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At least 883 records · Page 49

Selective ion transport through hydrated micropores in polymer membranes

Abstract Ion-conducting polymer membranes are essential in many separation processes and electrochemical devices, including electrodialysis 1 , redox flow batteries 2 , fuel cells 3 and electrolysers 4,5 . Controlling ion transport and selectivity in these membranes largely hinges on the manipulation of pore size. Although membrane pore structures can be designed in the dry state 6 , they are redefined upon hydration owing to swelling in electrolyte solutions. Strategies to control pore hydration and a deeper understanding of pore structure evolution are vital for accurate pore size tuning. Here we report polymer membranes containing pendant groups of varying hydrophobicity, strategically positioned near charged groups to regulate their hydration capacity and pore swelling. Modulation of the hydrated micropore size (less than two nanometres) enables direct control over water and ion transport across broad length scales, as quantified by spectroscopic and computational methods. Ion selectivity improves in hydration-restrained pores created by more hydrophobic pendant groups. These highly interconnected ion transport channels, with tuned pore gate sizes, show higher ionic conductivity and orders-of-magnitude lower permeation rates of redox-active species compared with conventional membranes, enabling stable cycling of energy-dense aqueous organic redox flow batteries. This pore size tailoring approach provides a promising avenue to membranes with precisely controlled ionic and molecular transport functions.

Science & Technology - Other Topics↗

Molecular basis of P[II] major human rotavirus VP8* domain recognition of histo-blood group antigens

Initial cell attachment of rotavirus (RV) to specific cell surface glycan receptors, which is the essential first step in RV infection, is mediated by the VP8* domain of the spike protein VP4. Recently, human histo-blood group antigens (HBGAs) have been identified as receptors or attachment factors for human RV strains. RV strains in the P[4] and P[8] genotypes of the P[II] genogroup share common recognition of the Lewis b (Le b ) and H type 1 antigens, however, the molecular basis of receptor recognition by the major human P[8] RVs remains unknown due to lack of experimental structural information. Here, we used nuclear magnetic resonance (NMR) spectroscopy-based titration experiments and NMR-derived high ambiguity driven docking (HADDOCK) methods to elucidate the molecular basis for P[8] VP8* recognition of the Leb (LNDFH I) and type 1 HBGAs. We also used X-ray crystallography to determine the molecular details underlying P[6] recognition of H type 1 HBGAs. Unlike P[6]/P[19] VP8*s that recognize H type 1 HBGAs in a binding surface composed of an α-helix and a β-sheet, referred as the “βα binding site”, the P[8] and P[4] VP8*s bind Le b HBGAs in a previously undescribed pocket formed by the edges of two β-sheets, referred to as the “ββ binding site”. Importantly, the P[8] and P[4] VP8*s retain binding capability to non-Le b type 1 HBGAs using the βα binding site. The presence of two distinct binding sites for Le b and non-Le b HBGA glycans in the P[8] and P[4] VP8* domains suggests host-pathogen co-evolution under structural and functional adaptation of RV pathogens to host glycan polymorphisms. Assessment and understanding of the precise impact of this co-evolutionary process in determining RV host ranges and cross-species RV transmission should facilitate improved RV vaccine development and prediction of future RV strain emergence and epidemics.

59 BASIC BIOLOGICAL SCIENCES↗

Programming Amphiphilic Peptoid Oligomers for Hierarchical Assembly and Inorganic Crystallization

