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Probing the Structures and Electronic Properties of Dual-Phosphorus-Doped Gold Cluster Anions (AunP-2, n = 1–8): A Density functional Theory Investigation

The geometries of gold clusters doped with two phosphorus atoms, (AunP-2, n = 1–8) were investigated using density functional theory (DFT) methods. Various two-dimensional (2D) and three-dimensional (3D) structures of the doped clusters were studied. The results indicate that the structures of dual-phosphorus-doped gold clusters exhibit large differences from those of pure gold clusters with small cluster sizes. In our study, as for Au6P-2, two cis–trans isomers were found. The global minimum of Au8P-2 presents a similar configuration to that of Au-20, a pyramid-shaped unit, and the potential novel optical and catalytic properties of this structure warrant further attention. The higher stability of AunP-2 clusters relative to Au-n+2 (n = 1–8) clusters was verified based on various energy parameters, and the results indicate that the phosphorus atom can improve the stabilities of the gold clusters. We then explored the evolutionary path of (n = 1–8) clusters. We found that AunP-2 clusters exhibit the 2D–3D structural transition at n = 6, which is much clearer and faster than that of pure gold clusters and single-phosphorus-doped clusters. The electronic properties of AunP-2 (n = 1–8) were then investigated. The photoelectron spectra provide additional fundamental information on the structures and molecular orbitals shed light on the evolution of AunP-2 (n = 1–8). Natural bond orbital (NBO) described the charge distribution in stabilizing structures and revealed the strong relativistic effects of the gold atoms.

Environmental Molecular Sciences Laboratory↗

Quantifying structural errors in cloud condensation nuclei activity from reduced representation of aerosol size distributions

Aerosol effects on clouds and radiation are the dominant contribution to uncertainty in radiative forcing relative to the pre-industrial atmosphere. While previous studies have assessed the impact of parametric uncertainty on modeled forcing, structural errors from the numerical representation of particle distributions have not been well quantified. Here we present a framework for quantifying error in aerosol size distributions and cloud condensation nuclei activity, which we apply to the widely used 4-mode version of the Modal Aerosol Module (MAM4). Box model predictions from the MAM4 are evaluated against the Particle Monte Carlo Model for Simulating Aerosol Interactions and Chemistry (PartMC-MOSAIC), a benchmark model that tracks the evolution of individual particles. We show that size distributions simulated by MAM4 diverge from those simulated by PartMC-MOSAIC after only a few hours of aging by condensation and coagulation in polluted conditions, which leads to large errors in modeled cloud condensation nuclei concentrations. We find that differences between MAM4 and PartMC-MOSAIC are largest under polluted conditions, where the size distribution evolves rapidly though aging by condensation of semi-volatile substances and coagulation among particles. These findings suggest that structural error in modeled aerosol properties contributes to the large inter-model variability in aerosol radiative forcing.

Fierce, Laura M.↗

Local atomic structure and lattice defect analysis in heavily Co-doped ZnS thin films using X-ray absorption fine structure spectroscopy

Iin this work, X-ray absorption fine structure (XAFS) spectroscopy was used to address both the local atomic structure and the local electronic structure around Zn, Co, and S in Co-doped ZnS thin films. X-ray absorption near-edge spectroscopy (XANES) revealed changes in the strong pre-edge feature of the S K-edge spectra that depend on the Co concentration and are related to atomic bound-state transitions through hybridization between $3d$ transition metal and $sp$ host semiconductor electronic states. These changes reveal intrinsic effects, such as S vacancies and dopant effects. From the Co K-edge XANES spectra, substitution of Co 2+ into ZnS is observed. The local atomic structure around the dopant, obtained by XAFS spectroscopy, indicates a reduction of the Co–S bond length. Optical analysis shows deep absorption centers or intermediate states in the bandgap, ascribed to $d$-$d$ transitions in the Co atoms that modify the electronic band structure and cause a decrease in the bandgap as a function of Co concentration. This work provides direct evidence of dopant effects in heavily Co-doped ZnS, including bond distances and Debye-Waller factors, providing key elements to generate a realistic atomic structural model, which is crucial to understand the observed electronic properties of this material.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Pushing the size limit of de novo structure ensemble prediction guided by sparse SDSL-EPR restraints to 200 residues: The monomeric and homodimeric forms of BAX

