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At least 739 records · Page 41

Examination of Short- and Long-Range Atomic Order Nanocrystalline SiC and Diamond by Powder Diffraction Methods

The real atomic structure of nanocrystals determines unique, key properties of the materials. Determination of the structure presents a challenge due to inherent limitations of standard powder diffraction techniques when applied to nanocrystals. Alternate methodology of the structural analysis of nanocrystals (several nanometers in size) based on Bragg-like scattering and called the "apparent lattice parameter" (alp) is proposed. Application of the alp methodology to examination of the core-shell model of nanocrystals will be presented. The results of application of the alp method to structural analysis of several nanopowders were complemented by those obtained by determination of the Atomic Pair Distribution Function, PDF. Based on synchrotron and neutron diffraction data measured in a large diffraction vector of up to Q = 25 Angstroms(exp -1), the surface stresses in nanocrystalline diamond and SiC were evaluated.

Palosz, B.↗

Peculiarities of plastic deformation nucleation in copper under nanoindentation

The computer simulation results on the atomic structure of the copper crystallite and its behavior in nanoindentation demonstrate the key role of local structural transformations in nucleation of plasticity. The generation of local structural transformations can be considered as an elementary event during the formation of higher scale defects, including partial dislocations and stacking faults. The cause for local structural transformations, both direct fcc-hcp and reverse hcp-fcc, is an abrupt local increase in atomic volume. A characteristic feature is that the values of local volume jumps in direct and reverse structural transformations are comparable with that in melting and lie in the range 5–7%.

36 MATERIALS SCIENCE↗

Multicell model of La{sub 3}Ga{sub 5}GeO{sub 14} crystal: A new approach to the description of the short-range order of atoms

The multicell model alternative to the model of mixed atomic sites used now is proposed for a single crystal of La{sub 3}Ga{sub 5}GeO{sub 14} belonging to the langasite family. The multicell consists of four unit cells. In three identical cells of the structure, atoms adapt to the Ge atom occupying one of the two 2d positions on the threefold symmetry axis. In the fourth cell, atoms surround the Ge atom located at the 1a position. The multicell model allows one to study the short-range order of atoms by the methods of classical structure analysis based on Bragg scattering. Four high-resolution data sets measured at 295 and 111.5 K are used in the study. The results are obtained with high relative precision (space group P321, Z = 1; at 295 K a = 8.2020(6) Å and c = 5.1065(6) Å, R/wR = 0.81/0.73% for 3829 unique ref lections; at 111.5 K a = 8.1939(1) Å and c = 5.1022(4) Å, R/wR = 0.85/0.76% for 3880 reflections).

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

The ever-evolving active site: transformation of single atoms to extended structures during the Rh-catalyzed reverse water–gas shift reaction

At low temperatures (< 400°C), single atoms of Rh supported on rutile TiO 2 (rTiO 2 ) are responsible for the formation of CO during the reverse water gas shift (RWGS), while methane production is associated with the Rh-TiO 2 interface due to the correlation between methane formation rates and the volume-averaged Rh nanoparticle diameter. As the temperature is increased to >540°C, there is a notable increase in CO selectivity and methane production rates tend towards zero. The time to reach zero depends on the temperature but independent of the initial Rh structure (single atoms and/or nanoparticles), which is controlled by the catalyst preparation method (wetness impregnation versus colloidal nanoparticles). At 600°C and > 4 h time on stream, the catalytic behaviour becomes completely agnostic to the initial Rh structure as well as weight loading, and the catalysts are highly selective for the reverse water gas-shift reaction. Post-reaction HR-TEM image analysis confirms Rh nanoparticles crystallize/order during the reaction; at 400°C, most of the Rh particles are disordered, while at 600°C, they are more ordered (i.e., development of defined faceting). Infrared spectroscopy of CO adsorption on Rh nanoparticles confirms the appearance of defined facets after annealing in nitrogen at high temperatures. Annealing the Rh/rTiO 2 catalysts prior to the RWGS reaction demonstrates the structural transformation of Rh depends only on time and temperature and not on reactant or product fugacity. Sites responsible for stabilizing Rh single atoms are no longer competent at higher temperatures, enabling their integration into existent nanoparticles. As the reaction temperature is increased to temperatures >540°C, the dominant active site for CO production evolves from single atoms to extended Rh structures.

