Atomic Structure Research Articles

Neutron diffraction: a primer

Abstract Because of the neutron’s special properties, neutron diffraction may be considered one of the most powerful techniques for structure determination of crystalline and related matter. Neutrons can be released from nuclear fission, from spallation processes, and also from low-energy nuclear reactions, and they can then be used in powder, time-of-flight, texture, single crystal, and other techniques, all of which are perfectly suited to clarify crystal and magnetic structures. With high neutron flux and sufficient brilliance, neutron diffraction also excels for diffuse scattering, for in situ and operando studies as well as for high-pressure experiments of today’s materials. For these, the wave-like neutron’s infinite advantage (isotope specific, magnetic) is crucial to answering important scientific questions, for example, on the structure and dynamics of light atoms in energy conversion and storage materials, magnetic matter, or protein structures. In this primer, we summarize the current state of neutron diffraction (and how it came to be), but also look at recent advances and new ideas, e.g., the design of new instruments, and what follows from that.

Numerical studies on lutetium isotopic selective photoionization based on a three-step ionization scheme

Numerical studies of lutetium selective photoionization have been carried out based on a three-step photoionization scheme, 5d6s2 2D3/2 → 5d6s6p4Fo5/2 → 5d6s7s4D3/2 → (53,375 cm−1)1/2 → Lu+, by the density matrix theory. Atomic hyperfine structures and magnetic sublevels are considered in our photoionization dynamics model. To examine the effectiveness of this model, the simulated 176Lu ion strengths are compared with the experimental results, and the simulated excitation cross sections of 176Lu excitation channels are compared with the analytical and experimental results. Semi-quantitative agreements are acquired for these two cases. On this basis, selective photoionization processes of two lutetium isotopes are simulated and discussed. Considering the ionization probability and abundance of target isotope, the 8.5-9.5-8.5 two-step excitation channel is optimal for 176Lu enrichment from natural lutetium. The influences of laser parameters and atomic Doppler broadening are presented numerically and optimization excitation conditions are identified. For the co-propagating excitation lasers, extra-narrow laser bandwidth (at the magnitude of 0.1 GHz) and atomic Doppler broadening (smaller than 0.3 GHz) is required. A new time-delayed configuration is proposed to implement multiple counter-propagating laser exposures for high target isotope abundance at the larger atomic Doppler broadening.

Morphology and kinetics of nanoheterogeneities in Fe81Ga19–Tb alloy: A small-angle neutron scattering study

The formation of nanoprecipitates in the Fe81Ga19 alloy doped with Tb (∼0.1 at. %) was studied by small-angle neutron scattering (SANS). Measurements at room temperature for several samples pre-aged at a fixed temperature in the range of (300–700)°C revealed a dilute system of precipitates with a characteristic size at nanoscale (<1000 Å) growing with an increase in ageing temperature. In situ measurements during isothermal ageing at 300 °C for 3 h revealed fast (order of 10 min) formation of precipitates. SANS analysis is consistent with the results of neutron diffraction experiments, which suggest the microstructure of this alloy as a matrix of disordered atomic structure (A2 phase) with embedded precipitates of the structurally and magnetically ordered D03 phase.

Surface and interface physics driven by quantum materials

Abstract Electronic states at boundaries of crystals, such as surfaces, interfaces, edges, hinges, corners, and extremities, play crucial roles in emerging quantum materials like graphene and similar monatomic-layer materials, van der Waals crystals, and topological insulators. Electronic states at such boundaries are different from those inside the three- or two-dimensional crystals, not only due to the truncation of crystal lattices, but also due to space-inversion-symmetry breaking and difference of topology in band structures across the boundaries. Such quantum materials are expected to advance energy-saving/-harvesting technology as well as quantum computing/information technology because of exotic phenomena such as electron’s spin-momentum locking, pure spin current, dissipation-less charge current, non-reciprocal current, possible Majorana fermions, and so on. In this review, their fundamental concepts are introduced from the viewpoint of surface physics, in which atomic and electronic structures as well as charge/spin transport properties are directly probed using state-of-art techniques.