Natural organisms make a wide variety of exquisitely complex, nano-, micro-, and macroscale structured materials in an energy-efficient and highly reproducible manner. During these processes, the information-carrying biomolecules (e.g., proteins, peptides, and carbohydrates) enable (1) hierarchical organization to assemble scaffold materials and execute high-level functions and (2) exquisite control over inorganic materials synthesis, generating biominerals whose properties are optimized for their functions. Inspired by nature, significant efforts have been devoted to developing functional materials that can rival those natural molecules by mimicking in vivo functions using engineered proteins, peptides, DNAs, sequence-defined synthetic molecules (e.g., peptoids), and other biomimetic polymers. Among them, peptoids, a new type of synthetic mimetics of peptides and proteins, have received particular attention because they combine the merits of both synthetic polymers (e.g., high chemical stability and efficient synthesis) and biomolecules (e.g., sequence programmability and biocompatibility). The lack of both chirality and hydrogen bonds in their backbone results in a highly designable peptoid-based system with reduced structural complexity and side chain-chemistry-dominated properties. Here in this Account, we present our recent efforts in this field by programming amphiphilic peptoid sequences for (1) the controlled self-assembly into different hierarchically structured nanomaterials with favorable properties and (2) manipulating inorganic (nano)crystal nucleation, growth, and assembly into superstructures. First, we designed a series of amphiphilic peptoids with controlled side chain chemistries that self-assembled into 1D highly stiff and dynamic nanotubes, 2D membrane-mimetic nanosheets, hexagonally patterned nanoribbons, and 3D nanoflowers. These crystalline nanostructures exhibited sequence-dependent properties and showed promise for different applications. The corresponding peptoid self-assembly pathways and mechanisms were also investigated by leveraging in situ atomic force microscopy studies and molecular dynamics simulations, which showed precise sequence dependency. Second, inspired by peptide- and protein-controlled formation of hierarchical inorganic nanostructures in nature, we developed peptoid-based biomimetic approaches for controlled synthesis of inorganic materials (e.g., noble metals and calcite), in which we took advantage of the substantial side chain chemistry of peptoids and investigated the relationship between the peptoid sequences and the morphology and growth kinetics of inorganic materials. For example, to overcome the challenges (e.g., complexity of protein- and peptide-folding, poor thermal and chemical stabilities) facing the area of protein- and peptide-controlled synthesis of inorganic materials, we recently reported the design of sequence-defined peptoids for controlled synthesis of highly branched plasmonic gold particles. Moreover, we developed a rule of thumb for designing peptoids that predictively enabled the morphological evolution from spherical to coral-shaped gold nanoparticles (NPs). With this Account, we hope to stimulate the research interest of chemists and materials scientists and promote the predictive synthesis of functional and robust materials through the design of sequence-defined synthetic molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Temperature and composition dependent screw dislocation mobility in austenitic stainless steels from large-scale molecular dynamics

Abstract Extensive molecular dynamics simulations are performed to determine screw dislocation mobility in austenitic Fe 0.7 Ni x Cr 0.3-x stainless steels as a function of temperature ranging from 100 to 1300 K, resolved shear stress from 30 to 140 MPa, and Ni composition from 0.0 to 30.0 at%. These mobility data are fitted to a linear mobility law with a nonzero stress offset, referred to as the threshold stress. We find that both the linear drag coefficient and the threshold stress increase with Ni composition. The drag coefficient increases with temperature, whereas the threshold stress decreases with temperature. Based on these calculations, we determine fitting functions for the linear solute drag coefficient as a function of temperature and composition. The mobility laws determined in this study may serve to inform dislocation dynamics simulations pertinent to dislocation network evolution at elevated temperatures for a wide composition range of austenitic stainless steels.

Chu, Kevin (ORCID:000000031929710X)↗

Hybridization of colloidal handlebodies with singular defects and topological solitons in chiral liquid crystals

Topology can manifest itself in colloids when quantified by invariants like Euler characteristics of nonzero-genus colloidal surfaces, albeit spherical colloidal particles are most often studied, and colloidal particles with complex topology are rarely considered. On the other hand, singular defects and topological solitons often define the physical behavior of the molecular alignment director fields in liquid crystals. Interestingly, nematic liquid crystalline dispersions of colloidal particles allow for probing the interplay between topologies of surfaces and fields, but only a limited number of such cases have been explored so far. Here, we study the hybridization of topological solitons, singular defects, and topologically nontrivial colloidal particles with the genus of surfaces different from zero in a chiral nematic liquid crystal phase. Hybridization occurs when distortions separately induced by colloidal particles and LC solitons overlap, leading to energy minimization-driven redistribution of director field deformations and defects. As a result, hybrid director configurations emerge, combining topological features from both components. We uncover a host of director field configurations complying with topological theorems, which can be controlled by applying electric fields. Rotational and translational dynamics arise due to the nonreciprocal evolution of the director fields in response to alternating electric fields of different frequencies. These findings help define a platform for controlling topologically hyper-complex colloidal structures and dynamics with electrically reconfigurable singular defects and topological solitons induced by colloidal handlebodies.

