STRUCTURES AND TRANSITIONS IN TUNGSTEN GRAIN BOUNDARIES AND THEIR ROLE IN THE ABSORPTION OF POINT DEFECTS
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Physics - Condensed matter physics↗
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Application of micro X-ray diffraction to investigate the reaction products formed by the alkali–silica reaction in concrete structures
Alkali–silica reaction (ASR) is one of the most important deterioration mechanisms in concrete leading to substantial damages of structures worldwide. Synchrotron-based micro-X-ray diffraction (micro-XRD) was employed to characterize the mineral phases formed in micro-cracks of concrete aggregates as a consequence of ASR. This high spatial resolution technique enables to directly gain structural information on ASR products formed in a 40-year old motorway bridge damaged due to ASR. Micro-X-ray-fluorescence was applied on thin sections to locate the reaction products formed in veins within concrete aggregates. Micro-XRD pattern were collected at selected points of interest along a vein by rotating the sample. Rietveld refinement determined the structure of the ASR product consisting of a new layered framework similar to mountainite and rhodesite. It is conceivable that understanding the structure of the ASR product may help developing new technical treatments inhibiting ASR.
36 MATERIALS SCIENCE↗
Monte Carlo Simulation of Borosilicate Glass Dissolution using Molecular Dynamics-Generated Glass Structures
Atomic-scale insights into the dissolution mechanisms of borosilicate glasses are critical to the development of the waste form corrosion models that inform performance assessments of nuclear waste disposal facilities. Monte Carlo (MC) simulations have been instrumental in advancing the state of knowledge of borosilicate glass dissolution; however, all such simulations to date have relied on lattices to represent the amorphous glass structure, thereby potentially introducing artifacts. Therefore, a new approach, referred to as the amorphous MC approach, has been developed whereby glass structures generated from molecular dynamics simulations are used as starting points for MC simulations of glass dissolution. MC simulations of sodium borosilicate glasses that covered a wide compositional range were performed and revealed correlations between dissolution rate and structural features of the glasses. Notably, the lattice MC approach predicted the fraction of tetrahedral boron to have a lesser influence on the dissolution rate than computed with the amorphous MC approach. The lattice MC simulations also overestimated the dissolution rate for a given glass composition. These findings highlight the importance of using truly amorphous structures in MC simulations of glass corrosion.
Kerisit, Sebastien N.↗
Competing Pathways for Nucleation of the Double Perovskite Structure in the Epitaxial Synthesis of La 2 MnNiO 6
Over the past decades a confluence of advanced synthesis techniques, data-driven characterization, and rapid increases in computing power has sparked a renaissance in materials engineering. The emerging “materials-by-design” approach, while radically transforming the development of multicomponent systems, has tended to overlook the complex kinetic pathways that define materials synthesis. Although we are able to envision almost limitless materials combinations, we are unable to synthesize all of them in practice, since existing characterization and modeling approaches often fail to capture the inherent complexity of such systems. There is currently a disconnect between highly local structural characterization and macroscale properties measurements, resulting in oversimplified or incomplete structure-property models. Here we describe a multi-technique approach that combines aberration-corrected transmission electron microscopy with emerging oxide atom probe tomography to measure chemical ordering and extended defects in the model complex oxide, La2MnNiO6. We visualize cation ordering, as well as a three-dimensional network of secondary phases, which we describe in terms of ab initio structure calculations. We propose a defect model in which these phases alter their surrounding octahedral environment, severely disrupting cation superexchange. Through this array of experimental and theoretical techniques, we uncover fundamental structure-property relationships and illustrate a new approach to engineer complex, multicomponent systems.
