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At least 1,081 records · Page 60
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Synthesis and symmetry of perovskite oxynitride CaW(O,N) 3

Perovskite oxynitrides, in addition to being promising electrocatalysts and photoabsorbers, present an interesting case study in crystal symmetry. Full or partial ordering of the O and N anions affects global symmetry and influences material performance and functionality; however, anion ordering is challenging to detect experimentally. In this work, we synthesize a novel perovskite oxynitride CaW(O,N) 3 and characterize its crystal structure using both X-ray and neutron diffraction. Through co-refinement of the diffraction patterns with a range of literature and theory-derived model structures, we demonstrate that CaW(O,N) 3 adopts an orthorhombic Pnma average structure and exhibits octahedral distortion with evidence for preferred anion site occupancy. However, through comparison with a large, low-symmetry unit cell, we identify the presence of disorder that is not fully accounted for by the high-symmetry model. We compare CaW(O,N) 3 with SrW(O,N) 3 to demonstrate the broader presence of such disorder and identify contrasting features in the electronic structures. This work signifies an updated perspective on the inherent crystal symmetry present in perovskite oxynitrides.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication

Abstract Mosquito-borne flaviviruses (MBFVs) including dengue, West Nile, yellow fever, and Zika viruses have an RNA genome encoding one open reading frame flanked by 5′ and 3′ untranslated regions (UTRs). The 3′ UTRs of MBFVs contain regions of high sequence conservation in structured RNA elements known as dumbbells (DBs). DBs regulate translation and replication of the viral RNA genome, functions proposed to depend on the formation of an RNA pseudoknot. To understand how DB structure provides this function, we solved the x-ray crystal structure of the Donggang virus DB to 2.1Å resolution and used structural modeling to reveal the details of its three-dimensional fold. The structure confirmed the predicted pseudoknot and molecular modeling revealed how conserved sequences form a four-way junction that appears to stabilize the pseudoknot. Single-molecule FRET suggests that the DB pseudoknot is a stable element that can regulate the switch between translation and replication during the viral lifecycle by modulating long-range RNA conformational changes.

Akiyama, Benjamin M.↗
DOE OSTI2022

gC1qR/C1qBP/HABP-1: Structural Analysis of the Trimeric Core Region, Interactions With a Novel Panel of Monoclonal Antibodies, and Their Influence on Binding to FXII

The protein gC1qR/C1qBP/HABP-1 plays an essential role in mitochondrial biogenesis, but becomes localized at the cellular surface in numerous pathophysiological states. When this occurs on endothelial cells, surface-exposed gC1qR activates the classical pathway of complement. It also promotes assembly of a multi-protein complex comprised of coagulation factor XII (FXII), pre-kallikrein (PK), and high-molecular weight kininogen (HMWK) that activates the contact system and the kinin-generating system. Since surface-exposed gC1qR triggers intravascular inflammatory pathways, there is interest in identifying molecules that block gC1qR function. Here we further that objective by reporting the outcome of a structure/function investigation of gC1qR, its interactions with FXII, and the impact of a panel of monoclonal anti-gC1qR antibodies on FXII binding to gC1qR. Although deletion mutants have been used extensively to assess gC1qR function, none of these proteins have been characterized structurally. To that end, we determined a 2.2 Å resolution crystal structure of a gC1qR mutant lacking both of its acidic loops, but which retained nanomolar-affinity binding to FXII and FXIIa. This structure revealed that the trimeric gC1qR assembly was maintained despite loss of roughly thirty residues. Characterization of a novel panel of anti-gC1qR monoclonal antibodies identified several with biochemical properties distinct from previously described antibodies, as well as one which bound to the first acidic loop of gC1qR. Intriguingly, we found that each of these antibodies could partly inhibit binding of FXII and FXIIa to gC1qR. Based on these results and previously published studies, we offer new perspectives for developing gC1qR inhibitors.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

