Electronic structure, local magnetism, and spin-orbit effects of Ir(IV)-, Ir(V)-, and Ir(VI)-based compounds
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Laguna-Marco, M. A.↗
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Results for “structures”
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Magnetic structure of NiS 2 - x Se x
NiS 2-2x Se x is revisited to determine the magnetic structure using neutron diffraction and magnetic representational analysis. Upon cooling, the insulating parent compound, NiS 2 , becomes antiferromagnetic with two successive magnetic transitions. The first transition (M1) occurs at T N similar to 39 K with Γ 1 Ψ 1 symmetry and a magnetic propagation vector of k = (000). The second transition (M2) occurs at T N similar to 30 K with k = (0.5,0.5,0.5) and a Γ 1 Ψ 2 symmetry with face-centered translations, giving rise to four possible magnetic domains. With doping, the system become smetallic. The transition to the M2 state is suppressed prior to x = 0.4 while the M1 state persists. The M1 magnetic structure gradually vanishes by x similar to 0.8 at a lower concentration than previously reported. The details of the magnetic structures are provided.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Fermi arc electronic structure and Chern numbers in the type-II Weyl semimetal candidate Mo x W 1 - x Te 2
It has recently been proposed that electronic band structures in crystals can give rise to a previously overlooked type of Weyl fermion, which violates Lorentz invariance and, consequently, is forbidden in particle physics. It was further predicted that Mo x W 1 - x Te 2 may realize such a type-II Weyl fermion. Here, we first show theoretically that it is crucial to access the band structure above the Fermi level ε F to show a Weyl semimetal in Mo x W 1 - x Te 2 . Then, we study Mo x W 1 - x Te 2 by pump-probe ARPES and we directly access the band structure > 0.2 eV above ε F in experiment. By comparing our results with ab initio calculations, we conclude that we directly observe the surface state containing the topological Fermi arc. We propose that a future study of Mo x W 1 - x Te 2 by pump-probe ARPES may directly pinpoint the Fermi arc. Our work sets the stage for the experimental discovery of the first type-II Weyl semimetal in Mo x W 1 - x Te 2 .
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Electronic band structure effects in the stopping of protons in copper [Electronic band structure non-linear effects in the stopping of protons in copper]
Here, we present an ab initio study of the electronic stopping power of protons in copper over a wide range of proton velocities v = 0.02–10a.u. where we take into account nonlinear effects. Time-dependent density functional theory coupled with molecular dynamics is used to study electronic excitations produced by energetic protons. A plane-wave pseudopotential scheme is employed to solve the time-dependent Kohn-Sham equations for a moving ion in a periodic crystal. The electronic excitations and the band structure determine the stopping power of the material and alter the interatomic forces for both channeling and off-channeling trajectories. Our off-channeling results are in quantitative agreement with experiments, and at low velocity they unveil a crossover region of superlinear velocity dependence (with a power of ~1.5) in the velocity range v = 0.07–0.3a.u., which we associate to the copper crystalline electronic band structure. The results are rationalized by simple band models connecting two separate regimes. We find that the limit of electronic stopping v → 0 is not as simple as phenomenological models suggest and it is plagued by band-structure effects.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Electronic structures of C u 2 O , C u 4 O 3 , and CuO: A joint experimental and theoretical study
We present a joint experimental and theoretical study for the electronic structures of copper oxides including Cu 2 O, CuO, and the metastable mixed-valence oxide Cu 4 O 3 . The optical band gap is determined by experimental optical absorption coefficient, and the electronic structure in valence and conduction bands is probed by photoemission and electron energy loss spectroscopies, respectively. Furthermore, we compare our experimental results with many-body GW calculations utilizing an additional on-site potential for d-orbital energies that facilitates tractable and predictive computations. The side-by-side comparison between the three oxides, including a band insulator (Cu2O) and two Mott/charge-transfer insulators (CuO, Cu 4 O 3 ) leads to a consistent picture for the optical and band-structure properties of the Cu oxides, strongly supporting indirect band gaps of about 1.2 and 0.8 eV in CuO and Cu 4 O 3 , respectively. This comparison also points towards surface oxidation and reduction effects that can complicate the interpretation of the photoemission spectra.
