Atomic Level Research Articles

Illuminating Protein Allostery by Chemically Accurate Contact Response Analysis (ChACRA).

Decoding allostery at the atomic level is essential for understanding the relationship between a protein's sequence, structure, and dynamics. Recently, we have shown that decomposing temperature responses of inter-residue contacts can reveal allosteric couplings and provide useful insight into the functional dynamics of proteins. The details of this Chemically Accurate Contact Response Analysis (ChACRA) are presented here along with its application to two well-known allosteric proteins. The first protein, IGPS, is a model of ensemble allostery that lacks clear structural differences between the active and inactive states. We show that the application of ChACRA reveals the experimentally identified allosteric coupling between effector and active sites of IGPS. The second protein, ATCase, is a classic example of allostery with distinct active and inactive structural states. Using ChACRA, we directly identify the most significant residue level interactions underlying the enzyme's cooperative behavior. Both test cases demonstrate the utility of ChACRA's unsupervised machine learning approach for dissecting allostery at the residue level.

Structure‐Activity Relationships of the Structural Analogs Au8Cu1 and Au8Ag1 in the Electrocatalytic CO2 Reduction Reaction

AbstractOwing to the significant attention directed toward alloy metal nanoclusters, it is crucial to explore the relationship between their structures and their performance during the electrocatalytic CO2 reduction reaction (eCO2RR) and discover potential synergistic effects for the design of novel functional nanoclusters. However, a lack of suitable analogs makes this investigation challenging. In this study, we synthesized a well‐defined pair of structural analogs, [Au8Cu1(SAdm)4(Dppm)3Cl]2+ and [Au8Ag1(SAdm)4(Dppm)3Cl]2+ (Au8Cu1 and Au8Ag1, respectively), and characterized them. Single‐crystal X‐ray diffraction analysis revealed that Au8M1 (M=Cu/Ag) consists of a tetrahedral Au3M1 core capped by three (Dppm)Au staples, one Au2(SR)3 staple, one lone SR ligand, and a terminal Cl ligand. Ag and Cu were doped at the same site in the Au8M1 nanoclusters, which has rarely been reported. Au8Cu1 exhibited a significantly higher CO Faradaic efficiency (FECO; ~82.2 %) during eCO2RR than that of Au8Ag1 (FECO; ~33.1 %). Density functional theory calculations demonstrated that *COOH is the key intermediate in the reduction of CO2 to CO. The formation of *COOH on Au8Cu1 is more thermodynamically stable than on Au8Ag1, and Au8Cu1 shows a smaller *CO formation energy than that on Au8Ag1, which promotes the reduction of CO2. We believe that the structural analogs Au8Cu1 and Au8Ag1 offer a suitable template for the in‐depth investigation of structure‐property correlations at the atomic level.

Stimuli‐Responsive Interconversion between Poly‐NHC‐Based Organometallic Assemblies and Their Self‐Aggregated Dimers

Comprehensive SummaryPoly‐NHC‐based organometallic assemblies 3‐PF6, 3‐SbF6 and 3‐OTf were obtained and verified by NMR spectroscopy, ESI mass spectrometry and single‐crystal X‐ray diffraction analyses. Controllable structural interconversion was observed between the poly‐NHC‐based organometallic assemblies and their self‐aggregated dimers in solution affected by concentration, solvent and metal ion. 1H NMR spectra of assembly 3‐PF6 in CD3CN at different concentrations demonstrated controllable structural interconversion, and 19F NMR spectrum of assembly 3‐PF6 at high concentration further evidenced the presence of the free hexafluorophosphate anion and encapsulated hexafluorophosphate anion for its two sets of signals. In addition, single‐crystal X‐ray diffraction analysis provided clear evidence that in the solid state, two assemblies 3‐PF6 were vertically stuck, forming a self‐aggregated dimer with an encapsulated hexafluorophosphate anion. Investigating the reversible structural interconversion is beneficial for revealing the intrinsic nature on the atom level and paving the way to design the stimuli‐responsive functional system.

