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Software to manipulate and describe crystal and molecular structures and set up structural refinements from multiple experimental inputs. Calculation and simulation of structure derived physical quantities. Library for creating customized refinements of atomic structures from available experimental and theoretical inputs.
A previous analysis by Albright and Tidman (1972) of the structure of an ionizing potential wave driven through a dense gas by a strong electric field is extended to include atomic structure details of the background atoms and radiative effects, especially, photoionization. It is found that photoionization plays an important role in avalanche propagation. Velocities, electron densities, and temperatures are presented as a function of electric field for both negative and positive breakdown waves in nitrogen.
Extended X ray absorption fine structure (EXAFS) is a powerful technique for probing the local atomic structure of battery and fuel cell materials. The major advantages of EXAFS are that both the probe and the signal are X rays and the technique is element selective and applicable to all states of matter. This permits in situ studies of electrodes and determination of the structure of single components in composite electrodes, or even complete cells. EXAFS specifically probes short range order and yields coordination numbers, bond distances, and chemical identity of nearest neighbors. Thus, it is ideal for structural studies of ions in solution and the poorly crystallized materials that are often the active materials or catalysts in batteries and fuel cells. Studies on typical battery and fuel cell components are used to describe the technique and the capability of EXAFS as a structural tool in these applications. Typical experimental and data analysis procedures are outlined. The advantages and limitations of the technique are also briefly discussed.
Software to manipulate and describe crystal and molecular structures and set up structural refinements from multiple experimental inputs. Calculation and simulation of structure derived physical quantities. Library for creating customized refinements of atomic structures from available experimental and theoretical inputs.
Monolayer molybdenum disulfide (MoS2) is a two-dimensional direct band gap semiconductor with distinctive mechanical, electronic, optical and chemical properties that can be utilized for novel nanoelectronics and optoelectronics devices. The performance of these electronic devices strongly depends on the quality and defect morphology of the MoS2 layers. Yet, little is known about the atomic structure of defects present in monolayer MoS2 and their influences on the material properties. Here we provide a systematic study of various intrinsic structural defects, including point defects, grain boundaries, and edges, in chemical vapor phase grown monolayer MoS2 via direct atomic resolution imaging, and explore their energy landscape and electronic properties using first-principles calculations. We discover that one-dimensional metallic wires can be created via two different types of 60 grain boundaries consisting of distinct 4-fold ring chains. A new type of edge reconstruction, representing a transition state during growth, was also identified, providing insights into the material growth mechanism. The atomic scale study of structural defects presented here brings new opportunities to tailor the properties of MoS2 via controlled synthesis and defect engineering.
Superhard materials consisting of light elements have recently received considerable attention because of their ultrahigh specific strength for a wide range of applications as structural and functional materials. However, the failure mechanisms of these materials subjected to high stresses and dynamic loading remain to be poorly known. We report asymmetric twins in a complex compound, boron carbide (B{sub 4}C), characterized by spherical-aberration-corrected transmission electron microscopy. The atomic structure of boron-rich icosahedra at rhombohedral vertices and cross-linked carbon-rich atomic chains can be clearly visualized, which reveals unusual asymmetric twins with detectable strains along the twin interfaces. This study offers atomic insights into the structure of twins in a complex material and has important implications in understanding the planar defect-related failure of superhard materials under high stresses and shock loading.
We reveal that the elastic moduli of metallic glasses (MGs) invariably vary in a much steeper manner than that predicted by the conventional “rule of mixtures” in individual alloy systems. Such deviations are proved to originate fundamentally from their disordered atomic structures and intrinsic local heterogeneities. By treating the MGs as atomic-level dual phase hybrids, we further propose universal relations to be capable of precisely predicting and designing the elastic constants of MGs. This may contribute to the development of MGs with intended properties and behaviors, and allow new understandings on the structures and properties as well as their relationships in MGs.
The atomic structure of a bacterial aryl acylamidase (EC 3.5.1.13; AAA) is reported and structural features are investigated to better understand the catalytic profile of this enzyme. Structures of AAA were determined in its native form and in complex with the analgesic acetanilide, p-acetaminophenol, at 1.70 Å and 1.73 Å resolutions, respectively. The overall structural fold of AAA was identified as an α/β fold class, exhibiting an open twisted β-sheet core surrounded by α-helices. The asymmetric unit contains one AAA molecule and the monomeric form is functionally active. The core structure enclosing the signature sequence region, including the canonical Ser-cisSer-Lys catalytic triad, is conserved in all members of the Amidase Signature enzyme family. The structure of AAA in a complex with its ligand reveals a unique organization in the substrate-binding pocket. The binding pocket consists of two loops (loop1 and loop2) in the amidase signature sequence and one helix (α10) in the non-amidase signature sequence. We identified two residues (Tyr{sup 136} and Thr{sup 330}) that interact with the ligand via water molecules, and a hydrogen-bonding network that explains the catalytic affinity over various aryl acyl compounds. The optimum activity of AAA at pH > 10 suggests that the reaction mechanism employs Lys{sup 84} as the catalytic base to polarize the Ser{sup 187} nucleophile in the catalytic triad. - Highlights: • We determined the first structure of a bacterial aryl acylamidase (EC 3.5.1.13). • Structure revealed spatially distinct architecture of the substrate-binding pocket. • Hydrogen-bonding with Tyr{sup 136} and Thr{sup 330} mediates ligand-binding and substrate.
