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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Structural and Biophysical Properties of a [4Fe-4S] Ferredoxin-Like Protein from Synechocystis sp. PCC 6803 with a Unique Two Domain Structure

Electron carrier proteins (ECPs), binding iron-sulfur clusters, are vital components within the intricate network of metabolic and photosynthetic reactions. They play a crucial role in the distribution of reducing equivalents. In Synechocystis sp. PCC 6803, the ECP network includes at least nine ferredoxins. Previous research, including global expression analyses and protein binding studies, has offered initial insights into the functional roles of individual ferredoxins within this network. This study primarily focuses on Ferredoxin 9 (slr2059). Through sequence analysis and computational modeling, Ferredoxin 9 emerges as a unique ECP with a distinctive two-domain architecture. It consists of a C-terminal iron-sulfur binding domain and an N-terminal domain with homology to Nil-domain proteins, connected by a structurally rigid 4-amino acid linker. Notably, in contrast to canonical [2Fe-2S] ferredoxins exemplified by PetF (ssl0020), which feature highly acidic surfaces facilitating electron transfer with photosystem I reaction centers, models of Ferredoxin 9 reveal a more neutral to basic protein surface. Using a combination of electron paramagnetic resonance spectroscopy and square-wave voltammetry on heterologously produced Ferredoxin 9, this study demonstrates that the protein coordinates 2x[4Fe-4S]2+/1+ redox-active and magnetically interacting clusters, with measured redox potentials of -420 +/- 9 mV and -516 +/- 10 mV vs SHE. A more in-depth analysis of Fdx9's unique structure and protein sequence suggests that this type of Nil-2[4Fe-4S] multi-domain ferredoxin is well conserved in cyanobacteria, bearing structural similarities to proteins involved in homocysteine synthesis in methanogens.

cyanobacteria↗
DOE OSTI2016

The influence of crystal structure on ion-irradiation tolerance in the Sm(x)Yb(2-x)TiO5 series

his ion-irradiation study covers the four major crystal structure types in the Ln(2)TiO(5) series (Ln = lanthanide), namely orthorhombic Pnma, hexagonal P63/mmc, cubic (pyrochlore-like) Fd-3m and cubic (fluorite-like) Fm-3m. This is the first systematic examination of the complete Ln(2)TiO(5) crystal system and the first reported examination of the hexagonal structure. A series of samples, based on the stoichiometry Sm(x)Yb(2-x)TiO5 (where x = 2, 1.4, 1, 0.6, and 0) have been irradiated using 1 MeV Kr2+ ions and characterised in-situ using a transmission electron microscope. Two quantities are used to define ion-irradiation tolerance: critical dose of amorphisation (D-c), which is the irradiating ion dose required for a crystalline to amorphous transition, and the critical temperature (T-c), above which the sample cannot be rendered amorphous by ion irradiation. The structure type plus elements of bonding are correlated to ion-irradiation tolerance. The cubic phases, Yb2TiO5 and Sm0.6Yb1.4TiO5, were found to be the most radiation tolerant, with Tc values of 479 and 697 K respectively. The improved radiation tolerance with a change in symmetry to cubic is consistent with previous studies of similar compounds.

Aughterson, R. D. (ORCID:000000021704024X)↗
DOE OSTI2014

Structure and elementary properties of the new Ir hollandite Rb{sub 0.17}IrO{sub 2}

We report the synthesis and structural characterization of the new Ir holladite, Rb{sub 0.17}IrO{sub 2}. Rb{sub 0.17}IrO{sub 2} crystallizes in the tetragonal hollandite structure. In contrast to the previously reported monoclinic Ir hollandite K{sub 0.25}IrO{sub 2}, we do not observe a difference in Ir–O bond lengths in Rb{sub 0.17}IrO{sub 2} and thus find Ir in an average oxidation state of + 3.83. We also report and compare the electronic and magnetic properties of Rb{sub 0.17}IrO{sub 2} and K{sub 0.25}IrO{sub 2}, finding that they are both metallic and Pauli paramagnets further supporting that the electrons are delocalized in the Ir 5d states. - Graphical abstract: Crystal structure of Rb{sub 0.17}IrO{sub 2} (right), and the SEM image of Rb{sub 0.17}IrO{sub 2}, showing the growth of thin needles (left). Display Omitted - Highlights: • New iridium hollandite. • Naturally grows in very thin wires. • Elementary physical properties of Ir holladites reported for the first time metallic conductor and paramagnetic.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Structure and properties of α-NaFeO{sub 2}-type ternary sodium iridates