Tribological behavior of graphene/h-BN vdW heterostructures: the role of defects at the BN layer

Molecular dynamics simulations and first principles calculations were performed to study the tribological behavior of graphene/h-BN (G/h-BN) heterostructures with vacancy and Stone–Wales (SW) defect under uniform normal load, revealing the mechanism of the effect of defect types on friction, and discussing the coupling effect of temperature and interfacial defects on the tribological behavior of G/h-BN heterostructures. Under the normal force of 0.2 nN/atom, the friction force of the four systems is 0.0057, 0.0096, 0.0077, and 0.26 nN, respectively. The friction force of SW defect heterostructure is 45 times that of perfect interface heterostructure. The influence of defect type on friction force is SW > SV > DV. By observing the dynamic change of the Z-direction coordinate position of the sliding layer atoms, the slip potential energy curves and the evolution law of the moiré pattern, the relationship between the structural morphology and the energy change of different defective heterostructures and the frictional behavior was investigated comprehensively and intuitively for the first time. From the perspective of atomic strain, the deformation of heterostructures at the atomic level was quantified. The results showed that at 300 K and 0 K, the maximum strain of atoms in the sliding layer was 11.25% and 9.85%, respectively. The thermal perturbation mainly occurs in the out-of-plane direction, which in turn affects the friction. Through density functional theory, it is found that under uniform load, it is difficult to form bonds between the graphene sliding layer and the substrate layer when the defects are in the h-BN substrate layer, which has less influence on the friction of the system, thus making the defective heterostructures also remainsuperlubricity state. These results provide a new understanding of the interfacial friction of G/h-BN defective heterostructure.

Structure-Activity Relationships of the Structural Analogs Au8Cu1 and Au8Ag1 in the Electrocatalytic CO2 Reduction Reaction.

Owing to the significant attention directed toward alloy metal nanoclusters, it is crucial to explore the relationship between their structures and their performance during the electrocatalytic CO2 reduction reaction (eCO2RR) and discover potential synergistic effects for the design of novel functional nanoclusters. However, a lack of suitable analogs makes this investigation challenging. In this study, we synthesized a well-defined pair of structural analogs, [Au8Cu1(SAdm)4(Dppm)3Cl]2+ and [Au8Ag1(SAdm)4(Dppm)3Cl]2+ (Au8Cu1 and Au8Ag1, respectively), and characterized them. Single-crystal X-ray diffraction analysis revealed that Au8M1 (M=Cu/Ag) consists of a tetrahedral Au3M1 core capped by three (Dppm)Au staples, one Au2(SR)3 staple, one lone SR ligand, and a terminal Cl ligand. Ag and Cu were doped at the same site in the Au8M1 nanoclusters, which has rarely been reported. Au8Cu1 exhibited a significantly higher CO Faradaic efficiency (FECO; ~82.2 %) during eCO2RR than that of Au8Ag1 (FECO; ~33.1 %). Density functional theory calculations demonstrated that *COOH is the key intermediate in the reduction of CO2 to CO. The formation of *COOH on Au8Cu1 is more thermodynamically stable than on Au8Ag1, and Au8Cu1 shows a smaller *CO formation energy than that on Au8Ag1, which promotes the reduction of CO2. We believe that the structural analogs Au8Cu1 and Au8Ag1 offer a suitable template for the in-depth investigation of structure-property correlations at the atomic level.

In silico monitoring of non-reactive gas blistering on crystalline substrates

Blistering from gas aggregation occurs very rarely on solid substrates; however, it is commonly observed under high-pressure gas or plasma environments. This is due to the repeated aggregation process of gas molecules penetrating beneath the surface, but it has been difficult to find cases that demonstrate the dynamic mechanism on the atomic level. In this study, the dynamics of physical bombardment of argon atoms on the flat monocrystalline silicon substrate are simulated to propose an initiation principle for gas-aggregate formation. Simulations of extremely large numbers of argon atoms bombarding a limited area of single crystal silicon revealed inhomogeneous aggregation properties consistent with the experimental observations. Particularly, the results suggest that momentum transfer formed by collisions between argon trapped in the surface grooves and the argon used for bombardment is the governing factor for the aggregation behavior. The aggregated argon clusters grow in the in-plane direction while generating stress propagation in the thickness direction, ultimately causing an expansion pressure that lifts the adjacent silicon surface upwards. Our work provides a deterministic understanding of the initiation process of blister formation, which rarely occurs in physical sputtering on defect-free substrates.

