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At least 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Insights from the Structure of Mycobacterium tuberculosis Topoisomerase I with a Novel Protein Fold

The DNA topoisomerase I enzyme of Mycobacterium tuberculosis (MtTOP1) is essential for the viability of the organism and survival in a murine model. This topoisomerase is being pursued as a novel target for the discovery of new therapeutic agents for the treatment of drug-resistant tuberculosis. In this study, we succeeded in obtaining a structure of MtTOP1 by first predicting that the C-terminal region of MtTOP1 contains four repeated domains that do not involve the Zn-binding tetracysteine motifs seen in the C-terminal domains of Escherichia coli topoisomerase I. A construct (amino acids A2-T704), MtTOP1-704t, that includes the N-terminal domains (D1-D4) and the first predicted C-terminal domain (D5) of MtTOP1 was expressed and found to retain DNA cleavage-religation activity and catalyze single-stranded DNA catenation. MtTOP1-704t was crystallized, and a structure of 2.52 angstrom resolution limit was obtained. The structure of the MtTOP1 N-terminal domains has features that have not been observed in other previously available bacterial topoisomerase I crystal structures. The first C-terminal domain D5 forms a novel protein fold of a four-stranded antiparallel beta-sheet stabilized by a crossing-over alpha-helix. Since there is only one type IA topoisomerase present in Mycobacteriaceae and related Actinobacteria, this subfamily of type IA topoisomerase may be required for multiple functions in DNA replication, transcription, recombination, and repair. The unique structural features observed for MtTOP1 may allow these topoisomerase I enzymes to carry out physiological functions associated with topoisomerase III enzyme in other bacteria.

crystallization↗
DOE OSTI2018

First principles study of the structural, electronic, and optical properties of Sn 2+ -doped ZnO–P 2 O 5 glasses [First principles study of the structural, electronic and optical properties of Sn-doped ZnO-P2O5 glasses]

The atomic-structural, electronic, and optical properties of Sn-doped ZnO–P 2 O 5 glasses are examined using combined semi-empirical and density functional theory calculations. From model structures for two different ZnO–P 2 O 5 glass compositions, it is found that these glasses consist of nearly ideal tetrahedral PO 4 unit and largely distorted ZnO 4 and ZnO 5 units. The concentration of ZnO 5 units is calculated to increase and exceed that of ZnO 4 as the amount of ZnO in the glass is increased. Also, the concentration of terminal oxygen atoms shared by two Zn neighbors is largely increased for 70ZnO:30P 2 O 5 (70:30) glass compared to 60:40 glass, which can be rationalized by electrostatic bond strength calculations. Regarding medium-range order, calculations show that Q 1 and Q 2 structures (where Q n refers to structures containing n bridging oxygen atoms on PO 4 tetrahedra) are dominant for the 60:40 glass, while Q 0 and Q 1 prevail for the 70:30 glass, in good agreement with experimental observations. For the Sn-doped ZnO–P 2 O 5 glass, various Sn coordination geometries are found, with trigonal pyramidal SnO 3 and largely distorted pyramidal SnO 4 configurations being dominant and a small fraction of two-fold and five-fold coordinated Sn configurations also present. From combined cluster and glass model calculations, two-fold coordinated Sn are found to exhibit slightly smaller optical transition energy than three-fold and four-fold coordinated Sn. However, local variations in coordination structures throughout the glass likely result in a broad singlet transition (S 0 →S 1 ) around 5.4 eV for all the different Sn configurations. Finally, a triplet transition (S 0 →T 1 ) driven by spin-orbit coupling can occur around 4.5 – 4.8 eV, but the magnitude of this transition is predicted to be much smaller than the spin-allowed singlet transition.

