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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Unveiling the ambipolar carrier transport property of SnO 2–X for multiple-functional interlayers in perovskite solar cells

Tin oxides are the most promising electron transport layers in perovskite solar cells. An ambipolar carrier transport property has been recently demonstrated which enables a simple interconnection structure for all-perovskite tandem solar cells. However, the underlying mechanism for its ambipolar behavior is unclear which cannot be explained by the intrinsic defects in SnO 2-x . Here by using density functional theory calculations, we unveil the origin of the ambipolar carrier transport of non-stoichiometry SnO 2-x with a structure of SnO embedded in SnO 2 matrix. The hybridization of O 2p and Sn 5s orbitals of SnO introduces mid-gap states in the bandgap of SnO 2 , enabling hole transport property for SnO 2-x when x is > 0.2. Increasing the percentage of SnO in SnO 2-x significantly enhances the hole transport capability of SnO 2-x due to the enlarged Sn-O-Sn angles that increases orbital overlapping between O and Sn atoms, thus providing strategies for the further tuning of the carrier transport properties of SnO 2-x by compositional and structural designs.

14 SOLAR ENERGY↗
DOE OSTI2023

Direct Transformation of SiH 4 to a Molecular L(H) 2 Co=Si=Co(H) 2 L Silicide Complex

The synthesis of bimetallic molecular silicide complexes is reported, based on the use of multiple Si–H bond activations in SiH 4 at the metal centers of 14-electron LCo I fragments (L = Tp", HB(3,5-diisopropylpyrazolyl) 3 – ; [BP 2 tBu Pz], PhB(CH 2 P t Bu 2 ) 2 (pyrazolyl)). Upon exposure of (Tp"Co) 2 (μ-N 2 ) (1) to SiH 4 , a mixture of (Tp"Co) 2 (μ-H) (2) and (Tp"Co) 2 (μ-H) 2 (3) was formed and no evidence for Si–H oxidative addition products was observed. In contrast, [BP 2 tBu Pz]-supported Co complexes led to Si–H oxidative additions with the generation of silylene and silicide complexes as products. Notably, the reaction of ([BP 2 tBu Pz]Co) 2 (μ-N 2 ) (5) with SiH 4 gave the dicobalt silicide complex [BP 2 tBu Pz](H) 2 Co=Si=Co(H) 2 [BP 2 tBu Pz] (8) in high yield, representing the first direct route to a symmetrical bimetallic silicide. Here, the effect of the [BP 2 tBu Pz] ligand on Co–Si bonding in 7 and 8 was explored by analysis of solid-state molecular structures and density functional theory (DFT) investigations. Upon exposure to CO or DMAP (DMAP = 4-dimethylaminopyridine), 8 converted to the corresponding [BP 2 tBu Pz]Co(L) x adducts (L = CO, x = 2; L = DMAP, x = 1) with concomitant loss of SiH 4 , despite the lack of significant Si–H interactions in the starting complex. On heating to 60 °C, 8 underwent reaction with MeCl to produce small quantities of Me x SiH 4–x (x = 1–3), demonstrating functionalization of the μ-silicon atom in a molecular silicide to form organosilanes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Sulfurized Polyacrylonitrile for High-Performance Lithium–Sulfur Batteries: In-Depth Computational Approach Revealing Multiple Sulfur’s Reduction Pathways and Hidden Li + Storage Mechanisms for Extra Discharge Capacity

Like no other sulfur host material, polyacrylonitrile-derived sulfurized carbon (SPAN) promises improved electrochemical performance for lithium–sulfur batteries, based on its compatibility with carbonate solvents and ability to prevent self-discharge and shuttle effect. However, a complete understanding of the SPAN’s lithiation mechanism is still missing because its structural features vary widely with synthesis conditions, and its electrochemical performance deviates from elemental sulfur. This study continues our research on the elucidation of the SPAN’s structural characteristics and lithiation mechanisms via computational approaches. Here, our models reproduce most experimental data regarding carbon’s graphitization level and conjugated ordering, sulfur–carbon covalent bonding, sulfur loading, and elemental composition. Our simulations emulate the discharge voltage observed in experiments for the first discharge, which reveals that sulfur follows multiple reduction pathways based on its interaction with the carbon backbone. Sulfur reduction takes place above 1.0 V vs Li/Li + mostly in the SPAN-like material, with no long-chain lithium polysulfide formation. Below 1.0 V vs Li/Li + , the backbone’s electrochemical activity occurs via multiple C–Li and N–Li interactions, mostly with edge carbon atoms and pyridinic nitrogen. Moreover, we identify Li + binding sites throughout the graphitized backbone that might lead to prohibited energy costs for Li + deintercalation, which may explain the irreversible capacity loss between the first and second discharges. This work improves understanding of lithiation mechanisms in sulfurized carbon, which is useful for rationally designing SPAN synthesis pathways tailored to increase sulfur loading and enhanced electrochemical performance.

