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The first 3D malonate bridged copper [Cu(O{sub 2}C-CH{sub 2}-CO{sub 2}H){sub 2}{center_dot}2H{sub 2}O]: Structure, properties and electronic structure

A new inorganic-organic compound [Cu(O{sub 2}C-CH{sub 2}-CO{sub 2}H){sub 2}{center_dot}2H{sub 2}O] ([Cumal]) was hydrothermally synthesized and characterized by IR spectroscopy, thermal analysis and single crystal X-ray diffraction. [Cumal] is the first three-dimensional compound existing in the system Cu(II)-malonic acid-H{sub 2}O. Its framework is built up through carboxyl bridged copper where CuO{sub 6} octahedra are elongated with an almost D{sub 4h} symmetry (4+2) due to the Jahn-Teller effect. The magnetic properties were studied by measuring its magnetic susceptibility in the temperature range of 2-300 K indicating the existence of weak ferromagnetic interactions. The electronic structure of [Cumal] was calculated within the density functional theory (DFT) framework. Structural features are well reproduced using DFT structural optimizations and the optical spectra, calculated within the dielectric formalism, explain very well the light blue colour of the compound. It is shown that a GGA+U approach with a U{sub eff} value of about 6 eV is necessary for a better correlation with the experiment. - Graphical abstract: [Cu(O{sub 2}C-CH{sub 2}-CO{sub 2}H){sub 2}{center_dot}2H{sub 2}O]: the first 3D hybrid organic-inorganic compound built up carboxyl groups. The network presents a diamond-like structure achieved via carboxyl. Highlights: Black-Right-Pointing-Pointer A new organic-inorganic material with an unprecedented topology is synthesized. Black-Right-Pointing-Pointer Crystallographic structure is determined using single crystal X-ray diffraction. Black-Right-Pointing-Pointer Electronic structure is obtained from DFT, GGA+U calculation. Black-Right-Pointing-Pointer Framework can be described as formed from CuC{sub 4} tetrahedron sharing four corners. Black-Right-Pointing-Pointer This structure can be classified as an extended diamond structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mild hydrothermal synthesis, crystal structure, photoluminescence properties and emission quantum yield of a new zirconium germanate with garnet-type structure

The mild hydrothermal synthesis, crystal structure, photoluminescence properties and emission quantum yield of a new sodium zirconium germanate are reported. This material and the method for its preparation represent for the first time a germanium garnet-type material synthesized at autogenous pressure and temperature at 230 Degree-Sign C. The crystal structure was determined by starting from the crystallographic parameters of a common garnet structure and it represents not only a new chemical combination of atoms but also combination of oxidation states in garnet structure. The framework consists of interconnected corner sharing GeO{sub 4} tetrahedra and ZrO{sub 6} octahedra which form small cavities that accommodate charge compensation Na{sup +} cations. In the course of synthesis the structure can be functionalized by in situ doping with different percentage of Eu{sup 3+} ions. This structural flexibility is used to explore the photoluminescent behavior of the active centers embedded in garnet-type host. The materials display the Eu{sup 3+5}D{sub 0}{yields}{sup 7}F{sub 0-4} transitions under excitation via intra-{sup 4}f{sub 6} excitation levels and through the O{sup 2-}{yields}Eu{sup 3+} ligand-to-metal charge transfer. A maximum {sup 5}D{sub 0} quantum efficiency and emission quantum yield values (ca. 0.28 and 0.04{+-}0.01, respectively) were found for the low Eu{sup 3+}-containing sample, suggesting the presence of concentration quenching effects at higher Eu{sup 3+}-content (5%). - Graphical abstract: Na{sub 3}Zr{sub 1.8}Ge{sub 3}O{sub 10}(OH){sub 2} prepared at mild hydrothermal conditions. Highlights: Black-Right-Pointing-Pointer New zirconogermanate with garnet-type structure. Black-Right-Pointing-Pointer Hydrothermal synthesis. Black-Right-Pointing-Pointer Crystal structure. Black-Right-Pointing-Pointer Photoluminescent properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

