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At least 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Impact of the d 0 transition metal on local structural transformations in disordered rock salt cathodes

Although it is widely accepted that the long-range (average) crystal structure plays a critical role in determining the electrochemical performance of battery materials, the relationship between local structural features and electrochemical performance is rarely studied. Disordered rock salt oxides (DRX), which have become serious contenders for next generation Li-ion electrode materials, provide an ideal platform for exploring correlations between local structure and electrochemical performance as they exhibit a simple face-centered cubic structure and combine long-range disorder and short-range order on the cation sublattice. This work examines the Li 1.1 Mn 0.7 Zr 0.2−x Ti x O 2 series of DRX cathodes and investigates the links between local structure rearrangements and capacity activation. The end-member Li 1.1 Mn 0.7 Zr 0.2 O 2 compound exhibits a low capacity in the as-synthesized state, attributed to unfavorable short-range order that hinders Li-ion transport, yet its capacity increases seven-fold, from 20 to 140 mAh g −1 , after chemical delithiation followed by a 400 °C heat treatment. Capacity activation is associated with the appearance of local spinel-like structural features that depart from the short-range order originally present in the material, without significant change to the bulk composition and average crystal structure. Investigation of a series of Li 1.1 Mn 0.7 Zr 0.2−x Ti x O 2 (x ≤ 0.2) DRX compounds reveals that the correlation length of the spinel-like ordering that emerges during the heat treatment strongly depends on the Zr : Ti ratio. Yet, dramatic capacity activation and electrochemical (pseudo-)plateaus reminiscent of Mn-based spinel cathodes are observed for all compounds irrespective of the size of the ordered domains. To explain this phenomenon, we propose that the DRX phase undergoes a complete transformation to a spinel-like domain structure, which improves bulk Li-ion transport regardless of domain size.

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

Li 7 P 3 S 11 electrolyte for all-solid-state lithium-ion batteries: structure, synthesis, and applications

Because of a high ion conductivity (10 -2 S cm -1 ) comparable with liquid electrolytes at room temperature, Li 7 P 3 S 11 , one of the most important solid state electrolytes (SSEs), has attracted significant attention for applications in all-solid-state lithium batteries (ASSLBs). The development of Li 7 P 3 S 11 has progressed impressively in recent years. A fundamental understanding of Li 7 P 3 S 11 SSE from its crystal structure and ion conductivity to practical applications is critical for the development of Li 7 P 3 S 11 SSE based ASSLBs. In light of that, this review presents an overview of the Li 7 P 3 S 11 SSE. Herein, the review addresses 1) the crystal structure and Li + diffusion mechanism; 2) developed synthesis methods and corresponding crystal growth mechanisms; 3) challenges and strategies of Li 7 P 3 S 11 SSE in practical applications. Finally, remaining challenges and future perspectives are highlighted.

25 ENERGY STORAGE↗
DOE OSTI2024

Large Angle Rocking Beam Electron Diffraction Utilizing Electron Direct Detector

Electron diffraction of a crystal is fundamentally a function of the potential of that crystal. The intensity of electron diffraction patterns is, as a result, sensitive to the charge density of atoms and bonding inside crystals. Experimentally, the traditional method to probe this information is quantitative Convergent Beam Electron Diffraction (CBED). Quantitative CBED or QCEBD is a method which uses dynamic diffraction theory to quantify CBED intensities and to extract information about crystal structure and bonding. The sensitivity of dynamical scattering is leveraged to measure crystal symmetry and crystal structure factors. At its limit, electron structure factors are measured at high accuracy allowing access to chemical bonding information, which corroborate theoretical calculations through multipole model refinements of the experimental charge density. The primary limit to QCBED is the requirement of a non-overlapping convergent beam. This subsequently limits QCBED to crystals with small unit cells which are stable under the focused probe.

Busch, Robert↗
DOE OSTI2023

Structural Basis of Clostridium perfringens Enterotoxin Activation and Oligomerization by Trypsin

Clostridium perfringens enterotoxin (CpE) is a β-pore forming toxin that disrupts gastrointestinal homeostasis in mammals by binding membrane protein receptors called claudins. Although structures of CpE fragments bound to claudins have been determined, the mechanisms that trigger CpE activation and oligomerization that lead to the formation of cytotoxic β-pores remain undetermined. Proteolysis of CpE in the gut by trypsin has been shown to play a role in this and subsequent cytotoxicity processes. Here, we report solution structures of full-length and trypsinized CpE using small-angle X-ray scattering (SAXS) and crystal structures of trypsinized CpE and its C-terminal claudin-binding domain (cCpE) using X-ray crystallography. Mass spectrometry and SAXS uncover that removal of the CpE N-terminus by trypsin alters the CpE structure to expose areas that are normally unexposed. Crystal structures of trypsinized CpE and cCpE reveal unique dimer interfaces that could serve as oligomerization sites. Moreover, comparisons of these structures to existing ones predict the functional implications of oligomerization in the contexts of cell receptor binding and β-pore formation. This study sheds light on trypsin’s role in altering CpE structure to activate its function via inducing oligomerization on its path toward cytotoxic β-pore formation. Its findings can incite new approaches to inhibit CpE-based cytotoxicity with oligomer-disrupting therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Liquid crystal defect structures with Möbius strip topology

