Atomic-level Understanding Research Articles

Reaction Pathways of the Selective Catalytic Reduction of NO with NH3 on the α-Fe2O3(012) Surface: a Combined Experimental and DFT Study.

Fe2O3-based catalysts have promising potential in the selective catalytic reduction (SCR) of NO with NH3 with the advantages of environmental friendliness, excellent medium-high SCR activity, good N2 selectivity, and high SO2 tolerance. However, the NH3-SCR mechanism over Fe2O3-based catalysts remains highly uncertain and controversial due to the complex nature of the SCR reaction. Herein, the NH3-SCR reaction pathways over the α-Fe2O3(012) surface are elucidated at the atomic level by density functional theory calculations and experimental measurements. We demonstrate that, different from the NH3 activation mechanism in numerous SCR catalytic systems, the reaction tends to follow the NO activation mechanism, in which NO activated at Fe sites reacts with NH3 to form a NH2NO intermediate and further decomposes into N2 and H2O, in synchronization with the formation of a surface OH group. Subsequently, the catalyst is regenerated by an O2-assisted surface-dehydrogenation process. The activation of NO as well as the formation of the NH2NO intermediate is the rate-determining step of the complete SCR cycle. This study enhances the atomic-level understanding toward the NH3-SCR reaction and provides insights for the development of Fe2O3-based SCR catalysts.

Toward an Atomic-Level Understanding of Ceria-Based Catalysts: When Experiment and Theory Go Hand in Hand.

ConspectusBecause ceria (CeO2) is a key ingredient in the formulation of many catalysts, its catalytic roles have received a great amount of attention from experiment and theory. Its primary function is to enhance the oxidation activity of catalysts, which is largely governed by the low activation barrier for creating lattice O vacancies. Such an important characteristic of ceria has been exploited in CO oxidation, methane partial oxidation, volatile organic compound oxidation, and the water–gas shift (WGS) reaction and in the context of automotive applications. A great challenge of such heterogeneously catalyzed processes remains the unambiguous identification of active sites.In oxidation reactions, closing the catalytic cycle requires ceria reoxidation by gas-phase oxygen, which includes oxygen adsorption and activation. While the general mechanistic framework of such processes is accepted, only very recently has an atomic-level understanding of oxygen activation on ceria powders been achieved by combined experimental and theoretical studies using in situ multiwavelength Raman spectroscopy and DFT.Recent studies have revealed that the adsorption and activation of gas-phase oxygen on ceria is strongly facet-dependent and involves different superoxide/peroxide species, which can now be unambiguously assigned to ceria surface sites using the combined Raman and DFT approach. Our results demonstrate that, as a result of oxygen dissociation, vacant ceria lattice sites are healed, highlighting the close relationship of surface processes with lattice oxygen dynamics, which is also of technical relevance in the context of oxygen storage-release applications.A recent DFT interpretation of Raman spectra of polycrystalline ceria enables us to take account of all (sub)surface and bulk vibrational features observed in the experimental spectra and has revealed new findings of great relevance for a mechanistic understanding of ceria-based catalysts. These include the identification of surface oxygen (Ce–O) modes and the quantification of subsurface oxygen defects. Combining these theoretical insights with operando Raman experiments now allows the (sub)surface oxygen dynamics of ceria and noble metal/ceria catalysts to be monitored under the reaction conditions.Applying these findings to Au/ceria catalysts provides univocal evidence for ceria support participation in heterogeneous catalysis. For room-temperature CO oxidation, operando Raman monitoring the (sub)surface defect dynamics clearly demonstrates the dependence of catalytic activity on the ceria reduction state. Extending the combined experimental/DFT approach to operando IR spectroscopy allows the elucidation of the nature of the active gold as (pseudo)single Au+ sites and enables us to develop a detailed mechanistic picture of the catalytic cycle. Temperature-dependent studies highlight the importance of facet-dependent defect formation energies and adsorbate stabilities (e.g., carbonates). While the latter aspects are also evidenced to play a role in the WGS reaction, the facet-dependent catalytic performance shows a correlation with the extent of gold agglomeration. Our findings are fully consistent with a redox mechanism, thus adding a new perspective to the ongoing discussion of the WGS reaction.As outlined above for ceria-based catalysts, closely combining state-of-the-art in situ/operando spectroscopy and theory constitutes a powerful approach to rational catalyst design by providing essential mechanistic information based on an atomic-level understanding of reactions.