36 MATERIALS SCIENCE↗
DOE OSTI2015

The U{sup 5+} compound Ba{sub 9}Ag{sub 10}U{sub 4}S{sub 24}: Synthesis, structure, and electronic properties

Black crystals of Ba{sub 9}Ag{sub 10}U{sub 4}S{sub 24} have been made by direct combination of BaS, Ag, U, and S at 1273 K. This compound crystallizes in a new structure type in the space group C{sub 4v}{sup 10}−I4cm of the tetragonal system with four formula units in a cell with lattice constants a=13.9189(6) Å and c=23.7641(11) Å (V=4604(5) Å{sup 3}). Multiphoton Luminescence Spectroscopy measurements are consistent with the noncentrosymmetric nature of the structure. In the structure each U atom is octahedrally coordinated by six S atoms, whereas three of the five crystallographically independent Ag atoms are tetrahedrally coordinated to four S atoms, another has a seesaw coordination to four S atoms, and the last has a triangular coordination to three S atoms. The overall structure consists of the three-dimensional stacking of the US{sub 6}, AgS{sub 4}, and AgS{sub 3} polyhedra to leave channels in which Ba atoms reside. Based on the values of the U–S interatomic distances, the compound Ba{sub 9}Ag{sub 10}U{sub 4}S{sub 24} contains U{sup 5+} and charge balance is achieved with the formal oxidation states of 9 Ba{sup 2+}, 10 Ag{sup 1+}, 4 U{sup 5+} and 24 S{sup 2−}. DFT calculations predict an antiferromagnetic ground state and a band gap of 2.1 eV. Resistivity measurements indicate that the compound is a semiconductor with a complex activation mechanism and activation energies ranging from 0.03(1) eV to 0.08(1) eV. - Graphical abstract: General view of the Ba{sub 9}Ag{sub 10}U{sub 4}S{sub 24} structure. - Highlights: • Black crystals of Ba{sub 9}Ag{sub 10}U{sub 4}S{sub 24} have been made by direct combination of BaS, Ag, U, and S at 1273 K. • Ba{sub 9}Ag{sub 10}U{sub 4}S{sub 24} contains U{sup 5+} and charge balance is achieved with 9 Ba{sup 2+}, 10 Ag{sup 1+}, 4 U{sup 5+}, and 24 S{sup 2−}. • DFT calculations predict an antiferromagnetic ground state and a band gap of 2.1 eV. • The compound is a semiconductor with activation energies ranging from 0.03(1) eV to 0.08(1) eV.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Synthesis, crystal structure, and magnetism of A{sub 2}Co{sub 12}As{sub 7} (A=Ca, Y, Ce–Yb)

Ternary intermetallics, A{sub 2}Co{sub 12}As{sub 7} (A=Ca, Y, Ce–Yb), have been synthesized by annealing mixtures of elements in molten Bi at 1223 K. The materials obtained crystallize in the P6{sub 3}/m variant of the Zr{sub 2}Fe{sub 12}P{sub 7} structure type. The unit cell volume shows a monotonic decrease with the increasing atomic number of the rare-earth metal, with the exception of Ce-, Eu-, and Yb-containing compounds. An examination of these outliers with X-ray absorption near edge structures (XANES) spectroscopy revealed mixed valence of Ce, Eu, and Yb, with the average oxidation states of +3.20(1), +2.47(5), and +2.91(1), respectively, at room temperature. Magnetic behavior of A{sub 2}Co{sub 12}As{sub 7} is generally characterized by ferromagnetic ordering of Co 3d moments at 100–140 K, followed by low-temperature ordering of rare-earth 4f moments. The 3d-4f magnetic coupling changes from antiferromagnetic for A=Pr–Sm to ferromagnetic for A=Ce and Eu–Yb. Polarized neutron scattering experiments were performed to support the postulated ferro- and ferrimagnetic ground states for Ce{sub 2}Co{sub 12}As{sub 7} and Nd{sub 2}Co{sub 12}As{sub 7}, respectively. - Graphical abstract: Title arsenides were synthesized by Bi‐flux method. They exhibit mixed valence for A = Ce, Eu, Yb, ferrimagnetism for A = Ca, Y, Pr–Sm, and ferromagnetism for A = Eu–Tm. - Highlights: • A2Co12As7 (A=Ca, Y, Ce–Yb) were synthesized in Bi flux. • Ce, Eu, Yb exhibit mixed valence in the corresponding structures. • The character of 3d‐4f magnetic coupling changes at the half‐filled f shell. • Materials behave as ferrimagnets for A=Ca, Y, Pr–Sm and as ferromagnets for A=Eu–Yb.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