High-Fidelity Mock Development for the Insensitive High Explosive TATB

Due to the violent reaction potential of high explosives, in tests where a reaction is not desired, it can be safe and convenient to use an inert mock that can mimic relevant properties of the associated explosive. Use of mock materials is well-established in explosives work, but most existing mocks are generally meant to mimic only one or two properties of a given explosive, potentially failing to match the explosive in other critical ways. Recently, there has been interest in developing robust thermomechanical mocks for many common explosives. Here, eleven materials are systematically chosen and investigated as potential thermomechanical mocks for TATB, the explosive component of PBX 9502. DSC, nanoindentation, and compression testing are used to narrow down to most appropriate mocks and identify their advantages and limitations. Hardness and elastic modulus are reported for the first time for the molecular crystals iodoanthranilic acid, hexamine, melamine, and trithiolane dioxide, and the crystal structure is reported for the first time for the molecular crystals iodoanthranilic acid and iodosalicylic acid.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Characterization of a broadly specific cadaverine N-hydroxylase involved in desferrioxamine B biosynthesis in Streptomyces sviceus

N-hydroxylating flavin-dependent monooxygenases (FMOs) are involved in the biosynthesis of hydroxamate siderophores, playing a key role in microbial virulence. Herein, we report the first structural and kinetic characterization of a novel alkyl diamine N-hydroxylase DesB from Streptomyces sviceus (SsDesB). This enzyme catalyzes the first committed step in the biosynthesis of desferrioxamine B, a clinical drug used to treat iron overload disorders. X-ray crystal structures of the SsDesB holoenzyme with FAD and the ternary complex with bound NADP + were solved at 2.86 Å and 2.37 Å resolution, respectively, providing a structural view of the active site environment. SsDesB crystallized as a tetramer and the structure of the individual protomers closely resembles the structures of homologous N-hydroxylating FMOs from Erwinia amylovora (DfoA), Pseudomonas aeruginosa (PvdA), and Aspergillus fumigatus (SidA). Using NADPH oxidation, oxygen consumption, and product formation assays, kinetic parameters were determined for various substrates with SsDesB. SsDesB exhibited typical saturation kinetics with substrate inhibition at high concentrations of NAD(P)H as well as cadaverine. The apparent k cat values for NADPH in steady-state NADPH oxidation and oxygen consumption assays were 0.28 ± 0.01 s -1 and 0.24 ± 0.01 s -1 , respectively. However, in product formation assays used to measure the rate of N-hydroxylation, the apparent k cat for NADPH (0.034 ± 0.008 s -1 ) was almost 10-fold lower under saturating FAD and cadaverine concentrations, reflecting an uncoupled reaction, and the apparent NADPH K M was 33 ± 24 μM. Under saturating FAD and NADPH concentrations, the apparent k cat and K M for cadaverine in Csaky assays were 0.048 ± 0.004 s -1 and 19 ± 9 μM, respectively. SsDesB also N-hydroxylated putrescine, spermidine, and L-lysine substrates but not alkyl (di)amines that were branched or had fewer than four methylene units in an alkyl chain. These data demonstrate that SsDesB has wider substrate scope compared to other well-studied ornithine and lysine N-hydroxylases, making it an amenable biocatalyst for the production of desferrioxamine B, derivatives, and other N-substituted products.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structural Flexibility of Metal Chelate Complexes and Its Relation to Supramolecular Chemistry

In this study, crystal structures of metal chelate and related complexes in the Cambridge Structural Database have been analyzed, with respect to their use as components in supramolecular metal-organic compounds. In β-diketonate complexes, the distribution of angles between ligands is relatively broad; other ligands, such as 2,2'-bipyridine, yield significantly narrower distributions. According to the principle of structure correlation, these distributions reflect the ease of distorting the various families of complexes. A comparison through density functional theory calculations also indicates that angular distortions require significantly less energy for M(β-diketonate) 3 than for M(2,2'-bipyridine) 3 . The differences are likely to affect the construction of supramolecular systems from different combinations of metals and ligands, including the likelihood that the desired structures will be obtained.

