) the experimentally determined structural compositions available in the literature. The LGS dataset is a valuable resource to advance lignin chemistry research, including computational simulation approaches and predictive modelling.
Structure and identification of the native PLP synthase complex from Methanosarcina acetivorans lysate
Many protein-protein interactions behave differently in biochemically purified forms as compared to their in vivo states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here, we apply the bottom-up structural proteomics method, cryoID , toward a model methanogenic archaeon. While they are keystone organisms in the global carbon cycle and active members of the human microbiome, there is a general lack of characterization of methanogen enzyme structure and function. Through the cryoID approach, we successfully reconstructed and identified the native Methanosarcina acetivorans pyridoxal 5′-phosphate (PLP) synthase (PdxS) complex directly from cryogenic electron microscopy (cryo-EM) images of fractionated cellular lysate. We found that the native PdxS complex exists as a homo-dodecamer of PdxS subunits, and the previously proposed supracomplex containing both the synthase (PdxS) and glutaminase (PdxT) was not observed in cellular lysate. Our structure shows that the native PdxS monomer fashions a single 8α/8β TIM-barrel domain, surrounded by seven additional helices to mediate solvent and interface contacts. A density is present at the active site in the cryo-EM map and is interpreted as ribose 5-phosphate. In addition to being the first reconstruction of the PdxS enzyme from a heterogeneous cellular sample, our results reveal a departure from previously published archaeal PdxS crystal structures, lacking the 37-amino-acid insertion present in these prior cases. This study demonstrates the potential of applying the cryoID workflow to capture native structural states at atomic resolution for archaeal systems, for which traditional biochemical sample preparation is nontrivial.
Fixed-target serial femtosecond crystallography using in cellulo grown microcrystals
The crystallization of recombinant proteins in living cells is an exciting new approach in structural biology. Recent success has highlighted the need for fast and efficient diffraction data collection, optimally directly exposing intact crystal-containing cells to the X-ray beam, thus protecting the in cellulo crystals from environmental challenges. Serial femtosecond crystallography (SFX) at free-electron lasers (XFELs) allows the collection of detectable diffraction even from tiny protein crystals, but requires very fast sample exchange to utilize each XFEL pulse. Here, an efficient approach is presented for high-resolution structure elucidation using serial femtosecond in cellulo diffraction of micometre-sized crystals of the protein HEX-1 from the fungus Neurospora crassa on a fixed target. Employing the fast and highly accurate Roadrunner II translation-stage system allowed efficient raster scanning of the pores of micro-patterned, single-crystalline silicon chips loaded with living, crystal-containing insect cells. Compared with liquid-jet and LCP injection systems, the increased hit rates of up to 30% and reduced background scattering enabled elucidation of the HEX-1 structure. Using diffraction data from only a single chip collected within 12 min at the Linac Coherent Light Source, a 1.8 Å resolution structure was obtained with significantly reduced sample consumption compared with previous SFX experiments using liquid-jet injection. This HEX-1 structure is almost superimposable with that previously determined using synchrotron radiation from single HEX-1 crystals grown by sitting-drop vapour diffusion, validating the approach. This study demonstrates that fixed-target SFX using micro-patterned silicon chips is ideally suited for efficient in cellulo diffraction data collection using living, crystal-containing cells, and offers huge potential for the straightforward structure elucidation of proteins that form intracellular crystals at both XFELs and synchrotron sources.
Free Energy Landscapes for Elucidating the Structural Consequences of Exon-20 mutations on the ErbB Family of Protein Kinases
The ErbB family of protein kinases plays an important role in major cellular functions and consequently mutations in the functional regions of these proteins are implicated in several types of cancer growths. To envision rational design of small molecule drugs that target the diseased proteins it is important to quantify the structural effects of the mutations, as some of these mutants render the protein resistant to tyrosine kinase inhibitors (TKIs). Herein we use advanced sampling techniques and long-timescale molecular dynamics simulations to predict the effect of major exon 20 mutations on the ErbB family, specifically EGFR and HER2 proteins. Exon 20 mutations have been clinically known to induce TKI resistance, though the mechanisms of such an effect is poorly understood. By mapping out the free energy landscape of the mutants and comparing them against the wild-type, we elucidate the structural differences in the binding pocket region that alter the nature of drug-protein interactions. We believe that these insights will play a pivotal role in developing small molecule drugs that overcome the TKI resistance.
Recent progress in understanding solid electrolyte interphase on lithium metal anode
Lithium (Li) metal batteries (LMBs) are among the most promising candidates of next-generation high-energy-density rechargeable batteries. Solid electrolyte interphase (SEI) on Li metal anode plays a significant role which influences the Li deposition morphology and the cycle life of LMBs. Although SEI is the most important part, a thorough understanding of SEI is inadequate. In this review, we focus on the progresses of understanding on structures, properties and influencing factors of SEI as well as efficient strategies of tailoring SEI. First, the compositions, models and recent progresses on characterizing atomic structure of SEI are summarized. Second, the properties of SEI, including electronic conduction, ionic conduction, stability and mechanical properties are elucidated. Structures and properties of SEI are greatly influenced by multiple factors such as solvent, salt, additive, solvation structure, impurity, current density, temperature, pressure and capacity utilization. Thus, interactions between these factors and SEI are comprehensively discussed. Correlations of SEI with Li deposition morphology, rate capability and cycle life are further summarized. Moreover, efficient strategies of tailoring SEI with desired properties, including in-situ SEI and ex-situ SEI are also reviewed. Despite the significant progresses that have been achieved in the researches of SEI, better understanding of SEI is still highly demand. Finally, future directions especially in-operando techniques, multi-modality approaches for characterization of SEI and artificial intelligence assisted understanding of correlation between electrolyte components and SEI properties are proposed.
