Direct motif extraction from high resolution crystalline STEM images

During the last decade, automatic data analysis methods concerning different aspects of crystal analysis have been developed, e.g., unsupervised primitive unit cell extraction and automated crystal distortion and defects detection. However, an automatic, unsupervised motif extraction method is still not widely available yet. Here, we propose and demonstrate a novel method for the automatic motif extraction in real space from crystalline images based on a variational approach involving the unit cell projection operator. Due to the non-convex nature of the resulting minimization problem, a multi-stage algorithm is used. First, we determine the primitive unit cell in form of two lattice vectors. Second, a motif image is estimated using the unit cell information. Finally, the motif is determined in terms of atom positions inside the unit cell. The method was tested on various synthetic and experimental HAADF STEM images. The results are a representation of the motif in form of an image, atomic positions, primitive unit cell vectors, and a denoised and a modeled reconstruction of the input image. The method was applied to extract the primitive cells of complex μ-phase structures Nb6.4Co6.6 and Nb7Co6, where subtle differences between their interplanar spacings were determined.

Understanding Alkaline Hydrogen Oxidation Reaction on PdNiRuIrRh High-Entropy-Alloy by Machine Learning Potential

High-entropy alloy (HEA) catalysts have been widely studied in electrolysis. However, identifying atomic structure of HEA with complex atomic arrangement is challenging, which seriously hinders the fundamental understanding of catalytic mechanism. Here, we report a HEA-PdNiRuIrRh catalyst with remarkable mass activity of 3.25 mA μg-1 for alkaline hydrogen oxidation reaction (HOR), which is 8-fold enhancement compared to that of commercial Pt/C. Through machine learning potential-based Monte Carlo simulation, we reveal that the dominant Pd-Pd-Ni/Pd-Pd-Pd bonding environments and Ni/Ru oxophilic sites on HEA surface are beneficial to the optimized adsorption/desorption of *H and enhanced *OH adsorption, contributing to the excellent HOR activity and stability. This work provides significant insights into atomic structure and catalytic mechanism for HEA and offers novel prospects for developing advanced HOR electrocatalysts.

Hydrogens and hydrogen-bond networks in macromolecular MicroED data

Microcrystal electron diffraction (MicroED) is a powerful technique utilizing electron cryo-microscopy (cryo-EM) for protein structure determination of crystalline samples too small for X-ray crystallography. Electrons interact with the electrostatic potential of the sample, which means that the scattered electrons carry information about the charged state of atoms and provide relatively stronger contrast for visualizing hydrogen atoms. Accurately identifying the positions of hydrogen atoms, and by extension the hydrogen bonding networks, is of importance for understanding protein structure and function, in particular for drug discovery. However, identification of individual hydrogen atom positions typically requires atomic resolution data, and has thus far remained elusive for macromolecular MicroED. Recently, we presented the ab initio structure of triclinic hen egg-white lysozyme at 0.87 Å resolution. The corresponding data were recorded under low exposure conditions using an electron-counting detector from thin crystalline lamellae. Here, using these subatomic resolution MicroED data, we identified over a third of all hydrogen atom positions based on strong difference peaks, and directly visualize hydrogen bonding interactions and the charged states of residues. Furthermore, we find that the hydrogen bond lengths are more accurately described by the inter-nuclei distances than the centers of mass of the corresponding electron clouds. We anticipate that MicroED, coupled with ongoing advances in data collection and refinement, can open further avenues for structural biology by uncovering the hydrogen atoms and hydrogen bonding interactions underlying protein structure and function.

Combining Electron Microscopy (EM) and Cross-Linking Mass Spectrometry (XL-MS) for Structural Characterization of Protein Complexes

Structural biology has recently witnessed the benefits of the combined use of two complementary techniques: electron microscopy (EM) and cross-linking mass spectrometry (XL-MS). EM (especially its cryogenic variant cryo-EM) has proven to be a very powerful tool for the structural determination of proteins and protein complexes, even at an atomic level. In a complementary way, XL-MS allows the precise characterization of particular interactions when residues are located in close proximity. When working from low-resolution, negative-staining images and less-defined regions of flexible domains (whose mapping is made possible by cryo-EM), XL-MS can provide critical information on specific amino acids, thus identifying interacting regions and helping to deduce the overall protein structure. The protocol described here is particularly well suited for the study of protein complexes whose intrinsically flexible or transient nature prevents their high-resolution characterization by any structural technique itself.

