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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Crystal structure of dihydrofolate reductase from the filarial nematode W. bancrofti in complex with NADPH and folate

Lymphatic filariasis is a debilitating illness with an estimated 50 million cases as of 2018. The majority of cases are caused by the parasitic worm W. bancrofti and additional cases by the worms B. malayi and B. timori. Dihydrofolate reductase (DHFR) is an established target in the treatment of cancer, bacterial, and protozoal infections and may be a potential target for drugs targeting parasitic worm infections, including filariasis. Recent studies have shown that known antifolate compounds, including methotrexate, inhibit the activity of W. bancrofti DHFR (WbDHFR). However, the absence of structural information for filarial DHFRs has limited the study of more in-depth structure-function relationships. We report the structure of WbDHFR complexed with NADPH and folate using X-ray diffraction data measured to 2.47 Å resolution. The structure of WbDHFR reveals the usual DHFR fold and is currently only the second nematode DHFR structure in the Protein Data Bank. The equilibrium dissociation constants for NADPH (90 ± 29 nM) and folate (23 ± 4 nM) were determined by equilibrium titrations. The interactions of known antifolates with WbDHFR were analyzed using molecular docking programs and molecular dynamics simulations. Antifolates with a hydrophobic core and extended linker formed favorable interactions with WbDHFR. These combined data should now facilitate the rational design of filarial DHFR inhibitors, which in turn can be used to determine whether DHFR is a viable drug target for filariasis and whether existing antifolates may be repurposed for its treatment.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

New layered quaternary Zintl pnictide oxides Ba 2 Zn 2 Pn 2 O ( Pn = Sb, Bi): Discovery, crystal structures, band engineering, and transport properties

Three new heteroanionic oxypnictides, Ba 2 Zn 2 Sb 2 O, Ba 2 Zn 2 Bi 2 O, and the solid solution Ba 2 Zn 2 Sb 2−x Bi x O (x ≈ 1.1–1.6), have been synthesized and structurally characterized. They are isostructural with their Mn-bearing analog, adopting the Ba 2 Mn 2 Sb 2 O-type structure (space group P6 3 /mmc, No. 194), and feature a double-layered 2D $^{2}_{∞}$ [Zn 2 Pn 2 O] 2- substructure (Pn = Sb, Bi, Sb/Bi) composed of corner-sharing, distorted tetrahedral ZnPn 3 O units. Electronic structure calculations reveal a systematic progression from semiconducting Ba 2 Zn 2 Sb 2 O to metallic Ba 2 Zn 2 Bi 2 O as Bi content increases. These trends are corroborated by transport property measurements, with Ba 2 Zn 2 Sb 0.9(1) Bi 1.1 O exhibiting relatively low electrical resistivity, high Hall mobilities of ∼160 cm 2 /V·s, and large Seebeck coefficients from 69 to 132 μV K −1 over the 300–600 K temperature range. Comparison with structurally related Zintl pnictides, such as SrIn 2 As 2 and PrZn 3 As 3 phases, situates Ba 2 Zn 2 Pn 2 O (Pn = Sb, Bi) within a broader family of heteroanionic oxypnictide Zintl compounds, highlighting their structural flexibility and amenability to band engineering. Finally, electronic structure and bonding considerations point to tunable semiconducting behavior and underscore the relevance of these materials for thermoelectric and topological applications.

Band engineering↗
DOE OSTI2023

Simultaneous measurements of volume, pressure, optical images, and crystal structure with a dynamic diamond anvil cell: A real-time event monitoring system

The dynamic diamond anvil cell (dDAC) technique has attracted great interest because it possibly provides a bridge between static and dynamic compression studies with fast, repeatable, and controllable compression rates. The dDAC can be a particularly useful tool to study the pathways and kinetics of phase transitions under dynamic pressurization if simultaneous measurements of physical quantities are possible as a function of time. We report the development of a real-time event monitoring (RTEM) system with dDAC, which can simultaneously record the volume, pressure, optical image, and structure of materials during dynamic compression runs. In particular, the volume measurement using both Fabry–Pérot interferogram and optical images facilitates the construction of an equation of state (EoS) using the dDAC in a home-laboratory. We also developed an in-line ruby pressure measurement (IRPM) system to be deployed at a synchrotron x-ray facility. This system provides simultaneous measurements of pressure and x-ray diffraction in low and narrow pressure ranges. The EoSs of ice VI obtained from the RTEM and the x-ray diffraction data with the IRPM are consistent with each other. The complementarity of both RTEM and IRPM systems will provide a great opportunity to scrutinize the detailed kinetic pathways of phase transitions using dDAC.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Crystal Structure and Atomic Vacancy Optimized Thermoelectric Properties in Gadolinium Selenides

