Atomic-level Understanding Research Articles

Effect of Al addition on structure and dynamics of Zr-Cu-Al glass-forming alloy

Classical molecular dynamics study of metallic glass-forming alloys, Zr36Cu64 and Zr47Cu46Al7, is carried out to acquire atomic level understanding of the microalloying effect of Al atoms on the structure and dynamics of the alloy. The results indicate that in comparison to hard sphere-like atomic packing in the binary alloy, microalloying of Al brings in a fundamental modification in the atomic packing due to soft sphere-like Cu-Al bonding due to chemical short-range ordering (CSRO). In the ternary alloy, CSRO is found to homogenize the topological packing of the icosahedra (<0,0,12,0 > ). Microalloying also impacts the single particle dynamics at the timescale of β-relaxation and could have important implications on the mechanical properties of the glasses prepared from this alloy.

Suppressed Lattice Disorder for Large Emission Enhancement and Structural Robustness in Hybrid Lead Iodide Perovskite Discovered by High‐Pressure Isotope Effect

AbstractThe soft nature of organic–inorganic halide perovskites renders their lattice particularly tunable to external stimuli such as pressure, undoubtedly offering an effective way to modify their structure for extraordinary optoelectronic properties. Here, using the methylammonium lead iodide as a representative exploratory platform, it is observed that the pressure‐driven lattice disorder can be significantly suppressed via hydrogen isotope effect, which is crucial for better optical and mechanical properties previously unattainable. By a comprehensive in situ neutron/synchrotron‐based analysis and optical characterizations, a remarkable photoluminescence (PL) enhancement by threefold is convinced in deuterated CD3ND3PbI3, which also shows much greater structural robustness with retainable PL after high peak‐pressure compression–decompression cycle. With the first‐principles calculations, an atomic level understanding of the strong correlation among the organic sublattice and lead iodide octahedral framework and structural photonics is proposed, where the less dynamic CD3ND3+ cations are vital to maintain the long‐range crystalline order through steric and Coulombic interactions. These results also show that CD3ND3PbI3‐based solar cell has comparable photovoltaic performance as CH3NH3PbI3‐based device but exhibits considerably slower degradation behavior, thus representing a paradigm by suggesting isotope‐functionalized perovskite materials for better materials‐by‐design and more stable photovoltaic application.

Atomic-level understanding layer-by-layer formation process of TiCx on carbon film

TiCx coating film was fabricated by a novel two-step deposition strategy in molten salts media, namely carbon film was prepared firstly on the substrate and then following transformation of C to TiCx by deposition of Ti on the C film. The latter step was achieved by electrochemical deposition of Ti in FLiNaK-K2TiF6-Ti, in which the Ti2+ ion was the dominant species. It was found that the transformation of C to TiCx is a diffusion control process rather than deposition control one, implying that the interdiffusion between Ti and C phase is the decision step. To reveal the formation process, calculation simulation was further conducted. The results of first-principle calculation demonstrate that the deposited Ti atom prefers to combine to the central site of the graphite surface. Then, formation of Ti layer will take place as the atom number increased by continuous deposition. Subsequently, the interdiffusion between Ti and C phase motivated by repulsion, concentration gradient and Gibbs free energy will contribute to the transformation of composite. Such initial formation process of TiCx on the C film was further confirmed by the results of charge transfer between Ti and C atoms and its electronic state. The results of deposition and diffusion of Ti and C atoms manifest that the formation of TiCx is a reconstruction rather than atom diffusion process.

(Invited) Electrolyte and Interphase Revealed By Cryogenic Electron Microscopy and Solvation Measurement

Obtaining atomic and molecular level understanding of electrolyte and electrode-electrolyte interphase is critical to the battery developments. In this talk, I will present a multimodal approach combining the powerful cryogenic electron microscopy technique, electrochemical technique and solvation entropy and free energy measurements. I will discover including: 1) atom-resolved images of solid electrolyte interphase for Li metal and Si anodes; 2) Insight on the debate on the existence of cathode electrolyte interphase; 3) the solvation structure and related thermodynamic parameters and their correlation with electrochemical performance.