Engineering of multiferroic BiFeO3 grain boundaries with head-to-head polarization configurations

Confined low dimensional charges with high density such as two-dimensional electron gas (2DEG) at interfaces and charged domain walls in ferroelectrics show great potential to serve as functional elements in future nanoelectronics. However, stabilization and control of low dimensional charges is challenging, as they are usually subject to enormous depolarization fields. Here, we demonstrate a method to fabricate tunable charged interfaces with ~77°, 86° and 94° head-to-head polarization configurations in multiferroic BiFeO₃ thin films by grain boundary engineering. The adjacent grains are cohesively bonded and the boundary is about 1 nm in width and devoid of any amorphous region. Remarkably, the polarization remains almost unchanged near the grain boundaries, indicating the polarization charges are well compensated, i.e., there should be two-dimensional charge gas confined at grain boundaries. Adjusting the tilt angle of the grain boundaries enables tuning the angle of polarization configurations from 71° to 109°, which in turn allows the control of charge density at the grain boundaries. This general and feasible method opens new doors for the application of charged interfaces in next generation nanoelectronics.

Natural abundance 17O MAS NMR and DFT simulations: New insights into the atomic structure of designed micas

Combining ¹⁷O Magic-Angle Spinning (MAS) NMR at natural abundance with DFT calculations is a promising methodology to shed light on the structure and disorder in tetrahedral sheets of designed micas with enhanced properties. Among brittle micas, synthetic mica is an important alternative to natural ones with a swelling sheet-like structure that results in many applications, by exploiting unique characteristics. Lowenstein's rule is one of the main chemical factor that determines the atomic structure of aluminosilicates and furthermore their properties. In the present article, ¹⁷O MAS NMR spectroscopy is used to validate (or not) the agreement of the Lowenstein's rule with the distribution of Si and Al sites in the tetrahedral sheets of synthetic micas. ¹⁷O MAS spectra of synthetic high-charged micas exhibit two regions of signals that revealed two distinguishable oxygen environments, namely Si-O-X (with X = Si, Al^tet, Mg) and Al^tet-O-Y (Y=Mg or Al^tet). DFT calculations were also conducted to obtain the ¹⁷O chemical shift and other NMR features like the quadrupolar coupling constant, C_Q, for all of the oxygen environments encountered in the two model structures, one respecting the Lowenstein's rule and the other involving Al^tet-O-Al^tet and Si-O-Si environments. Our DFT calculations support the ¹⁷O assignment, by confirming that Al^tet-O-3Mg and Al^tet-O-Al^tet oxygen environments show chemical shifts under 30 ppm and more important, with quadrupolar coupling constants of about 1 MHz, in line with the spectral observation. By quantifying the ¹⁷O MAS NMR spectra at natural abundance, we demonstrate that one of the synthetic mica compositions does not meet the Lowenstein's rule.

HRTEM study of individual bone apatite nanocrystals reveals symmetry reduction with respect to P63/m apatite

In this study we present the first crystal structure model for bone apatite based on the analysis of individual nanocrystals by high resolution transmission electron microscopy (HRTEM). Crystallographic image processing of the obtained HRTEM images from different projections indicates symmetry reduction with respect to P6₃/m stoichiometric apatites and the presence of threefold symmetry along the c axis. Based on HRTEM observations and the measured Ca/P = 2 ratio we propose a structural model with phosphate-to-carbonate substitution and O vacancies localized along c axis, which explains the observed loss of 6₃ screw axis parallel, and the shift of mirror plane perpendicular to the c axis. Also, the presence of non-equivalent (010) surfaces has been proven. These results on the atomic structure of bone apatite nanocrystals contribute to the understanding of their biochemically controlled nucleation processes.

Phase Fraction and Evolution of Additively Manufactured (AM) 15-5 Stainless Steel and Inconel 625 AM-Bench Artifacts

A proper understanding of the structure and microstructure of additively manufactured (AM) alloys is essential not only to the prediction and assessment of their material properties, but also to the validation and verification of computer models needed to advance AM technologies. To accelerate AM development, as part of the AM-Bench effort, we conducted rigorous synchrotron-based X-ray scattering and diffraction experiments on two types of AM alloys (AM 15-5 stainless steel and AM Inconel 625). Taking advantage of the high penetration of synchrotron hard X-rays, we determined the phases present in these alloys under different build conditions and their statistically meaningful phase fractions using high-resolution X-ray diffraction. Using in situ multi-scale X-ray scattering and diffraction, we quantitatively analyzed the phase evolution and development of major precipitates in these alloys as a function of time during stress relief heat treatments. These results serve to validate AM microstructure models and provide input to higher-level AM processing and property models to predict the material properties and performances.

