Atomic Displacements Research Articles

Single-Atom Substituents in Copper Surfaces May Adsorb Multiple CO Molecules.

Copper is a good CO2 electroreduction catalyst as products beyond CO form, but efficiency and selectivity is low. Experiments have shown that an admixture of other elements can help, and computational screening studies have pointed out various promising candidates based on the adsorption of a single CO molecule as a descriptor. Our calculations of CO adsorption on surfaces where a first row transition metal atom replaces a Cu atom show that multiple CO molecules, not just one, bind to the substitutional atom. For Fe, Co, and Ni atoms, a decrease in binding energy is found, but the reverse trend, namely, increasing bond strength, is found for V, Cr, and Mn and the first three CO molecules. Magnetic moment, charge, and position of the substitutional atom are also strongly affected by the CO adsorption in most cases. Magnetic moment is stepwise reduced to zero, and the outward displacement of the substitutional atom increased.

Measurement of atomic dispersion on buried Ag nanoparticles decomposed by Ne[formula omitted] ion irradiation

The effects of room temperature 200keV Ne+ ion irradiation on Ag nanoparticles (NPs) embedded in a silicon nitride film have been studied via Medium Energy Ion Scattering (MEIS), Scanning Transmission Electron Microscopy (STEM), and the results are discussed in comparison with Monte Carlo TRI3DYN simulations. The experiment was designed to test the mechanisms controlling the room temperature irradiation-induced microstructure evolution of individual NPs and the overall system. We present an innovative MEIS approach capable of quantitatively determining Ag’s content and spatial distribution in solution. The STEM observations demonstrate the nucleation of smaller Ag NPs distributed within the solute field. The TRI3DYN simulations suggest that a fraction of the solute content is reincorporated within the NPs. These results are discussed considering that room-temperature thermal diffusion processes are significantly retarded in silicon nitride substrates, which leads to an interpretation primarily based on the irradiation-induced atomic displacements that render a microstructure evolution driven by the minimization of chemical potential as an elemental thermodynamic force. Our findings are of applied interest concerning the application of ion beams to manipulate NP ensembles.

Van der Waals Engineering of Charge Density Waves in One-Dimensional Nb6Te6 Nanowires.

One-dimensional (1D) systems have played a crucial role in the development of fundamental physics and practical applications. Recently, transition metal monochalcogenide (TMM) wires based on molybdenum (Mo) and tungsten (W) have emerged as promising platforms for investigating 1D physics in pure van der Waals (vdW) platforms. Here, we report on the bottom-up fabrication of Nb6Te6 wires down to the single-wire limit. The unique properties of Nb6Te6 single wire enable the realization of 1D charge density wave (CDW) phases in an isolated single TMM wire. Moreover, we revealed the appealing regulation of 1D CDW orders by van der Waals interactions at either the 1D-2D interface (i.e., rotation of a single wire along its wire axis) or the 1D-1D interface. Two rotation angles (30° and 0°) give rise to 3 × 1 and zigzag chain CDW morphologies, respectively, which exhibit pronounced differences in atomic displacement by a factor of 2. The interwire vdW coupling overwhelms its counterpart at the 1D-2D interface, thus locking the rotation angle (at 0°) as well as the interwire atomic registries. In contrast, interestingly, the phases of the charge oscillations are independent of the adjacent wires. The ability to tailor 1D charge orders provides a crucial addition to the toll set of vdW integrations beyond two-dimensional materials.

Detection of dislocation motion in atomistic simulations of nanocrystalline materials

A method for identifying dislocation motion in atomistic simulations is presented. While identifying static and moving dislocations within a single crystal or a combination of such is well established, the method described here is tailored to identify dislocation motion by correlating the displacements of individual atoms. This facilitates the identification of dislocation motion in complex structural arrangements, and allows the specific contribution to plastic deformation, due to dislocation motion, to be separated from that of other mechanisms. The method is applied to test cases in crystals and grain boundaries (GBs), in which irradiation-induced creep (IIC) was induced. It is shown that the method singles out the moving dislocations from among the dislocation forest at GBs, thus identifying the specific reactions driving the distortion at any given time. This enables the study of dislocation processes in the presence of realistic obstacles, and the study of the effects of microstructure on dislocation mobility. As an example of such a study, the method is applied to rule out intragranular slip, and to estimate the contribution of dislocation motion to strain, in a NC undergoing IIC.