Sophisticated construction of single-atom cobalt catalyst based on microbial hyphae for high-performance hydrogenation

Utilizing biomass as a versatile catalyst building platform holds tremendous promise for catalyst design. In this study, we demonstrate a facile and effective method to fabricate high-performance catalysts using Trichoderma afroharzianum hyphae derived carbon fiber (TAHCF) embedded with Co1-N3P1 active sites for nitroaromatic hydrogenation. This strategy leverages the intrinsic self-assembly and metal ion adsorption capabilities of Trichoderma afroharzianum (TA). During the carbonization process, amino acid-rich fungi undergo transformation into biochar substrates co-doped with functional heteroatoms, facilitating the creation of TAHCF single-atom catalyst. Moreover, the catalytic performance can be further enhanced by tailoring the coordination structure of metal atoms on the carbon substrates. Remarkably, we achieve a high turnover frequency of 1553 h−1 for the hydrogenation of nitrobenzene, along with exceptional conversion and selectivity for various nitro compounds with the metal loading as low as 0.02 wt%. Our study presents a characteristic synthetic method that advances the design of single-atom catalysts by leveraging the inherent structure characteristics of biomass in the pursuit of energy sustainability.

Computational Screening of Promising Deep-Ultraviolet Light Emitters.

Deep-ultraviolet (DUV) light sources are technologically highly important, but DUV light-emitting materials are extremely rare; AlN and its alloys are the only materials known so far, significantly limiting the chemical and structural spaces for materials design. Here, we perform a high-throughput computational search for DUV light emitters based on a set of carefully designed screening criteria relating to the sophisticated electronic structure. In this way, we successfully identify 5 promising material candidates that exhibit comparable or higher radiative recombination coefficients than AlN, including BeGeN2, Mg3NF3, KCaBr3, KHS, and RbHS. Further, we unveil the unique features in the atomic and electronic structures of DUV light emitters and elucidate the fundamental genetic reasons why DUV light emitters are extremely rare. Our study not only guides the design and synthesis of efficient DUV light emitters but also establishes the genetic nature of ultrawide-band-gap semiconductors in general.

Topological ordering during flexible to rigid transitions in disordered networks

This contribution focuses on the structural origin of flexible to rigid transitions and the possible underlying intermediate phase which have been reported to occur in a variety of network glasses such as chalcogenides or modified oxides. Here, using molecular dynamics simulations of densified glass-forming liquids, 2SiO 2 -Na 2 O, which are known to display a numerical reversibility window as a signature of an intermediate phase, we focus on structural functions emphasizing topological ordering using the Bhatia–Thornton formalism. Results not only reveal that densified silicates display topological ordering on lengthscales of about 25 Å, but also display obvious threshold behaviors close to the isostatic condition when the network undergoes a flexible to rigid transition. The mechanical constraint count of the atomic network structure reveals that a typical lengthscale characterizing the decay of topological correlations emerges for stressed rigid systems at ≃3.5 Å, whereas small wavevector oscillations are found to be minimal when the isostatic condition is merely satisfied. An additional analysis building on diffusivity and liquid entropy suggests that the locus of flexible to rigid transitions has also connections with water-like anomalies of densified tetrahedral liquids.

Molecular dynamics simulations into rolling scraping of nickel-copper bilayer film

In order to investigate the nanoscale friction mechanism and deformation behavior of nickel-copper bilayer film under rolling scraping, the effects of different factors during friction process such as the translation velocity, rotation velocity, radius of abrasive grain, contact depth, texture direction and crystallographic orientation are analyzed through molecular dynamics methods in terms of contact force, atomic lattice structure, internal substrate dislocation, kinetic energy and temperature. Results show that the contact force increases with the increase of the translation velocity or the decrease of the rotation velocity. Abrasive grains in a purely rolling state cause the most serious damage to the substrate. The contact force increases with the increase of contact depth or the decrease of abrasive grain radius. The crystallographic orientation has a significant effect on rolling scraping process and there is a crystallographic orientation with the minimum contact force. The degrees of substrate dislocation and the numbers of lattice reconstruction atoms under different factors and levels vary widely.

Bragg Spot Finder (BSF): a new machine-learning-aided approach to deal with spot finding for rapidly filtering diffraction pattern images