Estimation of the thermal and photochemical stabilities of pheromones

The correlation between the kinetic stability of molecules against temperature and variations in their geometric structure under optical excitation is investigated by the example of different organic pheromone molecules sensitive to temperature or ultraviolet radiation using the density functional theory. The kinetic stability is determined by the previously developed method based on the calculation of the probability of extension of any structural bond by a value exceeding the limit value L_мах corresponding to the breaking of the bond under temperature excitation. The kinetic stability calculation only requires the eigenfrequencies and vibrational mode vectors in the molecule ground state to be calculated, without determining the transition states. The weakest bonds in molecules determined by the kinetic stability method are compared with the bond length variations in molecules in the excited state upon absorption of light by a molecule. Good agreement between the results obtained is demonstrated and the difference between them is discussed. The universality of formulations within both approaches used to estimate the stability of different pheromone molecules containing strained cycles and conjugated, double, and single bonds allows these approaches to be applied for studying other molecules. Graphical Abstract Estimation of the thermal and photochemical stabilities of pheromones.

Structural analysis of single nanoparticles in liquid by low-dose STEM nanodiffraction

Liquid-cell TEM has enabled an interdisciplinary community of scientists to carry out atomic- / nano-scale studies of solid/liquid interfaces. Nevertheless, the restricted resolution of TEM in liquid media and the necessity to reduce the electron dose to avoid harmful radiolytic effects induced by the beam have limited the use of high resolution imaging to study the atomic structure of nanomaterials in liquid. Here we show that STEM nanodiffraction can be exploited in liquid-cell TEM experiments to overcome these two limitations. We evidence that this technique allows quick analysis of the structure of single gold nanoparticles whatever their zone axis orientation, which substantially increases the percentage of analysable nanostructures with respect to HRTEM investigations. Moreover, STEM nanodiffraction can also be used in very low dose conditions. The electron dose irradiating the analyzed nanostructures during data acquisition can be reduced by almost four orders of magnitude compared to conventional HRTEM analysis. Finally, dynamical analyses in reciprocal space are used to provide new insights into the shape-dependent rotation of nanocrystals in the liquid-cell.

First-Principles Study on the Stability and STM Image of Borophene

Very recently, borophene (atomic-thin two-dimensional boron sheet) has been successfully synthesized on the Ag(111) surface by deposition. Two kinds of structures were found. However, the identification of the monolayer boron sheets grown on the metal substrate, as well as the stability of different 2D boron sheets, is controversial. By performing the first-principles calculations, present study investigates the atomic structure, stability, and electronic properties of the most possible boron sheets grown on metal surface, namely, buckled triangular, β12, and χ3 types of crystal lattice. Our result shows that all the three freestanding sheets are thermodynamically unstable and all are metallic. On the other hand, our result indicates the Ag(111) substrate stabilize these sheets. Additionally, our simulated STM images of these monoatomic-thin boron sheets on Ag(111) surface reproduce the experiment observations well and clearly identify the as-grown boron sheets.

Exploring the atomic structure of 1.8nm monolayer-protected gold clusters with aberration-corrected STEM

Monolayer-protected (MP) Au clusters present attractive quantum systems with a range of potential applications e.g. in catalysis. Knowledge of the atomic structure is needed to obtain a full understanding of their intriguing physical and chemical properties. Here we employed aberration-corrected scanning transmission electron microscopy (ac-STEM), combined with multislice simulations, to make a round-robin investigation of the atomic structure of chemically synthesised clusters with nominal composition Au₁₄₄(SCH₂CH₂Ph)₆₀ provided by two different research groups. The MP Au clusters were "weighed" by the atom counting method, based on their integrated intensities in the high angle annular dark field (HAADF) regime and calibrated exponent of the Z dependence. For atomic structure analysis, we compared experimental images of hundreds of clusters, with atomic resolution, against a variety of structural models. Across the size range 123-151 atoms, only 3% of clusters matched the theoretically predicted Au₁₄₄(SR)₆₀ structure, while a large proportion of the clusters were amorphous (i.e. did not match any model structure). However, a distinct ring-dot feature, characteristic of local icosahedral symmetry, was observed in about 20% of the clusters.