The structural response of gadolinium phosphate to pressure

Accurate elastic constants for gadolinium phosphate (GdPO{sub 4}) have been measured by single-crystal high-pressure diffraction methods. The bulk modulus of GdPO{sub 4} determined under hydrostatic conditions, 128.1(8) GPa (K′=5.8(2)), is markedly different from that obtained with GdPO{sub 4} under non-hydrostatic conditions (160(2) GPa), which indicates the importance of shear stresses on the elastic response of this phosphate. High pressure Raman and diffraction analysis indicate that the PO{sub 4} tetrahedra behave as rigid units in response to pressure and that contraction of the GdPO{sub 4} structure is facilitated by bending/twisting of the Gd–O–P links that result in increased distortion in the GdO{sub 9} polyhedra. - Graphical abstract: A high-pressure single crystal diffraction study of GdPO{sub 4} with the monazite structure is presented. The elastic behaviour of rare-earth phosphates are believed to be sensitive to shear forces. The bulk modulus of GdPO{sub 4} measured under hydrostatic conditions is 128.1(8) GPa. Compression of the structure is facilitated by bending/twisting of the Gd−O−P links that result in increased distortion in the GdO{sub 9} polyhedra. Display Omitted - Highlights: • The elastic responses of rare-earth phosphates are sensitive to shear forces. • The bulk modulus of GdPO{sub 4} measured under hydrostatic conditions is 128.1(8) GPa. • Twisting of the inter-polyhedral links allows compression of the GdPO{sub 4} structure. • Changes to the GdO{sub 9} polyhedra occur in response to pressure (<7.0 GPa).

36 MATERIALS SCIENCE↗
DOE OSTI2018

A family of rare earth uranium oxides, RE{sub 6}UO{sub 12-δ}, (RE = Rare Earth). Synthesis, structure and magnetic behavior

Highlights: • A series of rare earth urinates, RE{sub 6}UO{sub 12}, were synthesized using the solid state method. • The crystal structures of RE{sub 6}UO{sub 12} were refined using the Rietveld method. • Magnetic properties were measured and AF ordering was observed in RE = Gd, Tb, Dy. - Abstract: A series of rare earth uranates, RE{sub 6}UO{sub 12-δ} (RE = La, Nd, Sm – Dy, Er and Yb), were synthesized via the solid state method and their structures were determined using the Rietveld method. These compounds crystallize in the rhombohedral space group R-3H with the lattice parameters a = 10.47005(3) Å and c = 9.98034(3) Å for the La analogue. The temperature and field dependent magnetization are reported for each analogue. Antiferromagnetic ordering is observed for RE = Gd, Tb, and Dy with Néel temperatures of 2.1 K, 5.8 K, and 2.8 K, respectively. Magnetic measurements on the La{sub 6}UO{sub 12} analogue indicate the presence of some U{sup 5+}, and therefore, oxygen vacancies in the structure. The variability of the U valence is examined.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Analysis of the structural, electronic, elastic and thermodynamic properties of CuAl2X4 (X = O, S) spinel structure

Highlights: • Fundamental properties of CuAl{sub 2}X{sub 4} (X = O, S) aluminate spinels have been investigated. • The pressure dependence of the elastic constants C{sub ij} can be successfully fit by a straight line. • CuAl{sub 2}X{sub 4} (X = O, S) compounds are mechanically stable at ambient conditions. • Temperature and pressure dependences of some macroscopic parameters are achieved. - Abstract: The structural, electronic, elastic and thermodynamic properties of oxo- and thio-spinels have been predicted based on the ultrasoft pseudo-potential scheme as implemented in the CASTEP code. The exchange-correlation potential was treated within the generalized gradient approximation (GGA-PBE). The calculated structural parameters such as lattice constants and internal parameters are in good agreement with the available experimental data. The ground state electronic band structure revealed that CuAl{sub 2}X{sub 4} (XO, S) spinels are direct band gap semiconductors with a transition along Γ-Γ symmetry points. The calculated values of elastic constants satisfy the Born criteria at ambient conditions and confirm that the spinel structures of CuAl{sub 2}O{sub 4} and CuAl{sub 2}S{sub 4} are mechanically stable. The thiospinel structure may have a phase transition under pressure, due to the negative value of C{sub 44}. The influence of temperature and pressure on macroscopic characteristics of CuAl{sub 2}O{sub 4} and CuAl{sub 2}S{sub 4} compounds was estimated using the quasi-harmonic Debye model.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