36 MATERIALS SCIENCE↗
Magnetic structure and excitation spectrum of the hyperhoneycomb Kitaev magnet β – Li 2 IrO 3
We present a theoretical study of the static and dynamical properties of the three-dimensional, hyperhoneycomb Kitaev magnet β–Li 2 IrO 3 . We argue that the observed incommensurate order can be understood in terms of a long-wavelength twisting of a nearby commensurate period-3 state, with the same key qualitatively features. The period-3 state shows very different structure when either the Kitaev interaction K or the off-diagonal exchange anisotropy Γ is dominant. A comparison of the associated static spin structure factors with reported scattering experiments in zero and finite fields gives strong evidence that β–Li 2 IrO 3 lies in the regime of dominant Kitaev coupling, and that the Heisenberg exchange J is much weaker than both K and Γ. Furthermore, our predictions for the magnon excitation spectra, the dynamical spin structure factors, and their polarization dependence provide additional distinctive fingerprints that can be checked experimentally.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Structure and disorder in ice VII on the approach to hydrogen-bond symmetrization
Abstract not provided
Guthrie, M.↗
Direct Observation of Quark-Hadron Duality in the Free Neutron {ital F}{sub 2} Structure Function
Using the recently published data from the BONuS(Barely Off-shell Nucleon Structure) experiment at Jefferson Lab, which utilized a spectator tagging technique to extract the inclusive electron-free neutron scattering cross section, we obtain the first direct observation of quark-hadron duality in the neutron F-2 structure function. The data are used to reconstruct the lowest few (N = 2, 4, and 6) moments of F-2 in the three prominent nucleon resonance regions, as well as the moments integrated over the entire resonance region. Comparison with moments computed from global parametrizations of parton distribution functions suggest that quark-hadron duality holds locally for the neutron in the second and third resonance regions down to Q(2) approximate to 1 GeV2, with violations possibly up to 20% observed in the first resonance region.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Structure of Ne 20 states in resonance O 16 + α elastic scattering
Background: The nuclear structure of the cluster bands in 20 Ne presents a challenge for different theoretical approaches. It is especially difficult to explain the broad 0 + , 2 + states at 9 MeV excitation energy. Simultaneously, it is important to obtain more reliable experimental data for these levels in order to quantitatively assess the theoretical framework. Purpose: To obtain new data on 20 Ne α- cluster structure. Method: Thick target inverse kinematics technique was used to study the 16 O+α resonance elastic scattering and the data were analyzed using an R matrix approach. The 20 Ne spectrum, the cluster and nucleon spectroscopic factors were calculated using cluster-nucleon configuration interaction model (CNCIM). Results: We determined the parameters of the broad resonances in 20 Ne: 0 + level at 8.77 ± 0.150 MeV with a width of 750 $^{+500}_{-220}$ keV; 2 + level at 8.75 ± 0.100 MeV with the width of 695 ± 120 keV; the width of 9.48 MeV level of 65 ± 20 keV and showed that 9.19 MeV, 2 + level (if exists) should have width ≤ 10 keV. The detailed comparison of the theoretical CNCIM predictions with the experimental data on cluster states was made. Conclusions: Our experimental results by the TTIK method generally confirm the adopted data on α-cluster levels in 20 Ne. The CNCIM gives a good description of the 20 Ne positive parity states up to an excitation energy of ~7 MeV, predicting reasonably well the excitation energy of the states and their cluster and single particle properties. At higher excitations, the qualitative disagreement with the experimentally observed structure is evident, especially for broad resonances.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Neural network approach for characterizing structural transformations by X-ray absorption fine structure