Structure determination remains a challenge for many biologically important proteins. In particular, proteins that adopt multiple conformations often evade crystallization in all biologically relevant states. Although computational de novo protein folding approaches often sample biologically relevant conformations, the selection of the most accurate model for different functional states remains a formidable challenge, in particular, for proteins with more than about 150 residues. Electron paramagnetic resonance (EPR) spectroscopy can obtain limited structural information for proteins in well-defined biological states and thereby assist in selecting biologically relevant conformations. The present study demonstrates that de novo folding methods are able to accurately sample the folds of 192-residue long soluble monomeric Bcl-2-associated X protein (BAX). The tertiary structures of the monomeric and homodimeric forms of BAX were predicted using the primary structure as well as 25 and 11 EPR distance restraints, respectively. The predicted models were subsequently compared to respective NMR/X-ray structures of BAX. EPR restraints improve the protein-size normalized root-mean-square-deviation (RMSD100) of the most accurate models with respect to the NMR/crystal structure from 5.9 Å to 3.9 Å and from 5.7 Å to 3.3 Å, respectively. Additionally, the model discrimination is improved, which is demonstrated by an improvement of the enrichment from 5% to 15% and from 13% to 21%, respectively.

Biochemistry & Molecular Biology↗

Local structure of Rb{sub 2}Li{sub 4}(SeO{sub 4}){sub 3}{center_dot}2H{sub 2}O by the modeling of X-ray diffuse scattering - from average-structure to microdomain model

Local structure of dirubidium tetralithium tris(selenate(VI)) dihydrate - Rb{sub 2}Li{sub 4}(SeO{sub 4}){sub 3}{center_dot} 2H{sub 2}O has been determined basing on the modeling of X-ray diffuse scattering. The origin of observed structured diffuse streaks is SeO{sub 4} tetrahedra switching between two alternative positions in two quasi-planar layers existing in each unit cell and formation of domains with specific SeO{sub 4} tetrahedra configuration locally fulfilling condition for C-centering in the 2a Multiplication-Sign 2b Multiplication-Sign c superstructure cell. The local structure solution is characterized by a uniform distribution of rather large domains (ca. thousand of unit cells) in two layers, but also monodomains can be taken into account. Inside a single domain SeO{sub 4} tetrahedra are ordered along ab-diagonal forming two-string ribbons. Inside the ribbons SeO{sub 4} and LiO{sub 4} tetrahedra share the oxygen corners, whereas ribbons are bound to each other by a net of hydrogen bonds and fastened by corner sharing SeO{sub 4} tetrahedra of the neighboring layers. - Graphical abstract: Experimental sections of the reciprocal space showing diffraction effects observed for RLSO. Bragg spots are visible on sections with integer indices (1 kl section - on the left), streaks - on sections with fractional ones (1.5 kl section - on the right). At the center: resulting local structure of the A package modeled as a microdomain: two-string ribbons of ordered oxygen-corners-sharing SeO{sub 4} and LiO{sub 4} terahedra extended along ab-diagonal are seen; ribbons are bound by hydrogen bonds (shown in pink); the multiplied 2a Multiplication-Sign 2b unit cell is shown. Highlights: Black-Right-Pointing-Pointer X-ray diffuse scattering in RLSO was registered and modeled. Black-Right-Pointing-Pointer The origin of diffuse streaks is SeO{sub 4} tetrahedra switching in two structure layers. Black-Right-Pointing-Pointer The local structure is characterized by a uniform distribution of microdomains. Black-Right-Pointing-Pointer Inside a single domain SeO{sub 4} tetrahedra are ordered along ab-diagonal forming ribbons. Black-Right-Pointing-Pointer The ribbons are bound to each other by a net of hydrogen bonds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Six novel transition-metal phosphite compounds, with structure related to yavapaiite: Crystal structures and magnetic and thermal properties of A{sup I}[M{sup III}(HPO{sub 3}){sub 2}] (A=K, NH{sub 4}, Rb and M=V, Fe)

