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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↗

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↗

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.↗

Investigation of a Structural Phase Transition and Magnetic Structure of Na 2 BaFe(VO 4 ) 2 : A Triangular Magnetic Lattice with a Ferromagnetic Ground State

The structural and magnetic properties of a glaserite-type Na 2 BaFe(VO 4 ) 2 compound, featuring a triangular magnetic lattice of Fe 2+ (S = 2), are reported. Temperature dependent X-ray single crystal studies indicate that at room temperature the system adopts a trigonal P$\bar{3}$ m 1 structure and undergoes a structural phase transition to a C2/c monoclinic phase slightly below room temperature (T s = 288 K). This structural transition involves a tilting of Fe–O–V bond angles and strongly influences the magnetic correlation within the Fe triangular lattice. The magnetic susceptibility measurements reveal a ferromagnetic transition near 7 K. Single crystal neutron diffraction confirms the structural distortion and the ferromagnetic spin ordering in Na 2 BaFe(VO 4 ) 2 . The magnetic structure of the ordered state is modeled in the magnetic space group C2'/c' that implies a ferromagnetic order of the a and c moment components and antiferromagnetic arrangement for the b components. Altogether, the Fe magnetic moments form ferromagnetic layers that are stacked along the c-axis, where the spins point along one of the (111) facets of the FeO 6 octahedron.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Charge ordering and structural transition in the new organic conductor {delta}'-(BEDT-TTF){sub 2}CF{sub 3}CF{sub 2}SO{sub 3}.

We report structural, transport, and optical properties and electronic structure calculations of the delta'-(BEDT-TTF) 2CF3CF2SO3 (BEDT-TTF = bis(ethylenedithio)-tetrathiafulvalene) organic conductor that has been synthesized by electrocrystallization. Electronic structure calculations demonstrate the quasi-one-dimensional Fermi surfaces of the compound, while the optical spectra are characteristic for a dimer-Mott insulator. The single-crystal X-ray diffraction measurements reveal the structural phase transition at 200 K from the ambient-temperature monoclinic P2(1)/m phase to the low-temperature orthorhombic Pca2(1) phase, while the resistivity measurements clearly show the first order semiconductor-semiconductor transition at the same temperature. This transition is accompanied by charge-ordering as it is confirmed by splitting of charge-sensitive vibrational modes observed in the Raman and infrared spectra. The horizontal stripe charge-order pattern is suggested based on the crystal structure, band structure calculations, and optical spectra.

Olejniczak, Iwona↗

Molecular simulation of structure and diffusion at smectite-water interfaces: Using expanded clay interlayers as model nanopores

In geologic settings relevant to a number of extraction and potential sequestration processes, nanopores bounded by clay mineral surfaces play a critical role in the transport of aqueous species. Solution structure and dynamics at clay–water interfaces are quite different from their bulk values, and the spatial extent of this disruption remains a topic of current interest. We have used molecular dynamics simulations to investigate the structure and diffusion of aqueous solutions in clay nanopores approximately 6 nm thick, comparing the effect of clay composition with model Na-hectorite and Na-montmorillonite surfaces. In addition to structural properties at the interface, water and ion diffusion coefficients were calculated within each aqueous layer at the interface, as well as in the central bulk-like region of the nanopore. The results show similar solution structure and diffusion properties at each surface, with subtle differences in sodium adsorption complexes and water structure in the first adsorbed layer due to different arrangements of layer hydroxyl groups in the two clay models. Interestingly, the extent of surface disruption on bulk-like solution structure and diffusion extends to only a few water layers. Additionally, a comparison of sodium ion residence times confirms similar behavior of inner-sphere and outer-sphere surface complexes at each clay surface, but ~1% of sodium ions adsorb in ditrigonal cavities on the hectorite surface. Thus, the presence of these anhydrous ions is consistent with highly immobile anhydrous ions seen in previous nuclear magnetic resonance spectroscopic measurements of hectorite pastes.

36 MATERIALS SCIENCE↗

Clay Swelling in Dry Supercritical Carbon Dioxide: Effects of Interlayer Cations on the Structure, Dynamics, and Energetics of CO 2 Intercalation Probed by XRD, NMR, and GCMD Simulations

In situ X-ray diffraction (XRD) and nuclear magnetic resonance (NMR) experiments combined with molecular dynamics simulations using the grand canonical ensemble [grand canonical molecular dynamics (GCMD)] show that the cation size, charge, and solvation energy play critical roles in determining the interlayer expansion of smectite clay minerals when exposed to dry supercritical scCO2 (scCO2) under conditions relevant to petroleum reservoirs and geological CO2 sequestration conditions. The GCMD results show that the smectite mineral, hectorite, containing interlayer alkali and alkaline earth cations with small ionic radii and high solvation energies (e.g., Na+ and Ca2+) does not intercalate CO2 and that the fully collapsed interlayer structure is the most energetically stable configuration. With Cs+ and Ba2+, the monolayer structure is the stable configuration, and CO2 should spontaneously enter the interlayer. With Cs+, there is not even an energy barrier for CO2 intercalation, in agreement with the XRD and NMR results. 13C NMR and simulations show that the average orientation of the intercalated CO2 is with their O-C-O axes parallel to the basal clay surface and that they undergo a rapid rotation about an axis perpendicular to the main molecular axis. The simulations show that the strength of the interaction between the exchangeable cation and the clay structure dominates the intercalation energetics in dry scCO2.

Loganathan, Narasimhan (ORCID:0000000302515430)↗

ZnxMn1-xO Solid Solutions in the Rocksalt Structure: Optical, Charge Transport, and Photoelectrochemical Properties

Theoretical predictions of ZnO:MnO solid solutions (abbreviated here as ZMO) with the rocksalt-type structure suggest improved visible light absorption and suitable band edge positions for the overall water splitting reaction, but experimental efforts to produce such phases are limited by the low solubility of Zn within this structure type. Here, we produce solid solutions of ZnxMn1-xO, with x = 0.5 and 0.3 in the metastable rocksalt phase, using high-pressure and high-temperature (HPHT) techniques. X-ray diffraction and electron microscopy methods were employed to determine the crystal structure, chemical composition, and homogeneity on the submicron scale. The solid solutions exhibit increased optical absorbance in the visible spectral range as compared to those of the parent oxides ZnO and MnO. Our theoretical calculations for ZnxMn1-xO with x = 0.5, 0.25 predict band gaps of 2.53 and 2.98 eV, respectively, with an unusually large band gap bowing. Our calculations also show small effective electron mass for these materials indicating their potential for solar energy applications. Initial photoelectrochemical tests reveal that ZMO solid solutions are suitable for water oxidation and warrant further experimental optimization.

36 MATERIALS SCIENCE↗