36 MATERIALS SCIENCE↗

Probing the initiation of voltage decay in Li-rich layered cathode materials at the atomic scale

Li-rich layered oxides hold great promise for improving the energy density of present-day Li-ion batteries. However, their application is limited by the voltage decay upon cycling, and the origin of such a phenomenon is poorly understood. A major issue is determining the voltage range over which detrimental reactions originate. In the present study, a unique yet effective approach was employed to probe this issue. Instead of studying the materials during the first cycle, electrochemical behavior and evolution of the atomic structures were compared in extensively cycled specimens under varied charge/discharge voltages. With the upper cutoff voltage lowered from 4.8 to 4.4 V, the voltage decay ceased to occur even after 60 cycles. In the meantime, the material maintained its layered structure without any spinel phase emerging at the surface, which is unambiguously shown by the atomic-resolution Z-contrast imaging and electron energy loss spectroscopy. These results have conclusively demonstrated that structural/chemical changes responsible for the voltage decay began between 4.4 and 4.8 V, where the layered-to-spinel transition was the most dramatic structural change observed. Thus, this discovery lays important groundwork for the mechanistic understanding of the voltage decay in Li-rich layered cathode materials.

25 ENERGY STORAGE↗

Experimental Study into the Stability of Whitlockite and Hydroxylapatite in Basaltic Magmas

Apatite (Ca5(PO4)3(F,Cl,OH)), merrillite (Ca18Na2Mg2(PO4)14), and whitlockite (Ca9(Mg,Fe(2+))(PO4)6[PO3(OH)]) are the primary phosphate minerals found in most planetary materials including rocks from Earth, Moon, Mars, and asteroids. For many years, the terms merrillite and whitlockite have been used interchangeably in the meteorite literature. Much of the confusion regarding the relationship between terrestrial and extraterrestrial 'whitlockite' is based on the presence or absence of hydrogen in the mineral structure. Whitlockite has approximately 8500 ppm H2O, and the term 'merrillite' has been adopted to identify the hydrogen-free form of whitlockite. The atomic structures of merrillite and whitlockite were examined in detail by Hughes et al.. On Earth, whitlockite has been found in rocks from evolved pegmatitic systems and in some mantle rocks. Furthermore, terrestrial whitlockite has been shown to have some merrillite component. For the meteoritic and lunar materials that have been investigated, merrillite appears to be far more common than whitlockite, and it has been proposed that the whitlockite component is unique to terrestrial samples. There are some reports of 'whitlockite' in the meteorite literature; however, these may represent misidentifications of merrillite because there have been no reports of extraterrestrial whitlockite that have been verified through crystal structural studies or analyzed for their H contents. Hughes et al. reported the atomic arrangement of lunar merrillite and demonstrated that the phase is similar to meteoritic merrillite and, predictably, devoid of hydrogen. In a follow-up study, Hughes et al. reported the atomic arrangements of two natural samples of whitlockite, one synthetic whitlockite, and samples of synthetic whitlockite that were heated at 500 C or 1050 C for 24 h. The crystal chemistry and crystal structures of the phases were compared, and it was discovered that the latter treatment resulted in the dehydrogenation of whitlockite to form merrillite.