The synthesis, structure, and elementary magnetic and electronic properties are reported for layered compounds of the type Na{sub 3−x}MIr{sub 2}O{sub 6} and Na{sub 3−x}M{sub 2}IrO{sub 6}, where M is a transition metal from the 3d series (M=Zn, Cu, Ni, Co, Fe and Mn). The rhombohedral structures, in space group R−3m, were determined by refinement of neutron and synchrotron powder diffraction data. No clear evidence for long range 2:1 or 1:2 honeycomb-like M/Ir ordering was found in the neutron powder diffraction patterns except in the case of M=Zn, and thus in general the compounds are best designated as sodium deficient α-NaFeO{sub 2}-type phases with formulas Na{sub 1−x}M{sub 1/3}Ir{sub 2/3}O{sub 2} or Na{sub 1−x}M{sub 2/3}Ir{sub 1/3}O{sub 2}. Synchrotron powder diffraction patterns indicate that several of the compounds likely have honeycomb in-plane metal–iridium ordering with disordered stacking of the layers. All the compounds are sodium deficient under our synthetic conditions and are black and insulating. Weiss constants derived from magnetic susceptibility measurements indicate that Na{sub 0.62}Mn{sub 0.61}Ir{sub 0.39}O{sub 2}, Na{sub 0.80}Fe{sub 2/3}Ir{sub 1/3}O{sub 2}, Na{sub 0.92}Ni{sub 1/3}Ir{sub 2/3}O{sub 2}, Na{sub 0.86}Cu{sub 1/3}Ir{sub 2/3}O{sub 2}, and Na{sub 0.89}Zn{sub 1/3}Ir{sub 2/3}O{sub 2} display dominant antiferromagnetic interactions. For Na{sub 0.90}Co{sub 1/3}Ir{sub 2/3}O{sub 2} the dominant magnetic interactions at low temperature are ferromagnetic while at high temperatures they are antiferromagnetic; there is also a change in the effective moment. Low temperature specific heat measurements (to 2 K) on Na{sub 0.92}Ni{sub 1/3}Ir{sub 2/3}O{sub 2} indicate the presence of a broad magnetic ordering transition. X-ray absorption spectroscopy shows that iridium is at or close to the 4+ oxidation state in all compounds. {sup 23}Na nuclear magnetic resonance measurements comparing Na{sub 2}IrO{sub 3} to Na{sub 0.92}Ni{sub 1/3}Ir{sub 2/3}O{sub 2} and Na{sub 0.89}Zn{sub 1/3}Ir{sub 2/3}O{sub 2} provide strong indications that the electron spins are short-range ordered in the latter two materials. Na{sub 0.62}Mn{sub 0.61}Ir{sub 0.39}O{sub 2}, Na{sub 0.80}Fe{sub 2/3}Ir{sub 1/3}O{sub 2}, Na{sub 0.90}Co{sub 1/3}Ir{sub 2/3}O{sub 2}, Na{sub 0.92}Ni{sub 1/3}Ir{sub 2/3}O{sub 2}, Na{sub 0.86}Cu{sub 1/3}Ir{sub 2/3}O{sub 2} and Na{sub 0.89}Zn{sub 1/3}Ir{sub 2/3}O{sub 2} are spin glasses. (CSD-numbers: Na{sub 0.62}Mn{sub 0.61}Ir{sub 0.39}O{sub 2}: 426657, Na{sub 0.80}Fe{sub 2/3}Ir{sub 1/3}O{sub 2}: 426659, Na{sub 0.90}Co{sub 1/3}Ir{sub 2/3}O{sub 2}: 426658, Na{sub 0.92}Ni{sub 1/3}Ir{sub 2/3}O{sub 2}: 426656, Na{sub 0.86}Cu{sub 1/3}Ir{sub 2/3}O{sub 2}: 426655, and Na{sub 2.8}ZnIr{sub 2}O{sub 6}: 426660.) - Graphical abstract: Diffraction patterns of Na{sub 0.92}Ni{sub 1/3}Ir{sub 2/3}O{sub 2}, Na{sub 0.86}Cu{sub 1/3}Ir{sub 2/3}O{sub 2} and Na{sub 0.89}Zn{sub 1/3}Ir{sub 2/3}O{sub 2}: neutron diffraction patterns in the main panel and synchrotron diffraction in the insets. The patterns show a small amount of ordering in the transition metal iridium layer. Display Omitted - Highlights: • We report six ternary sodium iridates with the α-NaFeO{sub 2} structure. • Compounds Na{sub 1−x}M{sub 1/3}Ir{sub 2/3}O{sub 2}, M=Co, Ni, Cu, Zn and Na{sub 1−x}M{sub 2/3}Ir{sub 1/3}O{sub 2}, M=Mn, Fe. • Rietveld refinement of powder neutron diffraction data. • All compounds are spin glasses. • NMR comparison to Na{sub 2}IrO{sub 3}.

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

Structural integrity--Searching the key factor to suppress the voltage fade of Li-rich layered cathode materials through 3D X-ray imaging and spectroscopy techniques

Li-rich layered materials are important cathode compounds used in commercial lithium ion batteries, which, however, suffers from some drawbacks including the so-called voltage fade upon electrochemical cycling. Here, our study employs novel transmission X-ray microscopy to investigate the electrochemical reaction induced morphological and chemical changes in the Li-rich Li 2 Ru 0.5 Mn 0.5 O 3 cathode particles at the meso to nano scale. We performed combined X-ray spectroscopy, diffraction and microscopy experiments to systematically study this cathode material's evolution upon cycling as well as to establish a comprehensive understanding of the structural origin of capacity fade through 2D and 3D fine length scale morphology and heterogeneity change of this material. This work suggests that atomic manipulation (e.g. doping, substitution etc.) or nano engineering (e.g. nano-sizing, heterogeneous structure) are important strategies to mitigate the internal strain and defects induced by extensive lithium insertion/extraction. It also shows that maintaining the structural integrity is the key in designing and synthesizing lithium-rich layered materials with better cycle stability.

25 ENERGY STORAGE↗
DOE OSTI2015

Temperature effects on the atomic structure and kinetics in single crystal electrochemistry

The influence of temperature on the atomic structure at the electrochemical interface has been studied using in-situ surface x-ray scattering (SXS) during the formation of metal monolayers on a Au(111) electrode. For the surface reconstruction of Au(111), higher temperatures increase the mobility of surface atoms in the unreconstructed phase which then determines the surface ordering during the formation of the reconstruction. For the underpotential deposition (UPD) systems, the surface diffusion of the depositing metal adatoms is significantly reduced at low temperatures which results in the frustration of ordered structures in the case of Cu UPD, occurring on a Br-modified surface, and in the formation of a disordered Ag monolayer during Ag UPD. The results indicate that temperature changes affect the mass transport and diffusion of metal adatoms on the electrode surface. This demonstrates the importance of including temperature as a variable in studying surface structure and reactions at the electrochemical interface.

Gründer, Yvonne↗