25 ENERGY STORAGE↗
DOE OSTI2020

Catalytic consequences of hydrogen addition events and solvent-adsorbate interactions during guaiacol-H 2 reactions at the H 2 O-Ru(0 0 0 1) interface

Catalytic reactions of biomass-derived phenolics and H 2 occur on transition metal surfaces via competitive C–O cleavage and ring saturation pathways, with both requiring multiple hydrogen addition events before forming their respective rate limiting transition states. These events are markedly affected by solvent chemical identity, with polar protic solvents ionizing hydrogen adatoms (H*) to interfacial protons (H + ) and opening up new catalytic routes. Here, we establish the reaction coordinate space for guaiacol-H 2 reactions on Ru(0 0 0 1) using density functional theory and describe the atomic-scale effect of a polar protic solvent, H 2 O. Coupled H + and H* attack leads to quasi-equilibrated enol and keto intermediates as the precursors for C–O cleavage and ring saturation, respectively. For C–O cleavage, H 2 O solvent enables a lower energy pathway via concomitant transfer of the hydroxyl H + to the methoxy oxygen during C–OCH 3 cleavage, forming a charge separated [Ru(s)–(C 6 H 5 O – )…(H + )…OCH 3 ] transition state and reducing the barrier by up to 0.8 eV as compared to unassisted C–OCH 3 cleavage. For ring saturation, H* attack onto an unsaturated meta carbon is rate limiting with no direct solvent participation, suggesting that protic polar solvents selectively promote the C–O cleavage pathway. Taken together, we show that activating guaiacol for either C–O bond cleavage or ring saturation product formation depends on the reactive hydrogen identity (H* or H + ), enol/keto isomerization equilibrium, and accessibility of the proton assisted Car–OCH 3 cleavage transition state. Here, all such factors are tunable via changes to the solvent or metal identity.

09 BIOMASS FUELS↗
DOE OSTI2024

Understanding Process–Structure Relationships during Lamination of Halide Perovskite Interfaces

Fabrication of halide perovskite (HP) solar cells typically involves the sequential deposition of multiple layers to create a device stack, which is limited by the thermal and chemical incompatibility of top contact layers with the underlying HP semiconductor. One emerging strategy to overcome these restrictions on material selection and processing conditions is lamination, where two half-stacks are independently processed and then diffusion bonded to complete the device. Lamination reduces the processing constraints on the top side of the solar cell to allow new device designs, expanded use of deposition methods, and self-encapsulation of devices. While laminated perovskite solar cells with high efficiencies and novel interlayer combinations have been demonstrated, there is a limited understanding of how the lamination process parameters affect the diffusion-bond quality and material properties of the resulting HP layer. In this study, we systematically vary temperature, pressure, and time during lamination and quantify the resulting impacts on bonded area, grain domain size, and photoluminescence. A design of experiments is performed, and statistical analysis of the experimental results is used to quantitatively evaluate the resulting process–structure–property relationships. The lamination temperature is found to be the key parameter controlling these properties. Furthermore, a temperature of 150 °C enables successful bonding over 95% of the substrate area and also results in increases in apparent grain domain size and photoluminescence intensity. Based on these insights, the lamination temperature of functional perovskite solar cell devices is varied, demonstrating the importance of the resulting bond quality on device performance metrics.