Facile control of surface reconstruction with Co2+ or Co3+-rich (oxy)hydroxide surface on ZnCo phosphate for large-current-density hydrogen evolution in alkali

Surface reconstruction of transition metal based electrocatalysts is a highly efficient strategy for water splitting, which is usually observed in oxygen evolution reaction. However, most of them are not designed subjectively and it brings great difficulties to developing and understanding the catalysts with well-defined structure after the reconstruction. We demonstrate here the design and synthesis of ZnCo phosphate that allows a two-step treatment for controllable surface reconstruction with Co2+ or Co3+ (oxy)hydroxide. The surface reconstruction continuously boosts the HER performance in alkaline electrolytes. More aided experiments are designed to disclose that the depletion of PO43− in concentrated alkali and Zn2+ in following electrochemical etching serve as the key to trigger the reconstruction for Co2+-rich hydroxide and Co3+-rich oxyhydroxide, respectively. The reconstructed catalyst can work on hydrogen evolution for more than 50 h at high current density (1200 mA cm−2). Density functional theory simulations uncover the atomic-level understanding on the boosted catalytic performance. The energetically favorable electronic structure roots in the interfacial interaction and charge transfer. This work supplies valuable insights for the reconstruction chemistry and paves a new way to rational design heterogeneous catalysts associated with surface reconstruction in alkaline water electrolysers, and can cope with large-scale industrial water decomposition.

Electronic metal\u2013support interaction modulates single-atom platinum catalysis for hydrogen evolution reaction

Tuning metal–support interaction has been considered as an effective approach to modulate the electronic structure and catalytic activity of supported metal catalysts. At the atomic level, the understanding of the structure–activity relationship still remains obscure in heterogeneous catalysis, such as the conversion of water (alkaline) or hydronium ions (acid) to hydrogen (hydrogen evolution reaction, HER). Here, we reveal that the fine control over the oxidation states of single-atom Pt catalysts through electronic metal–support interaction significantly modulates the catalytic activities in either acidic or alkaline HER. Combined with detailed spectroscopic and electrochemical characterizations, the structure–activity relationship is established by correlating the acidic/alkaline HER activity with the average oxidation state of single-atom Pt and the Pt–H/Pt–OH interaction. This study sheds light on the atomic-level mechanistic understanding of acidic and alkaline HER, and further provides guidelines for the rational design of high-performance single-atom catalysts.

Atomistic investigation on the mechanical properties of 3D nanoporous metallic glasses under uniaxial tension and compression

Nanoporous metallic glasses (NPMGs) have a combination of superior properties of metallic glasses and porous structures. Comprehending the inherent deformation and failure mechanisms of NPMGs subjected to complex loading conditions is of great importance to transferring it from scientific research to realistic multifunctional applications, as well as optimize the bottom-up design of NPMGs working in extreme conditions. However, deficiencies in state-of-the-art positioning characterization methods and the microstructure complexity remain tremendous obstacles for the in-situ investigation of deformation processes completely based on real experiments. In this work, molecular dynamics simulations of tensile and compressive tests of 3D NPMGs with diamond and gyroid structures are presented to investigate the mechanical behaviors, as well as deformation processes at the atomic level. Our results suggest that the 3D NPMGs have excellent properties such as lightweight, high strength, and enhanced ductility, which is distinct from bulk metallic glasses lacking global-plasticity. The mechanical behaviors of NPMGs strongly depend on the relative density and ligament size. A tension-compression asymmetry is observed due to the non-negligible surface effects in NPMGs. The influence of surface stress on the mechanical properties becomes slighter with the increment of relative density. This work reveals an atomic-level understanding of the inherent deformation modes of NPMGs, promoting the multifunctional applications of metallic glasses-based materials.Subject Areas: material science, computational material

Formation of pyrophosphates across grain boundaries induces the formation of mismatched but oriented interfaces in silver phosphate polypods