We investigated the atomic structure and infrared spectra of the alumina(0001)/water interface, using first-principles molecular dynamics simulations based on density functional theory within the generalized gradient approximation. The computed structural properties of the interface are in good agreement with the results of synchrotron X-ray experiments. In this work detailed analyses of the computed infrared spectra revealed two types of water molecules at the hydrophilic oxide/water interface: molecules participating in strong “ice-like” hydrogen bonding with the oxide surface and molecules involved in weaker “liquid-like” hydrogen bonding. Our results provide a molecular interpretation of the “ice-like” and “liquid-like” bands observed in sum-frequency vibrational spectroscopy experiments and underscore the significance of strong hydrogen-bonding interactions in determining the orientation of interfacial water molecules.
This NEUP Project aimed to generate accurate atomic structural models of nuclear waste glasses by using large-scale molecular dynamics-based computer simulations and to use these models to investigate self-diffusion behaviors, interfacial structures, and hydrated gel structures formed during dissolution of these glasses. The goal was to obtain realistic and accurate short and medium range structures of these complex oxide glasses, to provide a mechanistic understanding of the dissolution behaviors, and to generate reliable information with predictive power in designing nuclear waste glasses for long-term geological storage. Looking back of the research accomplishments of this project, most of the scientific goals initially proposed have been achieved through intensive research in the three and a half year period of the project. This project has also generated a wealth of scientific data and vibrant discussions with various groups through collaborations within and outside of this project. Throughout the project one book chapter and 14 peer reviewed journal publications have been generated (including one under review) and 16 presentations (including 8 invited talks) have been made to disseminate the results of this project in national and international conference. Furthermore, this project has trained several outstanding graduate students and young researchers for future workforce in nuclear related field, especially on nuclear waste immobilization. One postdoc and four PhD students have been fully or partially supported through the project with intensive training in the field material science and engineering with expertise on glass science and nuclear waste disposal
Solid state {sup 93}Nb nuclear magnetic resonance spectroscopy has been employed to investigate the atomic and electronic structures in Ni-Nb based metallic glass (MG) model system. {sup 93}Nb nuclear magnetic resonance (NMR) isotropic metallic shift of Ni{sub 60}Nb{sub 35}Sn{sub 5} has been found to be ∼100 ppm lower than that of Ni{sub 60}Nb{sub 35}Zr{sub 5} MG, which is correlated with their intrinsic fracture toughness. The evolution of {sup 93}Nb NMR isotropic metallic shifts upon alloying is clearly an electronic origin, as revealed by both local hyperfine fields analysis and first-principle computations. This preliminary result indicates that, in addition to geometrical considerations, atomic form factors should be taken into a description of atomic structures for better understanding the mechanical behaviors of MGs.
High-temperature ultrafine-precipitate-strengthened (HT-UPS) steel has potential applications in advanced nuclear reactors as a structural material. However, little is currently known about its response to neutron irradiation. This research provides insight into the neutron irradiation-induced physicochemical changes of the major constituents in HT-UPS steels, including Fe, Cr, and Ni, using synchrotron X-ray absorption near edge structure (XANES) and diffraction. This study is the first known investigation using XANES to characterize HT-UPS steel to analyze the evolution of the atomic level chemistry. It was found that following irradiation, nucleation, ballistic dispersion, and/or coarsening of Cr 23 C 6 precipitates occurred at very low neutron irradiation fluences, from 0.003 displacements per atom (dpa) up to 0.3 dpa, at ~600°C, which were at least an order of magnitude lower than previous studies. Calculations of the angular momentum projections, partial density of states, and the XANES spectra confirmed the experimental findings of the Cr 23 C 6 precipitate evolution. In contrast, the local atomic structure around Fe and Ni atoms demonstrated irradiation resistance.
Here, the atomic structure of amorphous (FeCoNi) 70 Ti 10 B 20 alloy synthesized by mechanical alloying was investigated using high energy synchrotron X-ray diffraction and inverse Monte Carlo simulations of pair distribution functions. Empirical potential structure refinement indicates a chemical short-range order at the length scales of 2.1–2.5 Å via local atomic arrangements forming deformed bcc-like clusters. The structural model obtained was described by bond lengths, coordination numbers, and bond angle distribution functions determined for the first neighbor atoms by x-ray scattering supplemented with 3D Monte Carlo simulations.