14 SOLAR ENERGY↗
DOE OSTI2022

Multi-reward Reinforcement Learning Based Bond-Order Potential to Study Strain-Assisted Phase Transitions in Phosphorene

Here, we introduce a multi-reward reinforcement learning (RL) approach to train a flexible bond-order potential (BOP) for 2D phosphorene based on ab initio training data sets. Our approach is based on a continuous action space Monte Carlo tree search algorithm that is general and scalable and presents an efficient multiobjective optimization scheme for high-dimensional materials design problems. As a proof-of-concept, we deploy this scheme to parametrize multiple structural and dynamical properties of 2D phosphorene polymorphs. Our RL-trained BOP model adequately captures the structure, energetics, transformation barriers, equation of state, elastic constants, and phonon dispersions of various 2D P polymorphs. We use this model to probe the impact of temperature and strain rate on the phase transition from black (α-P) to blue phosphorene (β-P) through molecular dynamics simulations. A decrease in critical strain for this phase transition with increase in temperature is observed, and the underlying atomistic mechanisms are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Isolated Metal Sites in Cu–Zn–Y/Beta for Direct and Selective Butene-Rich C 3+ Olefin Formation from Ethanol

Direct and selective production of C 3+ olefins from bioethanol remains a critical challenge and important for the production of renewable transportation fuels such as aviation biofuels. In this study, we report a Cu–Zn–Y/Beta catalyst for selective ethanol conversion to butene-rich C 3+ olefins (88% selectivity at 100% ethanol conversion, 623 K), where the Cu, Zn, and Y sites are all highly dispersed. The ethanol-to-butene reaction network includes ethanol dehydrogenation, aldol condensation to crotonaldehyde, and hydrogenation to butyraldehyde, followed by further hydrogenation and dehydration reactions to form butenes. Cu sites play a critical role in promoting hydrogenation of the crotonaldehyde C═C bond to form butyraldehyde in the presence of hydrogen, making this a distinctive pathway from crotyl alcohol-based ethanol-to-butadiene reaction. Reaction rate measurements in the presence of ethanol and acetaldehyde (543 K, 12 kPa ethanol, 1.2 kPa acetaldehyde, 101.9 kPa H 2 ) over monometallic Zn/Beta and Y/Beta catalysts indicate that Y sites have higher C–C coupling rates than over Zn sites (initial C–C coupling rate, 6.1 × 10 –3 mol mol Y –1 s –1 vs 1.2 × 10 –3 mol mol Zn –1 s –1 ). Further, Lewis-acidic Y-site densities over Cu–Zn–Y/Beta with varied Y loadings are linearly correlated with the initial C–C coupling rates, suggesting that Lewis-acidic Y sites are the predominant sites that catalyze C–C coupling in Cu–Zn–Y/Beta catalysts. Control experiments show that the dealuminated Beta support is important to form higher density of Lewis-acidic Y sites in comparison with other supports such as silica, or deboronated MWW despite similar atomic dispersion of Y sites and Y–O coordination numbers over these supports, leading to more than 9 times higher C–C coupling rate per mole Y over dealuminated Beta relative to other supports. This study highlights the significance of unique combination of metal sites in contributing to the selective valorization of ethanol to C 3+ olefins, motivating for exploring multifunctional zeolite catalysts, where the presence of multiple sites with varying reactivities and functions allows for controlling the predominant molecular fluxes toward the desired products in complex reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

KARRIKIN INSENSITIVE2 regulates leaf development, root system architecture and arbuscular‐mycorrhizal symbiosis in Brachypodium distachyon

SUMMARY KARRIKIN INSENSITIVE2 (KAI2) is an α/β‐hydrolase required for plant responses to karrikins, which are abiotic butenolides that can influence seed germination and seedling growth. Although represented by four angiosperm species, loss‐of‐function kai2 mutants are phenotypically inconsistent and incompletely characterised, resulting in uncertainties about the core functions of KAI2 in plant development. Here we characterised the developmental functions of KAI2 in the grass Brachypodium distachyon using molecular, physiological and biochemical approaches. Bdkai2 mutants exhibit increased internode elongation and reduced leaf chlorophyll levels, but only a modest increase in water loss from detached leaves. Bdkai2 shows increased numbers of lateral roots and reduced root hair growth, and fails to support normal root colonisation by arbuscular‐mycorrhizal (AM) fungi. The karrikins KAR 1 and KAR 2 , and the strigolactone (SL) analogue rac ‐GR24, each elicit overlapping but distinct changes to the shoot transcriptome via BdKAI2. Finally, we show that BdKAI2 exhibits a clear ligand preference for desmethyl butenolides and weak responses to methyl‐substituted SL analogues such as GR24. Our findings suggest that KAI2 has multiple roles in shoot development, root system development and transcriptional regulation in grasses. Although KAI2‐dependent AM symbiosis is likely conserved within monocots, the magnitude of the effect of KAI2 on water relations may vary across angiosperms.