Atomistic-level analysis of nanoindentation-induced plasticity in arc-melted NiFeCrCo alloys: The role of stacking faults

Concentrated solid solution alloys (CSAs) have attracted attention for their promising properties; however, current manufacturing methods face challenges in complexity, high costs, and limited scalability, raising concerns about industrial viability. The prevalent technique, arc melting, yields high-purity samples with complex shapes. In this study, we explore nanoindentation tests at room temperature where arc-melted samples exhibit larger grain sizes, diminishing the effects of grain boundaries on the results. Motivated by these findings, our investigation focuses on the atomistic-level exploration of plasticity mechanisms, specifically dislocation nucleation and propagation during nanoindentation tests. The intricate chemistry of NiFeCrCo CSA influences pile-ups and slip traces, aiming to elucidate plastic deformation by considering both pristine and pre-existing stacking fault tetrahedra. Our analysis scrutinizes dynamic deformation processes, defect nucleation, and evolution, complemented by stress–strain and dislocation densities–strain curves illustrating the hardening mechanism of defective materials. Additionally, we examine surface morphology and plastic deformation through atomic shear strain and displacement mappings. This integrated approach provides insights into the complex interplay between the material structure and mechanical behavior, paving the way for an enhanced understanding and potential advancements in CSA applications.

B-Factor Rescaling for Protein Crystal Structure Analyses

The B-factor, also known as the atomic displacement parameter, is a fundamental metric in crystallography for quantifying the positional flexibility of atoms within crystal lattices. In structural biology, various developments have expanded the use of B-factors beyond conventional crystallographic analysis, allowing for a deeper understanding of protein flexibility, enzyme manipulation, and an improved understanding of molecular dynamics. However, the interpretation of B-factors is complicated by their sensitivity to various experimental and computational factors, necessitating rigorous rescaling methods to ensure meaningful comparisons across different structures. This article provides an in-depth description of rescaling approaches used for B-factors. It includes an examination of several methods for managing conformational disorder and selecting the atom types required for the analysis.

Bayesian inference of atomic column positions in scanning transmission electron microscopy images

Abstract Atomic-resolution scanning transmission electron microscopy combined with 2D Gaussian fitting enables the accurate and precise identification of atomic column positions within a few picometers. The measurement performance significantly depends on the signal-to-noise ratio of the atomic columns. In areas with low signal-to-noise ratios, such as near surfaces, the measurement performance was lower than that of the bulk. However, previous studies evaluated the accuracy and precision only in bulk areas, underscoring the need for a method that quantitatively evaluates the accuracy and precision of each atomic column position with various signal-to-noise ratios. This study introduced Bayesian inference to assess the accuracy and precision of determining individual atomic column positions under various signals. We applied this method to simulated and experimental images and demonstrated its effectiveness in identifying statistically significant displacements, particularly near surfaces with signal degradation. The use of vector maps and kernel density estimate plots obtained from Bayesian inference provided a probabilistic understanding of the atom displacement. Therefore, this study highlighted the potential benefits of Bayesian inference in high-resolution imaging to reveal material properties.

The Formation and Transformation of Low-Dimensional Carbon Nanomaterials by Electron Irradiation.

Low-dimensional materials based on graphene or graphite show a large variety of phenomena when they are subjected to irradiation with energetic electrons. Since the 1990s, electron microscopy studies, where a certain irradiation dose is unavoidable, have witnessed unexpected structural transformations of graphitic nanoparticles. It is recognized that electron irradiation is not only detrimental but also bears considerable potential in the formation of new graphitic structures. With the availability of aberration-corrected electron microscopes and the discovery of techniques to produce monolayers of graphene, detailed insight into the atomic processes occurring during electron irradiation became possible. Threshold energies for atom displacements are determined and models of different types of lattice vacancies are confirmed experimentally. However, experimental evidence for the configuration of interstitial atoms in graphite or adatoms on graphene remained indirect, and the understanding of defect dynamics still depends on theoretical concepts. This article reviews irradiation phenomena in graphene- or graphite-based nanomaterials from the scale of single atoms to tens of nanometers. Observations from the 1990s can now be explained on the basis of new results. The evolution of the understanding during three decades of research is presented, and the remaining problems are pointed out.

Visualizing the Internal Nanocrystallinity of Calcite Due to Nonclassical Crystallization by 3D Coherent X-Ray Diffraction Imaging.

