Structural and Dynamic Heterogeneity of Capillary Wave Fronts at Aqueous Interfaces
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Chemistry↗
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High-Pressure Crystal Structures of an Insensitive Energetic Crystal: 1,1-Diamino-2,2-dinitroethene
Abstract not provided
Dreger, Zbigniew A.↗
Effect of Functional and Electron Correlation on the Structure and Spectroscopy of the Al 2 O 3 (001)–H 2 O Interface
Oxide–water interfaces are ubiquitous, with many applications in industry and the environment, yet there is a great deal of controversy over their properties and microscopic structure. This controversy stems, in part, from the unique H-bond networks formed at different surface terminations and mineral compositions. Density functional theory simulations of these interfaces require an accurate description of both the oxide mineral and water in diverse H-bond environments. Thus, herein we simulate the Al 2 O 3 (001)–H 2 O interface using the PBE, PBE-TS, RPBE, SCAN, and HSE06-TS functionals to determine how calculated interfacial properties depend on the choice of functional. We find that the structure of the first few layers of water at the surface is determined by electron correlation in a way that cannot be approximated using semiemipirical van der Waals corrections. Of the functionals investigated, we find that SCAN yields the most accurate interfacial structure, dynamics, and sum frequency generation spectrum. Furthermore, SCAN leads to a reduction in the order of the 2D H-bond network of water at the alumina surface predicted by GGA functionals, leading to a significant decrease in the anisotropy of the diffusion coefficient at the surface. We emphasize the importance of using a functional which accurately describes electron correlation for more complex oxides, such as transition-metal oxides, where electron correlation may play an even greater role in determining the structure and dynamics of the oxide–water interface.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Contrast-Matched Small-Angle X-ray Scattering from a Heavy-Atom-Labeled Protein in Structure Determination: Application to a Lead-Substituted Calmodulin-Peptide Complex
The information content in 1-D solution X-ray scattering profiles is generally restricted to low-resolution shape and size information that, on its own, cannot lead to unique 3-D structures of biological macromolecules comparable to all-atom models derived from X-ray crystallography or NMR spectroscopy. Here we show that contrast-matched X-ray scattering data collected on a protein incorporating specific heavy-atom labels in 65% aqueous sucrose buffer can dramatically enhance the power of conventional small- and wide-angle X-ray scattering (SAXS/WAXS) measurements. Under contrast-matching conditions the protein is effectively invisible and the main contribution to the X-ray scattering intensity arises from the heavy atoms, allowing direct extraction of pairwise distances between them. In combination with conventional aqueous SAXS/WAXS data, supplemented by NMR-derived residual dipolar couplings (RDCs) measured in a weakly aligning medium, we show that it is possible to position protein domains relative to one another within a precision of 1 Å. We demonstrate this approach with respect to the determination of domain positions in a complex between calmodulin, in which the four Ca 2+ ions have been substituted by Pb 2+ , and a target peptide. The uniqueness of the resulting solution is established by an exhaustive search over all models compatible with the experimental data, and could not have been achieved using aqueous SAXS and RDC data alone. Moreover, we show that the correct structural solution can be recovered using only contrast-matched SAXS and aqueous SAXS/WAXS data.
Grishaev, Alexander↗
Three-dimensional atomic packing in amorphous solids with liquid-like structure
Liquids and solids are two fundamental states of matter. However, our understanding of their three-dimensional atomic structure is mostly based on physical models. Here we use atomic electron tomography to experimentally determine the three-dimensional atomic positions of monatomic amorphous solids, namely a Ta thin film and two Pd nanoparticles. We observe that pentagonal bipyramids are the most abundant atomic motifs in these amorphous materials. Instead of forming icosahedra, the majority of pentagonal bipyramids arrange into pentagonal bipyramid networks with medium-range order. Molecular dynamics simulations further reveal that pentagonal bipyramid networks are prevalent in monatomic metallic liquids, which rapidly grow in size and form more icosahedra during the quench from the liquid to the glass state. Furthermore, these results expand our understanding of the atomic structures of amorphous solids and will encourage future studies on amorphous–crystalline phase and glass transitions in non-crystalline materials with three-dimensional atomic resolution.