Meng, Yongjie↗
DOE OSTI2020

One Electron Multiple Proton Transfer in Model Organic Donor–Acceptor Systems: Implications for High-Frequency EPR

EPR spectroscopy is an important spectroscopic method for identification and characterization of radical species involved in many biological reactions. The tyrosyl radical is one of the most studied amino acid radical intermediates in biology. Often in conjunction with histidine residues, it is involved in many fundamental biological electron and proton transfer processes, such as in the water oxidation in photosystem II. As biological processes are typically extremely complicated and hard to control, molecular bio-mimetic model complexes are often used to clarify the mechanisms of the biological reactions. In this work, we present theoretical calculations to investigate the sensitivity of magnetic resonance parameters to proton-coupled electron transfer events, as well as conformational substates of the molecular constructs which mimic the tyrosine-histidine (Tyr-His) pairs found in a large variety of proteins. Upon oxidation of the phenol, the Tyr analog, these complexes can perform not only one-electron one-proton transfer (EPT), but also one-electron two-proton transfers (E2PT). It is shown that in aprotic environment the g X -components of the electronicg-tensor are extremely sensitive to the first proton transfer from the phenoxyl oxygen to the imidazole nitrogen (EPT product), leading to a significant increase of the g X -value of up to 0.003, but are not sensitive to the second proton transfer (E2PT). In the latter case, the change of the g X -value is much smaller (ca. 0.0001), which is too small to be distinguished even by high-frequency EPR. The 14 N hyperfine values are also too similar to allow differentiation between the different protonation states in EPT and E2PT. The magnetic resonance parameters were also calculated as a function of the rotation angles around single bonds. It was demonstrated that rotation of the phenoxyl group results in large positive changes (> 0.001) in the g X -values. Analysis of the data reveals that the main source of these changes is related to the strength of the H-bond between phenoxyl oxygen and the proton(s) on N 1 and N 2 positions of the imidazole.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

The Role of Ligand–Ligand Interactions in Multimodal Ligand Conformational Equilibria and Surface Pattern Formation

Multimodal chromatography uses multiple modes of interaction such as charge, hydrophobic, or hydrogen bonding to separate proteins. Recently, we used molecular dynamics (MD) simulations to show that ligands immobilized on surfaces can interact and associate with neighboring ligands to form hydrophobic and charge patches, which may have important implications for the nature of protein–surface interactions. Here, we study interfacial systems of increasing complexity—from a single immobilized multimodal ligand to high density surfaces—to better understand how ligand behavior is affected by the presence of a surface and the presence of other ligands in the vicinity, and how this behavior scales to larger systems. Furthermore, we find that tethering a ligand to a surface restricts its conformations to a subset of those observed in free solution, yet the ligand maintains flexibility in the plane of the surface and can form contacts with neighboring ligands. We find that although the formation of a contact between two neighboring ligands is slightly unfavorable, three neighboring ligands exhibit a preference for the formation of a fully connected cluster. To explore how these trends in ligand association extend to a larger surface with high density of ligands, we performed coarse-grained Monte Carlo (MC) simulations of a 132-ligand surface using ligand interactions parametrized based on free energies obtained from the three-ligand MD simulations. Despite their simplicity, the coarse-grained simulations qualitatively capture the cluster size distribution of ligands observed in detailed MD simulations. Quantitative differences between the two suggest opportunities for improvements in the coarse-grained energy function for efficient predictions of cluster and pattern formations. Our approach presents a promising route to the engineering of multimodal patterns for future chromatographic resin design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

High-Resolution Comonomer Sequencing of Blocky Brominated Syndiotactic Polystyrene Copolymers Using 13C NMR Spectroscopy and Computer Simulations