Lee, Jun-Yong [Hiroshima Univ. (Japan)]↗

Ab Initio Molecular Dynamics Insights into Stress Corrosion Cracking and Dissolution of Metal Oxides

Oxide phases such as α-Fe2O3 (hematite) and α-Al2O3 (corundum) are highly insoluble in water; however, subcritical crack growth has been observed in humidity nonetheless. Chemically induced bond breaking at the crack tip appears unlikely due to sterically hindered molecular transport. The molecular mechanics of a crack in corundum with a reactive force field reveal minimal lattice trapping, leading to bond breaking before sufficient space opens for water transport. To address this, we model a pre-built blunt crack with space for H2O molecule adsorption at the tip and show that it reduces fracture toughness by lowering the critical J-integral. Then, we explore stress-enhanced dissolution to understand the mechanism of crack tip blunting in the oxide/water system. Density functional theory combined with metadynamics was employed to describe atomic dissolution from flat hematite and corundum surfaces in pure water. Strain accelerates dissolution, stabilizing intermediate states with broken bonds before full atom detachment, while the free energy profile of unstrained surfaces is almost monotonic. The atomistic calculations provided input for a kinetic model, predicting the shape evolution of a blunt crack tip, which displays three distinct regimes: (i) dissolution primarily away from the tip, (ii) enhanced blunting near but not at the apex, and (iii) sharpening near the apex. The transition between regimes occurs at a low strain, highlighting the critical role of water in the subcritical crack growth of oxide scales, with dissolution as the fundamental microscopic mechanism behind this process.

Chemistry↗

NELL2-Robo3 complex structure reveals mechanisms of receptor activation for axon guidance

Axon pathfinding is critical for nervous system development, and it is orchestrated by molecular cues that activate receptors on the axonal growth cone. Robo family receptors bind Slit guidance cues to mediate axon repulsion. In mammals, the divergent family member Robo3 does not bind Slits, but instead signals axon repulsion from its own ligand, NELL2. Conversely, canonical Robos do not mediate NELL2 signaling. Here, we present the structures of NELL-Robo3 complexes, identifying a mode of ligand engagement for Robos that is orthogonal to Slit binding. We elucidate the structural basis for differential binding between NELL and Robo family members and show that NELL2 repulsive activity is a function of its Robo3 affinity and is enhanced by ligand trimerization. Our results reveal a mechanism of oligomerization-induced Robo activation for axon guidance and shed light on Robo family member ligand binding specificity, conformational variability, divergent modes of signaling, and evolution.

59 BASIC BIOLOGICAL SCIENCES↗

Fluorescence-mediated postcollision interaction in x-ray photoionization of the Xe 𝐾 edge

Postcollision interaction (PCI) in near-threshold photoionization of the K shell of atomic Xe is investigated with hard-x-ray synchrotron radiation. Applying Auger electron spectroscopy, line-shape distortion is monitored in the K-L 2 → L 2 M 4,5 M 4,5 decay channel, where the initial K-L 2 (Kα 2 ) x-ray-emission step mediates the emission of the two continuum electrons. The K-edge result is compared to similar data obtained on direct L 2 M 4,5 M 4,5 decay at the L 2 edge without x-ray-emission. In conclusion, it is found that the evolution of the PCI shift with excess photon energy is very similar at both edges, but a subtle decrease in the PCI shift is observable at the K edge due to the effect of the ultrafast x-ray emission step delaying the PCI energy exchange by a few attoseconds.