36 MATERIALS SCIENCE↗
I35W collapse, rebuild, and structural health monitoring - challenges associated with structural health monitoring of bridge systems
During evening rush hour traffic on August 1, 2007, the major interstate highway bridge carrying I35W over the Mississippi River in Minneapolis catastrophically failed, tragically taking the lives of thirteen people and injuring many more. The steel truss bridge, constructed in 1967, was undergoing deck reconstruction during the collapse, and was estimated to carry more than 140,000 vehicles daily. This tragedy generated great interest in employment of structural health monitoring systems. The I35W St. Anthony Falls Bridge, a post-tensioned concrete box bridge constructed to replace the collapsed steel truss bridge, contains over 500 instruments to monitor the structural behavior. Numerical models of the bridge are being developed and calibrated to the collected data obtained from truck load tests and thermal effects. The data obtained over the first few years of monitoring are being correlated with the calibrated models and used to develop the baseline bridge behavior. This information is being used to develop a system to monitor and interpret the long-term behavior of the bridge. This paper describes the instrumentation, preliminary results from the data and model calibration, the plan for developing long-term monitoring capabilities, and the challenges associated with structural health monitoring of bridge systems. In addition, opportunities and directions for future research required to fully realize the objectives of structural health monitoring are described.
42 ENGINEERING↗
Electronic structure of Pt based topological Heusler compounds with C1{sub b} structure and 'zero band gap'
Besides of their well-known wide range of properties it was recently shown that many of the heavy Heusler semiconductors with 1:1:1 composition and C1{sub b} structure exhibit a zero band gap behavior and are topological insulators induced by their inverted band structure. In the present study, the electronic structure of the Heusler compounds PtYSb and PtLaBi was investigated by bulk sensitive hard x-ray photoelectron spectroscopy. The measured valence band spectra are clearly resolved and in well agreement to the first-principles calculations of the electronic structure of the compounds. The experimental results give clear evidence for the zero band gap state.
36 MATERIALS SCIENCE↗
The Partonic Structure of the Pion at Large-x
Unlike the proton, whose parton distributions have been extracted using abundant data, the pion has been relatively ignored. The pion, nevertheless, is a crucial part of the current understanding of the nucleon's parton distributions and of the binding of the nucleon into a nucleus. The pion's structure becomes more intriguing when its dual roles as a light quark-antiquark system and as QCD's Goldstone boson are considered. One source of data on the pion's structure is pion-induced Drell-Yan scattering. Two recent re-analyses of such data are discussed here.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Structural evolution of Ga-Ge-Te glasses by combined EXAFS and XPS analysis
The structural evolution of Ga{sub x}Ge{sub y}Te{sub 100−x−y} glasses in the vicinity of GeTe{sub 4}-GaTe{sub 3} pseudo-binary tie-line is determined with high-resolution X-ray photoelectron (XPS) and extended X-ray absorption fine structure (EXAFS) spectroscopies. The analysis of XPS data is complicated by similar electronegativity values for the constituent chemical elements, but then the interpretation is facilitated by information from complementary EXAFS analysis of the structure around each element independently. The results show 4/4/2 coordination for Ga/Ge/Te atoms and absence of Ga(Ge)-Ge(Ga) bonds or extended Te clusters in significant concentrations within the whole range of studied composition. The observed structural features correlate well with the measured basic physical properties of Ga-containing germanium telluride glasses.
36 MATERIALS SCIENCE↗
Atomic and electronic structures of lattice mismatched Cu 2 O/TiO 2 interfaces
Heterojunction interfaces between metal oxides are often highly lattice mismatched. The atomic and electronic structures of such interfaces, however, are not well understood. Here, we have synthesized Cu 2 O/TiO 2 heterojunction thin films with 13% lattice mismatch and studied the interface via experimental methods and large-scale density function theory calculations of supercells containing 1300 atoms. We find that an interface of epitaxial quality is formed via a coincidence site lattice of 8 Cu 2 O unit cells matching 9 TiO 2 unit cells. Calculations reveal the existence of a dislocation core of the O sublattices at the interface and a random arrangement of one layer of interfacial Cu atoms. The interfacial electronic structure is found to be mostly determined by the interfacial Cu distribution, rather than by the O dislocation core. The conduction band minimum and valence band maximum states are spatially separated, and there is no strongly localized state near the core.