Materials design, synthesis, and transport properties of disordered rare-earth Zintl bismuthides with the anti -Th 3 P 4 structure type
The synthesis, structural elucidation, and transport properties of the extended series Ca 4–x RE x Bi 3 (RE = Y, La–Nd, Sm, Gd–Tm, and Lu; x ≈ 1) and Ca 4–x RE x Bi 3–δ Sb δ (RE = La, Ho, Er, and Lu; x ≈ 1, δ ≈ 1.5) are presented. Structural elucidation is based on single-crystal X-ray diffraction data and confirms the chemical drive of Ca4Bi3 with the cubic anti-Th 3 P 4 structure type (space group I4 ¯3d, no. 220, Z = 4) into a Zintl phase by the introduction of trivalent rare-earth atoms. The structure features complex bonding, heavy elements, and electron count akin to that of valence-precise semiconductors, making it an ideal target for thermoelectrics development. Introducing crystallographic site disorders at the cation site for the Ca 4–x RE x Bi 3 phase and both the cation and anion sites for the Ca 4–x RE x Bi 3–δ Sb δ phase brings about additional desirable characteristics for thermoelectric materials in the context of tuning knobs for lowering thermal conductivity. Electronic structure calculations of idealized Ca 3 YBi 3 and Ca 3 LaBi 3 compounds indicate the opening of indirect bandgaps at the Fermi level with magnitudes Eg = 0.38 eV and 0.57 eV, respectively. The electrical resistivity ρ(T) of some of the investigated phases measured on single crystals evolve in a metallic manner with magnitudes of order 1.4 mΩ cm near 500 K, thus supporting the notion of a degenerate semiconducting state, with the temperature dependence of the Seebeck coefficient α(T) suggesting the p-type behavior. Furthermore, the low electrical resistivity and the realization of a degenerate semiconducting state in the title phases present a window of opportunity for optimizing their carrier concentrations for enhanced thermoelectric performance.
Elucidating the Structural and Electronic Effects of Ni and Mn Cationic Incorporation on CoOOH for Efficient Benzyl Alcohol Electrooxidation
Transition-metal oxyhydroxides such as CoOOH are promising low-cost electrocatalysts for the selective electrooxidation of organic molecules, yet the influence of ubiquitous transition-metal impurities on their performance and durability remains poorly understood. Here, we experimentally probed the individual and synergistic electrochemical and structural effects of Ni and Mn incorporations into model CoOOH electrocatalysts toward an efficient benzyl alcohol oxidation reaction (BAOR). Comprehensive electrochemical, microscopic, and spectroscopic analyses reveal that Ni incorporation enhances charge-transfer kinetics and overall activity through the formation of catalytically active Ni 3+ sites, whereas Mn exhibited a more complex but interesting role. At the early stages of operation, Mn 4+ acts as a stabilizing surface layer that mitigates catalyst degradation but partially blocks Co sites before they undergo gradual leaching. The concurrent incorporation of both Ni and Mn yields a trimetallic 2NMC@NF electrocatalyst that integrates the activity benefits of Ni with the stability conferred by Mn, achieving 92.9% benzyl alcohol conversion and 91.4% Faradaic efficiency after 24 h at 1.5 V vs RHE. These findings elucidate how trace Ni and Mn impurities, often introduced from electrolytes or external sources, can modulate the lattice and electronic structure of CoOOH, offering a design strategy for enhancing both activity and long-term stability in electrocatalytic organic oxidation.
Elucidating the Structure of the Eu‐EDTA Complex in Solution at Various Protonation States
Abstract Ethylenediaminetetraacetic acid (EDTA), which has two amine and four carboxylate protonation sites, forms stable complexes with lanthanide ions. This work analyzes the coordination structure, in atomic resolution, of the Eu 3+ ion complexed with EDTA in all its protonation states in aqueous solution. Eu‐EDTA complexes were modeled using classical molecular dynamics (MD) simulations using force field parameters optimized with ab initio molecular dynamics (AIMD) simulations. Structures from the MD simulations were used to predict extended X‐ray absorption fine structure (EXAFS) spectra and compared with EXAFS measurements of the Eu 3+ aqua ion and Eu‐EDTA complexes at pH 3 and 11. This work details how Eu‐EDTA complex coordination structures change with increasing protonation of the EDTA ligand in the complex, from the tightly bound unprotonated complex to the unbinding of the fully protonated EDTA ligand from the Eu 3+ ion as both become solvated by water. Agreement between predicted and measured EXAFS spectra supports the findings from simulation.