Topological solitons commonly appear as energy-minimizing field configurations, but examples of stable, spatially localized objects with coexisting solitonic structures and singular defects are rare. Here we use a nonpolar chiral liquid crystal system to show how twist domain walls can co-self-assemble with vortices to form spatially localized topological objects with spontaneous folding. These soliton–vortex assemblies, which we call ‘möbiusons’, have a topology of the molecular alignment field resembling that of the Möbius strip’s surface and package localized field excitations into folded structures within a confinement-frustrated uniform far-field background. Upon supplying energy in the form of electric pulses, möbiusons with different overall symmetries of structure exhibit folding-dependent rotational and translational motions, as well as topological cargo-carrying abilities that can be controlled by tuning the amplitude and frequency of the applied fields. We demonstrate on-demand transformations between various möbiusons and show examples of encoding information by manipulating folds in such structures. A model based on the energetics of solitons and vortices provides insights into the origins of the folding instability, whereas minimization of the Landau–de Gennes free energy closely reproduces details of their internal structure. Our findings may provide a route towards topology-enabled light-steering designs.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Pd and octahedra do not get along: Square planar [PdS 4 ] units in non-centrosymmetric La 6 PdSi 2 S 14

Non-linear optical (NLO) materials require a balance of high second-harmonic generation (SHG) signal and laser damage threshold (LDT), as well as phase matchable behavior. Herein, we report a new member of the (RE) 6 (TM) x (Tt) 2 Q 14 family of compounds, La 6 PdSi 2 S 14 , which, unlike all other reported TM analogues crystallizing in hexagonal P6 3 space group, crystallizes in the non-centrosymmetric monoclinic P2 1 space group. The crystal structure contains chains of edge-sharing distorted square planar [PdS 4 ] units. The square-planar coordination of Pd in La 6 PdSi 2 S 14 exhibits remarkable NLO properties with high SHG (3.7 × AgGaS 2 ) and LDT (3 × AgGaS 2 ) values as well as phase matchability. This shows the promise of novel materials with distorted structural motifs for enhanced NLO properties. Further, upon formation of bimetallic chiral sulfides containing both Cu and Pd, Cu occupies the opposite faces of the octahedra forming [CuS 3 ] units while Pd can be stabilized in the center of PdS 6 octahedra in the hexagonal P6 3 crystal structure of La 6 Pd 0.5 CuSi 2 S 14 . This suggests that it is possible to form mixed metal systems which could further enhance NLO properties by incorporation of additional structural distortions.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Preference for a pressure-induced 3D structure after 1T-HfSe 2

Extensive crystal structure prediction searches provide evidence of two 3D structures with orthorhombic (Immm) and monoclinic (C2/m) space groups as reasonable candidates for the first pressure-induced phase of 1T-HfSe 2 . Our candidates are compared with two recent proposals that keep the 2D nature of the ambient conditions phase and display hexagonal (P6 3 /mmc) and monoclinic (C2/m) symmetry, although the latter has a different structure than our proposed C2/m phase. Both of these 2D-like structures are discarded based on simple thermodynamic and kinetic arguments that can be extended to explain the pressure-induced polymorphic sequence of other transition metal dichalcogenides. The computed observables of our orthorhombic phase are fully consistent with the experimental structural and Raman data observed at low and high-pressure.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Structure and pressure dependence of the Fermi surface of lithium

Here, we report studies of the Fermi surface (FS) of isotopically pure polycrystalline 7 Li from ambient pressure to 4.7 GPa. Shubnikov–de Haas (SdH) oscillations at 300 mK in external magnetic fields up to 35 T are measured to map the spherical parts of the FS of lithium. Our ambient pressure data show that the principal SdH frequencies consist of three distinct peaks at 41.25 ± 0.05, 41.65 ± 0.05, and 42.05 ± 0.05 kT, which are theoretically consistent with the presence of two crystal structure domains exhibiting nearly spherical FS. The size of the spherical parts of the FS is compatible with bcc and fcc crystal structures. The measured frequencies at 41.25 and 42.65 kT present direct quantitative evidence for the spherical deformation of the FS in fcc Li. Our high-pressure data show that while the FS of Li deforms under compression, it remains mostly spherical up to 4.7 GPa and the pressure dependence of the SdH frequency is consistent with the theoretically calculated pressure dependence in the fcc structure. Finally, we find that the electron effective mass does not deviate under pressure significantly from its ambient pressure value.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Localized Flexoelectric Effect Around Ba(CuNb) Nano‐Clusters in Epitaxial BiFeO 3 Films for Enhancement of Electric and Multiferroic Properties