atom probe tomography↗
Structure and Thermochemistry of Perrhenate Sodalite and Mixed Guest Perrhenate/Pertechnetate Sodalite
Treatment and immobilization of technetium-99 ( 99 Tc) contained in reprocessed nuclear waste and present in contaminated subsurface systems represents a major environmental challenge. One potential approach to managing this highly mobile and long-lived radionuclide is immobilization into micro- and meso-porous crystalline solids, specifically sodalite. We synthesized and characterized the structure of perrhenate sodalite, Na 8 [AlSiO 4 ]6(ReO 4 ) 2 , and the structure of a mixed guest perrhenate/pertechnetate sodalite, Na 8 [AlSiO 4 ] 6 (ReO 4 ) 2-x (TcO 4 ) x . Perrhenate was used as a chemical analogue for pertechnetate. Bulk analyses of each solid confirm a cubic sodalite-type structure (P$\overline{43}$n, No. 218 space group) with rhenium and technetium in the 7+ oxidation state. High-resolution nanometer scale characterization measurements provide first-of-a-kind evidence that the ReO 4 – anions are distributed in a periodic array in the sample, nanoscale clustering is not observed, and the ReO 4 – anion occupies the center of the sodalite β-cage in Na 8 [AlSiO 4 ] 6 (ReO 4 ) 2 . We also demonstrate, for the first time, that the TcO 4 – anion can be incorporated into the sodalite structure. Lastly, thermochemistry measurements for the perrhenate sodalite were used to estimate the thermochemistry of pertechnetate sodalite based on a relationship between ionic potential and the enthalpy and Gibbs free energy of formation for previously measured oxyanion-bearing feldspathoid phases. The results collected in this study suggest that micro- and mesoporous crystalline solids maybe viable candidates for the treatment and immobilization of 99 Tc present in reprocessed nuclear waste streams and contaminated subsurface environments.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
High-Pressure Structural Response of an Insensitive Energetic Crystal: Dihydroxylammonium 5,5'-Bistetrazole-1,1'-diolate (TKX-50)
The structural response of a novel, insensitive energetic crystal—dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)—was examined under high pressure. Using synchrotron single-crystal X-ray diffraction measurements, details of molecular, intermolecular, and crystal changes were determined to ~10 GPa to understand its structural stability. The experimental results showed that TKX-50 exhibits highly anisotropic compression and significantly lower volume compressibility than currently known energetic crystals. These results are found to be in general agreement with our previous predictions from the DFT calculations. Additionally, the experimental data revealed anomalous compression—an expansion of the unit cell along the a axis (negative linear compressibility, NLC) upon compression to ~3 GPa. The structural analyses demonstrated that this unusual effect, the first such observation in an energetic crystal, is a consequence of the highly anisotropic response of 3D motifs, comprised of two parallel anions [(C 2 N 8 O 2 ) 2– ] linked with two cations [(NH 3 OH) + ] through four strong hydrogen bonds. The present results demonstrate that the structural stability of TKX-50 is controlled by the strong and highly anisotropic intermolecular interactions, and these may contribute to its shock insensitivity.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Sequence of Silicon Monolayer Structures Grown on a Ru Surface: from a Herringbone Structure to Silicene
Silicon-based two-dimensional (2D) materials are uniquely suited for integration in Si-based electronics. Silicene, an analogue of graphene, was recently fabricated on several substrates and was used to make a field-effect transistor. Here, we report that when Ru(0001) is used as a substrate, a range of distinct monolayer silicon structures forms, evolving toward silicene with increasing Si coverage. Low Si coverage produces a herringbone structure, a hitherto undiscovered 2D phase of silicon. With increasing Si coverage, herringbone elbows evolve into silicene-like honeycomb stripes under tension, resulting in a herringbone-honeycomb 2D superlattice. At even higher coverage, the honeycomb stripes widen and merge coherently to form silicene in registry with the substrate. Scanning tunneling microscopy (STM) was used to image the structures. The structural stability and electronic properties of the Si 2D structures, the interaction between the Si 2D structures and the Ru substrate, and the evolution of the distinct monolayer Si structures were elucidated by density functional theory (DFT) calculations. This work paves the way for further investigations of monolayer Si structures, the corresponding growth mechanisms, and possible functionalization by impurities.
36 MATERIALS SCIENCE↗
Same Precursor, Two Different Products: Comparing the Structural Evolution of In–Ga–O “Gel-Derived” Powders and Solution-Cast Films Using Pair Distribution Function Analysis
Amorphous metal oxides are central to a variety of technological applications. In particular, indium gallium oxide has garnered attention as a thin-film transistor channel layer material. In this work we examine the structural evolution of indium gallium oxide gel-derived powders and thin films using infrared vibrational spectroscopy, X-ray diffraction, and pair distribution function (PDF) analysis of X-ray total scattering from standard and normal incidence thin-film geometries (tfPDF). We find that the gel-derived powders and films from the same aqueous precursor evolve differently with temperature, forming mixtures of Ga-substituted In2O3 and In-substituted β-Ga2O3 with different degrees of substitution. X-ray total scattering and PDF analysis indicate that the majority phase for both the powders and films is an amorphous/nanocrystalline β-Ga2O3 phase, with a minor constituent of In2O3 with significantly larger coherence lengths. This amorphous β-Ga2O3 phase could not be identified using the conventional Bragg diffraction techniques traditionally used to study crystalline metal oxide thin films. The combination of Bragg diffraction and tfPDF provides a much more complete description of film composition and structure, which can be used to detail the effect of processing conditions and structure–property relationships. This study also demonstrates how structural features of amorphous materials, traditionally difficult to characterize by standard diffraction, can be elucidated using tfPDF.