This work demonstrates the first high-resolution comonomer sequencing of Blocky brominated syndiotactic polystyrene (sPS-co-sPS-Br) copolymers based on pentad assign- ments of the quaternary carbon region of the nuclear magnetic resonance spectrum. Copolymers containing p-bromostyrene (Br-Sty) units were prepared in matched sets using postpolymerization bromination methods carried out in the heterogeneous gel state (Blocky) and homogeneous solution state (Random). Quantitative information from the quaternary carbon spectra, heteronuclear multiple bond correlation spectroscopy, electronic structure calculations, and simulated statistically random copolymers was correlated to confirm the carbon resonance assignments for all 20 possible pentad comonomer sequences. Using the experimental pentad sequence prevalences, a computer code was developed to simulate chains with microstructures typical of each sample as a means to visually represent the copolymer blockiness with quantitative precision. Based on the microstructure and distribution of run lengths in these chains, the simulations revealed that the Blocky copolymers contain a high degree of blockiness. By comparing the run lengths in the simulated chains to the average number of styrene units in a crystalline segment of sPS (found by small-angle X-ray scattering), copolymer crystallizability was predicted. For the simulated Blocky B-21% (21 mol % Br-Sty) chain, the probability of randomly selecting a styrene unit in a crystallizable block was 25.8%, while that in the simulated Random R-18% was zero, in excellent agreement with the experimental crystallization behavior measured by differential scanning calorimetry. Additionally, these predictions confirmed that the simulated chains accurately represent the ensemble of chains in their respective copolymer samples. Furthermore, each simulated Blocky chain contained one or more long sPS blocks that paralleled the measured 38-40 styrene units spanning a crystalline segment within the sPS/CCl4 gel. This finding affirmed that the long sPS segments originated from the precise lamellar structure within the heterogeneous gel morphology (i.e., block length is correlated with lamellar thickness). Overall, the ability to tailor the copolymer microstructure through control of the semicrystalline gel morphology opens the door to synthesizing ordered copolymers by postpolymerization functionalization processes with unprecedented levels of compositional control.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Partons as unique ground states of quantum Hall parent Hamiltonians: The case of Fibonacci anyons

We present microscopic, multiple Landau level, (frustration-free and positive semi-definite) parent Hamiltonians whose ground states, realizing different quantum Hall fluids, are parton-like and whose excitations display either Abelian or non-Abelian braiding statistics. We prove ground state energy monotonicity theorems for systems with different particle numbers in multiple Landau levels, demonstrate S-duality in the case of toroidal geometry, and establish complete sets of zero modes of special Hamiltonians stabilizing parton-like states, specifically at filling factor \nu=2/3 ν = 2 / 3 . The emergent Entangled Pauli Principle (EPP), introduced in [Phys. Rev. B 98, 161118(R) (2018)] and which defines the “DNA” of the quantum Hall fluid, is behind the exact determination of the topological characteristics of the fluid, including charge and braiding statistics of excitations, and effective edge theory descriptions. When the closed-shell condition is satisfied, the densest (i.e., the highest density and lowest total angular momentum) zero-energy mode is a unique parton state. We conjecture that parton-like states generally span the subspace of many-body wave functions with the two-body M M -clustering property within any given number of Landau levels, that is, wave functions with M M th-order coincidence plane zeroes and both holomorphic and anti-holomorphic dependence on variables. General arguments are supplemented by rigorous considerations for the M=3 M = 3 case of fermions in four Landau levels. For this case, we establish that the zero mode counting can be done by enumerating certain patterns consistent with an underlying EPP. We apply the coherent state approach of [Phys. Rev. X 1, 021015 (2011)] to show that the elementary (localized) bulk excitations are Fibonacci anyons. This demonstrates that the DNA associated with fractional quantum Hall states encodes all universal properties. Specifically, for parton-like states, we establish a link with tensor network structures of finite bond dimension that emerge via root level entanglement.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Identification of 2-Hydroxyacyl-CoA Synthases with High Acyloin Condensation Activity for Orthogonal One-Carbon Bioconversion

One-carbon (C1) compounds are emerging as cost-effective and potentially carbon-negative feedstocks for biomanufacturing, which require efficient, versatile metabolic platforms for the synthesis of value-added products. Synthetic formyl-CoA elongation (FORCE) pathways allow diverse product synthesis from C1 compounds via iterative C1 elongation, operating independently from the host metabolism with reduced engineering complexity and improved theoretical yields. However, a major bottleneck was identified as the suboptimal kinetics of the core C1–C1 condensation enzyme, 2-hydroxyacyl-CoA synthase (HACS), catalyzing the acyloin condensation reaction between formaldehyde and formyl-CoA. Furthermore, we used a combinatorial approach of bioprospecting and rational protein engineering to identify multiple HACS variants with significantly improved activities toward C1 substrates. Sequence and structure alignment of the active variants elucidated the key regions for the catalytic function, which were targeted for mutagenesis, leading to improved catalytic efficiency. In parallel, a consecutive round of bioprospecting for homologs with high similarity with active variants revealed a highly active HACS variant exhibiting up to 7-fold improvement in catalytic efficiency (k cat /K M ) and 14-fold improvement in the FORCE pathway flux in vivo compared to the previous reports. Upon further optimization of the downstream pathway, the orthogonal C1-to-product bioconversion system showed a metabolic flux of up to 700 μM glycolate OD –1 h –1 (2.1 mmol gDCW –1 h –1 ) and an industrially relevant glycolate titer, rate, and yield of 5.2 g L –1 (67.8 mM), 0.22 g L –1 h –1 , and 94% carbon yield, respectively.