74 ATOMIC AND MOLECULAR PHYSICS↗

Charge accumulation and solvation in $β$-NiOOH: Surface chemistry of an OER catalyst from ML-aided simulations

Electrochemical water splitting is a key technology for a sustainable energy transition, providing a route to store surplus electricity from renewable sources. A central bottleneck is the sluggish oxygen evolution reaction (OER), which drives the search for catalysts that are active, stable, and inexpensive enough for large-scale deployment. Within this context, pure and doped NiO x H y combine high activity with low cost, making them prime candidates for alkaline OER. Yet, despite extensive study, the atomistic structure of NiOOH under operando conditions and the associated reaction mechanisms remain debated. Here, we investigate the structural complexity of pure β-NiOOH, the scaffold for its doped derivatives. We systematically investigate the oxidation of the surface adsorbates via proton-coupled electron transfer steps across relevant facets and sites, identifying the most probable sequence of deprotonation events. Our results reveal asymmetric charge accumulation on Wulff-relevant surfaces and show how applied potential can promote morphological restructuring. Explicit solvation is included through machine-learning interatomic potential molecular dynamics of the NiOOH/water interface, which allows us to resolve the hydrophobic and hydrophilic character of different surfaces and the associated interfacial water structure. Together, these insights demonstrate how surface chemistry and solvation jointly govern the stability of NiOOH and the accumulation of surface charge, with possible implications for catalytic performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

New insights into fuel blending effects: Intermolecular chemical kinetic interactions affecting autoignition times and intermediate-temperature heat release

Fuel blending effects on chemically-dominated fuel properties, such as gasoline anti-knock quality, are influenced by fundamental chemical kinetic interactions between the blending agent and the base fuel. Historically, quantification of such interactions has focused on changes to the radical pool, including $\dot{O}$H and HO 2 , while intermolecular interactions pertaining to carbonated, non-fuel-specific intermediates are typically overlooked. In this regard, this work aims to derive new insight into intermolecular chemical kinetic interactions that are intrinsic to fuel blending effects via a case study on blends of 0–30% ethanol (by volume) into FGF-LLNL (a multi-component gasoline surrogate for FACE-F research gasoline) using a rapid compression machine at a diluted/stoichiometric fuel loading, compressed pressure of 40 bar and low- to intermediate-temperature regimes that are representative of boosted SI engine operation. Ethanol blending effects on the intermediate temperature heat release (ITHR) of FGF-LLNL are characterized using experimental measurements, where ethanol is found to promote the extent of ITHR and suppress the transition from ITHR to main ignition. Chemical kinetic modeling is undertaken using a recently updated gasoline surrogate model. Sensitivity analyses on ITHR characteristics further corroborate the ethanol blending effects, and highlight the significant dependence of ITHR on both fuel-specific and non-fuel-specific reactions. An approach allowing comprehensive characterization of the complex intermolecular chemical kinetic interactions between constitutes in a fuel blend is then proposed. Application of the approach to FGF-LLNL/E0–E30 reveals that ethanol perturbs the heat release and autoignition characteristics of FGF-LLNL not only by directly changing the $\dot{O}$H and HO 2 radical pools via fuel-specific reactions, but also through intermolecular interactions where participating intermediates can be produced and consumed by various sub-chemistries. Disabling the intermolecular interactions in carbonated species between ethanol and FGF-LLNL sub-chemistries leads to somewhat slower ITHR evolution and lower ignition reactivity. The role of the individual intermolecular interaction is also characterized using the proposed approach. Lastly, implications of intermolecular interactions for future studies that aim to improve model performance are highlighted, where it is found that further investigations on the core C0-C4 chemistry are needed for developing highly accurate chemistry models for complex fuel blends.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the United States National Science Foundation, National Institutes of Health, and Department of Energy, supports structural biologists and Protein Data Bank (PDB) data users around the world. The RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, serves as the US data center for the global PDB archive housing experimentally-determined three-dimensional (3D) structure data for biological macromolecules. As the wwPDB-designated Archive Keeper, RCSB PDB is also responsible for the security of PDB data and weekly update of the archive. RCSB PDB serves tens of thousands of data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) annually working on all permanently inhabited continents. RCSB PDB makes PDB data available from its research-focused web portal at no charge and without usage restrictions to many millions of PDB data consumers around the globe. It also provides educators, students, and the general public with an introduction to the PDB and related training materials through its outreach and education-focused web portal. This review article describes growth of the PDB, examines evolution of experimental methods for structure determination viewed through the lens of the PDB archive, and provides a detailed accounting of PDB archival holdings and their utilization by researchers, educators, and students worldwide.

