Atomic Resolution Analysis Research Articles

Atomic-Resolution Analysis of 2-D and Thin Film Quantum Materials

Atomic-Resolution Analysis of 2-D and Thin Film Quantum Materials

Atomic resolution analysis of extended defects and Mg agglomeration in Mg-ion-implanted GaN and their impacts on acceptor formation

We carried out atomic-scale observations of Mg-ion-implanted GaN by transmission electron microscopy (TEM) and atom probe tomography (APT) to clarify the crystallographic structures of extended defects and Mg agglomerations that form during post-implantation annealing. The complementary TEM and APT analyses have shown that Mg atoms agglomerate at dislocations that bound extended defects. The concentration of Mg is higher at the dislocations with a larger Burgers vector. This indicates that Mg agglomeration is caused by the pressure at the dislocations. Mg concentration in highly Mg-rich regions is 1 at. %, which exceeds the solubility limit of Mg in GaN. We investigated isothermal and isochronal evolution of the defects by TEM, cathodoluminescence analysis, and positron annihilation spectroscopy. The results indicated that the intensity of donor–acceptor pair emission increases with the annealing temperature and duration and reaches a maximum after elimination of the extended defects with highly Mg-rich regions. These results strongly suggest that such extended defects reduce the acceptor formation and that they as well as the previously reported compensating centers, such as N-related vacancies, can inhibit the formation of p-type GaN. The mechanism by which the extended defects reduce acceptor formation is discussed.

Evolution in X-ray analysis from micro to atomic scales in aberration-corrected scanning transmission electron microscopes.

X-ray analysis is one of the most robust approaches to extract quantitative information from various materials and is widely used in various fields ever since Raimond Castaing established procedures to analyze electron-induced X-ray signals for materials characterization '70 years ago'. The recent development of aberration-correction technology in a (scanning) transmission electron microscopes (S/TEMs) offers refined electron probes below the Å level, making atomic-resolution X-ray analysis possible. In addition, the latest silicon drift detectors allow complex detector arrangements and new configurational designs to maximize the collection efficiency of X-ray signals, which make it feasible to acquire X-ray signals from single atoms. In this review paper, recent progress and advantages related to S/TEM-based X-ray analysis will be discussed: (i) progress in quantification for materials characterization including the recent applications to light element analysis, (ii) progress in analytical spatial resolution for atomic-resolution analysis and (iii) progress in analytical sensitivity toward single-atom detection and analysis in materials. Both atomic-resolution analysis and single-atom analysis are evaluated theoretically through multislice-based calculation for electron propagation in oriented crystalline specimen in combination with X-ray spectrum simulation.

Driving force of biomolecular liquid-liquid phase separation probed by nuclear magnetic resonance spectroscopy.

The assembly of biomolecular condensates is driven by liquid-liquid phase separation. To understand the structure and functions of these condensates, it is essential to characterize the underlying driving forces, e.g., protein-protein and protein-RNA interactions. As both structured and low-complexity domains are involved in the phase separation process, NMR is probably the only technique that can be used to depict the binding topology and interaction modes for the structured and nonstructured domains simultaneously. Atomic-resolution analysis for the intramolecular and intermolecular interactions between any pair of components sheds light on the mechanism for phase separation and biomolecular condensate assembly and disassembly. Herein, we describe the procedures used for the most extensively employed NMR techniques to characterize key interactions for biomolecular phase separation.

Driving force of biomolecular liquid–liquid phase separation probed by nuclear magnetic resonance spectroscopy

The assembly of biomolecular condensates is driven by liquid–liquid phase separation. To understand the structure and functions of these condensates, it is essential to characterize the underlying driving forces, <i>e</i>.<i>g</i>., protein–protein and protein–RNA interactions. As both structured and low-complexity domains are involved in the phase separation process, NMR is probably the only technique that can be used to depict the binding topology and interaction modes for the structured and nonstructured domains simultaneously. Atomic-resolution analysis for the intramolecular and intermolecular interactions between any pair of components sheds light on the mechanism for phase separation and biomolecular condensate assembly and disassembly. Herein, we describe the procedures used for the most extensively employed NMR techniques to characterize key interactions for biomolecular phase separation.

Atomically precise single-crystal structures of electrically conducting 2D metal-organic frameworks.