Interfaces and their misfit defects determine the material properties of a wide range of applications, such as electronic devices, photocatalysts, and structural materials. However, current atomic-level understanding of interfacial structures is limited. Here we reveal that a special interfacial structure, a mismatched but oriented interface formed by two differently structured facets, gives rise to Ag3PO4 polypods at room temperature in aqueous solution. Transmission and scanning electron microscopy results suggest that interfaces of {100} and {110}({100}/(110}), {100}/{111}, {110}/{111}, and {100}/{100} have certain orientation relationships, corresponding to the structural energy minima and coincident site lattices of interfacial atoms, as demonstrated by molecular dynamics simulations. Density functional theory calculations indicate that the formation of pyrophosphates and/or phosphates rotation across the interface, as well as deformation of Ag-O bonds, compensate for the lattice mismatch at the interfaces. Our work opens a new avenue for a much wider range of interfacial structures, allow for a higher diversity of structures, and shines light on tailoring crystal structures, morphologies, and their resulting properties.

NMR unveils an N-terminal interaction interface on acetylated-α-synuclein monomers for recruitment to fibrils

Amyloid fibril formation of α-synuclein (αS) is associated with multiple neurodegenerative diseases, including Parkinson's disease (PD). Growing evidence suggests that progression of PD is linked to cell-to-cell propagation of αS fibrils, which leads to seeding of endogenous intrinsically disordered monomer via templated elongation and secondary nucleation. A molecular understanding of the seeding mechanism and driving interactions is crucial to inhibit progression of amyloid formation. Here, using relaxation-based solution NMR experiments designed to probe large complexes, we probe weak interactions of intrinsically disordered acetylated-αS (Ac-αS) monomers with seeding-competent Ac-αS fibrils and seeding-incompetent off-pathway oligomers to identify Ac-αS monomer residues at the binding interface. Under conditions that favor fibril elongation, we determine that the first 11 N-terminal residues on the monomer form a common binding site for both fibrils and off-pathway oligomers. Additionally, the presence of off-pathway oligomers within a fibril seeding environment suppresses seeded amyloid formation, as observed through thioflavin-T fluorescence experiments. This highlights that off-pathway αS oligomers can act as an auto-inhibitor against αS fibril elongation. Based on these data taken together with previous results, we propose a model in which Ac-αS monomer recruitment to the fibril is driven by interactions between the intrinsically disordered monomer N terminus and the intrinsically disordered flanking regions (IDR) on the fibril surface. We suggest that this monomer recruitment may play a role in the elongation of amyloid fibrils and highlight the potential of the IDRs of the fibril as important therapeutic targets against seeded amyloid formation.

Plasticity-induced stacking fault behaviors of γ’ precipitates in novel CoNi-based superalloys

Implementation of novel γ/γ’ Co-based superalloys with higher strength and improved creep durability is a challenging task for researchers. The lack of atomic-level understanding of plastic deformation behavior has seriously limited the exploration of the full capacity of Co-based alloys. We put forward a comprehensive study of generalized stacking fault energies by first principles to explore the effect of Ni and Al/W on the plastic deformation mechanism of γ’ precipitates in Co-based superalloys. It is found that alloying Ni and adjusting Al/W obviously change the dislocation glide and twinning nucleation in the γ’ precipitates by altering the stable fault energies and the unstable fault energy barriers. Excessive addition of either Ni or W deteriorates the strength even the stability of alloys. The ratio of effective planar fault energy (ΔEp) bridges intrinsic energy barriers and various deformation mechanisms of superalloys at elevated temperatures. Except for alloying effects, the grain orientation also significantly governs the operation of the plastic deformation of superalloys. Our theoretical results agree with the available measurements and well capture the observed phenomena in experiments.

Antigenic Peptide Loading into Major Histocompatibility Complex Class I Is Driven by the Substrate N-Terminus

Major histocompatibility complex class I (MHC-I), a key element of the acquired immune system, plays essential roles in activating CD8+ T cells by recognizing intracellular antigens derived from pa...

Thermal behaviour during initial stages of graphene oxidation: Implications for reaction kinetics and mechanisms

Atomic level understanding of graphene oxidation behaviour is presently far from complete. During large scale preparation of graphene from graphene oxide (GO), persistent presence of up to 8% residual oxygen is an issue of great concern. Such incomplete reduction is attributed to the presence of highly stable carbonyl and ether groups. Here we present a new approach for limiting the formation and behavior of these functional groups. We report high temperature molecular dynamics simulations on the oxidation process of pristine (Pr) and mono-vacancy (MV) graphene with O2 with specific focus on the initial reaction period. An abnormal thermal behaviour was observed in the onset times of oxidation reactions; significant differences were detected in the nucleation and growth mechanisms and reaction kinetics. Overall reaction kinetics was significantly slower in the thermal region (Pr: 4350–4450 K; MV: 4300–4450 K). By identifying this region experimentally or theoretically, a narrow window of minimal carbonyl group formation and residual oxygen could be created leading to a major breakthrough in the field.