74 ATOMIC AND MOLECULAR PHYSICS↗
Direct observation of the structural and electronic changes of Li{sub 2}MnO{sub 3} during electron irradiation
This study focuses on the effects of electron beam induced irradiation to the layered oxide Li{sub 2}MnO{sub 3}. Aberration-corrected scanning transmission electron microscopy and electron energy loss spectroscopy are used to characterize structural and electronic transitions in the material during irradiation, with a focus on changes in Mn valence and O content. This truly in situ irradiation allows for specific particle tracking, dose quantification, and real-time observation, while demonstrating many parallels to the oxide's structure evolution observed during electrochemical cycling. Furthermore, it is demonstrated that typical imaging conditions are not severe enough to induce damage to the pristine oxide.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis
Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe0.55Se0.45 (Tc = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe1 x Sex structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by their electronic signature and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Effect of interfacial structures on spin dependent tunneling in epitaxial L1{sub 0}-FePt/MgO/FePt perpendicular magnetic tunnel junctions
Epitaxial FePt(001)/MgO/FePt magnetic tunnel junctions with L1{sub 0}-FePt electrodes showing perpendicular magnetic anisotropy were fabricated by molecular beam epitaxial growth. Tunnel magnetoresistance ratios of 21% and 53% were obtained at 300 K and 10 K, respectively. Our previous work, based on transmission electron microscopy, confirmed a semi-coherent interfacial structure with atomic steps (Kohn et al., APL 102, 062403 (2013)). Here, we show by x-ray photoemission spectroscopy and first-principles calculation that the bottom FePt/MgO interface is either Pt-terminated for regular growth or when an Fe layer is inserted at the interface, it is chemically bonded to O. Both these structures have a dominant role in spin dependent tunneling across the MgO barrier resulting in a decrease of the tunneling magnetoresistance ratio compared with previous predictions.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Isotopic studies of trans- and cis-HOCO using rotational spectroscopy: Formation, chemical bonding, and molecular structures
HOCO is an important intermediate in combustion and atmospheric processes because the OH + CO → H + CO{sub 2} reaction represents the final step for the production of CO{sub 2} in hydrocarbon oxidation, and theoretical studies predict that this reaction proceeds via various intermediates, the most important being this radical. Isotopic investigations of trans- and cis-HOCO have been undertaken using Fourier transform microwave spectroscopy and millimeter-wave double resonance techniques in combination with a supersonic molecular beam discharge source to better understand the formation, chemical bonding, and molecular structures of this radical pair. We find that trans-HOCO can be produced almost equally well from either OH + CO or H + CO{sub 2} in our discharge source, but cis-HOCO appears to be roughly two times more abundant when starting from H + CO{sub 2}. Using isotopically labelled precursors, the OH + C{sup 18}O reaction predominately yields HOC{sup 18}O for both isomers, but H{sup 18}OCO is observed as well, typically at the level of 10%-20% that of HOC{sup 18}O; the opposite propensity is found for the {sup 18}OH + CO reaction. DO + C{sup 18}O yields similar ratios between DOC{sup 18}O and D{sup 18}OCO as those found for OH + C{sup 18}O, suggesting that some fraction of HOCO (or DOCO) may be formed from the back-reaction H + CO{sub 2}, which, at the high pressure of our gas expansion, can readily occur. The large {sup 13}C Fermi-contact term (a{sub F}) for trans- and cis-HO{sup 13}CO implicates significant unpaired electronic density in a σ-type orbital at the carbon atom, in good agreement with theoretical predictions. By correcting the experimental rotational constants for zero-point vibration motion calculated theoretically using second-order vibrational perturbation theory, precise geometrical structures have been derived for both isomers.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Gas phase structures and charge localization in small aluminum oxide anions: Infrared photodissociation spectroscopy and electronic structure calculations
We use cryogenic ion trap vibrational spectroscopy in combination with quantum chemical calculations to study the structure of mono- and dialuminum oxide anions. The infrared photodissociation spectra of D{sub 2}-tagged AlO{sub 1-4}{sup −} and Al{sub 2}O{sub 3-6}{sup −} are measured in the region from 400 to 1200 cm{sup −1}. Structures are assigned based on a comparison to simulated harmonic and anharmonic IR spectra derived from electronic structure calculations. The monoaluminum anions contain an even number of electrons and exhibit an electronic closed-shell ground state. The Al{sub 2}O{sub 3-6}{sup −} anions are oxygen-centered radicals. As a result of a delicate balance between localization and delocalization of the unpaired electron, only the BHLYP functional is able to qualitatively describe the observed IR spectra of all species with the exception of AlO{sub 3}{sup −}. Terminal Al–O stretching modes are found between 1140 and 960 cm{sup −1}. Superoxo and peroxo stretching modes are found at higher (1120-1010 cm{sup −1}) and lower energies (850-570 cm{sup −1}), respectively. Four modes in-between 910 and 530 cm{sup −1} represent the IR fingerprint of the common structural motif of dialuminum oxide anions, an asymmetric four-member Al–(O){sub 2}–Al ring.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Evolution of structure and transport properties of the Ba 8 Cu 16 P 30 clathrate-I framework with the introduction of Ga
