Structural Determinants of the 59-Methylthioinosine Specificity of Plasmodium Purine Nucleoside Phosphorylase
Abstract not provided
Donaldson, Teraya M.↗
SEARCH · Engineering Papers
Results for “Structured”
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Hydration Layer Structure at Solid-Water Interfaces
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catalysis (heterogeneous)↗
Elastic Fluctuations and Structural Heterogeneities in Metallic Glasses
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Liu, Chaoyang↗
Structure Sensitivity of Acrolein Hydrogenation by Platinum Nanoparticles on Ba x Sr 1- x TiO 3 Nanocuboids
The structure sensitivity of Pt nanoparticles (Pt N ) for gas-phase acrolein (AC) hydrogenation was probed for Pt N on Ba x Sr 1- x TiO 3 nanocuboid supports with (0 0 1) facets in a combined theoretical and experimental study. The in situ selectivity for allyl alcohol increased with the increase of the Sr concentration in the support, which corresponds to modifications in the stable Winterbottom shape and lattice strain of the Pt nanoparticles as a result of the interfacial energy between Pt and the Ba x Sr 1- x TiO 3 supports. “Local model” nanofacets of the Pt surface, edge, and corner morphologies were developed as compact representations of adsorption and reaction sites. DFT was used as the primary modeling tool for the equilibrium adsorption states. We argue that adsorption on edge sites is critically important for the overall allyl alcohol selectivity of Pt N catalysts. A simple model was developed to represent Pt N strain effects caused by its interaction with the substrate. Bader topological atom, spherical volume averaging charge, and modified bond valence sum analyses were used to understand the bonding structure. Density of states analysis was performed for the structures of Pt N , adsorbed AC, and intermediate products to examine adsorbate–particle interactions. The simulated hydrogenation of AC on Pt N nanofacets was compared to the in situ hydrogenation of AC by Pt N on Ba x Sr 1- x TiO 3 to examine the effects of facet, edge, and corner sites on the overall selectivity.
bio-inspired↗
Ionic and Optical Properties of Methylammonium Lead Iodide Perovskite across the Tetragonal–Cubic Structural Phase Transition
Abstract Practical hybrid perovskite solar cells (PSCs) must endure temperatures above the tetragonal–cubic structural phase transition of methylammonium lead iodide (MAPbI 3 ). However, the ionic and optical properties of MAPbI 3 in such a temperature range, and particularly, dramatic changes in these properties resulting from a structural phase transition, are not well studied. Herein, we report a striking contrast at approximately 45 °C in the ionic/electrical properties of MAPbI 3 owing to a change of the ion activation energy from 0.7 to 0.5 eV, whereas the optical properties exhibit no particular transition except for the steady increase of the bandgap with temperature. These observations can be explained by the “continuous” nature of perovskite phase transition. We speculate that the critical temperature at which the ionic/electrical properties change, although related to crystal symmetry variation, is not necessarily the same temperature as when tetragonal–cubic structural phase transition occurs.
Hoque, Md Nadim Ferdous↗
Synthesis, Structural Characterization and Chemical Bonding of Sr 7 Li 6 Sn 12 and its Quaternary Derivatives with Eu and Alkaline Earth Metal (Mg, Ca, Ba) Substitutions. A Tale of Seven Li‐Containing Stannides and Two Complex Crystal Structures
In this paper, we discuss the synthesis and the structural characterization of the new ternary compound Sr 7 Li 6 Sn 12 and its six quaternary derivatives, where alkaline earth metals (Ca, Mg, Ba) and the rare earth metal Eu are substituted, yielding crystalline phases of monoclinic or orthorhombic symmetry. The title compounds were synthesized via high‐temperature solid‐state reactions of the corresponding elements. The crystal structures were determined by single‐crystal X‐ray diffraction methods. The (Sr,Ca) 7 Li 6 Sn 12 and Eu 7 (Mg,Li) 6 Sn 12 phases represent a new structure type (space group P 2/ m , No. 10) while Sr 7 Li 6 Sn 12 and the rest of the title phases crystallize in the orthorhombic base‐centered space group Cmmm (No. 65) which is similar to the Eu 7 Li 8– x Sn 10+ x ( x ≈ 2.0) phase with the Ce 7 Li 8 Ge 10 structure type (Pearson code oC 50). Careful examination of the resulting structures shows intricate disordering between Li and Sn atoms, which is governed by the total number of valence electrons. The discussion of experimental results is also supported by DFT electronic structure calculations.
Osman, Hussien H.↗
The limiting layer of fish scales: structure and properties
Fish scales serve as a flexible natural armor that have received increasing attention across the materials community. Most efforts in this area have focused on the composite structure of the predominately organic elasmodine, and limited work addresses the highly mineralized external portion known as the Limiting Layer (LL). This coating serves as the first barrier to external threats and plays an important role in resisting puncture. In this investigation the structure, composition and mechanical behavior of the LL were explored for three different fish, including the arapaima (Arapaima gigas), the tarpon (Megalops atlanticus) and the carp (Cyprinus carpio). The scales of these three fish have received the most attention within the materials community. Features of the LL were evaluated with respect to anatomical position to distinguish site-specific functional differences. Results show that there are significant differences in the surface morphology of the LL from posterior and anterior regions in the scales, and between the three fish species. The calcium to phosphorus ratio and the mineral to collagen ratios of the LL are not equivalent among the three fish. Results from nanoindentation showed that the LL of tarpon scales is the hardest, followed by the carp and the arapaima and the differences in hardness are related to the apatite structure, possibly induced by the growth rate and environment of each fish.
Arola, Dwayne D.↗
3D printed structures for modeling the Young’s modulus of bamboo parenchyma
Not Available
Dixon, P. G.↗
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↗
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↗