Macromolecular crystallography contributes significantly to understanding diseases and, more importantly, how to treat them by providing atomic resolution 3D structures of proteins. This is achieved by collecting X-ray diffraction images of protein crystals from important biological pathways. Spotfinders are used to detect the presence of crystals with usable data, and the spots from such crystals are the primary data used to solve the relevant structures. Having fast and accurate spot finding is essential, but recent advances in synchrotron beamlines used to generate X-ray diffraction images have brought us to the limits of what the best existing spotfinders can do. This bottleneck must be removed so spotfinder software can keep pace with the X-ray beamline hardware improvements and be able to see the weak or diffuse spots required to solve the most challenging problems encountered when working with diffraction images. In this paper, we first present Bragg Spot Detection (BSD), a large benchmark Bragg spot image dataset that contains 304 images with more than 66 000 spots. We then discuss the open source extensible U-Net-based spotfinder Bragg Spot Finder (BSF), with image pre-processing, a U-Net segmentation backbone, and post-processing that includes artifact removal and watershed segmentation. Finally, we perform experiments on the BSD benchmark and obtain results that are (in terms of accuracy) comparable to or better than those obtained with two popular spotfinder software packages (Dozor and DIALS), demonstrating that this is an appropriate framework to support future extensions and improvements.

Electron impact broadening and atomic data for As IV-V, Mo V and In V spectral lines

Missing Stark broadening parameters for 33 spectral lines of several arsenic, molybdenum and indium ions (7 As IV, 4 As V, 12 Mo V and 10 In V lines) have been calculated using a quantum-mechanical method. All the considered spectral lines for As IV and As V have been detected for the first time in the atmospheres of cool DO white dwarfs HD 149499 B and p=HZ 21, these four As V lines that have been discovered in HD 149499 B are also present in the UV spectrum of hot white dwarf (WD) RE 0503−289. All the considered spectral lines for Mo V have been recently discovered for the first time in the ultraviolet (UV) spectrum of the DO-type white dwarf (WD) RE 0503−289. Also, the ten considered lines for In V have been detected in the ultraviolet (UV) spectrum of the DO-type white dwarf (WD) RE 0503−289, that five among those discovered — recently — for the first time. This recent discovery encourages us to calculate their Stark widths to fill the lack of the data base STARK-B and for use in investigations of observed spectra in such stars. Before the Stark widths evaluation, two calculation steps have been carried out : in the first step, we calculate the atomic structure and then the electron-ion collision as a second step using the sequence of the codes (superstructure, distorted wave, and jajom) of University College London. We provide our results for these lines at different temperature values and at density Ne=1017 cm−3.

Plutonium oxide melt structure and covalency.

Advances in nuclear power reactors include the use of mixed oxide fuel, containing uranium and plutonium oxides. The high-temperature behaviour and structure of PuO2-x above 1,800 K remain largely unexplored, and these conditions must be considered for reactor design and planning for the mitigation of severe accidents. Here, we measure the atomic structure of PuO2-x through the melting transition up to 3,000 ± 50 K using X-ray scattering of aerodynamically levitated and laser-beam-heated samples, with O/Pu ranging from 1.57 to 1.76. Liquid structural models consistent with the X-ray data are developed using machine-learned interatomic potentials and density functional theory. Molten PuO1.76 contains some degree of covalent Pu-O bonding, signalled by the degeneracy of Pu 5f and O 2p orbitals. The liquid is isomorphous with molten CeO1.75, demonstrating the latter as a non-radioactive, non-toxic, structural surrogate when differences in the oxidation potentials of Pu and Ce are accounted for. These characterizations provide essential constraints for modelling pertinent to reactor safety design.

Topographical and morphological changes of the single‐crystal (La0.3Sr0.7)(Al0.65Ta0.35)O3 (001) surface treated with high‐purity deionized water

The topological and morphological changes of the (001) surface of single‐crystal (La0.3Sr0.7)(Al0.65Ta0.35)O3 during treatment with high‐purity deionized water (DI) have been investigated by atomic force microscopy and scanning transmission electron microscopy (STEM). Etching by DI treatment at room temperature proceeded mainly in anisotropic etching mode, resulting in rectangular etch pits with {001} inner surfaces forming in the surface. The dominant etching mode changed from anisotropic to isotropic with increasing DI‐treatment temperature, and the lowest surface roughness occurred for DI treatment at 50°C for 60 min. Direct observation of the atomic structure of the surface by STEM showed that the etched surface was the B‐site‐terminated (001) surface after anisotropic etching at 50°C for 60 min, in which the B‐site‐terminated atomic layer was found to maintain the B‐site ordered structure existing in the crystal. This is because DI treatment, which does not require high‐temperature heat treatment of the substrate, suppresses element diffusion, sublimation, and formation of point defects on and in the vicinity of the surface.