2-hydroxyacyl-CoA synthase↗
DOE OSTI2022

Design of functional materials based on new principles of disorder. Final Report

Disorder is present to some extent in every material. The disorder can be sparse and localized – individual defects – or globally such as in a glass. Normally disorder is considered to be detrimental to function. However, this is not necessarily always the case. This project addressed the question: How does disorder provide new potentialities for the behavior of a material that would be absent in a crystalline material of the same composition? We have discovered a new principle for disordered matter: Independence of bond-level response. This work has introduced the possibility of creating new classes of mechanical meta-materials with applications everywhere from microscopic biological molecules (allostery) to large scale architectural disordered networks. During the course of this grant, we have subsequently elaborated on these novel ideas about bond-level independence of properties in disordered materials. In particular, this study has required that we understand the limits of disorder. That is, if crystals are perfect order, is there another diametrically opposed pole which is the most disordered state? We have shown that, in a well-defined way, jamming is one extreme disordered pole of rigid matter. Jamming is a far-from-equilibrium way of creating a rigid solid by rapidly quenching a random distribution of particles to a mechanically stable system at zero temperature. To understand the jammed state of matter, we have elucidated the low-frequency excitation of these systems. This has allowed a new way of understanding materials that cannot be easily classified as crystals or glasses. These ideas can be extended to address the mechanical properties of polycrystalline matter. Memory formation in matter can take inspiration from memory that occurs in a biological context. The issue of memory formation raises another set of questions at the heart of how the energy landscape is organized and how it can be manipulated to store information in a solid. This project has explored how to understand the degree to which multiple memories can be stored in a single system and has created a holistic understanding of how inputs can be used to create a desired response.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Unraveling the mechanism of recognition of the 3’ splice site of the adenovirus major late promoter intron by the alternative splicing factor PUF60

Pre-mRNA splicing is critical for achieving required amounts of a transcript at a given time and for regulating production of encoded protein. A given pre-mRNA may be spliced in many ways, or not at all, giving rise to multiple gene products. Numerous splicing factors are recruited to pre-mRNA splice sites to ensure proper splicing. One such factor, the 60 kDa poly(U)-binding splicing factor (PUF60), is recruited to sites that are not always spliced, but rather function as alternative splice sites. In this study, we characterized the interaction of PUF60 with a splice site from the adenovirus major late promoter (the AdML 3' splice site, AdML3’). We found that the PUF60–AdML3’ dissociation constants are in the micromolar range, with the binding affinity predominantly provided by PUF60’s two central RNA recognition motifs (RRMs). A 1.95 Å crystal structure of the two PUF60 RRMs in complex with AdML3’ revealed a dimeric organization placing two stretches of nucleic acid tracts in opposing directionalities, which can cause looping of nucleic acid and explain how PUF60 affects pre-mRNA geometry to effect splicing. Solution characterization of this complex by light-scattering and UV/Vis spectroscopy suggested a potential 2:1 (PUF60 2 :AdML3’) stoichiometry, consistent with the crystal structure. This work defines the sequence specificity of the alternative splicing factor PUF60 at the pre-mRNA 3’ splice site. Our observations suggest that control of pre-mRNA directionality is important in the early stage of spliceosome assembly, and advance our understanding of the molecular mechanism by which alternative and constitutive splicing factors differentiate among 3’ splice sites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The J-elongated conformation of β 2 -glycoprotein I predominates in solution: Implications for our understanding of antiphospholipid syndrome