Electrically conducting 2D metal-organic frameworks (MOFs) have attracted considerable interest, as their hexagonal 2D lattices mimic graphite and other 2D van der Waals stacked materials. However, understanding their intrinsic properties remains a challenge because their crystals are too small or of too poor quality for crystal structure determination. Here, we report atomically precise structures of a family of 2D π-conjugated MOFs derived from large single crystals of sizes up to 200 μm, allowing atomic-resolution analysis by a battery of high-resolution diffraction techniques. A designed ligand core rebalances the in-plane and out-of-plane interactions that define anisotropic crystal growth. We report two crystal structure types exhibiting analogous 2D honeycomb-like sheets but distinct packing modes and pore contents. Single-crystal electrical transport measurements distinctively demonstrate anisotropic transport normal and parallel to the π-conjugated sheets, revealing a clear correlation between absolute conductivity and the nature of the metal cation and 2D sheet packing motif.

A baculoviral system for the production of human β-glucocerebrosidase enables atomic resolution analysis.

The lysosomal glycoside hydrolase β-glucocerebrosidase (GBA; sometimes called GBA1 or GCase) catalyses the hydrolysis of glycosphingolipids. Inherited deficiencies in GBA cause the lysosomal storage disorder Gaucher disease (GD). Consequently, GBA is of considerable medical interest, with continuous advances in the development of inhibitors, chaperones and activity-based probes. The development of new GBA inhibitors requires a source of active protein; however, the majority of structural and mechanistic studies of GBA today rely on clinical enzyme-replacement therapy (ERT) formulations, which are incredibly costly and are often difficult to obtain in adequate supply. Here, the production of active crystallizable GBA in insect cells using a baculovirus expression system is reported, providing a nonclinical source of recombinant GBA with comparable activity and biophysical properties to ERT preparations. Furthermore, a novel crystal form of GBA is described which diffracts to give a 0.98 Å resolution unliganded structure. A structure in complex with the inactivator 2,4-dinitrophenyl-2-deoxy-2-fluoro-β-D-glucopyranoside was also obtained, demonstrating the ability of this GBA formulation to be used in ligand-binding studies. In light of its purity, stability and activity, the GBA production protocol described here should circumvent the need for ERT formulations for structural and biochemical studies and serve to support GD research.

Atomic Resolution Analyses of Isocoumarin Derivatives for Inhibition of Lysyl-tRNA Synthetase.

Aminoacyl-tRNA synthetases, the essential enzyme family for protein translation, are attractive targets for developing antibacterial, antifungal, and antiparasitic agents and for treating other human diseases. The antimalarial natural product cladosporin was discovered recently as a novel lysyl-tRNA synthetase (LysRS) specific inhibitor. Here, we report a thorough analysis of cladosporin derivatives using chemical synthesis, biophysical, and biochemical experiments. A series of isocoumarin derivatives with only one nonhydrogen atom/bond change per compound was synthesized. These changes include replacements of methyltetrahydropyran moiety by methylcyclohexane or cyclohexane, lactone by lactam, hydroxyl groups by methoxyl groups, and dismission of the chiral center at C3 with a Δ3,4 double bond. We evaluated these compounds by thermal shift assays and enzymatic experiments and further studied their molecular recognition by the Plasmodium falciparum LysRS through total five high-resolution crystal structures. Our results showed that the methyltetrahydropyran moiety of cladosporin could be replaced by a more stable methylcyclohexane without reducing binding ability. Removing the methyl group from the methylcyclohexane moiety slightly decreased the interaction with LysRS. Besides, the replacement with a lactam group or a conjugated Δ3,4 double bond within the scaffold could be two more options to optimize the compound. Lastly, the two phenolic hydroxyl groups were critical for the compounds to bind LysRS. The detailed analyses at atomic resolution in this study provide a foundation for the further development of new antibiotics from cladosporin derivatives.

Ultrafast 1H MAS NMR Crystallography for Natural Abundance Pharmaceutical Compounds.

Magic angle spinning (MAS) NMR is a powerful method for the study of pharmaceutical compounds, and probes with spinning frequencies above 100 kHz enable an atomic-resolution analysis of sub-micromole quantities of fully protonated solids. Here, we present an ultrafast NMR crystallography approach for structural characterization of organic solids at MAS frequencies of 100-111 kHz. We assess the efficiency of 1H-detected experiments in the solid state and demonstrate the utility of 2D and 3D homo- and heteronuclear correlation spectra for resonance assignments. These experiments are demonstrated for an amino acid, U-13C,15N-histidine, and also for the significantly larger, natural product Posaconazole, an antifungal compound investigated at natural abundance. Our results illustrate the power for characterizing organic molecules, enabled by exploiting the increased 1H resolution and sensitivity at MAS frequencies above 100 kHz.