Cluster-based multidimensional scaling embedding tool for data visualization

Abstract We present a new technique for visualizing high-dimensional data called cluster MDS (cl-MDS), which addresses a common difficulty of dimensionality reduction methods: preserving both local and global structures of the original sample in a single 2-dimensional visualization. Its algorithm combines the well-known multidimensional scaling (MDS) tool with the k-medoids data clustering technique, and enables hierarchical embedding, sparsification and estimation of 2-dimensional coordinates for additional points. While cl-MDS is a generally applicable tool, we also include specific recipes for atomic structure applications. We apply this method to non-linear data of increasing complexity where different layers of locality are relevant, showing a clear improvement in their retrieval and visualization quality.

Influence of Zr element on the atomic structure of Al-Cu alloy liquid

The relationship among chemical composition, structure and glass-forming ability in multicomponent alloys is a long-standing puzzle due to the complexity of compositions. In this work, Al77.8Cu22.2 and Al70Cu20Zr10 amorphous alloy liquids were investigated by combining high-energy X-ray diffraction at a synchrotron facility, ab-initio molecular dynamics and reverse Monte Carlo simulations. The analysis of short- and medium-range order structures of two liquid alloys show that the addition of Zr element increases the number of cluster types and makes the distribution of cluster content more uniform, and enhances the structural heterogeneity and correlation of clusters with high five-fold symmetry. These findings reveal the influence of Zr element on the atomic structure of the Al-Cu liquid alloy and deepen the understanding of Al-based metallic glasses formation.

Tailored Local Electronic Environment of Co-N4 Sites in Cobalt Phthalocyanines for Enhanced CO2 Reduction Reaction.

Atomically dispersed Co-N4-based catalysts have been recently emerging as one of the most promising candidates for facilitating CO2 reduction reaction (CO2RR). The local electronic environment of Co-N4 sites in these catalysts is considered to play a critical role in adjusting the catalytic performance, the effort of which however is not yet clearly verified. Herein, a series of cobalt phthalocyanines with different peripheral substituents including unsubstituted phthalocyanine Co(II) (CoPc), 2,9,16,23-tetramethoxyphthalocyaninato Co(II) (CoPc-4OCH3), and 2,9,16,23-tetranitrophthalocyaninato Co(II) (CoPc-4NO2) are supported onto the surface of the multi-walled carbon nanotubes (CNTs), affording CoPc@CNTs, CoPc-4OCH3@CNTs, and CoPc-4NO2@CNTs. X-ray photoelectron spectroscopy and X-ray absorption near-edge structure measurements disclose the influence of the peripheral substituents on the local electronic structure of Co atoms in these three catalysts. Electrochemical tests indicate the higher CO2RR performance of CoPc-4OCH3@CNTs compared to CoPc@CNTs and CoPc-4NO2@CNTs as exemplified by the higher Faraday efficiency of CO, larger part current densities, and better stability displayed by CoPc-4OCH3@CNTs at the applied voltage range from -0.6 to -1.0V versus RHE in both H-cell and flow cell. These results highlight the effect of the electron-donating -OCH3 substituent on the enhanced catalytic activity of CoPc-4OCH3@CNTs, which will help develop Co-N4-based catalysts with promising catalytic performance toward CO2RR.

Structural insights into human exon-defined spliceosome prior to activation.

Spliceosome is often assembled across an exon and undergoes rearrangement to span a neighboring intron. Most states of the intron-defined spliceosome have been structurally characterized. However, the structure of a fully assembled exon-defined spliceosome remains at large. During spliceosome assembly, the pre-catalytic state (B complex) is converted from its precursor (pre-B complex). Here we report atomic structures of the exon-defined human spliceosome in four sequential states: mature pre-B, late pre-B, early B, and mature B. In the previously unknown late pre-B state, U1 snRNP is already released but the remaining proteins are still in the pre-B state; unexpectedly, the RNAs are in the B state, with U6 snRNA forming a duplex with 5'-splice site and U5 snRNA recognizing the 3'-end of the exon. In the early and mature B complexes, the B-specific factors are stepwise recruited and specifically recognize the exon 3'-region. Our study reveals key insights into the assembly of the exon-defined spliceosomes and identifies mechanistic steps of the pre-B-to-B transition.