McCubbin, F. M.↗

Charge density wave order in 1D mirror twin boundaries of single-layer MoSe 2

Here, We provide direct evidence for the existence of isolated, one-dimensional charge density waves at mirror twin boundaries (MTBs) of single-layer semiconducting MoSe 2 . Such MTBs have been previously observed by transmission electron microscopy and have been predicted to be metallic in MoSe 2 and MoS 2 . Our low-temperature scanning tunnelling microscopy/spectroscopy measurements revealed a substantial bandgap of 100 meV opening at the Fermi energy in the otherwise metallic one-dimensional structures. We found a periodic modulation in the density of states along the MTB, with a wavelength of approximately three lattice constants. In addition to mapping the energy-dependent density of states, we determined the atomic structure and bonding of the MTB through simultaneous high-resolution non-contact atomic force microscopy. Density functional theory calculations based on the observed structure reproduced both the gap opening and the spatially resolved density of states.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Oxygen deficiency induced deterioration in microstructure and magnetic properties at Y{sub 3}Fe{sub 5}O{sub 12}/Pt interface

Transport efficiency of pure spin current across the ferromagnetic films adjacent with a nonmagnetic metal is strongly dependent on the spin mixing conductance, which is very sensitive to atomic-level interface conditions. Here, by the means of advanced electron microscopy techniques, atomic structure, electronic structure, and magnetic properties at Y{sub 3}Fe{sub 5}O{sub 12} (YIG)/Pt interface are detailed characterized to correlate the microstructure and magnetic properties with interfacial transport properties. It is found that the order-disorder structure transformation at the interface is accompanied with oxygen deficiency, thus the reduced iron valence and the break of magnetic atom-O-magnetic atom bridges, which is responsible for superexchange interaction and magnetic order. It is also found that the magnetic moment of interfacial iron ions is decreased. The disorder interfacial layer with suppressed magnetism finally contributes to the declined spin transport efficiency. Our results provide the knowledge to control and manipulate the interfacial structure and properties in order to obtain higher spin transport efficiency.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Structural and orientation effects on electronic energy transfer between silicon quantum dots with dopants and with silver adsorbates

Starting from the atomic structure of silicon quantum dots (QDs), and utilizing ab initio electronic structure calculations within the Förster resonance energy transfer (FRET) treatment, a model has been developed to characterize electronic excitation energy transfer between QDs. Electronic energy transfer rates, K{sub EET}, between selected identical pairs of crystalline silicon quantum dots systems, either bare, doped with Al or P, or adsorbed with Ag and Ag{sub 3}, have been calculated and analyzed to extend previous work on light absorption by QDs. The effects of their size and relative orientation on energy transfer rates for each system have also been considered. Using time-dependent density functional theory and the hybrid functional HSE06, the FRET treatment was employed to model electronic energy transfer rates within the dipole-dipole interaction approximation. Calculations with adsorbed Ag show that: (a) addition of Ag increases rates up to 100 times, (b) addition of Ag{sub 3} increases rates up to 1000 times, (c) collinear alignment of permanent dipoles increases transfer rates by an order of magnitude compared to parallel orientation, and (d) smaller QD-size increases transfer due to greater electronic orbitals overlap. Calculations with dopants show that: (a) p-type and n-type dopants enhance energy transfer up to two orders of magnitude, (b) surface-doping with P and center-doping with Al show the greatest rates, and (c) K{sub EET} is largest for collinear permanent dipoles when the dopant is on the outer surface and for parallel permanent dipoles when the dopant is inside the QD.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Na-Montmorillonite Edge Structure and Surface Complexes: An Atomistic Perspective

The edges of montmorillonite (MMT) react strongly with metals and organic matter, but the atomic structure of the edge and its surface complexes are not unambiguous since the experimental isolation of the edge is challenging. In this study, we introduce an atomistic model of a Na MMT edge that is suitable for classical molecular dynamics (MD) simulations, in particular for the B edge, a representative edge surface of 2:1 phyllosilicates. Our model possesses the surface groups identified through density functional theory (DFT) geometry optimizations performed with variation in the structural charge deficit and Mg substitution sites. The edge structure of the classical MD simulations agreed well with previous DFT-based MD simulation results. Our MD simulations revealed an extensive H-bond network stabilizing the Na-MMT edge surface, which required an extensive simulation trajectory. Some Na counter ions formed inner-sphere complexes at two edge sites. The stronger edge site coincided with the exposed vacancy in the dioctahedral sheet; a weaker site was associated with the cleaved hexagonal cavity of the tetrahedral sheet. The six-coordinate Na complexes were not directly associated with the Mg edge site. Our simulations have demonstrated the heterogeneous surface structures, the distribution of edge surface groups, and the reactivity of the MMT edge.