Here, a detailed account of the local atomic structure and disorder at 5 K across the phase diagram of the high-temperature superconductor K x Fe 2 - y Se 2 - z S z ( 0 ≤ z ≤ 2) is obtained from neutron total scattering and associated atomic pair distribution function (PDF) approaches. Various model-independent and model-dependent aspects of the analysis reveal a high level of structural complexity on the nanometer length scale. Evidence is found for considerable disorder in the c -axis stacking of the ${\mathrm{FeSe}}_{1{-}x}{\mathrm{S}}_{x}$ slabs without observable signs of turbostratic character of the disorder. In contrast to the related FeCh (Ch = S, Se)-type superconductors, substantial Fe-vacancies are present in ${\mathrm{K}}_{x}{\mathrm{Fe}}_{2{-}y}{\mathrm{Se}}_{2{-}z}{\mathrm{S}}_{z}$ deemed detrimental for superconductivity when ordered. Our study suggests that the distribution of vacancies significantly modifies the iron-chalcogen bond-length distribution, in agreement with observed evolution of the PDF signal. A crossoverlike transition is observed at a composition of z ≈ 1 , from a correlated disorder state at the selenium end to a more vacancy-ordered (VO) state closer to the sulfur end of the phase diagram. The S-content-dependent measures of the local structure are found to exhibit distinct behavior on either side of this crossover, correlating well with the evolution of the superconducting state to that of a magnetic semiconductor toward the z ≈ 2 end. The behavior reinforces the idea of the intimate relationship of correlated Fe-vacancy order in the local structure and the emergent electronic properties.
The electronic, optical and chemical properties of two-dimensional transition metal dichalcogenides strongly depend on their three-dimensional atomic structure and crystal defects. Using Re-doped MoS 2 as a model system, here we present scanning atomic electron tomography as a method to determine three-dimensional atomic positions as well as positions of crystal defects such as dopants, vacancies and ripples with a precision down to 4 pm. We further measure the three-dimensional bond distortion and local strain tensor induced by single dopants. By directly offering these experimental three-dimensional atomic coordinates to density functional theory, we obtain more accurate electronic band structures than derived from conventional density functional theory calculations that relies on relaxed three-dimensional atomic coordinates. We anticipate that scanning atomic electron tomography not only will be generally applicable to determine the three-dimensional atomic coordinates of two-dimensional materials, but also will enable ab initio calculations to better predict the physical, chemical and electronic properties of these materials.
The structure of MX 3 transition metal trichalcogenides (TMTs, with M a transition metal and X a chalcogen) is typified by one-dimensional (1D) chains weakly bound together via van der Waals interactions. This structural motif is common across a range of M and X atoms (e.g. NbSe 3 , HfTe 3 , TaS 3 ), but not all M and X combinations are stable. We report here that three new members of the MX 3 family which are not stable in bulk, specifically NbTe 3 , VTe 3 , and TiTe 3 , can be synthesized in the few- to single-chain limit via nano-confined growth within the stabilizing cavity of multi-walled carbon nanotubes. Transmission electron microscopy (TEM) and atomic-resolution scanning transmission electron microscopy (STEM) reveal the chain-like nature and the detailed atomic structure. The synthesized materials exhibit behavior unique to few-chain quasi-1D structures, such as multi-chain spiraling and a trigonal anti-prismatic rocking distortion in the single-chain limit. Density functional theory (DFT) calculations provide insight into the crystal structure and stability of the materials, as well as their electronic structure.
Nanoporous silica-rich gel formed on silicate glass surfaces during dissolution in aqueous environment is critical in elucidating the corrosion mechanisms and the long-term residual dissolution behaviors. Silica gel models were created using two types of methods with reactive force field-based molecular dynamics simulations. The results show that the remnant silica gels created from the ISG bulk structure have a more isolated and closed pore morphology and slightly higher glass network connectivity. This contrasts with the gel structures created by hydrogarnet defect formation that exhibit more connected pore morphologies. The remnant gel structures show lower water diffusivity which was explained by the nano-confinement effect of water molecules due to frequent interactions of water molecules with adjacent silica walls and the more isolated pore morphology in the remnant gel structures. These results reveal the complexity in terms of micro and atomic structures of these silica gels, and both structure features have impact on water transport in the gel layer hence the passivating effect that controls the long-term dissolution behavior of these glasses.
InGaAs is one of the III–V active semiconductors used in modern high-electron-mobility transistors or high-speed electronics. ZnO is a good candidate material to be inserted as a tunneling insulator layer at the metal–semiconductor junction. A key consideration in many modern devices is the atomic structure of the hetero-interface, which often ultimately governs the electronic or chemical process of interest. Here, a complementary suite of in situ synchrotron X-ray techniques (fluorescence, reflectivity and absorption) as well as modeling is used to investigate both structural and chemical evolution during the initial growth of ZnO by atomic layer deposition (ALD) on In 0.53 Ga 0.47 As substrates. Prior to steady-state growth behavior, we discover a transient regime characterized by two stages. First, substrate-inhibited ZnO growth takes place on InGaAs terraces. This leads eventually to the formation of a 1 nm-thick, two-dimensional (2D) amorphous layer. Second, the growth behavior and its modeling suggest the occurrence of dense island formation, with an aspect ratio and surface roughness that depends sensitively on the growth condition. Lastly, ZnO ALD on In 0.53 Ga 0.47 As is characterized by 2D steady-state growth with a linear growth rate of 0.21 nm cy -1 , as expected for layer-by-layer ZnO ALD.