The knowledge of coordination environment around various atomic species in many functional materials provides a key for explaining their properties and working mechanisms. Many structural motifs and their transformations are difficult to detect and quantify in the process of work (operando conditions), due to their local nature, small changes, low dimensionality of the material, and/or extreme conditions. Here we use artificial neural network approach to extract the information on the local structure and its in-situ changes directly from the X-ray absorption fine structure spectra. We illustrate this capability by extracting the radial distribution function (RDF) of atoms in ferritic and austenitic phases of bulk iron across the temperature-induced transition. Integration of RDFs allows us to quantify the changes in the iron coordination and material density, and to observe the transition from body-centered to face-centered cubic arrangement of iron atoms. Furthermore, this method is attractive for a broad range of materials and experimental conditions
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Site-Specific Structure at Multiple Length Scales in Kagome Quantum Spin Liquid Candidates
Realizing a quantum spin liquid (QSL) ground state in a real material is a leading issue in condensed matter physics research. In this pursuit, it is crucial to fully characterize the structure and influence of defects, as these can significantly affect the fragile QSL physics. In this work, we perform a variety of cutting-edge synchrotron x-ray scattering and spectroscopy techniques, and we advance new methodologies for site-specific diffraction and L-edge Zn absorption spectroscopy. The experimental results along with our first-principles calculations address outstanding questions about the local and long-range structures of the two leading kagome QSL candidates, Zn-substituted barlowite Cu 3 Zn x Cu 1-x (OH) 6 FBr and herbertsmithite Cu 3 Zn(OH) 6 Cl 2 . On all length scales probed, there is no evidence that Zn substitutes onto the kagome layers, thereby preserving the QSL physics of the kagome lattice. Our calculations show that antisite disorder is not energetically favorable and is even less favorable in Zn-barlowite compared to herbertsmithite. Site-specific x-ray diffraction measurements of Zn-barlowite reveal that Cu 2+ and Zn 2+ selectively occupy distinct interlayer sites, in contrast to herbertsmithite. Using the first measured Zn L-edge inelastic x-ray absorption spectra combined with calculations, we discover a systematic correlation between the loss of inversion symmetry from pseudo-octahedral (herbertsmithite) to trigonal prismatic coordination (Zn-barlowite) with the emergence of a new peak. Overall, our measurements suggest that Zn-barlowite has structural advantages over herbertsmithite that make its magnetic properties closer to an ideal QSL candidate: its kagome layers are highly resistant to nonmagnetic defects while the interlayers can accommodate a higher amount of Zn substitution.
36 MATERIALS SCIENCE↗
Structural evidence for the partially oxidized dipyrromethene and dipyrromethanone forms of the cofactor of porphobilinogen deaminase: structures of the Bacillus megaterium enzyme at near-atomic resolution
The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses a key early step in the biosynthesis of tetrapyrroles in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. Two near-atomic resolution structures of PBGD from B. megaterium are reported that demonstrate the time-dependent accumulation of partially oxidized forms of the cofactor, including one that possesses a tetrahedral C atom in the terminal pyrrole ring. The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses an early step of the tetrapyrrole-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor, which is covalently linked by a thioether bridge to an invariant cysteine residue (Cys241 in the Bacillus megaterium enzyme). The cofactor is extended during the reaction by the sequential addition of the four substrate molecules, which are released as a linear tetrapyrrole product. Expression in Escherichia coli of a His-tagged form of B. megaterium PBGD has permitted the X-ray analysis of the enzyme from this species at high resolution, showing that the cofactor becomes progressively oxidized to the dipyrromethene and dipyrromethanone forms. In previously solved PBGD structures, the oxidized cofactor is in the dipyromethenone form, in which both pyrrole rings are approximately coplanar. In contrast, the oxidized cofactor in the B. megaterium enzyme appears to be in the dipyrromethanone form, in which the C atom at the bridging α-position of the outer pyrrole ring is very clearly in a tetrahedral configuration. It is suggested that the pink colour of the freshly purified protein is owing to the presence of the dipyrromethene form of the cofactor which, in the structure reported here, adopts the same conformation as the fully reduced dipyrromethane form.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
The structure of allophycocyanin B from Synechocystis PCC 6803 reveals the structural basis for the extreme redshift of the terminal emitter in phycobilisomes