58 GEOSCIENCES↗

Atomic resolution scanning transmission electron microscopy at liquid helium temperatures for quantum materials

Fundamental quantum phenomena in condensed matter, ranging from correlated electron systems to quantum information processors, manifest their emergent characteristics and behaviors predominantly at low temperatures. This necessitates the use of liquid helium (LHe) cooling for experimental observation. Atomic resolution scanning transmission electron microscopy combined with LHe cooling (cryo-STEM) provides a powerful characterization technique to probe local atomic structural modulations and their coupling with charge, spin and orbital degrees-of-freedom in quantum materials. However, achieving atomic resolution in cryo-STEM is exceptionally challenging, primarily due to sample drifts arising from temperature changes and noises associated with LHe bubbling, turbulent gas flow, etc. In this work, we demonstrate atomic resolution cryo-STEM imaging at LHe temperatures using a commercial side-entry LHe cooling holder. Firstly, we examine STEM imaging performance as a function of He gas flow rate, identifying two primary noise sources: He-gas pulsing and He-gas bubbling. Secondly, we propose two strategies to achieve low noise conditions for atomic resolution STEM imaging: either by temporarily suppressing He gas flow rate using the needle valve or by acquiring images during the natural warming process. Lastly, we show the applications of image acquisition methods and image processing techniques in investigating structural phase transitions in Cr 2 Ge 2 Te 6 , CuIr 2 S 4 , and CrCl 3 . In conclusion, our findings represent an advance in the field of atomic resolution electron microscopy imaging for quantum materials and devices at LHe temperatures, which can be applied to other commercial side-entry LHe cooling TEM holders.

36 MATERIALS SCIENCE↗

Heterostructural interface engineering for ultrawide-gap nitrides from first principles: Ta C / Al N and Ta C / Ga N rocksalt-wurtzite interfaces

Epitaxial lattice matching is an important condition for the formation of coherent interfaces with low defect densities. However, lattice-matched substrates with the same crystal structure as the active layer are often not available, suggesting opportunities for utilizing heterostructural interfaces. For example, at high Al contents that are interesting for ultrawide-gap applications in power electronics, Al x ⁢Ga 1-x ⁢N semiconductor alloys in the (0001) orientation of the wurtzite (wz) structure become lattice-matched to (111)-oriented rocksalt (rs) Ta⁢C substrates. To predict the expected interface atomic structures under different synthesis conditions, we perform high-throughput density-functional-theory calculations, using an algorithm for systematic sampling of the possible stacking sequences of the atomic layers on the in-plane hexagonal lattice. The approach considers octahedral, tetrahedral, and prismatic coordination motifs, and is generally applicable for the modeling of commensurate rs/wz heterostructural interfaces. Our results provide guidance for synthesis control of substrate-film bonding and the polarity of ultrawide-gap Al x⁢ Ga 1-x⁢ N alloys on Ta⁢C substrates.

36 MATERIALS SCIENCE↗

Insights from 20 years of the Molecule of the Month

For 20 years, Molecule of the Month articles have highlighted the functional stories of 3D structures found in the Protein Data Bank (PDB). The PDB is the primary archive of atomic structures of biological molecules, currently providing open access to more than 150,000 structures studied by researchers around the world. The wealth of knowledge embodied in this resource is remarkable, with structures that allow exploration of nearly any biomolecular topic, including the basic science of genetic mechanisms, mechanisms of photosynthesis and bioenergetics, and central biomedical topics like cancer therapy and the fight against infectious disease. The central motivation behind the Molecule of the Month is to provide a user-friendly introduction to this rich body of data, charting a path for users to get started with finding and exploring the many available structures. The Molecule of the Month and related materials are updated regularly at the education portal PDB-101 (http://pdb101.rcsb.org/), offering an ongoing resource for molecular biology educators and students around the world.