Thermoelectric materials enable the energy conversion of waste heat into electricity, helpful to relieve global energy crisis. Here, we report a systematic investigation on high-temperature thermoelectric gadolinium selenides, cubic Gd 3-x Se 4 (x = 0.16, 0.21 and 0.25) and orthorhombic Gd 2 Se 3-y (y = 0.02, 0.06 and 0.08). High energy synchrotron x-ray diffraction and total scattering have been used to investigate the crystallographic and local structures. Atomic-scale clusters of Gd vacancy in the cubic phase are observed by employing the reverse Monte Carlo simulation. For cubic Gd 3-x Se 4 , adjusting Gd vacancy triggers the effect of multiple conduction bands, confirmed by the increase in effective masses and theoretical calculations. A reasonable peak zT value of 0.27 is achieved at 850 K for Gd 3-x Se 4 (x = 0.16). On the other hand, tuning Se vacancy enables the optimization of electron concentration for the orthorhombic Gd 2 Se 3-y . More significantly, its low deformation potential (Ξ = 12eV) gives rise to enhanced electron mobility and higher peak zT value of 0.54 at 850 K for Gd 2 Se 3-y (y = 0.02). Intriguingly, a higher zT of 1.2 at 1200 K is reasonably predicted by quality factor analysis. Finally, this work extends the scope of high-temperature thermoelectric materials and facilitates the exploration of novel high-temperature thermoelectric materials

36 MATERIALS SCIENCE↗
DOE OSTI2023

Molecular beam epitaxy and crystal structure of majority a -plane-oriented and substrate-strained Mn 3 Sn thin films grown directly on sapphire (0001)

The Kagome antiferromagnet Mn 3 Sn has garnered much attention due to the presence of exciting properties such as anomalous Hall and Nernst effects. This paper discusses the synthesis of crystalline Mn 3 Sn thin films, prepared on Al 2 O 3 (0001) substrates at 453 ± 5°C using molecular beam epitaxy. The growth is monitored in situ using reflection high energy electron diffraction and measured ex situ using x-ray diffraction, Rutherford back-scattering, and cross-sectional scanning transmission electron microscopy. Our analysis shows the in-plane lattice constants of a 1,M = 4.117 ± 0.027 Å and a 2,M = 4.943 ± 0.033 Å, which is a very unexpected result when compared to the bulk a-plane Mn 3 Sn. This indicates a strain in the film and makes it challenging to provide a straightforward explanation. In an effort to explain our results, we discuss two possible orientation relationships between the Mn 3 Sn films and the sapphire substrates. Samples prepared under these conditions appear to have smooth surfaces locally, but overall the film has a 3D island morphology. First-principles calculations provide atomic models of the Mn 3 Sn (112¯0) lattice on Al 2 O 3 (0001) high symmetry sites, indicating that the L3-R90° is the most stable configuration. A detailed discussion of the experimental data and theoretical results, as well as strain effects, is provided.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Crystal structure and synchrotron X-ray powder reference pattern for the porous pillared cyanonickelate, Ni(3-amino-4,4′-bipyridine)[Ni(CN) 4 ]

The structure of Ni(3-amino-4,4′-bipyridine)[Ni(CN) 4 ] (or known as Ni-BpyNH 2 ) in powder form was determined using synchrotron X-ray diffraction and refined using the Rietveld refinement technique (R = 8.8%). The orthorhombic (Cmca) cell parameters were determined to be a = 14.7218(3) Å, b = 22.6615(3) Å, c = 12.3833(3) Å, V = 4131.29(9) Å 3 , and Z = 8. Ni-BpyNH 2 forms a 3-D network, with a 2-D Ni(CN) 4 net connecting to each other via the BpyNH 2 ligands. Further, there are two independent Ni sites on the net. The 2-D nets are connected to each other via the bonding of the pyridine “N” atom to Ni2. The Ni2 site is of six-fold coordination to N with relatively long Ni2–N distances (average of 2.118 Å) as compared to the four-fold coordinated Ni1–C distances (average of 1.850 Å). The Ni(CN) 4 net is arranged in a wave-like fashion. The functional group, –NH 2 , is disordered and was found to be in the m-position relative to the N atom of the pyridine ring. Instead of having a unique position, N has ¼ site occupancy in each of the four m-positions. The powder reference diffraction pattern for Ni-BpyNH 2 was prepared and submitted to the Powder Diffraction File (PDF) at the International Centre of Diffraction Data (ICDD).