Interatomic potential of the MgAl2O4/Al interface and its application in strengthening mechanisms

MgAl2O4 ceramics possess outstanding mechanical properties, making them promising for use as reinforcing or interfacial modulating phase in Al-based metal composites. The challenge lies in the insufficient interatomic potential parameters to accurately characterize the MgAl2O4/Al interfacial interactions, which hampers a detailed understanding of the interfacial strengthening mechanisms at the atomic level. Since the pair potential satisfies the requirements for computational efficiency and accuracy, it has been widely used for investigating the interfacial properties of composite materials. In this study, the interatomic potential parameters for Al–Mg and Al–Al bonds were derived from Buckingham potential, while those for Al–O bonds were obtained from Morse potential via first principles calculations. The uniaxial tensile mechanical properties and interface-dislocation strengthening mechanisms of MgAl2O4/Al interface configuration were explored through molecular dynamics simulations. The analyses reveal that the strength enhancement of the MgAl2O4/Al interface is due to the generation of a large number of immovable 1/6<110> stair-rod dislocations therein. The thickness of MgAl2O4 layer significantly influences the mechanical properties. Below a thickness of 20 Å, the presence of movable dislocations reduces the strengthening effect. Conversely, increasing the thickness of MgAl2O4 encourages the emergence of immovable dislocations and increases the flow stress, while the corresponding yield strain decreases. These insights open up new prospects in the development of aluminum metal matrix composites with enhanced performance.

Dynamic STEM-EELS for single-atom and defect measurement during electron beam transformations.

This study introduces the integration of dynamic computer vision-enabled imaging with electron energy loss spectroscopy (EELS) in scanning transmission electron microscopy (STEM). This approach involves real-time discovery and analysis of atomic structures as they form, allowing us to observe the evolution of material properties at the atomic level, capturing transient states traditional techniques often miss. Rapid object detection and action system enhances the efficiency and accuracy of STEM-EELS by autonomously identifying and targeting only areas of interest. This machine learning (ML)-based approach differs from classical ML in that it must be executed on the fly, not using static data. We apply this technology to V-doped MoS2, uncovering insights into defect formation and evolution under electron beam exposure. This approach opens uncharted avenues for exploring and characterizing materials in dynamic states, offering a pathway to increase our understanding of dynamic phenomena in materials under thermal, chemical, and beam stimuli.

Crystalline‐amorphous dual‐phase ceramic nanocomposites regulated by entropy engineering

AbstractSolid‐state reaction (SSR) is frequently used to fabricate bulk high‐entropy ceramics (HECs). However, a high temperature and a long dwelling time are typically required to allow the occurrence of SSR. Meanwhile, conventional HECs were typically composed of single‐phase solid solution with micrograins. It is of great interest to develop nanocrystalline dual‐phase HECs under mild conditions. Here, we fabricated entropy‐mediated crystalline‐amorphous dual‐phase ceramic nanocomposites, and the fabrication process showed significantly higher energy and time efficiency than the conventional SSR. The nanocomposites were composed of entropy‐mediated nanoparticles (EM‐NPs) embedded in an amorphous SiO2 matrix. The constituent elements were homogeneously distributed in the EM‐NPs at the atomic level. The EM‐NPs were dislocations‐free but with lattice strain, and they showed a strong coarsening tendency during annealing. The nanocomposites showed a significant solid solution hardening effect. The reported results would provide useful guidance to fabricate nanocrystalline HECs with crystalline‐amorphous dual‐phase microstructure.