59 BASIC BIOLOGICAL SCIENCES↗

Building a Consistent and Reproducible Database for Adsorption Evaluation in Covalent–Organic Frameworks

We present a workflow that traces the path from the bulk structure of a crystalline material to assessing its performance in carbon capture from coal's postcombustion flue gases. This workflow is applied to a database of 324 covalent-organic frameworks (COFs) reported in the literature, to characterize their CO 2 adsorption properties using the following steps: (1) optimization of the crystal structure (atomic positions and unit cell) using density functional theory, (2) fitting atomic point charges based on the electron density, (3) characterizing the pore geometry of the structures before and after optimization, (4) computing carbon dioxide and nitrogen isotherms using grand canonical Monte Carlo simulations with an empirical interaction potential, and finally, (5) assessing the CO 2 parasitic energy via process modeling. The full workflow has been encoded in the Automated Interactive Infrastructure and Database for Computational Science (AiiDA). Both the workflow and the automatically generated provenance graph of our calculations are made available on the Materials Cloud, allowing peers to inspect every input parameter and result along the workflow, download structures and files at intermediate stages, and start their research right from where this work has left off. In particular, our set of CURATED (Clean, Uniform, and Refined with Automatic Tracking from Experimental Database) COFs, having optimized geometry and high-quality DFT-derived point charges, are available for further investigations of gas adsorption properties. We plan to update the database as new COFs are being reported.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multi-slice electron ptychographic tomography for three-dimensional phase-contrast microscopy beyond the depth of focus limits

Electron ptychography is a powerful computational method for atomic-resolution imaging with high contrast for weakly and strongly scattering elements. Modern algorithms coupled with fast and efficient detectors allow imaging specimens with tens of nanometers thicknesses with sub-0.5 Ångstrom lateral resolution. However, the axial resolution in these approaches is currently limited to a few nanometers, limiting their ability to solve novel atomic structures ab initio. Here, we experimentally demonstrate multi-slice ptychographic electron tomography, which allows atomic resolution three-dimensional phase-contrast imaging in a volume surpassing the depth of field limits. We reconstruct tilt-series 4D-STEM measurements of a $\mathrm{Co_3O_4}$ nanocube, yielding 2 Å axial and 0.7 Å transverse resolution in a reconstructed volume of $\mathrm{(18.2\,nm)^3}$. Our results demonstrate a 13.5-fold improvement in axial resolution compared to multi-slice ptychography while retaining the atomic lateral resolution and the capability to image volumes beyond the depth of field limit. Multi-slice ptychographic electron tomography significantly expands the volume of materials accessible using high-resolution electron microscopy. We discuss further experimental and algorithmic improvements necessary to also resolve single weakly scattering atoms in 3D.

36 MATERIALS SCIENCE↗

Dynamic STEM-EELS for single-atom and defect measurement during electron beam transformations

This study introduces the integration of dynamic computer vision–enabled imaging with electron energy loss spectroscopy (EELS) in scanning transmission electron microscopy (STEM). This approach involves real-time discovery and analysis of atomic structures as they form, allowing us to observe the evolution of material properties at the atomic level, capturing transient states traditional techniques often miss. Rapid object detection and action system enhances the efficiency and accuracy of STEM-EELS by autonomously identifying and targeting only areas of interest. This machine learning (ML)–based approach differs from classical ML in that it must be executed on the fly, not using static data. We apply this technology to V-doped MoS 2 , uncovering insights into defect formation and evolution under electron beam exposure. This approach opens uncharted avenues for exploring and characterizing materials in dynamic states, offering a pathway to increase our understanding of dynamic phenomena in materials under thermal, chemical, and beam stimuli.