Six new transition metal(III) phosphites A{sup I}[V{sup III}(HPO{sub 3}){sub 2}], where A=K (1), NH{sub 4} (2) and Rb (3) and A{sup I}[Fe{sup III}(HPO{sub 3}){sub 2}] where A=K (4), NH{sub 4} (5) and Rb (6) have been synthesized under hydrothermal conditions and the solid-state structures were solved from single-crystal X-ray diffraction data. These compounds crystallize in the hexagonal system, space group P6{sub 3}mc (no. 186), with a=5.3294(2) A and c=12.3130(5) A for 1, a=5.3330(2) A and c=12.8760(4) A for 2, a=5.3459(2) A and c=12.6850(8) A for 3, a=5.3256(1) A and c=12.2362(3) A for 4, a=5.3229(2) A and c=12.8562(4) A for 5, a=5.3393(2) A and c=12.6913(5) A for 6, with Z=2 in the six phases. The crystal structures of these compounds are isotypic and exhibit a layered structure stacked along the c-axis with the A{sup +} cations located in the interlayer space. The [M{sup III}(HPO{sub 3}){sub 2}]{sup -} sheets are formed by MO{sub 6} octahedra interconnected by HPO{sub 3} tetrahedral phosphite oxoanions through sharing vertices. Thermal analysis shows a large range of stability for compounds containing potassium and rubidium cations with decomposition starting around 550 K for stable compounds and above 840 K for the most stable compounds leading in general to pyrophosphate compounds. Triangular nets of metallic centers are observed within the layers in which antiferromagnetic interactions are evidenced by magnetic susceptibility measurements suggesting magnetic frustration. - Graphical abstract: Six new transition metal(III) phosphites A{sup I}[M{sup III}(HPO{sub 3}){sub 2}], where A=K, NH{sub 4}, Rb and M=V, Fe, have been synthesized. The crystal structures of these compounds are isotypic and exhibit a lamellar structure related to Yavapaiite. The M(HPO{sub 3}){sub 2} layers separated by cationic species present the metallic centers in a triangular arrangement. Bulk antiferromagnetic behavior is observed for all the studied compounds. Highlights: Black-Right-Pointing-Pointer A new family of transition metal phosphites has been prepared. Black-Right-Pointing-Pointer The structure of these compounds is related to layered minerals like Yavapaiite. Black-Right-Pointing-Pointer Antiferromagnetic coupling is evidenced suggesting possible magnetic frustration. Black-Right-Pointing-Pointer Thermal studies show, in general, oxidation of phosphites into pyrophosphates.

36 MATERIALS SCIENCE↗

New orthorhombic derivative of CaCu{sub 5}-type structure: RNi{sub 4}Si compounds (R=Y, La, Ce, Sm, Gd–Ho), crystal structure and some magnetic properties

The crystal structure of new YNi{sub 4}Si-type RNi{sub 4}Si (R=Y, La, Ce, Sm, Gd–Ho) compounds has been established using powder X-ray diffraction. The YNi{sub 4}Si structure is a new structure type, which is orthorhombic derivative of CaCu{sub 5}-type structure (space group Cmmm N 65, oC12). GdNi{sub 4}Si and DyNi{sub 4}Si compounds order ferromagnetically at 25 and 19 K, respectively whereas YNi{sub 4}Si shows antiferromagnetic nature. At 15 K, DyNi{sub 4}Si shows second antiferromagnetic-like transition. The magnetic moment of GdNi{sub 4}Si at 5 K in 50 kOe field is ∼7.2 μ{sub B}/f.u. suggesting a completely ordered ferromagnetic state. The magnetocaloric effect of GdNi{sub 4}Si is calculated in terms of isothermal magnetic entropy change and it reaches the maximum value of −12.8 J/kg K for a field change of 50 kOe near T{sub C} ∼25 K. - Graphical abstract: The RNi{sub 4}Si (R=Y, La, Ce, Sm, Gd–Ho) compounds crystallize in new YNi{sub 4}Si-type structure which is orthorhombic derivative of the basic CaCu{sub 5}-type structure. GdNi{sub 4}Si and DyNi{sub 4}Si compounds show the ferromagnetic-like ordering, whereas.YNi{sub 4}Si has the antiferromagnetic nature. The GdNi{sub 4}Si demonstrates the big magnetocaloric effect near temperature of ferromagnetic ordering. The relationship between initial CaCu{sub 5}-type DyNi{sub 5} and YNi{sub 4}Si-type DyNi{sub 4}Si lattices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Synthesis and crystal structure characterization of InGaZnO{sub 4} with a new defect structure