(Invited) Probing Redox Centers in Oxygen-Redox Electrodes Using Soft X-Ray Spectroscopy

High-energy-density batteries have been a long-standing target toward sustainability, but the energy density of state-of-the-art lithium-ion batteries is limited in part by the small capacity of positive electrode materials. Although employing the additional oxygen-redox reaction of Li-excess transition-metal oxides is an attractive approach to increase the capacity, an atomic-level understanding of the reaction mechanism has not been established so far. In this talk, using bulk-sensitive resonant inelastic X-ray scattering (RIXS) spectroscopy combined with ab initio computations, we show the presence of a localized oxygen 2p orbital weakly hybridized with transition metal t 2g orbitals that was theoretically predicted to play a key role in oxygen-redox reactions. The ex-situ RIXS spectroscopy also unveils the stabilization mechanism of oxidized phases. References Sudayama, et al., M. Okubo & A. Yamada, Energy Environ. Sci., 2020, 13, 1492-1500.Mortemard de Boisse, et al., M. Okubo & A. Yamada, Nature Commun., 2019, 10, 2185.Mortemard de Boisse, et al., M. Okubo & A. Yamada, Adv. Energy Mater., 2018, 8, 1800409.

An S/T motif controls reversible oligomerization of the Hsp40 chaperone DNAJB6b through subtle reorganization of a β sheet backbone

Chaperone oligomerization is often a key aspect of their function. Irrespective of whether chaperone oligomers act as reservoirs for active monomers or exhibit a chaperoning function themselves, understanding the mechanism of oligomerization will further our understanding of how chaperones maintain the proteome. Here, we focus on the class-II Hsp40, human DNAJB6b, a highly efficient inhibitor of protein self-assembly in vivo and in vitro that forms functional oligomers. Using single-quantum methyl-based relaxation dispersion NMR methods we identify critical residues for DNAJB6b oligomerization in its C-terminal domain (CTD). Detailed solution NMR studies on the structure of the CTD showed that a serine/threonine-rich stretch causes a backbone twist in the N-terminal β strand, stabilizing the monomeric form. Quantitative analysis of an array of NMR relaxation-based experiments (including Carr-Purcell-Meiboom-Gill relaxation dispersion, off-resonance R1ρ profiles, lifetime line broadening, and exchange-induced shifts) on the CTD of both wild type and a point mutant (T142A) within the S/T region of the first β strand delineates the kinetics of the interconversion between the major twisted-monomeric conformation and a more regular β strand configuration in an excited-state dimer, as well as exchange of both monomer and dimer species with high-molecular-weight oligomers. These data provide insights into the molecular origins of DNAJB6b oligomerization. Further, the results reported here have implications for the design of β sheet proteins with tunable self-assembling properties and pave the way to an atomic-level understanding of amyloid inhibition.

Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation

Combustion is a complex chemical system which involves thousands of chemical reactions and generates hundreds of molecular species and radicals during the process. In this work, a neural network-based molecular dynamics (MD) simulation is carried out to simulate the benchmark combustion of methane. During MD simulation, detailed reaction processes leading to the creation of specific molecular species including various intermediate radicals and the products are intimately revealed and characterized. Overall, a total of 798 different chemical reactions were recorded and some new chemical reaction pathways were discovered. We believe that the present work heralds the dawn of a new era in which neural network-based reactive MD simulation can be practically applied to simulating important complex reaction systems at ab initio level, which provides atomic-level understanding of chemical reaction processes as well as discovery of new reaction pathways at an unprecedented level of detail beyond what laboratory experiments could accomplish.

Ab Initio Investigation of Cooperativity in Ion Exchange

Ion exchange reactions are being increasingly employed for the templated synthesis of inorganic nanomaterials for plasmonics, topological quantum computing, and solid-state electrolytes. Some cation exchange reactions have been found to be cooperative akin to the nature of ligand binding processes in enzymes. What is the structural origin of this cooperative behavior? This question is answered here through computational simulations of Cd2+-to-Cu+ replacement reactions in a CdSe crystal. Density functional theory simulations show that the incorporation of Cu+, at the initial stages of exchange, induces a translocation of Cd2+ ions from their ideal tetrahedral sites to the otherwise unfavored octahedral sites. This reorganized structure has a lower energy cost for Cd2+-to-Cu+ replacement and is therefore much more amenable to further cation exchange. Thus, Cu+-insertion-induced reorganization of the cationic sublattice is at the origin of the cooperativity exhibited by the cation exchange reaction. This atomic-level understanding establishes a close link between solid-state chemical reactions and phase transitions and will lead to more precise transformations for accessing unusual material phases.

Exploring reactivity and product formation in N(4S) collisions with pristine and defected graphene with direct dynamics simulations.