Abstract Room‐temperature (RT) multiferroic materials have received significant research attention for various potential applications; however, their properties are not suitable for real‐world implementation. In this study, a nano‐scale localized flexoelectric effect is introduced to enhance the RT multiferroic performance of epitaxial bismuth iron oxide (BiFeO 3 ; BFO) thin films by embedding 10 mol% Ba(Cu 1/3 Nb 2/3 )O 3 (BCN) nano‐clusters into the host BFO film, which originally has a rhombohedral crystal structure. By utilizing nano‐clustering, a large out‐of‐plane coherent strain is localized around the nano‐clusters, resulting in a highly strained tetragonality of the BFO structure; subsequently, the films exhibit peculiar types of domains and domain walls, such as nano‐scale rotational vortices and antiparallel dipole configurations. These peculiar domain structures, which originate from the localized flexoelectric effect at the nano‐scale, enable excellent ferroelectric, ferromagnetic, and RT multiferroic magnetoelectric coupling. This study reveals that the local variation in the localized flexoelectric field around nano‐clusters considerably impacts the formation of unusual domain‐wall structures. This suggests that the controlled introduction of nano‐clusters with different crystal structures is promising for achieving the desired multiferroic properties.

Song, Hyunseok↗
DOE OSTI2020

D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

The Drug Design Data Resource (D3R) aims to identify best practice methods for computer aided drug design through blinded ligand pose prediction and affinity challenges. Herein, we report on the results of Grand Challenge 4 (GC4). GC4 focused on proteins beta secretase 1 and Cathepsin S, and was run in an analogous manner to prior challenges. In Stage 1, participant ability to predict the pose and affinity of BACE1 ligands were assessed. Following the completion of Stage 1, all BACE1 co-crystal structures were released, and Stage 2 tested affinity rankings with co-crystal structures. Finally, we provide an analysis of the results and discuss insights into determined best practice methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Mechanistic insights into a heterobifunctional degrader-induced PTPN2/N1 complex

PTPN2 (protein tyrosine phosphatase non-receptor type 2, or TC-PTP) and PTPN1 are attractive immuno-oncology targets, with the deletion of Ptpn1 and Ptpn2 improving response to immunotherapy in disease models. Targeted protein degradation has emerged as a promising approach to drug challenging targets including phosphatases. We developed potent PTPN2/N1 dual heterobifunctional degraders (Cmpd-1 and Cmpd-2) which facilitate efficient complex assembly with E3 ubiquitin ligase CRL4 CRBN , and mediate potent PTPN2/N1 degradation in cells and mice. To provide mechanistic insights into the cooperative complex formation introduced by degraders, we employed a combination of structural approaches. Our crystal structure reveals how PTPN2 is recognized by the tri-substituted thiophene moiety of the degrader. We further determined a high-resolution structure of DDB1-CRBN/Cmpd-1/PTPN2 using single-particle cryo-electron microscopy (cryo-EM). This structure reveals that the degrader induces proximity between CRBN and PTPN2, albeit the large conformational heterogeneity of this ternary complex. The molecular dynamic (MD)-simulations constructed based on the cryo-EM structure exhibited a large rigid body movement of PTPN2 and illustrated the dynamic interactions between PTPN2 and CRBN. Together, our study demonstrates the development of PTPN2/N1 heterobifunctional degraders with potential applications in cancer immunotherapy. Furthermore, the developed structural workflow could help to understand the dynamic nature of degrader-induced cooperative ternary complexes.