The Electronic Structure of the Metal Active Site Determines the Geometric Structure and Function of the Metalloregulator NikR

NikR is a nickel-responsive metalloregulator protein that controls the level of Ni 2+ ions in living cells. Previous studies have shown that NikR can bind a series of first-row transition metal ions but binds to DNA with high affinity only as a Ni 2+ complex. To understand this metal selectivity, S K-edge X-ray absorption spectroscopy of NikR bound to different metal ions was used to evaluate the different electronic structures. The experimental results are coupled with density functional theory calculations on relevant models. This study shows that both the Z eff of the metal ion and the donor nature of the ligands determine the electronic structure of the metal site. This impacts the geometric structure of the metal site and thus the conformation of the protein. Furthermore, this contribution of electronic structure to geometric structure can be extended to other metal selective metalloregulators.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Unraveling the Origin of Structural Disorder in High Temperature Transition Al2O3: Structure of θ-Al2O3

The crystallography of transition Al2O3 has been extensively studied in the past due to the advantageous properties of the oxide in catalytic and a range of other technological applications. However, existing crystallographic models are insufficient to describe the structure of many important Al2O3 polymorphs due to their highly disordered nature. In this work, we investigate structure and disorder in high-temperature treated transition Al2O3, and provide a structural description for θ-Al2O3 by using a suite of complementary imaging, spectroscopy and quantum calculation techniques. Contrary to current understanding, our high-resolution imaging shows that θ-Al2O3 is a disordered composite phase of at least two different end members. By correlating imaging and spectroscopy results with DFT calculations, we propose a model that describes θ-Al2O3 as a disordered intergrowth of two crystallographic variants at the unit cell level. One variant is based on β-Ga2O3, and the other on a monoclinic phase that is closely-related to δ-Al2O3. The overall findings and interpretations afford new insight into the origin of poor crystallinity in transition Al2O3, and also provide new perspectives on structural complexity that can emerge from intergrowth of closely related structural polymorphs.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2017

Investigation of Structural Evolution of Li 1.1 V 3 O 8 by In Situ X-ray Diffraction and Density Functional Theory Calculations

Li 1.1 V 3 O 8 is a promising cathode material for Li-ion batteries, because of its high theoretical capacity (362 mAh g-1) and good rate performance. In this study, the structural evolution of Li 1.1 V 3 O 8 material during electrochemical dis(charge) processes was investigated using a combination of theoretical calculations and experimental data. Density functional theory (DFT) was used to predict the intermediate structures at various lithiation states, as well as the stability of major phases. In order to validate these predictions, in situ X-ray diffraction (XRD) data was collected operando, allowing for the phase transformations to be monitored under current load and eliminating the possibilities of structural relaxation processes and environmental oxidation. Rietveld refinement was performed to fit the diffraction data with the DFT-derived structures and to analyze the fractions of major phases as a function of dis(charge). The DFT calculations identified three stable states that were validated by the in situ XRD result: a Li-poor α-phase (Li1), a Li-rich α-phase (Li2.5), and a β-phase (Li4). The DFT-predicted particle shape based on the surface energy of the (100), (001), and (010) planes rationalized the preferential orientation of Li 1.1 V 3 O 8 particles along the [010] direction in the electrode. Furthermore, the onset and offset of the α → β transition, as well as the phase fractions of α and β determined via in situ XRD, related well with the DFT-derived relative stability of each phase. Thus, by integrating DFT calculations with experimental work, this work provides a thorough understanding of the structural transformations in Li 1.1 V 3 O 8 during electrochemical dis(charge).