The internal crystallinity of calcite is investigated for samples synthesized using two approaches: precipitation from solution and the ammonium carbonate diffusion method. Scanning electron microscopy (SEM) analyses reveal that the calcite products precipitated using both approaches have a well-defined rhombohedron shape, consistent with the euhedral crystal habit of the mineral. The internal structure of these calcite crystals is characterized using Bragg coherent diffraction imaging (BCDI) to determine the 3D electron density and the atomic displacement field. BCDI reconstructions for crystals synthesized using the ammonium carbonate diffusion approach have the expected euhedral shape, with internal strain fields and few internal defects. In contrast, the crystals synthesized by precipitation from solution have very complex external shapes and defective internal structures, presenting null electron density regions and pronounced displacement field distributions. These heterogeneities are interpreted as multiple crystalline domains, created by a nonclassical crystallization mechanism, where smaller nanoparticles coalescence into the final euhedral particles. The combined use of SEM, X-ray diffraction (XRD), and BCDI allows for structurally differentiating calcite crystals grown with different approaches, opening new opportunities to understand how grain boundaries and internal defects alter calcite reactivity.

Unzipping hBN with ultrashort mid-infrared pulses.

Manipulating the nanostructure of materials is critical for numerous applications in electronics, magnetics, and photonics. However, conventional methods such as lithography and laser writing require cleanroom facilities or leave residue. We describe an approach to creating atomically sharp line defects in hexagonal boron nitride (hBN) at room temperature by direct optical phonon excitation with a mid-infrared pulsed laser from free space. We term this phenomenon "unzipping" to describe the rapid formation and growth of a crack tens of nanometers wide from a point within the laser-driven region. Formation of these features is attributed to the large atomic displacement and high local bond strain produced by strongly driving the crystal at a natural resonance. This process occurs only via coherent phonon excitation and is highly sensitive to the relative orientation of the crystal axes and the laser polarization. Its cleanliness, directionality, and sharpness enable applications such as polariton cavities, phonon-wave coupling, and in situ flake cleaving.

Pseudomagnetic fields in fully relaxed twisted bilayer and trilayer graphene

We present simple models to describe the in-plane and the out-of-plane lattice relaxation in twisted bilayer and symmetrically twisted trilayer graphene. Analytical results and series expansions show that for twist angles θ>1.4∘ , the in-plane atomic displacements lead to pseudomagnetic fields weakly dependent on θ. In symmetrically twisted trilayer graphene, the central layer in-plane relaxation is greatly enhanced. The joint effect of the relaxation-induced pseudoscalar potentials and the associated energy difference between interlayer dimer and non-dimer pairs resulted in a significant electron–hole asymmetry both in twisted bilayer and trilayer graphene.

Three-dimensional domain identification in a single hexagonal manganite nanocrystal

The three-dimensional domain structure of ferroelectric materials significantly influences their properties. The ferroelectric domain structure of improper multiferroics, such as YMnO3, is driven by a non-ferroelectric order parameter, leading to unique hexagonal vortex patterns and topologically protected domain walls. Characterizing the three-dimensional structure of these domains and domain walls has been elusive, however, due to a lack of suitable imaging techniques. Here, we present a multi-peak Bragg coherent x-ray diffraction imaging determination of the domain structure in single YMnO3 nanocrystals. We resolve two ferroelectric domains separated by a domain wall and confirm that the primary atomic displacements occur along the crystallographic c-axis. Correlation with atomistic simulations confirms the Mexican hat symmetry model of domain formation, identifying two domains with opposite ferroelectric polarization and adjacent trimerization, manifesting in a clockwise arrangement around the hat’s brim.

Effect of F− doping on structural, elastic, and electronic properties of SmO1−xFxBiS2: A first principles investigation

Structural, elastic, and electronic properties of SmO1−xFxBiS2 were studied using first principles method, and effects of F− doping were clearly observed. By increasing x, the increase of lattice parameter ‘a’ and decrease of ‘c’ are mainly due to the displacement of S1 and Sm atoms respectively. For x = 0.3, new (Bi–S1)2 bonds formation was observed. The gap between Bi- and S1-planes decreases and disappeared at x = 0.9. Cauchy pressures, B/G, and ν indicate ductile nature having metallic bonds with small ionic contribution. B, G, and E are highly anisotropic and show anomaly at x = 0.3, 0.5, and 0.8. Sm 4f states are mainly responsible for metallicity. For x = 0.3, total DOS decreases due to new bonds formation. Anomalous displacement of Sm-sites by doping at O- or Sm-sites induces anomalous displacement of S1 atoms which may be the main reason for change of different properties of SmO1-xFxBiS2.