Atomic nitrogen is formed in the high-temperature shock layer of hypersonic vehicles and contributes to the ablation of their thermal protection systems (TPSs). To gain atomic-level understanding of the ablation of carbon-based TPS, collisions of hyperthermal atomic nitrogen on representative carbon surfaces have recently be investigated using molecular beams. In this work, we report direct dynamics simulations of atomic-nitrogen [N(4S)] collisions with pristine, defected, and oxidized graphene. Apart from non-reactive scattering of nitrogen atoms, various forms of nitridation of graphene were observed in our simulations. Furthermore, a number of gaseous molecules, including the experimentally observed CN molecule, have been found to desorb as a result of N-atom bombardment. These results provide a foundation for understanding the molecular beam experiment and for modeling the ablation of carbon-based TPSs and for future improvement of their properties.

Atomic-scale microstructure of metal halide perovskite.

Hybrid organic-inorganic perovskites have high potential as materials for solar energy applications, but their microscopic properties are still not well understood. Atomic-resolution scanning transmission electron microscopy has provided invaluable insights for many crystalline solar cell materials, and we used this method to successfully image formamidinium lead triiodide [CH(NH2)2PbI3] thin films with a low dose of electron irradiation. Such images reveal a highly ordered atomic arrangement of sharp grain boundaries and coherent perovskite/PbI2 interfaces, with a striking absence of long-range disorder in the crystal. We found that beam-induced degradation of the perovskite leads to an initial loss of formamidinium [CH(NH2)2 +] ions, leaving behind a partially unoccupied perovskite lattice, which explains the unusual regenerative properties of these materials. We further observed aligned point defects and climb-dissociated dislocations. Our findings thus provide an atomic-level understanding of technologically important lead halide perovskites.

Dynamic Surface Reconstruction of Single-Atom Bimetallic Alloy under Operando Electrochemical Conditions.

The atomic-level understanding of the dynamic evolution of the surface structure of bimetallic nanoparticles under industrially relevant operando conditions provides a key guide for improving their catalytic performance. Here, we exploit operando X-ray absorption fine structure spectroscopy to determine the dynamic surface reconstruction of Cu/Au bimetallic alloy where single-atom Cu was embedded on the Au nanoparticle, under electrocatalytic conditions. We identify the migration of isolated Cu atoms from the vertex position of the Au nanoparticle to the stable (100) plane of the Au first atom layer, when the reduction potential is applied. Density functional theory calculations reveal that the surface atom migration would significantly modulate the Au electronic structure, thus serving as the real active site for the catalytic performance. These findings demonstrate the real structural change under electrochemical conditions and provide guidance for the rational design of high-activity bimetallic nanocatalysts.

Microwave synthesis conditions dependent catalytic performance of hydrothermally aged CuII-SSZ-13 for NH3-SCR of NO

To simplify the complicated synthetic techniques so that getting CuII-SSZ-13 zeolites with ideal structures and CuII cations distribution, and to interrogate CuII cations dynamics dependent NH3 mediated performance of selective catalytic reduction (NH3-SCR) of NO and hydrothermal stability, a microwave-assisted hydrothermal synthesis route was performed to prepare CuII exchanged SSZ-13 zeolite catalysts. The effects of synthetic temperature and time on the structure of SSZ-13 zeolite and NH3-SCR performance are clarified. The types and numbers of CuII species of fresh and hydrothermal aged samples were precisely explored. The NH3-SCR activity, N2 selectivity of fresh and aged CuII-SSZ-13 zeolites synthesized by different conditions are evaluated, respectively. Experimental characterizations demonstrate that the CuII-SSZ-13 zeolites can be synthesized with short crystallization time assisted with microwave treatment. The microwave synthesis temperature and time can affect the nucleation and growth process of SSZ-13 and thus resulting in SSZ-13 with different framework structures and various affinity to CuII ions. When the temperature and time are 175 °C and 9 h, the as-synthesized CuII-SSZ-13 sample shows a stable framework structure, large specific surface area, and more [Z2CuII] speciation. This sample also shows excellent catalytic activity and hydrothermal stability. Characterization results also show that the microwave treatment can strengthen the Al-O-Si bonds in the zeolite framework. Our work provides a facile strategy to synthesize CuII-SSZ-13 zeolite and atomic-level understanding of catalytic property and hydrothermal stability.