59 BASIC BIOLOGICAL SCIENCES↗

Evolving dual-trait EPSP synthase variants using a synthetic yeast selection system

The enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) functions in the shikimate pathway which is responsible for the production of aromatic amino acids and precursors of other essential secondary metabolites in all plant species. EPSPS is also the molecular target of the herbicide glyphosate. While some plant EPSPS variants have been characterized with reduced glyphosate sensitivity and have been used in biotechnology, the glyphosate insensitivity typically comes with a cost to catalytic efficiency. Thus, there exists a need to generate additional EPSPS variants that maintain both high catalytic efficiency and high glyphosate tolerance. Here, we create a synthetic yeast system to rapidly study and evolve heterologous EPSP synthases for these dual traits. Using known EPSPS variants, we first validate that our synthetic yeast system is capable of recapitulating growth characteristics observed in plants grown in varying levels of glyphosate. Next, we demonstrate that variants from mutagenesis libraries with distinct phenotypic traits can be isolated depending on the selection criteria applied. By applying strong dual-trait selection pressure, we identify a notable EPSPS mutant after just a single round of evolution that displays robust glyphosate tolerance (K i of nearly 1 mM) and improved enzymatic efficiency over the starting point (~2.5 fold). Finally, we show the crystal structure of corn EPSPS and the top resulting mutants and demonstrate that certain mutants have the potential to outperform previously reported glyphosate-resistant EPSPS mutants, such as T102I and P106S (denoted as TIPS), in whole-plant testing. Altogether, this platform helps explore the trade-off between glyphosate resistance and enzymatic efficiency.

Science & Technology - Other Topics↗

Discovering novel therapeutic V H Hs for emerging viruses: perspectives from VEEV selection strategies

Introduction: Evolution or emergence of a new viral variant is a significant public health concern. Alphaviruses, such as Venezuelan equine encephalitis virus (VEEV), are mosquito-borne viruses which are becoming more prevalent due to expansion of vector habitats. Despite this, there are currently no antiviral therapies or FDA-approved vaccines available to treat or prevent VEEV infection. The increased prevalence of such viruses provides opportunities for novel variants to evolve. Key therapeutic molecules that could be developed against viral pathogens are recombinant antibodies or antibody fragments, such as the variable heavy domain of heavy chain antibodies (V H Hs). Methods: In vitro selections offer a promising pathway for identification of therapeutic antibodies, here we explored isolation of V H Hs using phage and yeast display methodology with three antigen formats 1) recombinant E2, 2) linear peptides of E2, selected based on molecular dynamics analysis, and 3) UV inactivated virus. Results: Here we report four novel “human” V H Hs which bind to the VEEV E2 protein selected using different strategies that include both computational and biochemical design of suitable antigens and whole virus selections. These V H Hs have distinct complementarity-determining regions (CDRs). Multiple VHHs bind to the VEEV viral particles in ELISAs, and we report the peptide epitope recognized by these V H Hs. Discussion: Though non-neutralizing, these V H Hs bind to and sequester VEEV viral particles preventing infection, demonstrating the potential of these V H Hs to perform viral “sponging” which represents a novel therapeutic approach. The selection strategies we report may have applications to further antibody developments against other viruses.