36 MATERIALS SCIENCE↗
Structural crossover in a supercooled metallic liquid and the link to a liquid-to-liquid phase transition
Time-resolved synchrotron measurements were carried out to capture the structure evolution of an electrostatically levitated metallic-glass-forming liquid during free cooling. The experimental data shows a crossover in the liquid structure at ~1000 K, about 115 K below the melting temperature and 150 K above the crystallization temperature. The structure change is characterized by a dramatic growth in the extended-range order below the crossover temperature. Molecular dynamics simulations have identified that the growth of the extended-range order was due to an increased correlation between solute atoms. These results provide structural evidence for a liquid-to-liquid-phase-transition in the supercooled metallic liquid.
Glass transitions↗
Integrating solvation shell structure in experimentally driven molecular dynamics using x-ray solution scattering data
In the past few decades, prediction of macromolecular structures beyond the native conformation has been aided by the development of molecular dynamics (MD) protocols aimed at exploration of the energetic landscape of proteins. Yet, the computed structures do not always agree with experimental observables, calling for further development of the MD strategies to bring the computations and experiments closer together. Here, we report a scalable, efficient MD simulation approach that incorporates an x-ray solution scattering signal as a driving force for the conformational search of stable structural configurations outside of the native basin. We further demonstrate the importance of inclusion of the hydration layer effect for a precise description of the processes involving large changes in the solvent exposed area, such as unfolding. Utilization of the graphics processing unit allows for an efficient all-atom calculation of scattering patterns on-the-fly, even for large biomolecules, resulting in a speed-up of the calculation of the associated driving force. The utility of the methodology is demonstrated on two model protein systems, the structural transition of lysine-, arginine-, ornithine-binding protein and the folding of deca-alanine. We discuss how the present approach will aid in the interpretation of dynamical scattering experiments on protein folding and association.
Hsu, Darren J.↗
Crystal structure of the human NK 1 tachykinin receptor
The NK 1 tachykinin G-protein–coupled receptor (GPCR) binds substance P, the first neuropeptide to be discovered in mammals. Through activation of NK 1 R, substance P modulates a wide variety of physiological and disease processes including nociception, inflammation, and depression. Human NK 1 R (hNK 1 R) modulators have shown promise in clinical trials for migraine, depression, and emesis. However, the only currently approved drugs targeting hNK 1 R are inhibitors for chemotherapy-induced nausea and vomiting (CINV). To better understand the molecular basis of ligand recognition and selectivity, we solved the crystal structure of hNK 1 R bound to the inhibitor L760735, a close analog of the drug aprepitant. Our crystal structure reveals the basis for antagonist interaction in the deep and narrow orthosteric pocket of the receptor. We used our structure as a template for computational docking and molecular-dynamics simulations to dissect the energetic importance of binding pocket interactions and model the binding of aprepitant. Furthermore, the structure of hNK 1 R is a valuable tool in the further development of tachykinin receptor modulators for multiple clinical applications.
60 APPLIED LIFE SCIENCES↗
From cluster structures to nuclear molecules: The role of nodal structure of the single-particle wave functions
In this study, the nodal structure of the density distributions of the single-particle states occupied in rod-shaped, hyper- and megadeformed structures of non-rotating and rotating N ~ Z nuclei has been investigated in detail. The single-particle states with the Nilsson quantum numbers of the [NN0]1/2 (with N from 0 to 5) and [N,N – 1,1]Ω (with N from 1 to 3 and Ω = 1/2, 3/2) types are considered. These states are building blocks of extremely deformed shapes in the nuclei with mass numbers A ≤ 50. Because of (near) axial symmetry and large elongation of such structures, the wave functions of the single-particle states occupied are dominated by a single basis state in cylindrical basis. This basis state defines the nodal structure of the single-particle density distribution. The nodal structure of the single-particle density distributions allows us to understand in a relatively simple way the necessary conditions for α clusterization and the suppression of the α clusterization with the increase of mass number. It also explains in a natural way the coexistence of ellipsoidal mean-field-type structures and nuclear molecules at similar excitation energies and the features of particle-hole excitations connecting these two types of the structures. Lastly, our analysis of the nodal structure of the single-particle density distributions does not support the existence of quantum liquid phase for the deformations and nuclei under study.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Structure of the Fc fragment of the NIST reference antibody RM8671
As the link between antigen binding and immune activation, the antibody Fc region has received extensive structural study. In this report, the structure of the Fc fragment of the NIST IgG1 mAb (reference material 8671) is described at 2.1 Å resolution in space group P 2 1 2 1 2 1 , with approximate unit-cell parameters a = 50, b = 80, c = 138 Å. Prior Fc structures with a wide variety of modifications are also surveyed, focusing on those in the same crystal form. To facilitate the analysis of conformations, a reference frame and a two-parameter metric are proposed, considering the CH 2 domains as mobile with respect to a fixed dimeric CH 3 core. Over several human Fc structures, a significant variation in Fc elbow conformations is observed, which may serve to facilitate the regulation of Fc effector signaling.