New tetragonal derivatives of cubic NaZn{sub 13}-type structure: RNi{sub 6}Si{sub 6} compounds, crystal structure and magnetic ordering (R=Y, La, Ce, Sm, Gd–Yb)

Novel RNi{sub 6}Si{sub 6} compounds adopt the new CeNi{sub 6}Si{sub 6}-type structure for R=La–Ce (tP52, space group P4/nbm N 125-1) and new YNi{sub 6}Si{sub 6}-type structure for R=Y, Sm, Gd–Yb (tP52, space group P4{sup ¯}b2N 117) that are tetragonal derivative of NaZn{sub 13}-type structure, like LaCo{sub 9}Si{sub 4}-type. The CeNi{sub 6}Si{sub 6}, GdNi{sub 6}Si{sub 6}, TbNi{sub 6}Si{sub 6}, DyNi{sub 6}Si{sub 6} and HoNi{sub 6}Si{sub 6} compounds are Curie–Weiss paramagnets down to ∼30 K, and do not order magnetically down to 5 K. However, the inverse paramagnetic susceptibility of LaNi{sub 6}Si{sub 6} does not follow Curie–Weiss law. The DyNi{sub 6}Si{sub 6} shows ferromagnetic-like saturation behaviour at 5 K in applied fields of 50 kOe, giving rise to a magnetic moment value of 6.5 μ{sub B}/f.u. in 50 kOe. The powder neutron diffraction study in zero applied filed indicates square modulated the c-collinear antiferromagnetic ordering of TbNi{sub 6}Si{sub 6} with K=[±1/4, ±1/4, 0] wave vector below ∼10 K. - Graphical abstract: Novel (La, Ce)Ni{sub 6}Si{sub 6} compounds adopt the new CeNi{sub 6}Si{sub 6}-type structure and (Y, Sm, Gd–Yb) adopt the new YNi{sub 6}Si{sub 6}-type structure that are tetragonal derivative of NaZn{sub 13}-type structure, like LaCo{sub 9}Si{sub 4}-type. The CeNi{sub 6}Si{sub 6}, GdNi{sub 6}Si{sub 6}, TbNi{sub 6}Si{sub 6}, DyNi{sub 6}Si{sub 6} and HoNi{sub 6}Si{sub 6} compounds are Curie–Weiss paramagnets down to ∼30 K, and do not order magnetically down to 4.2 K. The powder neutron diffraction study in zero applied filed indicates square modulated the c-collinear antiferromagnetic ordering of TbNi{sub 6}Si{sub 6} with K=[±1/4, ±1/4, 0] wave vector below ∼10 K. Display Omitted - Highlights: • The new (La, Ce)Ni{sub 6}Si{sub 6} compounds adopt the new CeNi{sub 6}Si{sub 6}-type structure. • The new (Y, Sm, Gd–Yb)Ni{sub 6}Si{sub 6} compounds adopt the new YNi{sub 6}Si{sub 6}-type structure. • TbNi{sub 6}Si{sub 6} has square modulated c-collinear antiferromagnetic ordering below ∼10 K.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

GeP and (Ge{sub 1−x}Sn{sub x})(P{sub 1−y}Ge{sub y}) (x≈0.12, y≈0.05): Synthesis, structure, and properties of two-dimensional layered tetrel phosphides