25 ENERGY STORAGE↗
DOE OSTI2026

CoSn-type NiIn1–xSbx (0 ≤ x ≤ 0.17): Site-Selective Substitution, Electronic Structure, Chemical Bonding, and Structural Transformation

CoSn-type intermetallic compounds have emerged as a model platform for Kagome-derived flat-band physics, where subtle chemical perturbations can strongly influence electronic structure and phase stability. Here, we present a combined experimental and theoretical study of Sb-substitution in CoSn-type NiIn1–xSbx (0 ≤ x ≤ 0.17) to elucidate the interplay between site selectivity, solubility limit, chemical bonding, and electronic structure. Rietveld refinements on Neutron powder diffraction data confirmed the selective Sb-substitution at the electron-rich In2 (2d) site forming the honeycomb substructure, while the In1 (1a) site within the Kagome layer remains exclusively occupied by In. Density functional theory (DFT) calculations revealed that pristine CoSn-type NiIn hosts Ni 3d-dominated flat bands near the Fermi level (EF), originating from the Kagome-like Ni substructure. Partial replacement of In by Sb within the honeycomb layer alters these flat-band features below EF, reducing the density of states and suppressing the flat-band topology near the Fermi level. Orbital-resolved electronic structure and chemical-bonding analyses show that Sb-substitution enhances Ni-p-block (In/Sb) covalency and optimizes charge compensation, stabilizing the CoSn-type structure up to the solubility limit x ≈ 0.17. Beyond the limit, the higher-Sb compositions show satellite reflections consistent with an incommensurately modulated phase. These results establish a link between site-selective chemical substitution, bonding optimization, and flat-band electronic structure evolution, providing fundamental insights into how chemical substitution influences the electronic properties of Kagome-based intermetallic compounds.

Roy, Nilanjan [National Institute of Technology Si↗
DOE OSTI2016

Crystal Structure of AgBi 2 I 7 Thin Films

Synthesis of cubic-phase AgBi 2 I 7 iodobismuthate thin films and fabrication of air-stable Pb-free solar cells using the AgBi 2 I 7 absorber have recently been reported. Based on X-ray diffraction (XRD) analysis and nominal composition, it was suggested that the synthesized films have a cubic ThZr 2 H 7 crystal structure with AgBi 2 I 7 stoichiometry. Through careful examination of the proposed structure and computational evaluation of the phase stability and bandgap, we find that the reported “AgBi 2 I 7 ” films cannot be forming with the ThZr 2 H 7 -type structure, but rather more likely adopt an Ag-deficient AgBiI 4 type. Both the experimental X-ray diffraction pattern and band gap can be better explained by the AgBiI 4 structure. Additionally, the proposed AgBiI 4 structure, with octahedral bismuth coordination, removes unphysically short Bi–I bonding within the BiI8 hexahedra of the ThZr 2 I 7 model. Our results provide critical insights for assessing the photovoltaic properties of AgBi 2 I 7 iodobismuthate materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

New Insights on the Structure of Electrochemically Deposited Lithium Metal and Its Solid Electrolyte Interphases via Cryogenic TEM

Lithium metal has been considered as the “holy grail” anode material for rechargeable batteries though the dendritic growth and low Coulombic efficiency (CE) have crippled its practical use for decades. Its high chemical reactivity and low stability make it difficult to explore the intrinsic chemical and physical properties of the electrochemically deposited lithium (EDLi) and its accompanied solid electrolyte interphase (SEI). To prevent the dendritic growth and enhance the electrochemical reversibility, it is crucial to understand the nano- and meso- structures of EDLi. However, Li metal is very sensitive to beam damage and has low contrast for commonly used characterization techniques such as electron microscopy. Inspired by biological imaging techniques, this work demonstrates the power of cryogenic (cryo)- electron microscopy to reveal the detailed structure of EDLi and the SEI composition at the nano scale while minimizing beam damage during imaging. Surprisingly, the results show that the nucleation dominated EDLi (five minutes at 0.5 mA cm-2) is amorphous while there is some crystalline LiF present in the SEI. The EDLi grown from various electrolytes with different additives exhibits distinctive surface properties. Consequently, these results highlight the importance of the SEI and its relationship with the CE. Our findings not only illustrate the capabilities of cryogenic microscopy for beam (thermal)-sensitive materials, but it yields crucial structural information of the EDLi evolution with and without electrolyte additives.

electrochemical deposition↗
DOE OSTI2015

Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ~20° rotation between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. In conclusion, this structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