β 2 -Glycoprotein I (β 2 GPI) is an abundant plasma protein displaying phospholipid-binding properties. Because it binds phospholipids, it is a target of antiphospholipid antibodies (aPLs) in antiphospholipid syndrome (APS), a life-threatening autoimmune thrombotic disease. Indeed, aPLs prefer membrane-bound β 2 GPI to that in solution. β 2 GPI exists in two almost equally populated redox states: oxidized, in which all the disulfide bonds are formed, and reduced, in which one or more disulfide bonds are broken. Furthermore, β 2 GPI can adopt multiple conformations (i.e. J-elongated, S-twisted, and O-circular). While strong evidence indicates that the J-form is the structure bound to aPLs, which conformation exists and predominates in solution remains controversial, and so is the conformational pathway leading to the bound state. Here, we report that human recombinant β 2 GPI purified under native conditions is oxidized. Moreover, under physiological pH and salt concentrations, this oxidized form adopts a J-elongated, flexible conformation, not circular or twisted, in which the N-terminal domain I (DI) and the C-terminal domain V (DV) are exposed to the solvent. Consistent with this model, binding kinetics and mutagenesis experiments revealed that in solution the J-form interacts with negatively charged liposomes and with MBB2, a monoclonal anti-DI antibody that recapitulates most of the features of pathogenic aPLs. We conclude that the preferential binding of aPLs to phospholipid-bound β 2 GPI arises from the ability of its preexisting J-form to accumulate on the membranes, thereby offering an ideal environment for aPL binding. We propose that targeting the J-form of β 2 GPI provides a strategy to block pathogenic aPLs in APS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Elucidating ion capture and transport mechanisms of Preyssler anions in aqueous solutions using biased MACE-accelerated MD simulations

Equilibrium and biased multi-atomic cluster expansion (MACE) accelerated molecular dynamics (MD) simulations in aqueous solutions are performed to investigate the ion capture and transport mechanisms of the {P 5 W 30 } Preyssler anion (PA) as the smallest representative member of the extended polyoxometalate (POM) family with an internal cavity. The unique interatomic interactions present in the internal cavity vs the exterior of PA are carefully investigated using equilibrium MACE MD simulations for two representative Na(H 2 O)@PA and Na@PA complexes in aqueous solutions. Our careful analyses of radial distribution functions and coordination numbers show that the presence of confined water in Na(H 2 O)@PA has profound modulating effects on the nature of the interactions of the encapsulated ion with the oxygens of the PA cavity. Using well-converged MACE-accelerated multiple walker well-tempered metadynamics simulations with nanosecond timescales, two different associative (ion exchange) and dissociative (ion ejection) ion transport mechanisms were carefully investigated for Na + as one of the most abundant and representative ions present in seawater and saline solutions. By comparing systems with and without confined water, it was found that the presence of only one pre-encapsulated confined water in Na(H 2 O)@PA dramatically changes the free energy landscape of ion transport processes. It was also found that the contraction and dilation of the two windows present in PA directly influence the Na + and H 2 O transport. Furthermore, the results from this work are helpful, as they show a viable path toward tuning the ion exchange and transport phenomena in aqueous solutions of POM molecular clusters and frameworks.

25 ENERGY STORAGE↗
DOE OSTI2021

Electronic Origin of T c in Bulk and Monolayer FeSe

FeSe is classed as a Hund’s metal, with a multiplicity of d bands near the Fermi level. Correlations in Hund’s metals mostly originate from the exchange parameter J, which can drive a strong orbital selectivity in the correlations. The Fe-chalcogens are the most strongly correlated of the Fe-based superconductors, with d xy the most correlated orbital. Yet little is understood whether and how such correlations directly affect the superconducting instability in Hund’s systems. By applying a recently developed ab initio theory, we show explicitly the connections between correlations in d xy and the superconducting critical temperature T c . Starting from the ab initio results as a reference, we consider various kinds of excursions in parameter space around the reference to determine what controls T c . We show small excursions in J can cause colossal changes in T c . Additionally we consider changes in hopping by varying the Fe-Se bond length in bulk, in the free standing monolayer M-FeSe, and M-FeSe on a SrTiO 3 substrate (M-FeSe/STO). The twin conditions of proximity of the dxy state to the Fermi energy, and the strength of J emerge as the primary criteria for incoherent spectral response and enhanced single- and two-particle scattering that in turn controls T c . Using c-RPA, we show further that FeSe in monolayer form (M-FeSe) provides a natural mechanism to enhance J. We explain why M-FeSe/STO has a high T c , whereas M-FeSe in isolation should not. Our study opens a paradigm for a unified understanding what controls Tc in bulk, layers, and interfaces of Hund’s metals by hole pocket and electron screening cloud engineering.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