GeP and Sn-doped GeP were synthesized from elements in bismuth and tin flux, respectively. The layered crystal structures of these compounds were characterized by single crystal X-ray diffraction. Both phosphides crystallize in a GaTe structure type in the monoclinic space group C2/m (No. 12) with GeP: a=15.1948(7) Å, b=3.6337(2) Å, c=9.1941(4) Å, β=101.239(2)°; Ge{sub 0.93(3)}P{sub 0.95(1)}Sn{sub 0.12(3)}: a=15.284(9) Å, b=3.622(2) Å, c=9.207(5) Å, β=101.79(1)°. The crystal structure of GeP consists of 2-dimensional GeP layers held together by weak electron lone pair interactions between the phosphorus atoms that confine the layer. Each layer is built of Ge–Ge dumbbells surrounded by a distorted antiprism of phosphorus atoms. Sn-doped GeP has a similar structural motif, but with a significant degree of disorder emphasized by the splitting of all atomic positions. Resistivity measurements together with quantum-chemical calculations reveal semiconducting behavior for the investigated phosphides. - Graphical abstract: Layered phosphides GeP and Sn-doped GeP were synthesized from elements in bismuth and tin flux, respectively. The crystal structure of GeP consists of 2-dimensional GeP layers held together by weak electron lone pair interactions between the phosphorus atoms that confine the layer. Sn-doped GeP has a similar structural motif with a significant degree of disorder emphasized by the splitting of all atomic positions. Resistivity measurements together with quantum-chemical calculations reveal semiconducting behavior for the investigated phosphides. - Highlights: • GeP crystallizes in a layered crystal structure. • Doping of Sn into GeP causes large structural distortions. • GeP is narrow bandgap semiconductor. • Sn-doped GeP exhibits an order of magnitude higher resistivity due to disorder.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Structure Determination of Mycobacterium tuberculosis Serine Protease Hip1 (Rv2224c)

The Mycobacterium tuberculosis (Mtb) serine protease Hip1 (hydrolase important for pathogenesis; Rv2224c) promotes tuberculosis (TB) pathogenesis by impairing host immune responses through proteolysis of a protein substrate, Mtb GroEL2. The cell surface localization of Hip1 and its immunomodulatory functions make Hip1 a good drug target for new adjunctive immune therapies for TB. Here, we report the crystal structure of Hip1 to a resolution of 2.6 Å and the kinetic studies of the enzyme against model substrates and the protein GroEL2. The structure shows a two-domain protein, one of which contains the catalytic residues that are the signature of a serine protease. Surprisingly, a threonine is located within the active site close enough to hydrogen bond with the catalytic residues Asp463 and His490. Mutation of this residue, Thr466, to alanine established its importance for function. Our studies provide insights into the structure of a member of a novel family of proteases. Knowledge of the Hip1 structure will aid in designing inhibitors that could block Hip1 activity

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Crystal Structures of Xanthomonas campestris OleA Reveal Features That Promote Head-to-Head Condensation of Two Long-Chain Fatty Acids

OleA is a thiolase superfamily enzyme that has been shown to catalyze the condensation of two long-chain fatty acyl-coenzyme A (CoA) substrates. The enzyme is part of a larger gene cluster responsible for generating long-chain olefin products, a potential biofuel precursor. In thiolase superfamily enzymes, catalysis is achieved via a ping-pong mechanism. The first substrate forms a covalent intermediate with an active site cysteine that is followed by reaction with the second substrate. For OleA, this conjugation proceeds by a nondecarboxylative Claisen condensation. The OleA from Xanthomonas campestris has been crystallized and its structure determined, along with inhibitor-bound and xenon-derivatized structures, to improve our understanding of substrate positioning in the context of enzyme turnover. OleA is the first characterized thiolase superfamily member that has two long-chain alkyl substrates that need to be bound simultaneously and therefore uniquely requires an additional alkyl binding channel. The location of the fatty acid biosynthesis inhibitor, cerulenin, that possesses an alkyl chain length in the range of known OleA substrates, in conjunction with a single xenon binding site, leads to the putative assignment of this novel alkyl binding channel. Structural overlays between the OleA homologues, 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) synthase and the fatty acid biosynthesis enzyme FabH, allow assignment of the two remaining channels: one for the thioester-containing pantetheinate arm and the second for the alkyl group of one substrate. A short {beta}-hairpin region is ordered in only one of the crystal forms, and that may suggest open and closed states relevant for substrate binding. Cys143 is the conserved catalytic cysteine within the superfamily, and the site of alkylation by cerulenin. The alkylated structure suggests that a glutamic acid residue (Glu117{beta}) likely promotes Claisen condensation by acting as the catalytic base. Unexpectedly, Glu117{beta} comes from the other monomer of the physiological dimer.