36 MATERIALS SCIENCE↗
DOE OSTI2023

Crystal structures of polymerized lithium chloride and dimethyl sulfoxide in the form of {2LiCl·3DMSO} n and {LiCl·DMSO} n

Two novel LiCl·DMSO polymer structures were created by combining dry LiCl salt with dimethyl sulfoxide (DMSO), namely, catena-poly[[chlorido­lithium(I)]-μ-(dimethyl sulfoxide)-κ 2 O:O-[chlorido­lithium(I)]-di-μ-(dimethyl sulfoxide)-κ 4 O:O], [Li 2 Cl 2 (C 2 H 6 OS) 3 ]n, and catena-poly[lithium(I)-μ-chlorido-μ-(dimethyl sulfoxide)-κ 2 O:O], [LiCl(C 2 H 6 OS)]n. The initial synthesized phase had very small block-shaped crystals (<0.08 mm) with monoclinic symmetry and a 2 LiCl: 3 DMSO ratio. As the solution evaporated, a second phase formed with a plate-shaped crystal morphology. After about 20 minutes, large (>0.20 mm) octa­hedron-shaped crystals formed. The plate crystals and the octa­hedron crystals are the same tetra­gonal structure with a 1 LiCl: 1 DMSO ratio. These structures are reported and compared to other known LiCl·solvent compounds.

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

The electronic structure, crystal fields, and magnetic anisotropy in RECo 5 magnets

The current progress in describing rare-earth-based magnets' electronic structure and magnetic properties is discussed. We use several currently popular electronic structure methods to show the typical values of critical parameters that define the physics of RECo 5 (RE = rare earth atom) materials. The magnetic moments and magnetic anisotropy of 4f atoms are obtained using several approaches, including anisotropic 4f-charge density-constrained DFT and DFT+HI methods. We also suggest the introduction of "penalty" functional for obtaining correct variational total energy in the traditional Hund's rule-constrained DFT-based techniques. The applicability and future extensions are discussed. The proposed combination of methods is potentially suitable for high-throughput computational searches of new rare-earth-containing magnetic materials.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Heterogeneous Composition of Oxygen-Evolving Complexes in Crystal Structures of Dark-Adapted Photosystem II

Photosystem II (PSII) is a homodimeric protein complex that catalyzes water oxidation at the oxygen-evolving complex (OEC), a heterocubanoid calcium-tetra-manganese cluster. Here, we analyze the omit electron-density peaks of the OEC’s metal ions in five X-ray free-electron laser PSII structures at a resolution between 2.15 Å and 1.95 Å. The omit peaks can be described by the total number of electrons and approximated by the variance of electron density distribution when the distributions are spherically symmetric. We show that the number of electrons of metal centers are different in the two OECs of PSII dimers, implying that either the oxidation states and/or occupancies of individual metal ions are different in the two monomers. In either case, we find that the two OECs of dark-adapted PSII dimers in crystals are not fully synchronized in the same expected S 1 state. Differences in redox states of the OEC in PSII only partially account for the observation that the electron densities integrate to a smaller number of electrons than expected. Differences between the determined and expected relative electron numbers are much larger than the estimated errors, indicating heterogeneity in the OEC composition. Here, the reported findings suggest that two OECs of dark-adapted PSII crystals are typically not fully synchronized in the S 1 state and likely generate heterogeneity in the crystallographical data of PSII intermediate structures.