Atomic-scale observation of localized phonons at FeSe/SrTiO3 interface

In single unit-cell FeSe grown on SrTiO3, the superconductivity transition temperature features a significant enhancement. Local phonon modes at the interface associated with electron-phonon coupling may play an important role in the interface-induced enhancement. However, such phonon modes have eluded direct experimental observations. The complicated atomic structure of the interface brings challenges to obtain the accurate structure-phonon relation knowledge. Here, we achieve direct characterizations of atomic structure and phonon modes at the FeSe/SrTiO3 interface with atomically resolved imaging and electron energy loss spectroscopy in an electron microscope. We find several phonon modes highly localized (~1.3 nm) at the unique double layer Ti-O terminated interface, one of which (~ 83 meV) engages in strong interactions with the electrons in FeSe based on ab initio calculations. This finding of the localized interfacial phonon associated with strong electron-phonon coupling provides new insights into understanding the origin of superconductivity enhancement at the FeSe/SrTiO3 interface.

First-principles study of the structures and redox mechanisms of Ni-rich lithium nickel manganese cobalt oxides

To reduce the cobalt (Co) content in lithium-ion batteries, Ni-rich (high-Ni) lithium nickel manganese cobalt oxides (NMC) are pursued as one of the next-generation cathode materials. However, there is still debate on the crystal and electronic structures of the baseline, LiNiO2. Density Functional Theory (DFT) calculations were performed to provide a theoretical understanding of Ni-rich NMC. First, it was found that the commonly used R3¯m structure for LiNiO2 is metallic, contrary to the experimentally reported mix-conducting behavior. Among the four different space groups, R3¯m, C2/m, P21/c, and P2/c, P2/c with charge disproportionation of Ni2+ and Ni4+ is the most energetically stable and semiconducting structure of LiNiO2. Therefore, the atomic structures of representative Ni-rich NMC were built by partially replacing Ni with Co or Mn in the P2/c LiNiO2 to form LixNiyMnzCo1-y-zO2. In the fully lithiated (x = 1.0) high Ni content NMC (y > 0.5), the oxidation state of all Mn ions becomes 4+, while Co ions still maintain 3+, and part of the Ni ions become 2+ to compensate for the charge. Upon delithiation, the local environment shows more variation of the charge states on the transition metal (TM) ions. The average oxidation on each TM follows a sequence of losing electrons that starts from Ni2+ to Ni3+, then oxidizing Ni3+ and Co3+, while Mn4+ remains electrochemically inactive till x = 0. A general relationship for the oxidation state change in each TM as a function of x and y is derived and shows agreement with both modeling and experimental data.

Atomistic insights into chemical vapor deposition process of preparing silicon carbide materials using ReaxFF-MD simulation

SiC is a kind of key advanced coating material used widely. The in-depth understanding of the CVD process of preparing SiC materials at the atomic scale is beneficial for studying the CVD mechanism and then optimizing the materials. Here, a CVD model of preparing SiC materials is established based on ReaxFF-MD considering the whole pyrolysis-adsorption-desorption-growth mechanism. The accuracy of the ReaxFF potential and its parameters is verified by DFT at first. Then an energy-based Monte Carlo (EMC)-MD-CVD model is proposed based on the bonding formation energy originating from DFT. It is used to simulate the CVD process of preparing SiC materials. The CVD of MTS is studied by deposition efficiency and deposited film components at different temperatures, and it can be found it in good agreement with experimental results. Finally, the crystallization of SiC film prepared by the CVD of MTS is studied by energy evolution and atomic structure evolution. The results are helpful to understand the CVD mechanism for preparing coatings and it can be used to optimize the CVD parameters of preparing SiC materials in the future.

Analysis of extreme ultraviolet radiation and hydrodynamics simulation at the core of laser-produced nickel plasmas

The non-uniformity and transient nature of laser-produced plasma are critical factors that affect the analysis of the extreme ultraviolet spectra of highly charged ions and the diagnosis of plasma states. This paper systematically investigates the characteristics of extreme ultraviolet radiation and the hydrodynamic evolution of laser-produced nickel plasmas from two perspectives: high-spatio-temporal-resolution extreme-ultraviolet spectroscopic measurement and radiation hydrodynamics simulation. The consistency between the four-band experimental spectra and their theoretically simulated spectra confirms the accuracy of the atomic structure parameters and plasma state parameters. We also analyze the significant contribution of the 3d-4f double-excited state radiation to the spectral profile and discuss the influence of the self-absorption caused by plasma opacity on the characteristics of extreme ultraviolet radiation. The findings are crucial for accurately understanding the characteristics of extreme ultraviolet radiation, the hydrodynamic evolution, and the application of medium- and high-Z laser-produced plasma as a pulsed short-wavelength light source.