59 BASIC BIOLOGICAL SCIENCES↗

Atomic Structure of Pt 3 Ni Nanoframe Electrocatalysts by in Situ X-ray Absorption Spectroscopy

Understanding the atomic structure of a catalyst is crucial to exposing the source of its performance characteristics. It is highly unlikely that a catalyst remains the same under reaction conditions when compared to as-synthesized. Hence, the ideal experiment to study the catalyst structure should be performed in situ. Here, we use X-ray absorption spectroscopy (XAS) as an in situ technique to study Pt3Ni nanoframe particles which have been proven to be an excellent electro catalyst for the oxygen reduction reaction (ORR). The surface characteristics of the nanoframes were probed through electrochemical hydrogen underpotential deposition and carbon monoxide electrooxidation, which showed that nanoframe surfaces with different structure exhibit varying levels of binding strength to adsorbate molecules. It is well-known that Pt-skin formation on Pt-Ni catalysts will enhance ORR activity by weakening the binding energy between the surface and adsorbates. Ex situ and in situ XAS results reveal that nanoframes which bind adsorbates more strongly have a rougher Pt surface caused by insufficient segregation of Pt to the surface and consequent Ni dissolution. In contrast, nanoframes which exhibit extremely high ORR activity simultaneously demonstrate more significant segregation of Pt over Ni-rich subsurface layers, allowing better formation of the critical Pt-skin. This work demonstrates that the high ORR activity of the Pt3Ni hollow nanoframes depends on successful formation of the Pt-skin surface structure.

Becknell, Nigel↗

Structure, Morphology, and Assembly Behavior of Kafirin

Prolamins from grains have attracted intensive attention in recent years due to their potential in satisfying the demand for environmentally friendly (biodegradable), abundantly available (sustainable), and cost-effective biomaterials. However, for kafirin, the prolamin from sorghum, its composition, structure, morphology, and self-assembly behaviors have not been fully characterized. In this paper, kafirin was extracted from the whole sorghum grain and found to contain 68, 14, 6, and 12% of α-, β-, and γ-fractions and cross-linked kafirin, respectively. Freeze-dried kafirin contained ~49% α-helix in the solid state. When dissolved in 65% (v/v) isopropanol, 60% (v/v) tert-butanol, and 85% (v/v) ethanol aqueous solvents, the relative α-helix content in kafirin increased with the decrease of solvent polarity. Structural analysis using small-angle X-ray scattering (SAXS) indicated that kafirin (2 mg/mL) took stretched and extended conformations with dimensions of 118 × 15 × 15 and 100 × 11 × 11 Å in 60% tert-butanol and 65% isopropanol, respectively. More elongated conformation of individual kafirin with high-order assembly was observed in 85% ethanol. Protein aggregation occurred as protein concentration increased in its good solvent. The morphology of kafirin assemblies captured by atomic force microscopy (AFM) revealed that kafirin protein took uniform particle morphology at low concentration, and disk-like or rod-like structures resulting from solvent evaporation induced particle interactions emerged at high concentrations. These results suggest that both protein concentration and solvent polarity can effectively regulate kafirin assemblies from thick rod-like to slim rod-like structures, a convenient way to tune the fibrillation of prolamin-based biomaterials.

60 APPLIED LIFE SCIENCES↗

Structure and dynamics of cadmium telluride studied by x-ray and inelastic neutron scattering

We present a combined study of density functional theory, x-ray diffraction, and inelastic neutron scattering examining the temperature dependent structure and lattice dynamics of commercially available cadmium telluride. A subtle change in the structure is evinced near 80 K, which manifests also in the measured phonon density of states. There is no change to the long-range ordered structure. The implications of the change in relation to structural defects are discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Local structure and polarization resistance of Ce doped SrMnO{sub 3} using extended x-ray fine structure analysis