Allophycocyanin B (AP-B) is one of the two terminal emitters in phycobilisomes, the unique light-harvesting complexes of cyanobacteria and red algae. Its low excitation-energy level and the correspondingly redshifted absorption and fluorescence emission play an important role in funnelling excitation energy from the hundreds of chromophores of the extramembraneous phycobilisome to the reaction centres within the photosynthetic membrane. In the absence of crystal structures of these low-abundance terminal emitters, the molecular basis for the extreme redshift and directional energy transfer is largely unknown. Here, the crystal structure of trimeric AP-B [(ApcD/ApcB) 3 ] from Synechocystis sp. PCC 6803 at 1.75 Å resolution is reported. In the crystal lattice, eight trimers of AP-B form a porous, spherical, 48-subunit assembly of 193 Å in diameter with an internal cavity of 1.1 × 10 6 Å 3 . While the overall structure of trimeric AP-B is similar to those reported for many other phycobiliprotein trimers, the chromophore pocket of the α-subunit, ApcD, has more bulky residues that tightly pack the phycocyanobilin (PCB). Ring D of the chromophores is further stabilized by close interactions with ApcB from the adjacent monomer. The combined contributions from both subunits render the conjugated rings B, C and D of the PCB in ApcD almost perfectly coplanar. Together with mutagenesis data, it is proposed that the enhanced planarity effectively extends the conjugation system of PCB and leads to the redshifted absorption (λ max = 669 nm) and fluorescence emission (679 nm) of the ApcD chromophore in AP-B, thereby enabling highly efficient energy transfer from the phycobilisome core to the reaction centres.
Peng, Pan-Pan↗
Structural basis for light control of cell development revealed by crystal structures of a myxobacterial phytochrome
Phytochromes are red-light photoreceptors that were first characterized in plants, with homologs in photosynthetic and non-photosynthetic bacteria known as bacteriophytochromes (BphPs). Upon absorption of light, BphPs interconvert between two states denoted Pr and Pfr with distinct absorption spectra in the red and far-red. They have recently been engineered as enzymatic photoswitches for fluorescent-marker applications in non-invasive tissue imaging of mammals. This article presents cryo- and room-temperature crystal structures of the unusual phytochrome from the non-photosynthetic myxobacterium Stigmatella aurantiaca (SaBphP1) and reveals its role in the fruiting-body formation of this photomorphogenic bacterium. SaBphP1 lacks a conserved histidine (His) in the chromophore-binding domain that stabilizes the Pr state in the classical BphPs. Instead it contains a threonine (Thr), a feature that is restricted to several myxobacterial phytochromes and is not evolutionarily understood. SaBphP1 structures of the chromophore binding domain (CBD) and the complete photosensory core module (PCM) in wild-type and Thr-to-His mutant forms reveal details of the molecular mechanism of the Pr/Pfr transition associated with the physiological response of this myxobacterium to red light. Specifically, key structural differences in the CBD and PCM between the wild-type and the Thr-to-His mutant involve essential chromophore contacts with proximal amino acids, and point to how the photosignal is transduced through the rest of the protein, impacting the essential enzymatic activity in the photomorphogenic response of this myxobacterium.
Woitowich, Nicole C.↗
Structure of Plasmodium falciparum orotate phosphoribosyltransferase with autologous inhibitory protein-protein interactions
Abstract not provided
Kumar, Shiva↗
High-resolution crystal structures of the D1 and D2 domains of protein tyrosine phosphatase epsilon for structure-based drug design
Here, new crystal structures are presented of the isolated membrane-proximal D1 and distal D2 domains of protein tyrosine phosphatase epsilon (PTPε), a protein tyrosine phosphatase that has been shown to play a positive role in the survival of human breast cancer cells. A triple mutant of the PTPε D2 domain (A455N/V457Y/E597D) was also constructed to reconstitute the residues of the PTPε D1 catalytic domain that are important for phosphatase activity, resulting in only a slight increase in the phosphatase activity compared with the native D2 protein. The structures reported here are of sufficient resolution for structure-based drug design, and a microarray-based assay for high-throughput screening to identify small-molecule inhibitors of the PTPε D1 domain is also described.
Lountos, George T.↗