Crystal structure of raptor adenovirus 1 fibre head and role of the beta-hairpin in siadenovirus fibre head domains

BACKGROUND

Most adenoviruses recognize their host cells via an interaction of their fibre head domains with a primary receptor. The structural framework of adenovirus fibre heads is conserved between the different adenovirus genera for which crystal structures have been determined (Mastadenovirus, Aviadenovirus, Atadenovirus and Siadenovirus), but genus-specific differences have also been observed. The only known siadenovirus fibre head structure, that of turkey adenovirus 3 (TAdV-3), revealed a twisted beta-sandwich resembling the reovirus fibre head architecture more than that of other adenovirus fibre heads, plus a unique beta-hairpin embracing a neighbouring monomer. The TAdV-3 fibre head was shown to bind sialyllactose.

METHODS

Raptor adenovirus 1 (RAdV-1) fibre head was expressed, crystallized and its structure was solved and refined at 1.5 Å resolution. The structure could be solved by molecular replacement using the TAdV-3 fibre head structure as a search model, despite them sharing a sequence identity of only 19 %. Versions of both the RAdV-1 and TAdV-3 fibre heads with their beta-hairpin arm deleted were prepared and their stabilities were compared with the non-mutated proteins by a thermal unfolding assay.

RESULTS

The structure of the RAdV-1 fibre head contains the same twisted ABCJ-GHID beta-sandwich and beta-hairpin arm as the TAdV-3 fibre head. However, while the predicted electro-potential surface charge of the TAdV-3 fibre head is mainly positive, the RAdV-1 fibre head shows positively and negatively charged patches and does not appear to bind sialyllactose. Deletion of the beta-hairpin arm does not affect the structure of the raptor adenovirus 1 fibre head and only affects the stability of the RAdV-1 and TAdV-3 fibre heads slightly.

CONCLUSIONS

The high-resolution structure of RAdV-1 fibre head is the second known structure of a siadenovirus fibre head domain. The structure shows that the siadenovirus fibre head structure is conserved, but differences in the predicted surface charge suggest that RAdV-1 uses a different natural receptor for cell attachment than TAdV-3. Deletion of the beta-hairpin arm shows little impact on the structure and stability of the siadenovirus fibre heads.

Multifunctional facets of retrovirus integrase

The retrovirus integrase (IN) is responsible for integration of the reverse transcribed linear cDNA into the host DNA genome. First, IN cleaves a dinucleotide from the 3’ OH blunt ends of the viral DNA exposing the highly conserved CA sequence in the recessed ends. IN utilizes the 3’ OH ends to catalyze the concerted integration of the two ends into opposite strands of the cellular DNA producing 4 to 6 bp staggered insertions, depending on the retrovirus species. The staggered ends are repaired by host cell machinery that results in a permanent copy of the viral DNA in the cellular genome. Besides integration, IN performs other functions in the replication cycle of several studied retroviruses. The proper organization of IN within the viral internal core is essential for the correct maturation of the virus. IN plays a major role in reverse transcription by interacting directly with the reverse transcriptase and by binding to the viral capsid protein and a cellular protein. Recruitment of several other host proteins into the viral particle are also promoted by IN. IN assists with the nuclear transport of the preintegration complex across the nuclear membrane. With several retroviruses, IN specifically interacts with different host protein factors that guide the preintegration complex to preferentially integrate the viral genome into specific regions of the host chromosomal target. Human gene therapy using retrovirus vectors is directly affected by the interactions of IN with these host factors. Inhibitors directed against the human immunodeficiency virus (HIV) IN bind within the active site of IN containing viral DNA ends thus preventing integration and subsequent HIV/AIDS.

Analysis of grain boundary dynamics using event detection and cumulative averaging

To analyze extended time series of high resolution images, we have employed automated frame-by-frame comparisons that are able to detect dynamic changes in the structure of a grain boundary in Au. Using cumulative averaging of images between events allowed high resolution measurements of the atomic relaxation in the interface with sufficient accuracy for comparison with atomistic models. Cumulative averaging was also used to observe the structural rearrangement of atomic columns at a moving step in the grain boundary. The technique of analyzing changing features in high resolution images by averaging between incidents can be used to deconvolute stochastic events that occur at random intervals and on time scales well beyond that accessible to single-shot imaging.