Atomic layer deposition of Al-doped ZnO nanomembrane with in situ monitoring

Due to shortcomings such as poor homogeneity of Al doping, precisely controlling the thickness, inability to conformally deposit on high aspect ratio devices and high pinhole rate, the applications of Al-doped ZnO (AZO) nanomembrane in integrated optoelectronic devices are remarkably influenced. Here, we report in situ monitoring during the atomic layer deposition (ALD) of AZO nanomembrane by using an integrated spectroscopic ellipsometer. AZO nanomembranes with different compositions were deposited with real-time and precise atomic level monitoring of the deposition process. We specifically investigate the half-reaction and thickness evolution during the ALD processes and the influence of the chamber temperature is also disclosed. Structural characterizations demonstrate that the obtained AZO nanomembranes without any post-treatment are uniform, dense and pinhole-free. The transmittances of the nanomembranes in visible range are >94%, and the optimal conductivity can reach up to 1210 S cm−1. The output of current research may pave the way for AZO nanomembrane to become promising in integrated optoelectronic devices.

Interactions between Iron Minerals and Dissolved Organic Matter Derived from Microplastics Inhibited the Ferrihydrite Transformation as Revealed at the Molecular Scale.

Microplastic-derived dissolved organic matter (MP-DOM) is an emerging carbon source in the environment. Interactions between MP-DOM and iron minerals alter the transformation of ferrihydrite (Fh) as well as the distribution and fate of MP-DOM. However, these interactions and their effects on both two components are not fully elucidated. In this study, we selected three types of MP-DOM as model substances and utilized Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and extended X-ray absorption fine structure (EXAFS) spectroscopy to characterize the structural features of DOMs and DOM-mineral complexes at the molecular and atomic levels. Our results suggest that carboxyl and hydroxyl groups in MP-DOM increased the Fe-O bond length by 0.02-0.03 Å through interacting with Fe atoms in the first shell, thereby inhibiting the transformation of Fh to hematite (Hm). The most significant inhibition of Fh transformation was found in PS-DOM, followed by PBAT-DOM and PE-DOM. MP-DOM components, such as phenolic compounds and condensed polycyclic aromatics (MW > 360 Da) with high oxygen content and high unsaturation, exhibited stronger mineral adsorption affinity. These findings provide a profound theoretical basis for accurately predicting the behavior and fate of iron minerals as well as MP-DOM in complex natural environments.

Electrochemical Stability of MXenes in Water Based on Constant Potential AIMD Simulations.

MXene has been recently explored as promising electrocatalytic materials to accelerate the electrocatalytic process for hydrogen evolution, but their dynamic stability under electrochemical conditions remains elusive. Here we performed first-principle ab initio molecular dynamics calculations to reveal the electrochemical stability of Ti2CTx MXene in different aqueous environments. The results revealed the high vulnerability of the pure and vacancy-defected Ti2CO2 MXene towards water attack, leading to surface oxidation of MXene under neutral electrochemical condition that formed adsorbed oxygen species to Ti and dissociated proton in solution. The surface oxidation of Ti2CO2 could be prevented in the acid condition or in the neutral condition under the negative potential. Differently, the fully F- or OH-functionalized Ti2CF2 and Ti2C(OH)2 as well as the mixed functionalized Ti2C(O0.5OH0.5)2 and Ti2CO1.12F0.88 are highly stable under various electrochemical conditions, which can effectively prevent close contact between water and surface Ti atoms via electronic repulsion or steric hindrance. These findings provide atomic level understanding of the aqueous stability of MXene and provide useful strategies to prevent degradation and achieve highly stable MXenes.

Mass transfer at vapor-liquid interfaces of H2O + CO2 mixtures studied by molecular dynamics simulation

Abstract In many industrial applications as well as in nature, the mass transfer of CO2 at vapor-liquid interfaces in aqueous systems plays an important role. In this work, this process was studied on the atomistic level using non-equilibrium molecular dynamics simulations. In a first step, a molecular model of the system water + CO2 was developed that represents both bulk and interfacial equilibrium properties well. This system is characterized by a very large adsorption and enrichment of CO2 at the vapor-liquid interface. Then, non-equilibrium mass transfer simulations were carried out using a method that was developed recently: CO2 is inserted into the vapor phase of a simulation box which contains a liquid slab. Surprising effects are observed at the interface such as a net repulsion of CO2 particles from the interface and a complex time dependence of the amount of CO2 adsorbed at the interface.