Changes to the local structure of Sr and Mn atoms in Sr{sub 1−x}Ce{sub x}MnO{sub 3} (SCM) according to increasing Ce content and the effect of the structural change on the polarization resistance of SCM were investigated. The reduction of manganese was confirmed by the absorption edge shift of the Mn K-edge toward lower energies. The noise of oscillation in extended X-ray absorption fine structure k{sup 3}χ data at Mn K-edge reveals the distortion of the local structure of Mn atoms, and the peak that indicates the bonding length of Mn-O, Sr/Ce, and -Mn decreased with the addition of Ce content in Fourier transformations of the Mn K-edge. The distortion of the local structure at Mn atoms was affected by the reduced manganese ions having larger ionic radii than Mn{sup 4+}. Meanwhile, few distortions of local atomic structures of Sr atoms occurred, and the average nearest neighboring distances of Sr-O and Sr-Mn are ∼2.13 Å and ∼2.95 Å, respectively. The average bonding lengths of the Ce-O and Ce-Mn increased because the ionic radius of substituted Ce ion with 12 coordination number is smaller than that of Sr ion, which leads the reduction of Mn ions and the distortion of local structure at the substituted A-site. Therefore, we reasoned that the distortion of the local atomic structure at Mn atoms in MnO{sub 6} and Ce atoms in A-site is one of the causes for interrupting oxygen ion transfers as a geometric factor, which results in an increase in the polarization resistance of SCM within the Ce composition range from 10 mol. % to 30 mol. %.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Structural and electrical properties of In-implanted Ge

We report on the effects of dopant concentration on the structural and electrical properties of In-implanted Ge. For In concentrations of ≤ 0.2 at. %, extended x-ray absorption fine structure and x-ray absorption near-edge structure measurements demonstrate that all In atoms occupy a substitutional lattice site while metallic In precipitates are apparent in transmission electron micrographs for In concentrations ≥0.6 at. %. Evidence of the formation of In-vacancy complexes deduced from extended x-ray absorption fine structure measurements is complimented by density functional theory simulations. Hall effect measurements of the conductivity, carrier density, and carrier mobility are then correlated with the substitutional In fraction.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Ab initio electronic structure of quasi-two-dimensional materials: A “native” Gaussian–plane wave approach

Ab initio electronic structure calculations of two-dimensional layered structures are typically performed using codes that were developed for three-dimensional structures, which are periodic in all three directions. The introduction of a periodicity in the third direction (perpendicular to the layer) is completely artificial and may lead in some cases to spurious results and to difficulties in treating the action of external fields. In this paper we develop a new approach, which is “native” to quasi-2D materials, making use of basis function that are periodic in the plane, but atomic-like in the perpendicular direction. We show how some of the basic tools of ab initio electronic structure theory — density functional theory, GW approximation and Bethe-Salpeter equation — are implemented in the new basis. We argue that the new approach will be preferable to the conventional one in treating the peculiarities of layered materials, including the long range of the unscreened Coulomb interaction in insulators, and the effects of strain, corrugations, and external fields.

Trevisanutto, Paolo E.↗

Experimental evidence for pressure-induced first order transition in cerium nitride from B1 to B10 structure type

Here, the crystal structure of CeN was investigated up to pressures of 82 GPa, using diamond anvil cell powder X-ray diffraction in two experiments with He and Si-oil as the pressure transmitting media. In contrast to previous reports, we do not observe the B2 (CsCl type) structure at high pressure. Instead, the structural phase transition, starting at 65 GPa, from the ambient rock salt B1 structure results in a distorted CsCl-like B10 structure, irrespective of the pressure medium. Our result unambiguously confirms two recent density functional theory (DFT) studies predicting the B10 phase to be stable at these pressures, rather than the B2 (CsCl type) phase previously reported. The B10 structure appears to approach the B2 structure as pressure is increased further, but DFT calculations indicate that an L1 0 structure (AuCu type) is energetically favored

36 MATERIALS SCIENCE↗

Modeling adsorption properties of structurally deformed metal–organic frameworks using structure–property map

Structural deformation and collapse in metal-organic frameworks (MOFs) can lead to loss of long-range order, making it a challenge to model these amorphous materials using conventional computational methods. In this work, we show that a structure–property map consisting of simulated data for crystalline MOFs can be used to indirectly obtain adsorption properties of structurally deformed MOFs. The structure–property map (with dimensions such as Henry coefficient, heat of adsorption, and pore volume) was constructed using a large data set of over 12000 crystalline MOFs from molecular simulations. By mapping the experimental data points of deformed SNU-200, MOF-5, and Ni-MOF-74 onto this structure–property map, we show that the experimentally deformed MOFs share similar adsorption properties with their nearest neighbor crystalline structures. Furthermore, once the nearest neighbor crystalline MOFs for a deformed MOF are selected from a structure–property map at a specific condition, then the adsorption properties of these MOFs can be successfully transformed onto the degraded MOFs, leading to a new way to obtain properties of materials whose structural information is lost.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Heterogeneous Seeding of a Prion Structure by a Generic Amyloid Form of the Fungal Prion-forming Domain HET-s(218-289)