59 BASIC BIOLOGICAL SCIENCES↗

Unlocking High Capacity and Reversible Alkaline Iron Redox Using Silicate-Sodium Hydroxide Hybrid Electrolytes

Alkaline iron (Fe) batteries are attractive due to the high abundance, low cost, and multiple valent states of Fe but show limited columbic efficiency and storage capacity when forming electrochemically inert Fe 3 O 4 on discharging and parasitic H 2 on charging. Herein, sodium silicate is found to promote Fe(OH) 2 /FeOOH against Fe(OH) 2 /Fe 3 O 4 conversions. Electrochemical experiments, operando X-ray characterization, and atomistic simulations reveal that improved Fe(OH) 2 /FeOOH conversion originates from (i) strong interaction between sodium silicate and iron oxide and (ii) silicate-induced strengthening of hydrogen-bond networks in electrolytes that inhibits water transport. Furthermore, the silicate additive suppresses hydrogen evolution by impairing energetics of water dissociation and hydroxyl de-sorption on iron surfaces. In conclusion, this new silicate-assisted redox chemistry mitigates H 2 and Fe 3 O 4 formation, improving storage capacity (199 mAh g -1 in half-cells) and coulombic efficiency (94 % after 400 full-cell cycles), paving a path to realizing green battery systems built from earth-abundant materials.

36 MATERIALS SCIENCE↗

Tantalum oxide and nitride spectral features from a laser-produced plasma

Here, we report measurements of time-resolved Ta, TaO and TaN emission spectroscopic signatures from a laser-produced plasma. Plasmas were generated using 1064 nm, 6 ns pulses from an Nd:YAG laser focused onto a pure Ta metal target in a gaseous environment with varying percentages of O 2 /N 2 for controlling gas-phase oxidation/plasma chemistry. Time-resolved analysis showed that Ta oxide emission is prominent at later times in plasma evolution, whereas strong atomic emission is present at early times in air. Emission spectral features as a function of O 2 partial pressure showed that TaO emission intensity increases, while the peak intensity of TaO appears earlier with increasing O 2 availability. We also report emission spectra of TaN, and show that plasma chemistry favors TaO formation instead of TaN when O 2 is present in the environment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Proteomic and phosphoproteomic measurements enhance ability to predict ex vivo drug response in AML

Acute Myeloid Leukemia (AML) affects 20,000 patients in the US annually with a five-year survival rate of approximately 25%. One reason for the low survival rate is the high prevalence of clonal evolution that gives rise to heterogeneous sub-populations of leukemic cells with diverse mutation spectra, which eventually leads to disease relapse. This genetic heterogeneity drives the activation of complex signaling pathways that is reflected at the protein level. This diversity makes it difficult to treat AML with targeted therapy, requiring custom patient treatment protocols tailored to each individual’s leukemia. Toward this end, the Beat AML research program prospectively collected genomic and transcriptomic data from over 1000 AML patients and carried out ex vivo drug sensitivity assays to identify genomic signatures that could predict patient-specific drug responses. However, there are inherent weaknesses in using only genetic and transcriptomic measurements as surrogates of drug response, particularly the absence of direct information about phosphorylation-mediated signal transduction. As a member of the Clinical Proteomic Tumor Analysis Consortium, we have extended the molecular characterization of this cohort by collecting proteomic and phosphoproteomic measurements from a subset of these patient samples (38 in total) to evaluate the hypothesis that proteomic signatures can improve the ability to predict response to 26 drugs in AML ex vivo samples. In this work we describe our systematic, multi-omic approach to evaluate proteomic signatures of drug response and compare protein levels to other markers of drug response such as mutational patterns. We explore the nuances of this approach using two drugs that target key pathways activated in AML: quizartinib (FLT3) and trametinib (Ras/MEK), and show how patient-derived signatures can be interpreted biologically and validated in cell lines. In conclusion, this pilot study demonstrates strong promise for proteomics-based patient stratification to assess drug sensitivity in AML.

60 APPLIED LIFE SCIENCES↗