Green Synthesis of Au‐Ag@TiO2 Nanocomposite for Photocatalytic Oxidation of Substituted Benzyl Alcohols

AbstractThe scaling‐up of methodologies in the oxidation of alcohols to carbonyl compounds faced widespread hindrance in industries due to large‐scale use of toxic and expensive metal oxidants. Novel, cost‐effective and eco‐friendly approaches need to be developed to address these problems. Bimetallic nanoparticles (BMNPs) show synergistic effects at atomic level, which makes them excellent catalysts for organic transformations. Transition metal nanocomposite with unique physicochemical properties and high surface area offers a promising alternative to traditional catalysts. Herein, an environment‐friendly methodology was adopted for the synthesis of Au−Ag BMNPs using phenolic‐rich Ocimum basilicum (L.) leaf extract, which was then incorporated into TiO2 matrix for the synthesis of plasmonic Au−Ag@TiO2 nanocomposite. The formation of the nanocomposite was confirmed through analytical characterizations, such as UV–Vis. DRS, FT‐IR, PL, SEM, TEM and XRD. The nanocomposite exhibited excellent catalytic activity in the selective oxidation of primary and secondary alcohols in aqueous media using H2O2 as an oxidant under visible light irradiation at room temperature. The nanocomposite also demonstrated good reusability of 84 % in the fifth cycle, which established its promising candidature for wide‐scale applications. This work holds significant relevance for industries dealing with pharmaceuticals and personal care products, and thus, offers sustainable solution for organic transformations.

Neuropilin-1 Protein May Serve as a Receptor for SARS-CoV-2 Infection: Evidence from Molecular Dynamics Simulations.

The binding of the virus to host cells is the first step in viral infection. Human cell angiotensin converting enzyme 2 (ACE2) is the most popular receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), while other receptors have recently been observed in experiments. Neuropilin-1 protein (NRP1) is one of them, but the mechanism of its binding to the wild type (WT) and different variants of the virus remain unclear at the atomic level. In this work, all-atom umbrella sampling simulations were performed to clarify the binding mechanism of NRP1 to the spike protein fragments 679-685 of the WT, Delta, and Omicron BA.1 variants. We found that the Delta variant binds most strongly to NRP1, while the affinity for Omicron BA.1 slightly decreases for NRP1 compared to that of WT, and the van der Waals interaction plays a key role in stabilizing the studied complexes. The change in the protonation state of the His amino acid results in different binding free energies between variants. Consistent with the experiment, decreasing the pH was shown to increase the binding affinity of the virus to NRP1. Our results indicate that Delta and Omicron mutations not only affect fusogenicity but also affect NRP1 binding. In addition, we argue that viral evolution does not further improve NRP1 binding affinity which remains in the μM range but may increase immune evasion.

19F Fast Magic-Angle Spinning NMR Spectroscopy on Microcrystalline Complexes of Fluorinated Ligands and the Carbohydrate Recognition Domain of Galectin-3.

Structural characterization of protein-ligand binding interfaces at atomic resolution is essential for improving the design of specific and potent inhibitors. Herein, we explored fast 19F- and 1H-detected magic angle spinning NMR spectroscopy to investigate the interaction between two fluorinated ligand diastereomers with the microcrystalline galectin-3 carbohydrate recognition domain. The detailed environment around the fluorine atoms was mapped by 2D 13C-19F and 1H-19F dipolar correlation experiments and permitted characterization of the binding interface. Our results demonstrate that 19F MAS NMR is a powerful tool for detailed characterization of protein-ligand interfaces and protein interactions at the atomic level.

Atomic-scale tribological behavior of pressure-induced MoO3(0 1 0)/Ag(1 1 1) heterogeneous sliding interface

The atomic-scale tribological properties of the MoO3(010)/Ag(111) heterogeneous sliding interface were studied by first-principles calculation method. The interface binding energy, sliding potential energy, friction force, charge density difference, partial density of states, Mulliken bond population and HiRshfeld charge were analyzed, and the essence of the friction was revealed. The results show that the sliding potential energy and friction exhibit anisotropy for the pressure-induced MoO3(010)/Ag(111) heterogeneous sliding interface. The friction force can be described by the change of the sliding potential energy, and the charge redistribution between interface atoms is the intrinsic reason for the change of tribological properties. This work provides atomic and electronic level insights for understanding the tribological characteristics between two-dimensional materials and soft metals.