Static and dynamic atom displacements in nanocrystalline powders from diffraction analysis at finite temperature

We evaluate the accuracy of x-ray diffraction analysis performed by Rietveld refinement in extracting the static and dynamic atomic displacement parameters of spherical gold nanocrystals with sizes of 30 nm and below and within a temperature interval of 10–300 K. A self-consistent computational workflow composed of real- and reciprocal- space analyses is designed for this purpose. We obtain average lattice parameters, static and thermal atomic displacements as well as their temperature and particle size dependence in an ideally monodispersed and realistic nanocrystalline powder generated by molecular dynamics simulations. Then, we compare crystallographic parameters obtained from real- and reciprocal- space analyses to evaluate the accuracy of diffraction analysis. We also extend the comparison to local variations of crystallographic parameters in the nanocrystals and show how Rietveld refinement relates to the average parameters of the core and surface regions separately. We show that 1) average lattice parameters obtained from Rietveld refinement are greater than the mean lattice parameter of small nanocrystals and converge to the core lattice parameter with increasing particle size, 2) Rietveld refinement significantly underestimates static atom displacements of surface atoms in small nanocrystals, 3) dynamic atomic displacements in nanocrystalline gold powders are reliably obtained within 5 % error by Rietveld refinement, provided that thermal diffuse scattering is adequately removed from the diffraction data, 4) the discrepancy between real- and reciprocal-space analysis increases for the smallest gold nanocrystal.

Study of the Surface-Layer Softening Effects in xLi2ZrO3–(1−x)Li4SiO4 Ceramics under Irradiation with He2+ Ions

The study investigates alterations in the mechanical and thermophysical properties of ceramics composed of xLi2ZrO3–(1−x)Li4SiO4 as radiation damage accumulates, mainly linked to helium agglomeration in the surface layer. This research is motivated by the potential to develop lithium-containing ceramics characterized by exceptional strength properties and a resistance to the accumulation of radiation damage and ensuing deformation distortions in the near-surface layer. The study of the radiation damage accumulation processes in the near-surface layer was conducted through intense irradiation of ceramics using He2+ ions at a temperature of 700 °C, simulating conditions closely resembling operation conditions. Following this, a correlation between the accumulation of structural modifications (value of atomic displacements) and variations in strength and thermophysical characteristics was established. During the research, it was observed that two-component ceramics exhibit significantly greater resistance to external influences and damage accumulation related to radiation exposure compared to their single-component counterparts. Furthermore, the composition that provides the highest resistance to softening in two-component ceramics is an equal ratio of the components of 0.5Li2ZrO3–0.5Li4SiO4 ceramics.

Raman, ATRIR and NMR spectra, conformational stability, vibrational assignments, normal coordinates analysis and DFT calculations of hydrochlorothiazide drug

The Raman (4000-50 cm−1), attenuated total reflectance (ATR) infrared (4000-400 cm−1) spectra of Hydrochlorothiazide (C7H8ClN3O4S2; HCTZ) have been recorded in the solid state in addition to LCMS in the dimer and trimer ranges. The 1H, 13C and 15N NMR spectra were also recorded in addition to DEPT (45, 90 and 135) of HCTZ sample dissolved DMSO‑d6. Initially, three conformers resulting from the rotation of -SO2NH2 moiety around C9-S11 were proposed, namely gauche, trans and cis conformers. And then Density Functional Theory (DFT) calculations for an isolated molecule were carried out employing both B3LYP and P3PW91 methods at 6-31G(d), 6-311+G(d), 6–311++G(d,p) basis set. The cis isomer is a transition state owing to the prediction of an imaginary wavenumber, while the gauche being more stable than trans by ∼438–538 cm−1 (∼1.25–1.54 kcal) employing the afore-mentioned computations. Moreover, we carried out a potential surface scan for the gauche to determine SO2NH2 barriers to internal rotations and to ensure the optimal gauche is the most stable conformer. Aided by normal coordinate analysis (NCA) in addition to the atomic displacements in Cartesian coordinates (ADCC), confident vibrational assignment of the observed infrared and Raman bands are proposed for all fundamentals of the gauche rotamer. Nevertheless, force constants (FCs) in internal coordinates were also estimated using the above-mentioned methods and basis sets as well. The 1H, 13C and 15N chemical shifts were also correlated to their corresponding atoms. The results are reported herein and compared with HCTZ and its cocrystals whenever appropriate.

Giant Modulation of Refractive Index from Picoscale Atomic Displacements.