Carbon dioxide adsorption and activation on gallium phosphide surface monitored by ambient pressure x-ray photoelectron spectroscopy

Gallium phosphide (GaP) is a promising catalyst material used in the photo-electrochemical carbon dioxide (CO2) reduction reaction (CO2RR). However, experimental data needed to interpret the interactions between CO2 and GaP at their interfaces must be gathered in order to develop advanced GaP based catalysts for the CO2RR. Here we used ambient pressure x-ray photoelectron spectroscopy to characterize the surface chemistry at 298 K on the GaP surface exposed to CO2 alone and in the presence of H2O under both dark and illuminated conditions. We found that a carbonate-like configuration is stable on the GaP surface exposed solely to 0.35 Torr CO2. Shining solar light promoted the CO2 dissociation process on the surface while negligibly influencing the CO2 adsorption configuration on GaP. Based on the surface chemistry change under dark and illuminated conditions, we propose a CO2 dissociation pathway on GaP. We also found that linear physisorbed CO2 formed on the surface of GaP when 0.35 Torr CO2 is co-dosed with 0.35 Torr H2O. Co-dosing H2O with CO2 also created a surface dipole, which is further influenced by solar light illumination. This work provides a fundamental atomic level understanding of how CO2 adsorption and activation happened on the GaP surface and how it was further influenced by solar light.

Atomic mechanism of cyclic healing effect in dual-phase metastable high entropy alloy

While many experiments and simulations on the high entropy alloy have focused on the deformation mechanisms under monotonic loading, the cyclic deformation behaviors remain largely elusive. In this work, the cyclic deformation behaviors of the dual-phase metastable high entropy alloy Ta0.5HfZrTi were investigated using molecular dynamics simulations with special focus on the interaction between phase boundaries and dislocations. Unlike the monotonic loading, the complex dislocation network formed in the growth of the martensite can be dramatically modified with different cyclic loading patterns. Both cyclic growth and cyclic healing effect were observed in simulations with different loading patterns. As the minimum strain reduces, the isolated dislocations and the unpinned partial dislocation on the stacking fault are found compressed and absorbed by the phase boundaries with the repeated straining. This cyclic healing effect is in distinct contrast to conventional cyclic straining hardening mechanisms with the increased dislocation density in metals and in agreement with the recent experimental observation of absent strain hardening effect in the cyclic response conduced on the metastable HEA recently. The present study provides a platform to probe an atomic-level understanding of the fundamental mechanisms in fatigue of dual-phase metastable HEAs.

Whole pair distribution function modeling: the bridging of Bragg and Debye scattering theories.

Microstructure-based design of materials requires an atomic level understanding of the mechanisms underlying structure-dependent properties. Methods for analyzing either the traditional diffraction profile or the pair distribution function (PDF) differ in how the information is accessed and in the approximations usually applied. Any variation of structural and microstructural features over the whole sample affects the Bragg peaks as well as any diffuse scattering. Accuracy of characterization relies, therefore, on the reliability of the analysis methods. Methods based on Bragg's law investigate the diffraction peaks in the intensity plot as distinct pieces of information. This approach reaches a limitation when dealing with disorder scenarios that do not conform to such a peak-by-peak basis. Methods based on the Debye scattering equation (DSE) are, otherwise, well suited to evaluate the scattering from a disordered phase but the structure information is averaged over short-range distances usually accessed by experiments. Moreover, statistical reliability is usually sacrificed to recover some of the computing-efficiency loss compared with traditional line-profile-analysis methods. Here, models based on Bragg's law are used to facilitate the computation of a whole PDF and then model powder-scattering data via the DSE. Models based on Bragg's law allow the efficient solution of the dispersion of a crystal's properties in a powder sample with statistical reliability, and the PDF provides the flexibility of the DSE. The whole PDF is decomposed into the independent directional components, and the number of atom pairs separated by a given distance is statistically estimated using the common-volume functions. This approach overcomes the need for an atomistic model of the material sample and the computation of billions of pair distances. The results of this combined method are in agreement with the explicit solution of the DSE although the computing efficiency is comparable with that of methods based on Bragg's law. Most importantly, the method exploits the strengths and different sensitivities of the Bragg and Debye theories.