Unveiling Atomic-Scaled Local Chemical Order of High-Entropy Intermetallic Catalyst for Alkyl-Substitution-Dependent Alkyne Semihydrogenation.

High-entropy intermetallic (HEI) nanocrystals, composed of multiple elements with an ordered structure, are of immense interest in heterogeneous catalysis due to their unique geometric and electronic structures and the cocktail effect. Despite tremendous efforts dedicated to regulating the metal composition and structures with advanced synthetic methodologies to improve the performance, the surface structure, and local chemical order of HEI and their correlation with activity at the atomic level remain obscure yet challenging. Herein, by determining the three-dimensional (3D) atomic structure of quinary PdFeCoNiCu (PdM) HEI using atomic-resolution electron tomography, we reveal that the local chemical order of HEI regulates the surface electronic structures, which further mediates the alkyl-substitution-dependent alkyne semihydrogenation. The 3D structures of HEI PdM nanocrystals feature an ordered (intermetallic) core enclosed by a disordered (solid-solution) shell rather than an ordered surface. The lattice mismatch between the core and shell results in apparent near-surface distortion. The chemical order of the intermetallic core increases with annealing temperature, driving the electron redistribution between Pd and M at the surface, but the surface geometrical (chemically disordered) configurations and compositions are essentially unchanged. We investigate the catalytic performance of HEI PdM with different local chemical orders toward semihydrogenation across a broad range of alkynes, finding that the electron density of surface Pd and the hindrance effect of alkyl substitutions on alkynes are two key factors regulating selective semihydrogenation. We anticipate that these findings on surface atomic structure will clarify the controversy regarding the geometric and/or electronic effects of HEI catalysts and inspire future studies on tuning local chemical order and surface engineering toward enhanced catalysts.

Quantitative Analysis of the Synergy of Doping and Nanostructuring of Oxide Photocatalysts.

In this paper, the effect of doping and nanostructuring on the electrostatic potential across the electrochemical interface between a transition metal oxide and a water electrolyte is investigated by means of the Poisson-Boltzmann model. For spherical nanoparticles and nanorods, compact expressions for the limiting potentials at which the space charge layer includes the whole semiconductor are reported. We provide a quantitative analysis of the distribution of the potential drop between the solid and the liquid and show that the relative importance changes with doping. It is usually assumed that high doping improves charge dynamics in the semiconductor but reduces the width of the space charge layer. However, nanostructuring counterbalances the latter negative effect; we show quantitatively that in highly doped nanoparticles the space charge layer can occupy a similar volume fraction as in low-doped microparticles. Moreover, as shown by some recent experiments, under conditions of high doping the electric fields in the Helmholtz layer can be as high as 100 mV/Å, comparable to electric fields inducing freezing in water. This work provides a systematic quantitative framework for understanding the effects of doping and nanostructuring on electrochemical interfaces, and suggests that it is necessary to better characterize the interface at the atomistic level.

Dynamic Evolution and Reversibility of a Single Au25 Nanocluster for the Oxygen Reduction Reaction.

Ultrasmall metallic nanoclusters (NCs) protected by surface ligands represent the most promising catalytic materials; yet understanding the structure and catalytic activity of these NCs remains a challenge due to dynamic evolution of their active sites under reaction conditions. Herein, we employed a single-nanoparticle collision electrochemistry method for real-time monitoring of the dynamic electrocatalytic activity of a single fully ligand-protected Au25(PPh3)10(SC2H4Ph)5Cl22+ nanocluster (Au252+ NC) at a cavity carbon nanoelectrode toward the oxygen reduction reaction (ORR). Our experimental results and computational simulations indicated that the reversible depassivation and passivation of ligands on the surface of the Au252+ NC, combined with the dynamic conformation evolution of the Au259+ core, led to a characteristic current signal that involves "ON-OFF" switches and "ON" fluctuations during the ORR process of a single Au252+ NC. Our findings reinvent the new perception and comprehension of the structure-activity correlation of NCs at the atomic level.