Direct evaluation of threading dislocations in 4H-SiC through large-angle convergent beam electron diffraction

ABSTRACTIn this study, the structures of threading dislocations (TDs) in a 4H-SiC epilayer were directly characterised using large-angle convergent beam electron diffraction (LACBED) via transmission electron microscopy (TEM), by examining the splitting of reflections due to the presence of dislocation lines. Previously, X-ray topography (XRT) mapping in combination with ray-tracing simulations has been shown to be an efficient method for imaging and differentiating common TD types and variants in 4H-SiC. In this work, the validity of XRT-based results was verified by LACBED through direct evaluation and differentiation of the Burgers vectors and physical crystallographic features of all threading edge, threading screw, and threading mixed dislocations variants. The LACBED results agreed with the XRT-based results with respect to TD type and variant. The screw-sense or half-plane orientation and Burgers vector determined from LACBED analysis for each TD were self-consistent. For the case of -TEDs, atomic-resolution analysis of the core structure, through high-angle annular dark field scanning TEM, directly revealed two half-planes, each with a Burgers vector component, and the sum of these components was confirmed to be . Finally, an algorithm for efficient LACBED analysis of TDs in 4H-SiC was discussed.

Atomic resolution analyses on defects in nanocrystalline Cu-based alloys generated by severe plastic deformation

Bulk nanocrystalline (NC) materials possess high volume fraction (up to 50%) of grain boundaries (GBs), which contributes significantly to their mechanical and physical properties. Nevertheless, high density of dislocations at GBs and the associated strain fields complicate the analyses on the fine GBs structures of NC materials. Here, taking NC Cu-based alloys as model systems, the atomic-scale configurations of dislocations and typical GBs triggered by severe plastic deformation are well investigated using aberration-corrected high-resolution transmission electron microscopy and geometric phase analysis. A periodic array of extended dislocations with a spacing of 2.2 nm is found to form low-angle GBs (LAGBs) in NC Cu-based alloys. The interaction between dislocations and twins play a crucial role in forming the GBs of NC. Twin boundaries (TBs) in NC Cu-based alloys can serve as barriers for trapping dislocations, which in turn tune the TBs directly evolving into LAGBs or high-angle GBs. In addition, a symmetric 6° [001] tilt LAGB is also analyzed to be composed of a/2〈100〉 edge dislocations, which are activated by the a/2〈110〉 full dislocation dissociation or simple shear deformation of {100} planes. Our study offers insights into the atomic resolution structures of dislocations and GBs in NC materials.

Microscopic origin of highly enhanced current carrying capabilities of thin NdFeAs(O,F) films.

Fe-based superconductors present a large variety of compounds whose physical properties strongly depend on the crystal structure and chemical composition. Among them, the so-called 1111 compounds show the highest critical temperature Tc in the bulk form. Here we demonstrate the realization of excellent superconducting properties in NdFeAs(O1−xFx). We systematically investigated the correlation between the microstructure at the nanoscale and superconductivity in an epitaxial 22 nm NdFeAs(O1−xFx) thin film on a MgO single crystalline substrate (Tc = 44.7 K). Atomic resolution analysis of the microstructure by transmission electron microscopy and atom probe tomography identified several defects and other inhomogeneities at the nanoscale that can act as extrinsic pinning centers. X-Ray diffraction and transmission electron microscopy displayed a broad variation of the a-axis lattice parameter either due to a partially strained layer at the interface to the substrate, high local strain at dislocation arrays, mosaicity, or due to composition variation within the film. The electrical transport properties are substantially affected by intrinsic pinning and a matching field corresponding to the film thickness and associated with the Bean–Livingston surface barrier of the surfaces. The thin film showed a self-field critical current density Jc(4.2 K) of ∼7.6 MA cm−2 and a record pinning force density of Fp ≈ 1 TN m−3 near 35 T for H‖ab at 4.2 K. These investigations highlight the role of the microstructure in fine-tuning and possibly functionalizing the superconductivity of Fe-based superconductors.

Localization of Yttrium Segregation within YSZ Grain Boundary Dislocation Cores

Ionic conductivity blocking at grain boundaries in polycrystalline electrolytes is one of the main obstacles that need to be overcome in order to improve the performance of solid state fuel cells and batteries. To this aim, harnessing the physical properties of grain boundaries in ionic conducting materials such as yttria‐stabilized zirconia (YSZ) down to the atomic scale arises as a greatly important task. Here a structural and compositional analysis of a single grain boundary in a 9 mol.% yttria content YSZ bicrystal by means of aberration‐corrected scanning transmission electron microscopy is presented. Studies here combine strain and compositional atomic resolution analysis with density‐functional‐theory calculations in order to find a preferential segregation of yttrium to the expansive atomic sites at the grain boundary dislocation cores. These results address a crucial step toward the understanding of the physical properties of grain boundaries down to atomic dimensions.