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

3D domain swapping in the TIM barrel of the α subunit of Streptococcus pneumoniae tryptophan synthase

Tryptophan synthase catalyzes the last two steps of tryptophan biosynthesis in plants, fungi and bacteria. It consists of two protein chains, designated α and β, encoded by trpA and trpB genes, that function as an αββα complex. Structural and functional features of tryptophan synthase have been extensively studied, explaining the roles of individual residues in the two active sites in catalysis and allosteric regulation. TrpA serves as a model for protein-folding studies. In 1969, Jackson and Yanofsky observed that the typically monomeric TrpA forms a small population of dimers. Dimerization was postulated to take place through an exchange of structural elements of the monomeric chains, a phenomenon later termed 3D domain swapping. The structural details of the TrpA dimer have remained unknown. Here, the crystal structure of the Streptococcus pneumoniae TrpA homodimer is reported, demonstrating 3D domain swapping in a TIM-barrel fold for the first time. The N-terminal domain comprising the H0–S1–H1–S2 elements is exchanged, while the hinge region corresponds to loop L2 linking strand S2 to helix H2′. The structural elements S2 and L2 carry the catalytic residues Glu52 and Asp63. As the S2 element is part of the swapped domain, the architecture of the catalytic apparatus in the dimer is recreated from two protein chains. The homodimer interface overlaps with the α–β interface of the tryptophan synthase αββα heterotetramer, suggesting that the 3D domain-swapped dimer cannot form a complex with the β subunit. In the crystal, the dimers assemble into a decamer comprising two pentameric rings.

3D domain swapping↗
DOE OSTI2020

Structural and thermal properties of Na 2 Mn(SO 4 ) 2 ·4H 2 O and Na 2 Ni(SO 4 ) 2 ·10H 2 O

The title compounds were prepared via a wet chemistry route and their crystal structures were determined from single crystal X-ray diffraction data. Na 2 Mn(SO 4 ) 2 ·4H 2 O crystallizes with a monoclinic symmetry, space group P2 1 /c, with a = 5.5415(2), b = 8.3447(3), c = 11.2281(3) Å, β = 100.172(1)°, V = 511.05(3) Å 3 and Z = 2. Na 2 Ni(SO 4 ) 2 ·10H 2 O also crystallizes with a monoclinic symmetry, space group P2 1 /c, with a = 12.5050(8), b = 6.4812(4), c = 10.0210(6) Å, β = 106.138(2)°, V = 780.17(8) Å3 and Z = 2. Na 2 Mn(SO 4 ) 2 ·4H 2 O is a new member of the blödite family of compounds, whereas Na 2 Ni(SO 4 ) 2 ·10H 2 O is isostructural with Na 2 Mg(SO 4 ) 2 ·10H 2 O. The structure of Na 2 Mn(SO 4 ) 2 ·4H 2 O is built up of [Mn(SO 4 ) 2 (H 2 O) 4 ] 2– building blocks connected through moderate O–H…O hydrogen bonds with the sodium atoms occupying the large tunnels along the a axis and the manganese atom lying on an inversion center, whereas the structure of Na 2 Ni(SO 4 ) 2 ·10H 2 O is built up of [Ni(H 2 O) 6 ] 2+ and [Na 2 (SO 4 ) 2 (H 2 O) 4 ] 2– layers. These layers which are parallel to the (100) plane are interconnected through moderate O–H…O hydrogen bonds. Here, the thermal gravimetric- and the powder X-ray diffraction-analyzes showed that only the nickel phase was almost pure. At a temperature above 300 °C, all the water molecules evaporated and a structural phase transition from P2 1 /c-Na 2 Ni(SO 4 ) 2 ·10H 2 O to C2/c-Na 2 Ni(SO 4 ) 2 was observed. C2/c-Na 2 Ni(SO 4 ) 2 is thermally more stable than Na 2 Fe(SO 4 ) 2 and therefore it would be suitable as the positive electrode for sodium ion batteries if a stable electrolyte at high voltage is developed.