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

Nonlinear propagating modes beyond the phonons in fluorite-structured crystals

The vibrational energy of crystals is known to propagate in a fixed number of phonon branches allowed by symmetry. In the realm of nonlinear dynamics, however, additional nonlinear propagating modes are possible. Nonlinear propagating modes have unique properties that are important in many disciplines including optical communications, conducting polymers, biology, magnetism, and nuclear physics. Yet, despite the crucial importance of crystal lattice vibrations in fundamental and applied science, such additional propagating modes have not been observed in ordinary crystals. Here, we show that propagating modes exist beyond the phonons in fluorite-structured thoria, urania, and natural calcium fluoride using neutron scattering and first-principles calculations. These modes are observed at temperatures ranging from 5 K up to 1200 K, extend to frequencies 30–40% higher than the maximum phonon frequency, and travel at velocities comparable to or higher than the fastest phonon. The nonlinear origin of the modes is explained in part via perturbation theory, which approximately accounts for nonlinearity. Given that these modes are still clearly observed at 5 K, they are likely an inherent feature of the quantum ground state. The existence of these waves in three-dimensional crystals may have ramifications for material properties.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Spatiotemporal control of liquid crystal structure and dynamics through activity patterning

Active materials are capable of converting free energy into mechanical work to produce autonomous motion, and exhibit striking collective dynamics that biology relies on for essential functions. Controlling those dynamics and transport in synthetic systems has been particularly challenging. Here, we introduce the concept of spatially structured activity as a means of controlling and manipulating transport in active nematic liquid crystals consisting of actin filaments and light-sensitive myosin motors. In this work, simulations and experiments are used to demonstrate that topological defects can be generated at will and then constrained to move along specified trajectories by inducing local stresses in an otherwise passive material. These results provide a foundation for the design of autonomous and reconfigurable microfluidic systems where transport is controlled by modulating activity with light.

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

Multimodal Characterization of Crystal Structure and Formation in Rubrene Thin Films Reveals Erasure of Orientational Discontinuities

Abstract Multimodal multiscale characterization provide opportunities to study organic semiconducting thin films with multiple length scales, across multiple platforms, to elucidate crystallization mechanisms of the various microstructures that impact functionality. With polarized scanning transmission X‐ray and 4D‐scanning transmission electron microscopy, hybrid crystalline structures in rubrene thin films in which large crystalline domains surround a common nucleus and transition to a spherulite morphology at larger radii is observed. These high‐resolution techniques reveal how azimuthal orientational discontinuities at smaller radii are erased as spherulite morphology takes hold. In situ crystallization in the films with optical microscopy is also captured, discovering the importance of considering the initial temperature increase of a film during thermal annealing over the crystallization timescale. This kinetic information of the radial crystallization rate and of corresponding film heating kinetics is used to estimate the temperature at which the larger crystalline regions transition into a spherulite. By combining the results obtained from the different characterization modes, it is learned that thermal conditions can sensitively affect the crystallization of rubrene and other organic thin films. The observations suggest opportunities for more complex temperature‐dependent processing to maximize hybrid structures’ functionality in organic thin films and demonstrate that multimodal studies deepen the understanding of structure‐function dynamics.

Tan, Jenna A.↗
DOE OSTI2023

The Crystal Structure of BaZn 2 Se 2 (OH) 2 Featuring Brownmillerite‐Type Layers

Abstract A bimetallic hydroxychalcogenide, BaZn 2 Se 2 (OH) 2 , was synthesized through hydrothermal pouch methods. The single crystal X‐ray diffraction and electron diffraction indicates that the phase crystallizes in the orthorhombic space group Pnma and is composed of anionic layers [ZnSe 3/3 (OH) 1/1 ] − that are separated and charged balanced by Ba 2+ cations. The [ZnSe 3/3 (OH) 1/1 ] – layer comprises two unique Zn sites, which form interpenetrating zigzag chains with an in‐plane dipole moment and adopts a brownmillerite‐type structural motif. The adjacent layers contain tetrahedrally coordinated Zn chains of opposite handedness related by an inversion center, which cancel the microscopic dipoles to minimize the macroscopic electric polarization. The adoption of a brownmillerite structural motif in BaZn 2 Se 2 (OH) 2 can be rationalized by the distinct charge difference between Se 2− and OH − anions, which creates a sufficient dipole moment in the ZnSe 3 (OH) tetrahedra to allow the occurrence of twisted chains. FTIR spectroscopy confirms the existence of OH − anions and DFT calculations indicate that BaZn 2 Se 2 (OH) 2 is a semiconductor with a direct band gap. This work expands the chemistry of the brownmillerite family from traditional homoanionic oxides to multianion hydroxychalcogenides, offering a new opportunity to explore tunable structural complexity for better design of functional materials.