The fungal prion-forming domain HET-s(218–289) forms infectious amyloid fibrils at physiological pH that were shown by solid-state NMR to be assemblies of a two-rung β-solenoid structure. Under acidic conditions, HET-s(218–289) has been shown to form amyloid fibrils that have very low infectivity in vivo, but structural information about these fibrils has been very limited. We show by x-ray fiber diffraction that the HET-s(218–289) fibrils formed under acidic conditions have a stacked β-sheet architecture commonly found in short amyloidogenic peptides and denatured protein aggregates. At physiological pH, stacked β-sheet fibrils nucleate the formation of the infectious β-solenoid prions in a process of heterogeneous seeding, but do so with kinetic profiles distinct from those of spontaneous or homogeneous (seeded with infectious β-solenoid fibrils) fibrillization. Several serial passages of stacked β-sheet-seeded solutions lead to fibrillization kinetics similar to homogeneously seeded solutions. Our results directly show that structural mutation can occur between substantially different amyloid architectures, lending credence to the suggestion that the processes of strain adaptation and crossing species barriers are facilitated by structural mutation.

Wan, William↗

Human γ-glutamyl transpeptidase 1: Structures of the free enzyme, inhibitor-bound tetrahedral transition states, and glutamate-bound enzyme reveal novel movement within the active site during catalysis [Human gamma-glutamyl transpeptidase: Inhibitor binding and movement within the active site]

γ-Glutamyl transpeptidase 1 (GGT1) is a cell surface, N-terminal nucleophile hydrolase that cleaves glutathione and other γ-glutamyl compounds. GGT1 expression is essential in cysteine homeostasis, and its induction has been implicated in the pathology of asthma, reperfusion injury, and cancer. In this study, we report four new crystal structures of human GGT1 (hGGT1) that show conformational changes within the active site as the enzyme progresses from the free enzyme to inhibitor-bound tetrahedral transition states and finally to the glutamate-bound structure prior to the release of this final product of the reaction. The structure of the apoenzyme shows flexibility within the active site. The serine-borate-bound hGGT1 crystal structure demonstrates that serine-borate occupies the active site of the enzyme, resulting in an enzyme-inhibitor complex that replicates the enzyme's tetrahedral intermediate/transition state. The structure of GGsTop-bound hGGT1 reveals its interactions with the enzyme and why neutral phosphonate diesters are more potent inhibitors than monoanionic phosphonates. These structures are the first structures for any eukaryotic GGT that include a molecule in the active site covalently bound to the catalytic Thr-381. The glutamate-bound structure shows the conformation of the enzyme prior to release of the final product and reveals novel information regarding the displacement of the main chain atoms that form the oxyanion hole and movement of the lid loop region when the active site is occupied. Lastly,tThese data provide new insights into the mechanism of hGGT1-catalyzed reactions and will be invaluable in the development of new classes of hGGT1 inhibitors for therapeutic use.

36 MATERIALS SCIENCE↗

Structure of the human MLH1 N-terminus: implications for predisposition to Lynch syndrome

Mismatch repair prevents the accumulation of erroneous insertions/deletions and non-Watson–Crick base pairs in the genome. Pathogenic mutations in the MLH1 gene are associated with a predisposition to Lynch and Turcot's syndromes. Although genetic testing for these mutations is available, robust classification of variants requires strong clinical and functional support. Here, the first structure of the N-terminus of human MLH1, determined by X-ray crystallography, is described. Lastly, the structure shares a high degree of similarity with previously determined prokaryotic MLH1 homologs; however, this structure affords a more accurate platform for the classification of MLH1 variants.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