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

Structural and physical properties of two distinct 2D lead halides with intercalated Cu( II )

Transition metal cation intercalation between the layers of two-dimensional (2D) metal halides is an underexplored research area. In this work we focus on the synthesis and physical property characterizations of two layered hybrid lead halides: a new compound [Cu(O 2 C–CH 2 –NH 2 ) 2 ]Pb 2 Br 4 and the previously reported [Cu(O 2 C–(CH 2 ) 3 –NH 3 ) 2 ]PbBr 4 . These compounds exhibit 2D layered crystal structures with incorporated Cu 2+ between the metal halide layers, which is achieved by combining Cu(II) and lead bromide with suitable amino acid precursors. The resultant [Cu(O 2 C–(CH 2 ) 3 –NH 3 ) 2 ]PbBr 4 adopts a 2D layered perovskite structure, whereas the new compound [Cu(O 2 C–CH 2 –NH 2 ) 2 ]Pb 2 Br 4 crystallizes with a new structure type based on edge-sharing dodecahedral PbBr5O3 building blocks. [Cu(O 2 C–CH 2 –NH 2 ) 2 ]Pb 2 Br 4 is a semiconductor with a bandgap of 3.25 eV. It shows anisotropic charge transport properties with a semiconductor resistivity of 1.44 × 10 10 Ω cm (measured along the a-axis) and 2.17 × 10 10 Ω cm (along the bc-plane), respectively. The fabricated prototype detector based on this material showed response to soft low-energy X-rays at 8 keV with a detector sensitivity of 1462.7 μCGy –1 cm –2 , indicating its potential application for ionizing radiation detection. Finally, these encouraging results are discussed together with the results from density functional theory calculations, optical, magnetic, and thermal property characterization experiments.

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

Structure and disorder resulting in ultralow thermal conductivity in the defect chalcopyrite AgInSnSe 4

Quaternary chalcogenides are attractive for a variety of technological fields of interest due to the diverse physical properties these materials possess. Herein, the structural and thermal properties of the disordered chalcopyrite AgInSnSe 4 are reported revealing a distinct relation between its structure and physical properties. Modeling of the experimental temperature-dependent thermal properties revealed an ultralow thermal conductivity (0.47 Wm -1 K -1 at room temperature) due to lattice anharmonicity, a low speed of sound and a low Debye temperature. Moreover, first principles electronic structure calculations revealed that the Ag-Se tetrahedra within the crystal structure possess relatively weak bonds due to occupied antibonding states from p-d orbital hybridization, which suppress the thermal conductivity. Here, in order to further quantify our findings, we extended our analyses to include comparisons with other ternary and quaternary adamantine materials, all of which possess a fourfold tetrahedral coordination of atoms, in revealing the origin of the thermal properties in AgInSnSe 4 .

36 MATERIALS SCIENCE↗
DOE OSTI2024

FeSi 4 P 4 and CoSi 3 P 3 : Hidden Gems of Ternary Tetrel Pnictides with Outstanding Nonlinear Optical Properties

Metal silicon phosphides have shown promise as nonlinear optical materials. To be practically useful and cheap, earth-abundant 3d transition metals are preferred over their scarcer and more expensive 4d and 5d counterparts. Here, we developed a synthetic method to produce polycrystalline bulk powders and millimeter-sized single crystals of ternary compounds FeSi 4 P 4 and CoSi 3 P 3 . Both studied compounds have noncentrosymmetric and chiral crystal structures with ordered Si/P arrangements as was confirmed by single-crystal X-ray diffraction and solid-state NMR. Despite the presence of the transition metal, FeSi 4 P 4 and CoSi 3 P 3 are semiconductors with direct band gaps of 1.3 and 1.6 eV, respectively, indicating low-spin d 6 electronic configuration for octahedral Fe 2+ and Co 3+ . Relative to reported sulfide materials, FeSi 4 P 4 and CoSi 3 P 3 small band gap semiconductors demonstrate an outstanding combination of second-harmonic generation (SHG) activity and laser damage threshold (LDT). Both studied materials are phase-matchable with a 2.09 μm laser and not only exhibit 2.5–3.0 times stronger SHG signal than that of the state-of-the-art AgGaS 2 standard but also demonstrate an LDT response of 2.3–2.5 times higher than that of AgGaS 2 (at 1.09 μm laser with a pulse width of 10 ns)-which is unprecedented for small band gap semiconductors.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Unraveling the Effects of Cobalt on Crystal Growth and Solution Behavior of Nb 6 P 2 W 12 -based Dimeric Clusters