Gallagher, D. Travis↗
Role of structure imperfection in the formation of the magnetotransport properties of rare-earth manganites with a perovskite structure
The structure, the structure imperfection, and the magnetoresistance, magnetotransport, and microstructure properties of rare-earth perovskite La{sub 0.3}Ln{sub 0.3}Sr{sub 0.3}Mn{sub 1.1}O{sub 3–δ} manganites are studied by X-ray diffraction, thermogravimetry, electrical resistivity measurement, magnetic, {sup 55}Mn NMR, magnetoresistance measurement, and scanning electron microscopy. It is found that the structure imperfection increases, and the symmetry of a rhombohedrally distorted R3̅c perovskite structure changes into its pseudocubic type during isovalent substitution for Ln = La{sup 3+}, Pr{sup 3+}, Nd{sup 3+}, Sm{sup 3+}, or Eu{sup 3+} when the ionic radius of an A cation decreases. Defect molar formulas are determined for a real perovskite structure, which contains anion and cation vacancies. The decrease in the temperatures of the metal–semiconductor (T{sub ms}) and ferromagnet–paramagnet (T{sub C}) phase transitions and the increase in electrical resistivity ρ and activation energy E{sub a} with increasing serial number of Ln are caused by an increase in the concentration of vacancy point defects, which weaken the double exchange 3d{sup 4}(Mn{sup 3+})–2p{sup 6}(O{sup 2–})–3d{sup 3}(Mn{sup 4+})–V{sup (a)}–3d{sup 4}(Mn{sup 3+}). The crystal structure of the compositions with Ln = La contains nanostructured planar clusters, which induce an anomalous magnetic hysteresis at T = 77 K. Broad and asymmetric {sup 55}Mn NMR spectra support the high-frequency electronic double exchange Mn{sup 3+}(3d{sup 4}) ↔ O{sup 2–}(2p{sup 6}) ↔ Mn{sup 4+}(3d{sup 3}) and indicate a heterogeneous surrounding of manganese by other ions and vacancies. A correlation is revealed between the tunneling magnetoresistance effect and the crystallite size. A composition–structure imperfection–property experimental phase diagram is plotted. This diagram supports the conclusion about a strong influence of structure imperfection on the formation of the magnetic, magnetotransport, and magnetoresistance properties of rare-earth perovskite manganites.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Crystal structure of the receptor-binding domain of botulinum neurotoxin type HA, also known as type FA or H
Botulinum neurotoxins (BoNTs), which have been exploited as cosmetics and muscle-disorder treatment medicines for decades, are well known for their extreme neurotoxicity to humans. They pose a potential bioterrorism threat because they cause botulism, a flaccid muscular paralysis-associated disease that requires immediate antitoxin treatment and intensive care over a long period of time. In addition to the existing seven established BoNT serotypes (BoNT/A–G), a new mosaic toxin type termed BoNT/HA (aka type FA or H) was reported recently. Sequence analyses indicate that the receptor-binding domain (HC) of BoNT/HA is ~84% identical to that of BoNT/A1. However, BoNT/HA responds differently to some potent BoNT/A-neutralizing antibodies (e.g., CR2) that target the HC. Therefore, it raises a serious concern as to whether BoNT/HA poses a new threat to our biosecurity. In this study, we report the first high-resolution crystal structure of BoNT/HA-HC at 1.8 Å. Sequence and structure analyses reveal that BoNT/HA and BoNT/A1 are different regarding their binding to cell-surface receptors including both polysialoganglioside (PSG) and synaptic vesicle glycoprotein 2 (SV2). Furthermore, the new structure also provides explanations for the ~540-fold decreased affinity of antibody CR2 towards BoNT/HA compared to BoNT/A1. Altogether, these new findings advance our understanding of the structure and function of this newly identified toxin at the molecular level, and pave the way for the future development of more effective countermeasures.
59 BASIC BIOLOGICAL SCIENCES↗
Structure-based analysis of CysZ-mediated cellular uptake of sulfate
Sulfur, most abundantly found in the environment as sulfate (SO 4 2- ), is an essential element in metabolites required by all living cells, including amino acids, co-factors and vitamins. However, current understanding of the cellular delivery of SO 4 2- at the molecular level is limited. CysZ has been described as a SO 4 2- permease, but its sequence family is without known structural precedent. Based on crystallographic structure information, SO 4 2- binding and flux experiments, we provide insight into the molecular mechanism of CysZ-mediated translocation of SO 4 2- across membranes. CysZ structures from three different bacterial species display a hitherto unknown fold and have subunits organized with inverted transmembrane topology. CysZ from Pseudomonas denitrificans assembles as a trimer of antiparallel dimers and the CysZ structures from two other species recapitulate dimers from this assembly. In conclusion, mutational studies highlight the functional relevance of conserved CysZ residues.
59 BASIC BIOLOGICAL SCIENCES↗