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

Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics

SARS-CoV-2 depends on -1 programmed ribosomal frameshifting (-1 PRF) to express proteins essential for its replication. The RNA pseudoknot stimulating -1 PRF is thus an attractive drug target. However, the structural models of this pseudoknot obtained from cryo-EM and crystallography differ in some important features, leaving the pseudoknot structure unclear. We measured the solution structure of the pseudoknot using small-angle X-ray scattering (SAXS). The measured profile did not agree with profiles computed from the previously solved structures. Beginning with each of these solved structures, we used the SAXS data to direct all atom molecular dynamics (MD) simulations to improve the agreement in profiles. In all cases, this refinement resulted in a bent conformation that more closely resembled the cryo-EM structures than the crystal structure. Applying the same approach to a point mutant abolishing -1 PRF revealed a notably more bent structure with reoriented helices. This work clarifies the dynamic structures of the SARS-CoV-2 pseudoknot in solution.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Structural analysis and functional evaluation of the disordered ß–hexosyltransferase region from Hamamotoa (Sporobolomyces) singularis

Hamamotoa (Sporobolomyces) singularis codes for an industrially important membrane bound ß-hexosyltransferase (BHT), (BglA, UniprotKB: Q564N5) that has applications in the production of natural fibers such as galacto-oligosaccharides (GOS) and natural sugars found in human milk. When heterologously expressed by Komagataella phaffii GS115, BHT is found both membrane bound and soluble secreted into the culture medium. In silico structural predictions and crystal structures support a glycosylated homodimeric enzyme and the presence of an intrinsically disordered region (IDR) with membrane binding potential within its novel N-terminal region (1–110 amino acids). Additional in silico analysis showed that the IDR may not be essential for stable homodimerization. Thus, we performed progressive deletion analyses targeting segments within the suspected disordered region, to determine the N-terminal disorder region’s impact on the ratio of membrane-bound to secreted soluble enzyme and its contribution to enzyme activity. The ratio of the soluble secreted to membrane-bound enzyme shifted from 40% to 53% after the disordered N-terminal region was completely removed, while the specific activity was unaffected. Furthermore, functional analysis of each glycosylation site found within the C-terminal domain revealed reduced total secreted protein activity by 58%–97% in both the presence and absence of the IDR, indicating that glycosylation at all four locations is required by the host for the secretion of active enzyme and independent of the removed disordered N-terminal region. Overall, the data provides evidence that the disordered region only partially influences the secretion and membrane localization of BHT.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Superconductivity in Y 4 RuGe 8 with a Vacancy-Ordered CeNiSi 2 -Type Superstructure

In this work, we report a new compound, Y 4 RuGe 8 , with a transition metal vacancy-ordered CeNiSi 2 -type superstructure, which has a superconducting transition at 1.3 K. Y 4 RuGe 8 crystals were grown by indium flux at relatively low temperatures (below 1273 K), which makes it possible to stabilize such a vacancy-ordered phase. The crystal structure of Y 4 RuGe 8 was solved by single-crystal X-ray diffraction and confirmed by transmission electron microscopy. The as-grown Y 4 RuGe 8 crystals are always twinned, crystallizing in the space group $P\bar{1}$(no. 2) with the lattice parameters a = 5.7680(1) Å, b = 8.2042(2) Å, c = 11.5093(3) Å, α = 79.696(1)degrees, β = 88.491(1)degrees, and γ = 79.637(2)degrees; this structure is a superstructure deriving from the higher symmetry CeNiSi 2 -type structure (Cmcm, no. 63) due to the ordering of Ru vacancies. The ordering of Ru sites breaks slightly distorted Ge planes in the CeNiSi 2 prototype into infinite cis-trans Ge chains in Y 4 RuGe 8 . The presence of bulk superconductivity in Y 4 RuGe 8 is well supported by zero resistance and a jump in specific heat at the critical transition temperature. The Sommerfeld coefficient (19 mJ K -2 mol -1 ) of the specific heat is greater than that (11 mJ K -2 mol -1 ) estimated using the bare density of states (4.7 states/eV/f.u.) from first-principles calculations. The ab initio calculations indicate that 4d electrons of both Y and Ru and 4p electrons of Ge are the main contributors to the total density of states at the Fermi level in Y 4 RuGe 8 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Structural Insights into the Mechanism of a Polyketide Synthase Thiocysteine Lyase Domain

Polyketide synthases (PKSs) are renowned for the structural diversity of the polyketide natural products they produce, but sulfur-containing functionalities are rarely installed by PKSs. We previously characterized thiocysteine lyase (SH) domains involved in the biosynthesis of the leinamycin (LNM) family of natural products, exemplified by LnmJ-SH and guangnanmycin (GnmT-SH). Here we report a detailed investigation into the PLP-dependent reaction catalyzed by the SH domains, guided by a 1.8 Å resolution crystal structure of GnmT-SH. A series of elaborate substrate mimics were synthesized to answer specific questions garnered from the crystal structure and from the biosynthetic logic of the LNM family of natural products. Here, through a combination of bioinformatics, molecular modeling, in vitro assays, and mutagenesis, we have developed a detailed model of acyl carrier protein (ACP)-tethered substrate-SH, and interdomain interactions, that contribute to the observed substrate specificity. Comparison of the GnmT-SH structure with archetypical PLP-dependent enzyme structures revealed how Nature, via evolution, has modified a common protein structural motif to accommodate an ACP-tethered substrate, which is significantly larger than any of those previously characterized. Overall, this study demonstrates how PLP-dependent chemistry can be incorporated into the context of PKS assembly lines and sets the stage for engineering PKSs to produce sulfur-containing polyketides.