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

Crystal structure of [Th 3 (Cp*) 3 (O)(OH) 3 ] 2 Cl 2 (N 3 ) 6 : a discrete molecular capsule built from multinuclear organothorium cluster cations

An unusually large and structurally complex charge-neutral polynuclear cluster, hexa-μ 2 -azido-di-μ 3 -chlorido-hexa-μ 2 -hydroxido-di-μ 3 -oxido-hexakis(pentamethylcyclopentadienyl)hexathorium–diethyl ether–tetrahydrofuran (1/0.56/1.44), [Th 3 (C 10 H 15 ) 6 Cl 3 (N 3 ) 6 (OH) 6 O 2 ]·0.56C 4 H 10 O·1.44C 4 H 8 O or [Th 3 (Cp*) 3 (O)(OH) 3 ] 2 Cl 2 (N 3 ) 6 ·0.56C 4 H 10 O·1.44C 4 H 8 O (Cp* = [pentamethylcyclopentadienyl]) − , has been crystallized as a mixed tetrahydrofuran/diethyl ether solvate and structurally characterized. The molecule contains a number of unusual features, the most notable being a finite yet exceptionally long cyclic metal-azido chain. These rare features are the consequence of both sterically protecting Cp* ligands and highly bridging oxide and hydroxide ligands in the same system and illustrate the interesting new possibilities that can arise from combining organometallic and solvothermal f -block element chemistry.

Kelley, Steven P.↗
DOE OSTI2026

The Modulated Crystal Structure of K 2 V 3 O 8

Weak lattice distortions can tune exchange pathways and magnetic interactions in square-lattice quantum magnets. K 2 V 3 O 8 is a mixed valence (V 4+ /V 5+ ) fresnoite oxide that exhibits strong spin–lattice coupling at low temperature. Here, we combine single-crystal neutron diffraction (90 K) and laboratory X-ray diffraction (50 K) to solve the low-temperature structure as an orthorhombic (3 + 1)D incommensurately modulated phase in superspace group Cmm2(β,0,1/2)0s0 [No. 196]. What initially appeared as two independent modulation vectors, q 1 = 0.3132(6)[$110$] + 1/2c* and q 2 = 0.3132(6)[$1\bar{10}$] + 1/2c*, are more naturally described as a single one-dimensional modulation wave q = 0.626(1)a* + 1/2c* in a C-centered orthorhombic lattice, related to the parent tetragonal cell by the transformation a + b, −a + b, c. Refinement with a 4-fold rotational twin inherited from the P4bm parent structure solves oxygen-dominated framework distortions and K + displacements. A de Wolff section (t = 0.40) enables a symmetry-mode decomposition, identifying three dominant mm2 (C 2v ) modes: GM3 for framework tilt, A5 for interlayer shear, and Z5 for c-axis breathing. The mode-resolved structure provides a unified, symmetry-based explanation for reported low-temperature Raman and IR anomalies and clarifies the structural origin of the spin–lattice coupling in the S = 1/2 two-dimensional quantum spin compound.

K2V3O8↗
DOE OSTI2023

Rapid and efficient ambient temperature X-ray crystal structure determination at Turkish Light Source

High-resolution biomacromolecular structure determination is essential to better understand protein function and dynamics. Serial crystallography is an emerging structural biology technique which has fundamental limitations due to either sample volume requirements or immediate access to the competitive X-ray beamtime. Obtaining a high volume of well-diffracting, sufficient-size crystals while mitigating radiation damage remains a critical bottleneck of serial crystallography. As an alternative, we introduce the plate-reader module adapted for using a 72-well Terasaki plate for biomacromolecule structure determination at a convenience of a home X-ray source. We also present the first ambient temperature lysozyme structure determined at the Turkish light source (Turkish DeLight). The complete dataset was collected in 18.5 min with resolution extending to 2.39 Å and 100% completeness. Combined with our previous cryogenic structure (PDB ID: 7Y6A), the ambient temperature structure provides invaluable information about the structural dynamics of the lysozyme. Turkish DeLight provides robust and rapid ambient temperature biomacromolecular structure determination with limited radiation damage.

59 BASIC BIOLOGICAL SCIENCES↗