We report the synthesis, characterization, and solution self-assembly of plenary Nb 6 P 2 W 12 -based transition-metal substituted polyoxometalate, which is obtained by simply adding transition metals (Co 2+ ) into aqueous solution containing cluster [(NbO 2 ) 6 P 2 W 12 O 56 ] 12- , which is obtained by an in situ synthetic method. The incorporation of Co 2+ ions significantly affects the crystal structure, resulting in the formation of a 1D chain-like crystal and the first example of a niobotungstate-based cobalt derivative cluster. The behavior and stability of this cluster in solution are confirmed by time-resolved static light scattering, dynamic light scattering, small-angle X-ray scattering, and electrospray mass spectrometry studies.

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

In situ observation of the atomic shuffles during the {${{11}}\bar{{{2}}}{{1}}$} twinning in hexagonal close-packed rhenium

Twinning, on par with dislocations, is critically required in plastic deformation of hexagonal close-packed crystals at low temperatures. In contrast to that in cubic-structured crystals, twinning in hexagonal close-packed crystals requires atomic shuffles in addition to shear. Though the twinning shear that is carried by twinning dislocations has been captured for decades, direct experimental observation of the atomic shuffles, especially when the shuffling mode is not unique and does not confine to the plane of shear, remains a formidable challenge to date. Here, by using in-situ transmission electron microscopy, we directly capture the atomic mechanism of the {${{11}}\bar{{{2}}}{{1}}$} twinning in hexagonal close packed rhenium nanocrystals. Results show that the {${{11}}\bar{{{2}}}{{1}}$} twinning is dominated by the ($\textbf{b}$ 1/2 , h 1/2 ) twinning disconnections. In contrast to conventional expectations, the atomic shuffles accompanying the twinning disconnections proceed on alternative basal planes along 1/6 {${{1\bar1}}{{{0}}}{{0}}$} , which may be attributed to the free surface in nanocrystal samples, leading to a lack of mirror symmetry across the {${{11}}\bar{{{2}}}{{1}}$} twin boundary.

(S)TEM↗
DOE OSTI2022

Quaternary structure independent folding of voltage-gated ion channel pore domain subunits

Every voltage-gated ion channel (VGIC) has a pore domain (PD) made from four subunits, each comprising an antiparallel transmembrane helix pair bridged by a loop. The extent to which PD subunit structure requires quaternary interactions is unclear. In this report we present crystal structures of a set of bacterial voltage-gated sodium channel (BacNa V ) 'pore only' proteins that reveal a surprising collection of non-canonical quaternary arrangements in which the PD tertiary structure is maintained. This context-independent structural robustness, supported by molecular dynamics simulations, indicates that VGIC-PD tertiary structure is independent of quaternary interactions. This fold occurs throughout the VGIC superfamily and in diverse transmembrane and soluble proteins. Strikingly, characterization of PD subunit-binding Fabs indicates that non-canonical quaternary PD conformations can occur in full-length VGICs. Together, our data demonstrate that the VGIC-PD is an autonomously folded unit. This property has implications for VGIC biogenesis, understanding functional states, de novo channel design, and VGIC structural origins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Electron transfer in polysaccharide monooxygenase catalysis