A Perspective on New Opportunities in Atom-by-Atom Synthesis of Heterogeneous Catalysts Using Atomic Layer Deposition

Catalyst precise synthesis at the atomic level is of great importance for establishing structure–activity relationships and developing advanced catalysts with high efficiency. Atomic layer deposition (ALD) relies on sequential self-limiting molecular surface reactions on substrates. Such unique features not only ensures to achieve uniform deposition on powder surfaces with high surface areas, but also offers a powerful capability of control of the deposited materials with near atomic precision. This perspective will discuss new opportunities in atomically-precise synthesis of heterogeneous catalysts using ALD. As examples, I will describe the recent key developments in ALD synthesis of supported metal single atoms, homonuclear and heteronuclear dimers, bimetallic nanoparticles as well as atomically-dispersed metal (hydro)oxide species on metal nanoparticles to form 3-dimentional metal–oxide interfaces. Such atom-by-atom construction of supported catalysts from the bottom up is hardly achieved by other synthetic methods, thus would greatly deepen atomic-level understanding of structure–activity relationships. Given the rapid development of technologies in ALD coating on powders at a large scale, atom-by-atom synthesis of heterogeneous catalysts using ALD sheds dawn light on precise catalysis for industrial applications in the near future.

Fatigue of Metallic Glasses

AbstractMetallic glasses (MGs) are often perceived as quintessential structural materials due to their superior mechanical properties such as high strength and large elastic limit. In practical applications, service conditions that introduce cyclic variations in stresses and strains are inevitably involved. The fatigue of MGs is thus a topic of research and practical interest. In this review, a brief introduction on MGs, their applications and challenges, is first provided. Next, experimental studies on fatigue behaviors of both macroscopic and nanoscale MGs are summarized. The range of topics covered include the stress-life behavior, fatigue-crack growth behavior, fatigue-fracture morphology, fatigue-failure mechanisms, as well as the effects of chemical composition, cycling frequency, loading condition, and sample size on the fatigue limits. Finally, recent progresses in simulation studies on the fatigue of MGs are discussed, with an emphasis placed on the atomic-level understanding of the fatigue mechanisms.

Frictional characteristics of heterostructure film composed of graphene and H-BN with the consideration of defects

The heterostructure film composed of graphene and h-BN has good long-term corrosion protection and excellent lubricity. For the heterostructure film, the dependence of lubrication performance on its structure is first investigated by molecular dynamics simulations, and an optimum structure with the minimum friction coefficient is determined. Based on this structure, the effect of various point defects on lubrication and wear properties of the film are investigated. Results show the Stone-Wales defect distributed on the top-most layer of the film has the most obvious effect on the lubrication, and the single vacancy defect plays a significant role in promoting the adhesive wear of the film. This study provides an atomic-level understanding of the frictional characteristics of heterostructure film composed of graphene and h-BN with the consideration of defects.

Atomic-level understanding on the evolution behavior of subnanometric Pt and Sn species during high-temperature treatments for generation of dense PtSn clusters in zeolites

To achieve high-loading of stable subnanometric metal clusters on solid carriers is a challenge since those small metal clusters have strong tendency to sinter into larger nanoparticles. Development of facile synthesis methodologies to obtain subnanometric metal catalysts with high metal loading and high stability against sintering at high temperature (>500 °C) in reductive atmosphere (such as H2) is critical for the practical applications. In this work, we will present and discuss the generation of high-loading (~1.4 wt%) subnanometric Pt clusters confined in the sinusoidal channels of MFI zeolite, on the basis of the atomic-level understanding on the evolution of Pt and Sn species during high-temperature oxidation–reduction treatments. It will be shown that the structural evolution of Pt and Sn species is dependent on the post-synthesis treatments. The Pt particles on the external surface can disintegrate into subnanometric Pt species and get stabilized in the zeolite channels during high-temperature calcination in air while Sn species migrate from surface region to internal region during high-temperature reduction treatment at 650 °C. The resultant material containing bimetallic PtSn clusters confined in the 10MR sinusoidal channels of the purely siliceous MFI zeolite show excellent catalytic activity and stability, as demonstrated for dehydrogenation of light alkanes at high reaction temperature.

Structural and Photophysical Templating of Conjugated Polyelectrolytes with Single-Stranded DNA.