Unusual solute segregation phenomenon in coherent twin boundaries

Interface segregation of solute atoms has a profound effect on properties of engineering alloys. The occurrence of solute segregation in coherent twin boundaries (CTBs) in Mg alloys is commonly considered to be induced by atomic size effect where solute atoms larger than Mg take extension sites and those smaller ones take compression sites in CTBs. Here we report an unusual solute segregation phenomenon in a group of Mg alloys—solute atoms larger than Mg unexpectedly segregate to compression sites of {10overline 11} fully coherent twin boundary and do not segregate to the extension or compression site of {10overline 12} fully coherent twin boundary. We propose that such segregation is dominated by chemical bonding (coordination and solute electronic configuration) rather than elastic strain minimization. We further demonstrate that the chemical bonding factor can also predict the solute segregation phenomena reported previously. Our findings advance the atomic-level understanding of the role of electronic structure in solute segregation in fully coherent twin boundaries, and more broadly grain boundaries, in Mg alloys. They are likely to provide insights into interface boundaries in other metals and alloys of different structures.

First-principles study of sulfur vacancy concentration effect on the electronic structures and hydrogen evolution reaction of MoS2

Defect engineering has been widely used in experiments to modulate the electrocatalytic properties of molybdenum disulfide (MoS2). However, the effect of vacancy concentration on the vacancy distribution, electronic properties, and hydrogen evolution reaction (HER) activity remains elusive. Herein, we perform density functional theory (DFT) studies to investigate defective MoS2 with different numbers of sulfur vacancies. In the case of low S-vacancy concentration, the vacancies prefer to agglomerate rather than being dispersed, while at the higher-vacancy concentration, the combination of local point defect and clustered vacancy chain is preferred. The coupling between S-vacancies leads to decreased band gap and increased Mo–H adsorption strength with increasing vacancy concentration. The optimal HER activity is identified to occur below vacancy concentration of 12.50%. Our work provides an atomic-level understanding about the role of S-vacancies in the HER performance of MoS2, and offers useful guidelines for the design of defective MoS2 and other TMDs electrocatalysts.

Examining learning of atomic level ideas about precipitation reactions with a resources framework

One particular challenge in chemistry learning is developing students’ atomic level understanding of chemical processes. It is necessary to help students learn how to critique atomic models rather than accept them as “truth.” In this study, we used a resources-based framework to examine how students made sense of macroscopic level information to account for what was happening at the atomic level. We interviewed 20 students enrolled in the first semester of general chemistry. Each student completed three exercises. The first exercise involved a card sorting task and the second exercise involved constructing an atomic model to learn how students made sense of the atomic level of a reaction involving the mixing of aqueous silver nitrate and aqueous sodium chloride to produce a precipitate. Next, students engaged in an exercise in which they were shown three conflicting atomic level animations of the same experiment and they were charged with selecting the animation that was most scientifically accurate. We analyzed the general patterns of characterization that emerged when students engaged in the card sorting and modeling exercise and the conflicting animation exercise using a resources framework. We contend that students apply and sometimes misapply knowledge resources to make sense of the atomic level. The process affects decisions that they make and stances that they develop about the accuracy of atomic level models.

Amorphous Si1-yCy composite anode materials: ab initio molecular dynamics for behaviors of Li and Na in the framework.

Although amorphous Si/C composite anode materials with various types of nanostructures Si/C materials have been experimentally proposed for rechargeable ion batteries for their structural durability, the atomistic mechanism primarily suggesting Li and Na monovalent ion intercalation into an amorphous Si/C composite matrix has not theoretically been understood to explore the thermodynamic and kinetic features of the a-Si/C composite phase regarding the effects on the carbon addition to an amorphous Si matrix. In this work, systematic ab initio molecular dynamics calculations (AIMDs) were conducted to identify electrochemical intercalation reactions involved in nanostructure evolutions, which correspond to favorable ion-intercalated formations, volume expansions, pair correlations, charge transfers, and diffusion behaviors of metals in a-MxSi1-yCy (Mx: Lix and Nax) alloys with increasing x contents of atomic concentrations. AIMDs using the a-Si1-yCy composite phase might allow one to have an atomic-level understanding of the composite phase and further insightful comprehension of any implementations such as the controlled ratio of the Si1-yCy composite and multivalent ions inserted into the framework.