Single crystals of InGaZnO{sub 4} were synthesized in a sealed Pt-tube at elevated temperatures under normal pressure without flux. InGaZnO{sub 4} has a trigonal crystal system (R3{sup ¯}m; No. 166) deduced from convergent beam electron diffraction (CBED). Single crystal structure refinement from XRD data at −150 °C (a=3.275(1) Å; c=25.99(1) Å; Z=3) revealed an alternate stacking of InO{sub 6/3}{sup −} and (Ga,Zn)O{sub 4/4}{sup +} layers, iso-structural to YbFe{sub 2}O{sub 4}. The cell parameters at room temperature were refined from powder X-ray diffraction data (a=3.284(3) Å and c=26.037(3) Å). The transparent crystals have a gray-bluish color and exhibit an excess of Ga expressed by the cation ratio of In:Ga:Zn=30.2(9):39(1):31(1) determined by energy dispersive X-ray spectroscopy (EDXS). While the isovalent substitution of In{sup 3+} by Ga{sup 3+} is known, an additional aliovalent substitution of Zn{sup 2+} by Ga{sup 3+} is observed. This results in the formula (In{sub 0.9}Ga{sub 0.1})Ga{sub 1.06}Zn{sub 0.91}□{sub 0.03}O{sub 4} where 3% of the cations in 4+1 coordination are vacant due to aliovalent substitution. Further evidence of that defect structure is found in the lattice parameter a which is substantially smaller than in stoichiometric InGaZnO{sub 4}, as well as in the strong absorption in the near-IR from transitions correlated with the defect structure. The bluish color of the crystals is due to an enhanced absorption in the red of the visible spectrum. For the first time, we achieved to image InGaZnO{sub 4} at atomic resolution in the electron microscope proving a perfect periodic stacking of atomic layers. - Graphical abstract: Single crystals of InGaZnO{sub 4} have been synthesized at ambient pressure and analyzed with X-ray diffraction, electron microscopy, and optical absorption. Optical band gap and optical transmission have been determined. - Highlights: • Preparation of single crystals of InGaO{sub 3}(ZnO){sub 1} at ambient pressure for the first time. • Non-stoichiometric compound (In{sub 0.9}Ga{sub 0.1})Ga{sub 1.06}Zn{sub 0.91}□{sub 0.03}O{sub 4} with defect structure, excess of Ga, depletion of Zn. • Real structure of InGaO{sub 3}(ZnO){sub 1} imaged by high resolution TEM for the first time. • Optical band gap and transmission of InGaO{sub 3}(ZnO){sub 1} single crystal.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Synthesis, structure, and magnetic characterization of Cr{sub 4}US{sub 8}

The compound Cr{sub 4}US{sub 8} has been synthesized at 1073 K and its crystal structure has been determined at 100 K. The structure is modulated with a two-fold commensurate supercell. The subcell may be indexed in an orthorhombic cell but weak supercell reflections lead to the monoclinic superspace group P2{sub 1}/c(α0γ)0s with two Cr sites, one U site, and four S sites. The structure comprises a three-dimensional framework of CrS{sub 6} octahedra with channels that are partially occupied by U atoms. Each U atom in these channels is coordinated by eight S atoms in a bicapped trigonal-prismatic arrangement. The magnetic behavior of Cr{sub 4}US{sub 8} is complex. At temperatures above ~120 K at all measured fields, there is little difference between field-cooled and zero field-cooled data and χ(T) decreases monotonously with temperature, which is reminiscent of the Curie–Weiss law. At lower temperatures, the temperature dependence of χ(T) is complex and strongly dependent on the magnetic field strength. - Graphical abstract: Structure of Cr{sub 4}US{sub 8} viewed down the a axis. - Highlights: • At 1073 K Cr{sub 4}US{sub 8} was synthesized and at 100 K its crystal structure was determined. • The 3D structure comprises CrS{sub 6} octahedra with channels partially occupied by U. • The magnetic behavior of Cr{sub 4}US{sub 8} is complex.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effects of geometric structure, orientation and size on structural stability and thermal behavior of zinc oxide nanowires