Two type-I clathrates were synthesized by introducing Ga into the framework of the Ba 8 Cu 16 P 30 type-I clathrate. The introduction of minute amounts of Ga, 1.9% Ga/M total (where M total = Cu + Ga), resulted in the disturbance of the completely ordered Pbcn superstructure of Ba 8 Cu 16 P 30 . Ba 8 Cu 15.43(2) Ga 0.3 P 30.26(3) crystallizes in a partially ordered orthorhombic Pmna clathrate-I superstructure with five out of 15 framework sites being jointly occupied by metal+phosphorus. Increasing the Ga content resulted in all framework sites being occupied by metal + phosphorus in the archetype cubic Pm n clathrate-I crystal structure of Ba 8 Cu 14.5(3) Ga 1.3 P 30.2(4) with 8.2% Ga/M total . A combination of energy dispersive x-ray spectroscopy, inductively coupled plasma mass spectroscopy, and single crystal x-ray diffraction was used to determine the structures alongside the compositions. The positional disorder was verified by 31 P solid state NMR spectroscopy. Characterization of the transport properties indicated that the Ga-substituted samples exhibit higher Seebeck coefficients and electrical resistivities compared to its pristine counterpart, in line with the expected reduction of the hole concentration due to Ga/Cu substitution. Moderate improvements in the thermoelectric power factor and overall figure-of-merit were observed for samples with 6.9% and 3.8% Ga/M total as compared to those for the pristine Ba 8 Cu 16 P 30 clathrate. Finally, band structure calculations shed light on how Ga substitution affects the electronic structure and thermoelectric properties of studied clathrates.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structures of the cGMP-dependent protein kinase in malaria parasites reveal a unique structural relay mechanism for activation
The cyclic guanosine-3',5'-monophosphate (cGMP)-dependent protein kinase (PKG) was identified >25 y ago; however, efforts to obtain a structure of the entire PKG enzyme or catalytic domain from any species have failed. In malaria parasites, cooperative activation of PKG triggers crucial developmental transitions throughout the complex life cycle. We have determined the cGMP-free crystallographic structures of PKG from Plasmodium falciparum and Plasmodium vivax, revealing how key structural components, including an N-terminal autoinhibitory segment (AIS), four predicted cyclic nucleotide-binding domains (CNBs), and a kinase domain (KD), are arranged when the enzyme is inactive. The four CNBs and the KD are in a pentagonal configuration, with the AIS docked in the substrate site of the KD in a swapped-domain dimeric arrangement. We show that although the protein is predominantly a monomer (the dimer is unlikely to be representative of the physiological form), the binding of the AIS is necessary to keep Plasmodium PKG inactive. A major feature is a helix serving the dual role of the N-terminal helix of the KD as well as the capping helix of the neighboring CNB. A network of connecting helices between neighboring CNBs contributes to maintaining the kinase in its inactive conformation. We propose a scheme in which cooperative binding of cGMP, beginning at the CNB closest to the KD, transmits conformational changes around the pentagonal molecule in a structural relay mechanism, enabling PKG to orchestrate rapid, highly regulated developmental switches in response to dynamic modulation of cGMP levels in the parasite.
59 BASIC BIOLOGICAL SCIENCES↗
Structural Basis for the Acyltransferase Activity of Lecithin: Retinol Acyltransferase-like Proteins
Lecithin:retinol acyltransferase-like proteins, also referred to as HRAS-like tumor suppressors, comprise a vertebrate subfamily of papain-like or NlpC/P60 thiol proteases that function as phospholipid-metabolizing enzymes. HRAS-like tumor suppressor 3, a representative member of this group, plays a key role in regulating triglyceride accumulation and energy expenditure in adipocytes and therefore constitutes a novel pharmacological target for treatment of metabolic disorders causing obesity. Here, we delineate a catalytic mechanism common to lecithin:retinol acyltransferase-like proteins and provide evidence for their alternative robust lipid-dependent acyltransferase enzymatic activity. We also determined high resolution crystal structures of HRAS-like tumor suppressor 2 and 3 to gain insight into their active site architecture. Based on this structural analysis, two conformational states of the catalytic Cys-113 were identified that differ in reactivity and thus could define the catalytic properties of these two proteins. Finally, these structures provide a model for the topology of these enzymes and allow identification of the protein-lipid bilayer interface. This study contributes to the enzymatic and structural understanding of HRAS-like tumor suppressor enzymes.
59 BASIC BIOLOGICAL SCIENCES↗