47 OTHER INSTRUMENTATION↗

Structure-based discovery of fiber-binding compounds that reduce the cytotoxicity of amyloid beta

Amyloid protein aggregates are associated with dozens of devastating diseases including Alzheimer’s, Parkinson’s, ALS, and diabetes type 2. While structure-based discovery of compounds has been effective in combating numerous infectious and metabolic diseases, ignorance of amyloid structure has hindered similar approaches to amyloid disease. Here we show that knowledge of the atomic structure of one of the adhesive, steric-zipper segments of the amyloid-beta (Aβ) protein of Alzheimer’s disease, when coupled with computational methods, identifies eight diverse but mainly flat compounds and three compound derivatives that reduce Aβ cytotoxicity against mammalian cells by up to 90%. Although these compounds bind to Aβ fibers, they do not reduce fiber formation of Aβ. Structure-activity relationship studies of the fiber-binding compounds and their derivatives suggest that compound binding increases fiber stability and decreases fiber toxicity, perhaps by shifting the equilibrium of Aβ from oligomers to fibers.

59 BASIC BIOLOGICAL SCIENCES↗

Experimental Study into the Stability of Whitlockite in Basaltic Magmas

Apatite Ca5(PO4)3(F,Cl,OH), merrillite Ca18Na2Mg2(PO4)14, and whitlockite Ca9(Mg,Fe2+)(PO4)6[PO3(OH)] are the primary phosphate minerals found in most planetary materials including rocks from Earth, Moon, Mars, and asteroids [1-2]. For many years, the terms merrillite and whitlockite have been used interchangeably in the meteorite literature. Much of the confusion regarding the relationship between terrestrial and extraterrestrial "whitlockite" is based on the presence or absence of hydrogen in the mineral structure. Whitlockite has approximately 8500 ppm H2O, and the term "merrillite" has been adopted to identify the hydrogen-free form of whitlockite [2]. The atomic structures of merrillite and whitlockite were examined in detail by Hughes et al. [3-4]. On Earth, whitlockite has been found in rocks from evolved pegmatitic systems [2-4] and in some mantle rocks [e.g., 5]. Furthermore, terrestrial whitlockite has been shown to have some merrillite component [4]. For the meteoritic and lunar materials that have been investigated, merrillite appears to be far more common than whitlockite, and it has been proposed that the whitlockite component is unique to terrestrial samples [4]. There are some reports of "whitlockite" in the meteorite literature; however, these likely represent misidentifications of merrillite because there have been no reports of extraterrestrial whitlockite that have been verified through crystal structural studies or analyzed for their H contents. Hughes et al. [3] reported the atomic arrangement of lunar merrillite and demonstrated that the phase is similar to meteoritic merrillite and, predictably, devoid of hydrogen. In a follow-up study, Hughes et al. [4] reported the atomic arrangements of two natural samples of whitlockite, one synthetic whitlockite, and samples of synthetic whitlockite that were heated at 500degC and 1050degC for 24 h. The crystal chemistry and crystal structures of the phases were compared, and it was discovered that the latter treatment resulted in the dehydrogenation of whitlockite to form merrillite. The presence of merrillite vs. whitlockite was widely thought to serve as an indication that magmas were anhydrous [e.g., 6-7]. However, McCubbin et al., [8] determined that merrillite in the martian meteorite Shergotty had no discernible whitlockite component despite its coexistence with OH-rich apatite. Consequently, McCubbin et al., (2014) speculated that the absence of a whitlockite component in Shergotty merrillite and other planetary merrillites may be a consequence of the limited thermal stability of H in whitlockite (stable only at T less than1050degC), which would prohibit merrillite-whitlockite solid-solution at high temperatures. In the present study, we have aimed to test this hypothesis experimentally by examining the stability of whitlockite in basaltic magmas at 1.2 GPa and a temperature range of -1000- 1300degC.

McCubbin, F. M.↗