Highlights: {yields} The structural stability, orientation effect and melting characteristic of zinc oxide (ZnO) nanowires are simulated by using the molecular dynamics with many-body tightbinding potential. {yields} The nanowire with a hexagonal cross section is more stable than that with other cross section type, namely, a rectangular, triangular, rhombohedral, octagonal, and circular cross section. {yields} The structural stability and melting temperature of a nanowire is sensitive to its diameter because of the surface energy and unfavorable coordination. -- Abstract: The structural stability, orientation effect and melting characteristic of zinc oxide (ZnO) nanowires are simulated by using the molecular dynamics with many-body tightbinding potential. The structural stability is affected by the geometric shape of the cross section of a nanowire. The nanowire with a hexagonal cross section is more stable than that with another cross section type, namely, a rectangular, triangular, rhombohedral, octagonal, and circular cross section. The structural stability and melting temperature of a nanowire is sensitive to its diameter because of the surface energy and unfavorable coordination. Remarkably, it is observed that hexagonal ZnO nanowires transform to metastable circular-type structures at temperatures lower than the melting point.

36 MATERIALS SCIENCE↗

Structures of minute virus of mice replication initiator protein N-terminal domain: Insights into DNA nicking and origin binding

Members of the Parvoviridae family all encode a non-structural protein 1 (NS1) that directs replication of single-stranded viral DNA, packages viral DNA into capsid, and serves as a potent transcriptional activator. Here we report the X-ray structure of the minute virus of mice (MVM) NS1 N-terminal domain at 1.45 Å resolution, showing that sites for dsDNA binding, ssDNA binding and cleavage, nuclear localization, and other functions are integrated on a canonical fold of the histidine-hydrophobic-histidine superfamily of nucleases, including elements specific for this Protoparvovirus but distinct from its Bocaparvovirus or Dependoparvovirus orthologs. High resolution structural analysis reveals a nickase active site with an architecture that allows highly versatile metal ligand binding. The structures support a unified mechanism of replication origin recognition for homotelomeric and heterotelomeric parvoviruses, mediated by a basic-residue-rich hairpin and an adjacent helix in the initiator proteins and by tandem tetranucleotide motifs in the replication origins. - Highlights: • The structure of a parvovirus replication initiator protein has been determined; • The structure sheds light on mechanisms of ssDNA binding and cleavage; • The nickase active site is preconfigured for versatile metal ligand binding; • The binding site for the double-stranded replication origin DNA is identified; • A single domain integrates multiple functions in virus replication.

60 APPLIED LIFE SCIENCES↗

Simulation of Probe Position-Dependent Electron Energy-Loss Fine Structure

We present a theoretical framework for calculating probe-position-dependent electron energy-loss near-edge structure for the scanning transmission electron microscope by combining density functional theory with dynamical scattering theory. We show how simpler approaches to calculating near-edge structure fail to include the fundamental physics needed to understand the evolution of near-edge structure as a function of probe position and investigate the dependence of near-edge structure on probe size. It is within this framework that density functional theory should be presented, in order to ensure that variations of near-edge structure are truly due to local electronic structure and how much from the diffraction and focusing of the electron beam.