Polysaccharide monooxygenase (PMO) catalysis involves the chemically difficult hydroxylation of unactivated C–H bonds in carbohydrates. The reaction requires reducing equivalents and will utilize either oxygen or hydrogen peroxide as a cosubstrate. Two key mechanistic questions are addressed here: 1) How does the enzyme regulate the timely and tightly controlled electron delivery to the mononuclear copper active site, especially when bound substrate occludes the active site? and 2) How does this electron delivery differ when utilizing oxygen or hydrogen peroxide as a cosubstrate? Using a computational approach, potential paths of electron transfer (ET) to the active site copper ion were identified in a representative AA9 family PMO from Myceliophthora thermophila ( Mt PMO9E). When Y62, a buried residue 12 Å from the active site, is mutated to F, lower activity is observed with O 2 . However, a WT-level activity is observed with H 2 O 2 as a cosubstrate indicating an important role in ET for O 2 activation. To better understand the structural effects of mutations to Y62 and axial copper ligand Y168, crystal structures were solved of the wild type Mt PMO9E and the variants Y62W, Y62F, and Y168F. A bioinformatic analysis revealed that position 62 is conserved as either Y or W in the AA9 family. The Mt PMO9E Y62W variant has restored activity with O 2 . Overall, the use of redox-active residues to supply electrons for the reaction with O 2 appears to be widespread in the AA9 family. Furthermore, the results provide a molecular framework to understand catalysis with O 2 versus H 2 O 2 .

Sayler, Richard I. (ORCID:000000017252707X)↗
DOE OSTI2022

Crystals of $\mathrm{TELSAM}$–target protein fusions that exhibit minimal crystal contacts and lack direct inter-$\mathrm{TELSAM}$ contacts

While conducting pilot studies into the usefulness of fusion to TELSAM polymers as a potential protein crystallization strategy, we observed novel properties in crystals of two TELSAM–target protein fusions, as follows. (i) A TELSAM–target protein fusion can crystallize more rapidly and with greater propensity than the same target protein alone. (ii) TELSAM–target protein fusions can be crystallized at low protein concentrations. This unprecedented observation suggests a route to crystallize proteins that can only be produced in microgram amounts. (iii) The TELSAM polymers themselves need not directly contact one another in the crystal lattice in order to form well-diffracting crystals. This novel observation is important because it suggests that TELSAM may be able to crystallize target proteins too large to allow direct inter-polymer contacts. (iv) Flexible TELSAM–target protein linkers can allow target proteins to find productive binding modes against the TELSAM polymer. (v) TELSAM polymers can adjust their helical rise to allow fused target proteins to make productive crystal contacts. (vi). Fusion to TELSAM polymers can stabilize weak inter-target protein crystal contacts. We report features of these TELSAM–target protein crystal structures and outline future work needed to validate TELSAM as a crystallization chaperone and determine best practices for its use.

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

The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature

The nonstructural protein 3 (NSP3) macrodomain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Mac1) removes adenosine diphosphate (ADP) ribosylation posttranslational modifications, playing a key role in the immune evasion capabilities of the virus responsible for the coronavirus disease 2019 pandemic. Here, we determined neutron and x-ray crystal structures of the SARS-CoV-2 NSP3 macrodomain using multiple crystal forms, temperatures, and pHs, across the apo and ADP-ribose–bound states. We characterize extensive solvation in the Mac1 active site and visualize how water networks reorganize upon binding of ADP-ribose and non-native ligands, inspiring strategies for displacing waters to increase the potency of Mac1 inhibitors. Determining the precise orientations of active site water molecules and the protonation states of key catalytic site residues by neutron crystallography suggests a catalytic mechanism for coronavirus macrodomains distinct from the substrate-assisted mechanism proposed for human MacroD2. These data provoke a reevaluation of macrodomain catalytic mechanisms and will guide the optimization of Mac1 inhibitors.

60 APPLIED LIFE SCIENCES↗