A promising approach to influence and control the photophysical properties of conjugated polymers is directing their molecular conformation by templating. We explore here the templating effect of single-stranded DNA oligomers (ssDNAs) on cationic polythiophenes with the goal to uncover the intermolecular interactions that direct the polymer backbone conformation. We have comprehensively characterized the optical behavior and structure of the polythiophenes in conformationally distinct complexes depending on the sequence of nucleic bases and addressed the effect on the ultrafast excited-state relaxation. This, in combination with molecular dynamics simulations, allowed us a detailed atomistic-level understanding of the structure–property correlations. We find that electrostatic and other noncovalent interactions direct the assembly with the polymer, and we identify that optimal templating is achieved with (ideally 10–20) consecutive cytosine bases through numerous π-stacking interactions with the thiophene rings and side groups of the polymer, leading to a rigid assembly with ssDNA, with highly ordered chains and unique optical signatures. Our insights are an important step forward in an effective approach to structural templating and optoelectronic control of conjugated polymers and organic materials in general.

Defect engineering on MoS2 surface with argon ion bombardments and thermal annealing

Various approaches have been developed to produce MoS2 monolayers and multilayers. Using plasma and thermal thinning, layer-by-layer thinning processes were developed to produce MoS2 monolayer and multilayers. However, an atomic-level understanding of the thinning mechanism and defects created in these processes is not clear. In this paper, we studied the impact on surface structures of bulk MoS2 by argon ion (Ar+) bombardments and thermal annealing using an ultra-high vacuum (UHV) scanning tunneling microscope (STM). The STM images obtained before and after Ar+ bombardments show that low-energy (50 eV) Ar+ ions can remove single atoms from the surface and fragment the top sulfur layer resulting in single sulfur vacancy point defects and atomic pits on the MoS2 surface. Higher energy (100 eV) Ar+ ions can penetrate deeper and remove the topmost MoS2 trilayer. After bombardment with an Ar+ beam of 500 eV, the MoS2 surface appeared as granulated nanostructures consisting of 1–3 nm nanoparticles. Upon thermal annealing, topmost sulfur atoms were removed through sublimation after heating at 650 °C for 5 min and deeper atom sublimation was observed with longer annealing time, resulting in granulated nanostructures on the MoS2 surface.

Atomic-Level Characterization of the Methadone-Stabilized Active Conformation of µ-Opioid Receptor

Methadone is a synthetic opioid agonist with notoriously unique properties, such as lower abuse liability and induced relief of withdrawal symptoms and drug cravings, despite acting on the same opioid receptors triggered by classic opioids—in particular the µ-opioid receptor (MOR). Its distinct pharmacologic properties, which have recently been attributed to the preferential activation of β-arrestin over G proteins, make methadone a standard-of-care maintenance medication for opioid addiction. Although a recent biophysical study suggests that methadone stabilizes different MOR active conformations from those stabilized by classic opioid drugs or G protein–biased agonists, how this drug modulates the conformational equilibrium of MOR and what specific active conformation of the receptor it stabilizes are unknown. Here, we report the results of submillisecond adaptive sampling molecular dynamics simulations of a predicted methadone-bound MOR complex and compare them with analogous data obtained for the classic opioid morphine and the G protein–biased ligand TRV130. The model, which is supported by existing experimental data, is analyzed using Markov state models and transfer entropy analysis to provide testable hypotheses of methadone-specific conformational dynamics and activation kinetics of MOR.SIGNIFICANCE STATEMENTOpioid addiction has reached epidemic proportions in both industrialized and developing countries. Although methadone maintenance treatment represents an effective therapeutic approach for opioid addiction, it is not as widely used as needed. In this study, we contribute an atomic-level understanding of how methadone exerts its unique function in pursuit of more accessible treatments for opioid addiction. In particular, we present details of a methadone-specific active conformation of the µ-opioid receptor that has thus far eluded experimental structural characterization.

Atomic-scale understanding of the γ/α2 interface in a TiAl alloy

The eutectoid reaction often produces lamellar structure of two alternating phases, which exhibits promising mechanical properties because of high density interfaces. However, the atomic-level understanding of these interfacial structures remains controversial. Here we report the atomic structure of γ/α2 interface in a fully lamellar TiAl alloy investigated by the aberration corrected transmission electron microscopy and density functional theory (DFT) simulations. The results reveal that the orientation relationship between α2/γ interface in TiAl alloy always follows (0001)α2||{111}γ and ⟨11–20⟩α2||⟨1–10⟩γ with a semi-coherent lattice match due to the ultralow interfacial energy predicated by DFT calculation.