Oxley, M. P.↗

Structural Evolution of Reversible Mg Insertion into a Bilayer Structure of V 2 O 5 · n H 2 O Xerogel Material

Functional multivalent intercalation cathodes represent one of the largest hurdles in the development of Mg batteries. While there are many reports of Mg cathodes, many times the evidence of intercalation chemistry is only circumstantial. In this work, direct evidence of Mg intercalation into a bilayer structure of V2O5·nH2O xerogel is confirmed, and the nature of the Mg intercalated species is reported. The interlayer spacing of V2O5·nH2O contracts upon Mg intercalation and expands for Mg deintercalation due to the strong electrostatic interaction between the divalent cation and the cathode. A combination of NMR, pair distribution function (PDF) analysis, and X-ray absorption near edge spectroscopy (XANES) confirmed reversible Mg insertion into the V2O5·nH2O material, and structural evolution of Mg intercalation leads to the formation of multiple new phases. Structures of V2O5·nH2O with Mg intercalation were further supported by the first principle simulations. A solvent cointercalated Mg in V2O5·nH2O is observed for the first time, and the 25Mg magic angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy was used to elucidate the structure obtained upon electrochemical cycling. Specifically, existence of a well-defined Mg–O environment is revealed for the Mg intercalated structures. Information reported here reveals the fundamental Mg ion intercalation mechanism in a bilayer structure of V2O5·nH2O material and provides insightful design metrics for future Mg cathodes.

36 MATERIALS SCIENCE↗

From the ternary Eu(Au/In) 2 and EuAu 4 (Au/In) 2 with remarkable Au/In distributions to a new structure type: The gold-rich Eu 5 Au 16 (Au/In) 6 structure

The ternary Eu(Au/In) 2 (EuAu 0.46 In 1.54 (2) ) (I), EuAu 4 (Au/In) 2 (EuAu 4+x In 2–x with x = 0.75(2) (II), 0.93(2), and 1.03(2)), and Eu 5 Au 16 (Au/In) 6 (Eu 5 Au 17.29 In 4.71(3) ) (III) have been synthesized, and their structures were characterized by single-crystal X-ray diffraction. I and II crystallize with the CeCu 2 -type (Pearson Symbol oI 12; Imma ; Z = 4; a = 4.9018(4) Å; b = 7.8237(5) Å; c = 8.4457(5) Å) and the YbAl 4 Mo 2 -type (tI14; I4/ mmm ; Z = 2; a = 7.1612(7) Å; c = 5.5268(7) Å) and exhibit significant Au/In disorder. I is composed of an Au/In-mixed diamond-related host lattice encapsulating Eu atoms, while the structure of II features ribbons of distorted, squared Au 8 prisms enclosing Eu, Au, and In atoms. Combination of these structural motifs leads to a new structure type as observed for Eu 5 Au 16 (Au/In) 6 (Eu 5 Au 17.29 In 4.71(3) ) (oS108; Cmcm ; Z = 4; a = 7.2283(4) Å; b = 9.0499(6) Å; c = 34.619(2) Å), which formally represents a one-dimensional intergrowth of the series EuAu 2 –“EuAu 4 In 2 ”. The site preferences of the disordered Au/In positions in II were investigated for different hypothetical “EuAu 4 (Au/In) 2 ” models using the projector-augmented wave method and indicate that these structures attempt to optimize the frequencies of the heteroatomic Au–In contacts. Furthermore, a chemical bonding analysis on two “EuAu 5 In” and “EuAu 4 In 2 ” models employed the TB-LMTO-ASA method and reveals that the subtle interplay between the local atomic environments and the bond energies determines the structural and site preferences for these systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effect of Pressure on Valence and Structural Properties of YbFe 2 Ge 2 Heavy Fermion Compound A Combined Inelastic X-ray Spectroscopy, X-ray Diffraction, and Theoretical Investigation

The crystal structure and the Yb valence of the YbFe 2 Ge 2 heavy fermion compound was measured at room temperature and under high pressures using high-pressure powder X-ray diffraction and X-ray absorption spectroscopy via both partial fluorescence yield and resonant inelastic X-ray emission techniques. Furthermore, the measurements are complemented by first-principles density functional theoretical calculations using the self-interaction corrected local spin density approximation investigating in particular the magnetic structure and the Yb valence. While the ThCr 2 Si 2 -type tetragonal (I4/mmm) structure is stable up to 53 GPa, the X-ray emission results show an increase of the Yb valence from v = 2.72(2) at ambient pressure to v = 2.93(3) at ~9 GPa, where at low temperature a pressure-induced quantum critical state was reported.

Kumar, Ravhi S.↗