Effect of external electric field on diffusivity and flash sintering of 8YSZ: A molecular dynamics study

The atomistic structural modification and ionic diffusivity in 8YSZ at elevated temperature with the presence of an external electric field (E-field) were investigated by molecular dynamics (MD) simulations. As an example, a sufficiently large system of atomic configuration for a bi-crystal ∑5(310)/[001] grain boundary (GB) model was studied. MD results show that the E-field promotes the formation of Frenkel pair defects. Notably, some Zr ions diffuse out of GB regions at E-field>∼500-1000V/cm, resulting in an “avalanche” of cation vacancies at GBs and reduction of GB space charge. Consequently, the diffusivities of cations and anions are enhanced in the 8YSZ system with the presence of E-field. The atomistic level understanding of E-field induced structural modifications and ionic diffusivities provide an in-depth insight to unravel the flash sintering mechanisms of ionic ceramics, especially the coupled thermal-field effect during the flash sintering process.

Elucidation of Active Sites in Aldol Condensation of Acetone over Single-Facet Dominant Anatase TiO2 (101) and (001) Catalysts.

Aldol condensations of carbonyl compounds for C–C bond formation are a very important class of reactions in organic synthesis and upgrading of biomass-derived feedstocks. However, the atomic level understanding of reaction mechanisms and structure–activity correlation on widely used transition metal oxide catalysts are limited due to the high degree of structural heterogeneity of catalysts such as commercial TiO2 powders. Here, we provide a deep understanding of the reaction mechanisms, kinetics, and structure–function relationships for vapor phase acetone aldol condensation through the controlled synthesis of two catalysts with high surface areas and clean, dominant facets, coupled with detailed characterization and kinetic studies that are further assisted by density functional theory (DFT) calculations. Temperature-dependent diffuse reflectance infrared Fourier transform spectroscopy showed the existence of abundant acetone bonded to surface hydroxyl groups (acetone-OsH) and acetone bonded to Lewis acid sites (acetone-Ti5c) on the surface of both {101} and {001} facet dominant TiO2. Intermolecular C–C coupling of theenolate intermediate from acetone-Ti5c and a vicinal acetone-OsH is a kinetically relevant step, which is consistent with kinetic and isotopic studies as well as DFT calculations. The {001} facet showed a lower apparent activation energy (or higher activity) than the {101} facet. This is likely caused by the weaker Lewis acid and Brønsted base strengths of the {001} facet which favors the reprotonation–desorption of the coupled intermediate, making the C–C coupling step more exothermic on the {001} facet and resulting in an earlier transition state with a lower activation barrier. It is also possible that the {001} facet has a smoother surface configuration and less steric hindrance during intermolecular C–C bond formation than the {101} facet.

PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins.

The Protein Ensemble Database (PED) (https://proteinensemble.org), which holds structural ensembles of intrinsically disordered proteins (IDPs), has been significantly updated and upgraded since its last release in 2016. The new version, PED 4.0, has been completely redesigned and reimplemented with cutting-edge technology and now holds about six times more data (162 versus 24 entries and 242 versus 60 structural ensembles) and a broader representation of state of the art ensemble generation methods than the previous version. The database has a completely renewed graphical interface with an interactive feature viewer for region-based annotations, and provides a series of descriptors of the qualitative and quantitative properties of the ensembles. High quality of the data is guaranteed by a new submission process, which combines both automatic and manual evaluation steps. A team of biocurators integrate structured metadata describing the ensemble generation methodology, experimental constraints and conditions. A new search engine allows the user to build advanced queries and search all entry fields including cross-references to IDP-related resources such as DisProt, MobiDB, BMRB and SASBDB. We expect that the renewed PED will be useful for researchers interested in the atomic-level understanding of IDP function, and promote the rational, structure-based design of IDP-targeting drugs.