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At least 1,387 records · Page 77
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DOE OSTI2026

Structural modulation, physical properties, and electronic band structure of the kagome metal UCr 6 ⁢Ge 6

The chemical flexibility of the 𝑅⁢𝑀 6 ⁢𝑋 6 stoichiometry, where an 𝑓-block element is intercalated in the CoSn structure type, allows for the tuning of flatbands associated with kagome lattices to the Fermi level and for emergent phenomena due to interactions between the 𝑓- and 𝑑-electron lattices. Yet, 5⁢𝑓 members of the “166” compounds are underrepresented compared with 4⁢𝑓 members. In this work, we report single-crystal growth of UCr 6 ⁢Ge 6 , which crystallizes in a monoclinically distorted Y 0.5⁢ Co 3 ⁢Ge 3 -type structure. The real-space character of the modulation, which is unique within the 𝑅⁢𝑀 6 ⁢𝑋 6 family, is approximated by a 3×1×2 supercell of the average monoclinic cell. The compound has kagome-lattice flatbands near the Fermi level and a moderately enhanced electronic heat capacity, as evidenced by its low-temperature Sommerfeld coefficient (𝛾=86.5 mJ mol −1 K −2 ) paired with band structure calculations. The small, isotropic magnetization and featureless resistivity of UCr 6 ⁢Ge 6 suggest itinerant uranium 5⁢𝑓 electrons and Pauli paramagnetism. Angle-resolved photoemission spectroscopy results provide evidence for uranium 5⁢𝑓 weight at the Fermi level and for a flatband near the Fermi level associated with the chromium 3⁢𝑑 kagome lattice. The isotropic magnetic behavior of the uranium 5⁢𝑓 electrons starkly contrasts with localized behavior in other uranium 166 compounds, highlighting the high tunability of the magnetic ground state across the material family.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Evolution of the electronic structure in Ta 2 NiSe 5 across the structural transition revealed by resonant inelastic x-ray scattering

We utilized high-energy-resolution resonant inelastic X-ray scattering (RIXS) at both the Ta and Ni L 3 -edges to map out element-specific particle-hole excitations in Ta 2 NiSe 5 across the phase transition. Our results reveal a momentum dependent gap-like feature in the low energy spectrum, which agrees well with the band gap in element-specific joint density of states calculations based on ab initio estimates of the electronic structure in both the low temperature monoclinic and the high temperature orthorhombic structure. Below T c , the RIXS energy-momentum map shows a minimal gap at the Brillouin zone center (~0.16 eV), conforming that Ta 2 NiSe 5 possesses a direct band gap in its low temperature ground state. However, inside the gap, no signature of anticipated collective modes with an energy scale comparable to the gap size can be identified. Upon increasing the temperature to above T c , whereas the gap at the zone center closes, the RIXS map at finite momenta still possesses the gross features of the low temperature map, suggesting a substantial mixing between the Ta and Ni orbits in the conduction and valence bands, which does not change substantially across the phase transition. Our experimental observations and comparison to the theoretical calculations lend further support that the phase transition and the corresponding gap opening in Ta 2 NiSe 5 is largely structural by nature with possible minor contribution from the putative exciton condensate.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2011

Electronic structure and physical properties of the spinel-type phase of BeP{sub 2}N{sub 4} from all-electron density functional calculations

Using density-functional-theory-based ab initio methods, the electronic structure and physical properties of the newly synthesized nitride BeP{sub 2}N{sub 4} with a phenakite-type structure and the predicted high-pressure spinel phase of BeP{sub 2}N{sub 4} are studied in detail. It is shown that both polymorphs are wide band-gap semiconductors with relatively small electron effective masses at the conduction-band minima. The spinel-type phase is more covalently bonded due to the increased number of P-N bonds for P at the octahedral sites. Calculations of mechanical properties indicate that the spinel-type polymorph is a promising superhard material with notably large bulk, shear, and Young's moduli. Also calculated are the Be K, P K, P L{sub 3}, and N K edges of the electron energy-loss near-edge structure for both phases. They show marked differences because of the different local environments of the atoms in the two crystalline polymorphs. These differences will be very useful for the experimental identification of the products of high-pressure syntheses targeting the predicted spinel-type phase of BeP{sub 2}N{sub 4}.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Structural and dynamical properties of liquid Cu[subscript 80]Si[subscript 20] alloy studied experimentally and by ab initio molecular dynamics simulations

The local structures and dynamical properties of the liquid Cu{sub 80}Si{sub 20} alloy have been studied by x-ray diffraction and ab initio molecular dynamics (MD) simulations. The pair-correlation functions and the structure factors derived from the three-dimensional coordinates of the MD configurations agree well with the experimental results. The local structure of the liquids is analyzed using Honeycutt-Andersen (HA) indices, Voronoi tessellation (VT), and an atomic cluster-alignment method. The HA indices analysis shows that the pentagonal bipyramid, a fragment of an icosahedron (ICO), plays a dominant role in the short-range order (SRO) of the Cu{sub 80}Si{sub 20} liquid. The HA indices corresponding to the pentagonal bipyramid increase dramatically with decreasing temperature. VT analysis indicates that, while the liquid does exhibit a strong icosahedral SRO, fcc-like SRO is also measurable. The results from VT analysis are further confirmed using the recently developed atomic cluster-alignment method. Finally, self-diffusion constants, as a function of temperature for both Cu and Si species, are calculated.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2012