It is shown that structural disorder-in the form of anisotropic, picoscale atomic displacements-modulates the refractive index tensor and results in the giant optical anisotropy observed in BaTiS3, a quasi-1D hexagonal chalcogenide. Single-crystal X-ray diffraction studies reveal the presence of antipolar displacements of Ti atoms within adjacent TiS6 chains along the c-axis, and threefold degenerate Ti displacements in the a-b plane. 47/49Ti solid-state NMR provides additional evidence for those Ti displacements in the form of a three-horned NMR lineshape resulting from a low symmetry local environment around Ti atoms. Scanning transmission electron microscopy is used to directly observe the globally disordered Ti a-b plane displacements and find them to be ordered locally over a few unit cells. First-principles calculations show that the Ti a-b plane displacements selectively reduce the refractive index along the ab-plane, while having minimal impact on the refractive index along the chain direction, thus resulting in a giant enhancement in the optical anisotropy. By showing a strong connection between structural disorder with picoscale displacements and the optical response in BaTiS3, this study opens a pathway for designing optical materials with high refractive index and functionalities such as large optical anisotropy and nonlinearity.

Atomic displacement threshold energies and defect generation in GaN, AlN, and AlGaN: A high-throughput molecular dynamics investigation

Gallium nitride, aluminum nitride, and their ternary alloys form an important class of wide-bandgap semiconductors employed in a variety of applications, including radiation-hard electronics. To better understand the effects of irradiation in these materials, molecular dynamics simulations were employed to determine the threshold recoil energies to permanently displace atoms from crystalline sites. Threshold displacement energies were calculated with the lattices at 0 K. Thermal effects are found to lower the threshold energies by ∼1 eV. The threshold energy knockout events observed result in Frenkel pair defects. The electronic structure and dynamics of these Frenkel pair defects are analyzed and the consequences for device operation are discussed.

Electrochemical Reduction of Perfluorooctanoic Acid (PFOA): An Experimental and Theoretical Approach.

Perfluorooctanoic acid (PFOA) is an artificial chemical of global concern due to its high environmental persistence and potential human health risk. Electrochemical methods are promising technologies for water treatment because they are efficient, cheap, and scalable. The electrochemical reduction of PFOA is one of the current methodologies. This process leads to defluorination of the carbon chain to hydrogenated products. Here, we describe a mechanistic study of the electrochemical reduction of PFOA in gold electrodes. By using linear sweep voltammetry (LSV), an E0' of -1.80 V vs Ag/AgCl was estimated. Using a scan rate diagnosis, we determined an electron-transfer coefficient (αexp) of 0.37, corresponding to a concerted mechanism. The strong adsorption of PFOA into the gold surface is confirmed by the Langmuir-like isotherm in the absence (KA = 1.89 × 1012 cm3 mol-1) and presence of a negative potential (KA = 3.94 × 107 cm3 mol-1, at -1.40 V vs Ag/AgCl). Based on Marcus-Hush's theory, calculations show a solvent reorganization energy (λ0) of 0.9 eV, suggesting a large electrostatic repulsion between the perfluorinated chain and water. The estimated free energy of the transition state of the electron transfer (ΔG‡ = 2.42 eV) suggests that it is thermodynamically the reaction-limiting step. 19F - 1H NMR, UV-vis, and mass spectrometry studies confirm the displacement of fluorine atoms by hydrogen. Density functional theory (DFT) calculations also support the concerted mechanism for the reductive defluorination of PFOA, in agreement with the experimental values.

Origin of discrete donor–acceptor pair transitions in 2D Ruddlesden–Popper perovskites

Two-dimensional (2D) van der Waals nanomaterials have attracted considerable attention for potential use in photonic and light–matter applications at the nanoscale. Thanks to their excitonic properties, 2D perovskites are also promising active materials to be included in devices working at room temperature. In this work, we study the presence of very narrow and spatially localized optical transitions in 2D lead halide perovskites by μ-photoluminescence and time-decay measurements. These discrete optical transitions are characterized by sub-millielectronvolt linewidths (≃120μeV) and long decay times (5–8 ns). X-ray photoemission and density-functional theory calculations have been employed to investigate the chemical origin of electronic states responsible of these transitions. The association of phenethylammonium with methylammonium cations into 2D Ruddlesden–Popper perovskites, (PEA)2(MA)n−1PbnI3n+1, particularly in phases with n≥2, has been identified as a mechanism of donor–acceptor pair (DAP) formation, corresponding to the displacement of lead atoms and their replacement by methylammonium. Ionized DAP recombination is identified as the most likely physical source of the observed discrete optical emission lines. The analysis of the experimental data with a simple model, which evaluates the Coulombic interaction between ionized acceptors and donors, returns a donor in Bohr radius of the order of ≃10 nm. The analysis of the spectral and electronic characteristics of these single donor–acceptor states in 2D perovskites is of particular importance both from the point of view of fundamental research, as well as to be able to link the emission of these states with new optoelectronic applications that require long-range optically controllable interactions.