Atomic Resolution Imaging and Analysis of Graphene at Low Acceleration Voltages using Aberration Corrected Microscope with Cold Field Emission Gun

Atomic Resolution Imaging and Analysis of Graphene at Low Acceleration Voltages using Aberration Corrected Microscope with Cold Field Emission Gun

Sublattice reversal in GaAs/Ge/GaAs heterostructures grown on (113)B GaAs substrates

GaAs/Ge/GaAs heterostructures were grown on high-index (113)B GaAs substrates by molecular beam epitaxy. Sublattice reversal in GaAs/Ge/GaAs was identified by comparing the anisotropic etching profile of the epitaxial sample with that for reference (113)A and (113)B GaAs substrates. The shape of the resulting mesa for the lower GaAs layer was similar to that for the reference (113)B GaAs substrate, whereas that for the upper GaAs layer was similar to that for the reference (113)A GaAs substrate. An atomic-resolution analysis was also conducted by mapping using energy-dispersive X-ray spectroscopy, whereby the sublattice reversal was directly observed through the atomic arrangements.

Atomic resolution structure of serine protease proteinase K at ambient temperature

Atomic resolution structures (beyond 1.20 Å) at ambient temperature, which is usually hampered by the radiation damage in synchrotron X-ray crystallography (SRX), will add to our understanding of the structure-function relationships of enzymes. Serial femtosecond crystallography (SFX) has attracted surging interest by providing a route to bypass such challenges. Yet the progress on atomic resolution analysis with SFX has been rather slow. In this report, we describe the 1.20 Å resolution structure of proteinase K using 13 keV photon energy. Hydrogen atoms, water molecules, and a number of alternative side-chain conformations have been resolved. The increase in the value of B-factor in SFX suggests that the residues and water molecules adjacent to active sites were flexible and exhibited dynamic motions at specific substrate-recognition sites.

Atomically resolved chemical ordering at the nm-thick TiO precipitate/matrix interface in V-4Ti-4Cr alloy

We have used advanced analytical electron microscopy to characterise the local structure and chemistry at the interface between nm-thick TiO precipitates and the V-based matrix in a V-4Ti-4Cr alloy. Our results reveal the presence of an intergrowth between the fcc TiO and bcc vanadium structures, with a repeat lattice distance that equals 2.5 times the vanadium lattice parameter along the c-axis. Our atomic resolution analysis of the interface will impact the mechanistic understanding of its interaction with interstitials and radiation-induced lattice defects, and consequently trigger the development of improved alloy structures with interfaces engineered for enhanced radiation tolerance.

Atomic-Resolution Analysis of Perovskite from the Early Solar System

Atomic-Resolution Analysis of Perovskite from the Early Solar System

Atomic-resolution analysis of degradation phenomena in SOFCS: A case study of SO2 poisoning in LSM cathodes

Solid oxide fuel cell (SOFC) degradation studies are often performed by scanning transmission electron microscopy (STEM), scanning electron microscopy (SEM), and X-ray diffraction (XRD). However, it is difficult to use these techniques to observe processes occurring at the smallest scales. Here, we study sulfur poisoning of La0.8Sr0.2MnO3−δ (LSM) cathodes as a model case for atomic resolution scanning transmission electron microscopy (STEM) analysis with energy dispersive X-ray diffraction (EDX). Significant SrSO4 nanoparticle formation is observed after SO2 exposure, especially at grain boundaries in the LSM. In addition, La2O3 formation inside the grain was also confirmed. The formation of SrSO4 is identified with irreversible SOFC degradation, in addition to simple SO2 adsorption, which is reversible.

Atomic-resolution analysis for the effects of heat treatment temperatures on the growth of chemically-ordered regions in Pb(Mg&lt;sub&gt;1/3&lt;/sub&gt;Nb&lt;sub&gt;2/3&lt;/sub&gt;)O&lt;sub&gt;3&lt;/sub&gt; thin films

Atomic-resolution analysis for the effects of heat treatment temperatures on the growth of chemically-ordered regions in Pb(Mg&lt;sub&gt;1/3&lt;/sub&gt;Nb&lt;sub&gt;2/3&lt;/sub&gt;)O&lt;sub&gt;3&lt;/sub&gt; thin films