Structure of human dual-specificity phosphatase 27 at 2.38 Å resolution

There are over 100 genes in the human genome that encode protein tyrosine phosphatases (PTPs) and approximately 60 of these are classified as dual-specificity phosphatases (DUSPs). Although many dual-specificity phosphatases are still not well characterized, novel functions have been discovered for some of them that have led to new insights into a variety of biological processes and the molecular basis for certain diseases. Indeed, as the functions of DUSPs continue to be elucidated, a growing number of them are emerging as potential therapeutic targets for diseases such as cancer, diabetes and inflammatory disorders. Here, the overexpression, purification and structure determination of DUSP27 at 2.38 {angstrom} resolution are presented.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Three-dimensional structure of a schistosome serpin revealing an unusual configuration of the helical subdomain

The crystal structure of ShSPI, a serpin from the blood fluke S. haematobium, reveals some peculiar features of the helical subdomain which have not been observed previously in the serpin superfamily. Parasitic organisms are constantly challenged by the defence mechanisms of their respective hosts, which often depend on serine protease activities. Consequently, protease inhibitors such as those belonging to the serpin superfamily have emerged as protective elements that support the survival of the parasites. This report describes the crystal structure of ShSPI, a serpin from the trematode Schistosoma haematobium. The protein is exposed on the surface of invading cercaria as well as of adult worms, suggesting its involvement in the parasite–host interaction. While generally conforming to the well established serpin fold, the structure reveals several distinctive features, mostly concerning the helical subdomain of the protein. It is proposed that these peculiarities are related to the unique biological properties of a small serpin subfamily which is conserved among pathogenic schistosomes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2013

Context-dependent protein folding of a virulence peptide in the bacterial and host environments: structure of an SycH–YopH chaperone–effector complex

The structure of a SycH–YopH chaperone–effector complex from Yersinia reveals the bacterial state of a protein that adopts different folds in the host and pathogen environments. Yersinia pestis injects numerous bacterial proteins into host cells through an organic nanomachine called the type 3 secretion system. One such substrate is the tyrosine phosphatase YopH, which requires an interaction with a cognate chaperone in order to be effectively injected. Here, the first crystal structure of a SycH–YopH complex is reported, determined to 1.9 Å resolution. The structure reveals the presence of (i) a nonglobular polypeptide in YopH, (ii) a so-called β-motif in YopH and (iii) a conserved hydrophobic patch in SycH that recognizes the β-motif. Biochemical studies establish that the β-motif is critical to the stability of this complex. Finally, since previous work has shown that the N-terminal portion of YopH adopts a globular fold that is functional in the host cell, aspects of how this polypeptide adopts radically different folds in the host and in the bacterial environments are analysed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

The structure of cytomegalovirus immune modulator UL141 highlights structural Ig-fold versatility for receptor binding

The crystal structure of Human cytomegalovirus immune modulator UL141 was solved at 3.25 Å resolution. Here, a detailed analysis of its intimate dimerization interface and the biophysical properties of its receptor (TRAIL-R2 and CD155) binding interactions are presented. Natural killer (NK) cells are critical components of the innate immune system as they rapidly detect and destroy infected cells. To avoid immune recognition and to allow long-term persistence in the host, Human cytomegalovirus (HCMV) has evolved a number of genes to evade or inhibit immune effector pathways. In particular, UL141 can inhibit cell-surface expression of both the NK cell-activating ligand CD155 as well as the TRAIL death receptors (TRAIL-R1 and TRAIL-R2). The crystal structure of unliganded HCMV UL141 refined to 3.25 Å resolution allowed analysis of its head-to-tail dimerization interface. A ‘dimerization-deficient’ mutant of UL141 (ddUL141) was further designed, which retained the ability to bind to TRAIL-R2 or CD155 while losing the ability to cross-link two receptor monomers. Structural comparison of unliganded UL141 with UL141 bound to TRAIL-R2 further identified a mobile loop that makes intimate contacts with TRAIL-R2 upon receptor engagement. Superposition of the Ig-like domain of UL141 on the CD155 ligand T-cell immunoreceptor with Ig and ITIM domains (TIGIT) revealed that UL141 can potentially engage CD155 similar to TIGIT by using the C′C′′ and GF loops. Further mutations in the TIGIT binding site of CD155 (Q63R and F128R) abrogated UL141 binding, suggesting that the Ig-like domain of UL141 is a viral mimic of TIGIT, as it targets the same binding site on CD155 using similar ‘lock-and-key’ interactions. Sequence alignment of the UL141 gene and its orthologues also showed conservation in this highly hydrophobic (L/A)X{sub 6}G ‘lock’ motif for CD155 binding as well as conservation of the TRAIL-R2 binding patches, suggesting that these host–receptor interactions are evolutionary conserved.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2010

Structure of the endonuclease IV homologue from Thermotoga maritima in the presence of active-site divalent metal ions

The most frequent lesion in DNA is at apurinic/apyrimidinic (AP) sites resulting from DNA-base losses. These AP-site lesions can stall DNA replication and lead to genome instability if left unrepaired. The AP endonucleases are an important class of enzymes that are involved in the repair of AP-site intermediates during damage-general DNA base-excision repair pathways. These enzymes hydrolytically cleave the 5{prime}-phosphodiester bond at an AP site to generate a free 3{prime}-hydroxyl group and a 5{prime}-terminal sugar phosphate using their AP nuclease activity. Specifically, Thermotoga maritima endonuclease IV is a member of the second conserved AP endonuclease family that includes Escherichia coli endonuclease IV, which is the archetype of the AP endonuclease superfamily. In order to more fully characterize the AP endonuclease family of enzymes, two X-ray crystal structures of the T. maritima endonuclease IV homologue were determined in the presence of divalent metal ions bound in the active-site region. These structures of the T. maritima endonuclease IV homologue further revealed the use of the TIM-barrel fold and the trinuclear metal binding site as important highly conserved structural elements that are involved in DNA-binding and AP-site repair processes in the AP endonuclease superfamily.

36 MATERIALS SCIENCE↗