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

Combining Organic Cations of Different Sizes Grants Improved Control over Perovskitoid Dimensionality and Bandgap

Because mixed-halide wide-bandgap (1.6-2.0 eV) perovskite solar cells suffer from operating instability related to light-induced halide segregation, it is of interest to study alternative means of bandgap widening. Perovskitoids combine wide bandgaps and structural stability resulting from face- or edge-sharing octahedral connections in their crystal structures. Unfortunately, there existed no prior reports of three-dimensional (3D) perovskitoids having direct bandgaps with optical absorption edges less than 2.2 eV. As the most significant predictor of perovskitoid bandgaps is the fraction of corner-sharing in their crystal structures, we hypothesized that increasing the amount of corner-sharing would access lower bandgaps than previously reported. Here, we accomplished this by mixing a spacer cation within the size range for 3D perovskitoid formation with a smaller perovskite-forming cation. We explored three spacer cations of different sizes: ethylammonium (EA), cyclopropylammonium (c-C3A), and cyclobutylammonium (c-C4A), combining these with methylammonium (MA), and found that the middle cation, c-C3A, pairs with MA to form a 3D perovskitoid with the formula (c-C3A) 3 (MA) 3 Pb 5 I 16 and a direct bandgap with an optical absorption edge at 2.0 eV. Solution-processed films of this perovskitoid showed improved light stability over mixed-halide perovskites, and solar cells based on these films exhibit increased maximum power point operating stability compared to reference mixed-halide devices.

Gilley, Isaiah W. [Northwestern University, Evanst↗
DOE OSTI2021

Iridate Li8IrO 6 : An Antiferromagnetic Insulator

In this work, a polycrystalline iridate Li 8 IrO 6 material was prepared via heating Li 2 O and IrO 2 starting materials in a sealed quartz tube at 650 °C for 48 h. The structure was determined from Rietveld refinement of room-temperature powder neutron diffraction data. Li 8 IrO 6 adopts the nonpolar space group $R\bar{3}$ with Li atoms occupying the tetrahedral and octahedral sites, which is supported by the electron diffraction and solid-state 7Li NMR. This results in a crystal structure consisting of LiO 4 tetrahedral layers alternating with mixed IrO 6 and LiO 6 octahedral layers along the crystallographic c -axis. The +4 oxidation state of Ir 4+ was confirmed by near-edge X-ray absorption spectroscopy. An in situ synchrotron X-ray diffraction study of Li 8 IrO 6 indicates that the sample is stable up to 1000 °C and exhibits no structural transitions. Magnetic measurements suggest long-range antiferromagnetic ordering with a Néel temperature (TN) of 4 K, which is corroborated by heat capacity measurements. The localized effective moment $μ_{\text{eff}}$ (Ir) = 1.73 $μ_{\text{B}}$ and insulating character indicate that Li 8 IrO 6 is a correlated insulator. First-principles calculations support the nonpolar crystal structure and reveal the insulating behavior both in paramagnetic and antiferromagnetic states.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Neutron scattering study of tantalum monohydride and monodeuteride

Powder samples of TaH 0.89 and TaD0.96 are synthesized under a hydrogen (deuterium) pressure of 2.8 GPa and a temperature of 250 °C, then quenched to the liquid nitrogen temperature, recovered to ambient pressure and studied by neutron diffraction (ND) and inelastic neutron scattering (INS). The ND study shows that both hydrogen and deuterium atoms occupy tetrahedral interstitial sites in a distorted body centered cubic (bcc) crystal structure of metal atoms, while the ordering scenarios in TaH 0.89 and TaD 0.96 are different. Hydrogen and deuterium atoms are ordered in a layered fashion, forming long period superstructures with space groups P$\bar{4}$ and P222, respectively, so that the unit cells of the crystal structures of TaH 0.89 and TaD 0.96 are $\sqrt{2}$ × $\sqrt{2}$ × 7 and $\sqrt{2}$ × $\sqrt{2}$ × 8 supercells of the initial cubic unit cell. The INS study demonstrates a pronounced “soft” (trumpet-like) anharmonicity of the potential well for H and D atoms.

08 HYDROGEN↗