Atomic Level Research Articles

Insight into the direct carbonation process of Ca2SiO4 based on ReaxFF MD simulation and experiments

Ca2SiO4 is the primary carbonation-reactive mineral in steel slag, and demonstrates significant carbon sequestration potential, yet its microscopic reaction processes remain unclear. This study investigated the carbonation behavior of Ca2SiO4 using ReaxFF MD simulations. The results indicated that as CO2 concentration increased, the capture rate of Ca2SiO4 decreased, and the molecular structure of the resulting CaCO3 varied in oxygen origin. At room temperature, the carbonation rate of Ca₂SiO₄ gradually decreased over time until it reached equilibrium. Increasing the temperature could reactivate the carbonation, but the rate would still decline until it reached equilibrium again. Higher temperatures could accelerate the formation of the intermediate C2O52− and internal CO32− diffusion, thereby boosting the carbonation and increasing CO2 adsorption. This study investigated the carbonation of Ca2SiO4 at the atomic level, aiming to link microscopic molecular processes with macroscopic experimental phenomena, thereby providing a theoretical foundation for enhancing the carbonation efficiency of steel slag.

Engineering of hyperentangled complex quantum networks

Abstract We propose a novel scheme to engineer the atomic hyperentangled cluster and ring graph states invoking cavity-QED technique for applicative relevance to quantum biology and quantum communications utilizing the complex quantum networks. These states are engineered using both external quantized momenta states and energy levels of neutral atoms under off-resonant and resonant Atomic Bragg Diffraction (ABD) technique. The study of dynamical capacity and potential efficiency have certainly enhanced the range of usefulness of these states. In order to assess the operational behavior of such states when subjected to a realistic noise environment has also been simulated, demonstrating long enough sustainability of the proposed states. Moreover, experimental feasibility of the proposed scheme has also been elucidated under the prevailing cavity-QED research scenario.

Uncovering structure-activity relationships in Brønsted acidic deep eutectic solvents for extractive and oxidative desulfurization

Modeling the structure-activity relationships (SARs) of deep eutectic solvents (DESs) is crucial for upgrading their catalytic performance in targeted reactions. Herein, a series of Brønsted acidic DESs are developed for the SARs research at molecular and atomic levels. Experimental and theoretical results suggest that the catalytic activity increases with the decreasing distances between O atom of active sites in DESs and S atom in sulfur compounds, and the R2 between EODS efficiency and the valid distances of O···S is above 0.9. Such geometric configuration can be optimized by altering the composition of DESs, which in turn substantially triggers the reaction acceleration between active intermediates and substrates. The resulting DES (TEAC/2BSA) achieved deep desulfurization for various sulfur compounds based on the optimal valid distances of O···S. This work contributes to a deep understanding of the reaction mechanism and enables the effective screening of task-specific DESs.

Atomistic origin of montmorillonite clay subjected to freeze-thaw hysteresis

The freeze-thaw cycles of frozen soil could significantly affect its thermo-hydro-mechanical-chemical (THMC) properties, causing the frost heaving and thawing settlement. The microscale essence is the water-ice phase transition, but the microscale details are still poorly understood, especially at ultra-low temperatures. Nuclear magnetic resonance (NMR) technology and molecular dynamics (MD) simulation methods were performed to explore the freeze-thaw behaviors of montmorillonite clay under temperature of 210 - 293 K. Then, the water-ice phase transition, freeze-thaw hysteresis, ice nucleation mechanism, and surface effect of clay at an atomistic level were discussed. A classification method of different types of unfrozen water through NMR experiment was proposed, including bulk, capillary, and bound water. Here, it is found that: (1) the freeze-thaw process of frozen soil at the macroscale was essentially the occurrence of ice-water phase transition at the microscale. (2) The freeze-thaw hysteresis was caused by different growth and melting rates of ice crystals, where the ice growth/nucleation on clay surface was more difficult to develop. (3) The surface effect of clay was essential for the ice nucleation and the existence of bound water. For example, little unfrozen water still existed in unfrozen soil even at 213 K. (4) For unsaturated frozen soil, the quasi-liquid water was an essential component of unfrozen water that cannot be ignored. This work could provide an atomistic insight to unravel the atomistic origin of the freeze-thaw mechanism of montmorillonite clay and complement relevant experimental evidence.

Drug expiration study using Raman spectroscopy and super paramagnetic clustering

Currently, there is a belief that drugs used after the expiration date no longer work, or even these can cause some damage. In the present work, several types of drugs on the market with different expiration dates are analyzed to find out if these, with the expired expiration date, present spectroscopic differences from those drugs whose expiration date is still valid. This study used the Raman spectroscopy technique to determine the chemical composition of drugs. To measure the drug Raman spectra, Horiba equipment, LabRam HR800, was used with an Olympus confocal microscope focusing a laser of 830 nm and 17 mW on the drugs through a 50 X Leica long-range objective. The Super Paramagnetic Clustering (SPC) method was applied to classify the Raman spectra. In the SPC method, the clustering process is based on a phenomenon of clustering observed in nature at the atomic level and perfectly described by a statistical physics model known as the Potts model, which describes the interacting spins on a crystalline lattice. This clustering method allows for identifying hierarchical structures in the spectra data banks. Fourteen drugs were analyzed, including 2 capsules, 5 tablets, 2 liquid samples, 4 ointments, and one spray with 1 to 3 expired expiration dates. Comparing drugs with expiration dates that are still valid and expired, the SPC results applied to the Raman spectra showed that, although some drugs indicated chemical differences, others indicated no chemical differences, even among those with up to two expired expiration dates. The results showed that Raman spectroscopy and SPC are excellent tools for discriminating between expired and non-expired drugs. The Principal Components Analysis (PCA) was also applied as a cross-checking method of the SPC result, obtaining consistent results. To our knowledge, it is the first preliminary result evaluating the usefulness of Raman spectroscopy and SPC in identifying expired drugs distributed on the market.

Partitioning of an Enzyme-Polymer Surfactant Nanocomplex into Lipid-Rich Cellular Compartments Drives In Situ Hydrolysis of Organophosphates.

Most organophosphates (OPs) are hydrophobic, and after exposure, can sequester into lipophilic regions within the body, such as adipose tissue, resulting in long term chronic effects. Consequently, there is an urgent need for therapeutic agents that can decontaminate OPs in these hydrophobic regions. Accordingly, an enzyme-polymer surfactant nanocomplex is designed and tested comprising chemically supercharged phosphotriesterase (Agrobacterium radiobacter; arPTE) electrostatically conjugated to amphiphilic polymer surfactant chains ([cat.arPTE][S-]). Experimentally-derived structural data are combined with molecular dynamics (MD) simulations to provide atomic level detail on conformational ensembles of the nanocomplex using dielectric constants relevant to aqueous and lipidic microenvironments. These show the formation of a compact admicelle pseudophase surfactant corona under aqueous conditions, which reconfigures to yield an extended conformation at a low dielectric constant, providing insight into the mechanism underpinning cell membrane binding. Significantly, it demonstrated that [cat.arPTE][S-] spontaneously binds to human mesenchymal stem cell membranes (hMSCs), resulting in on-cell OP hydrolysis. Moreover, the nanoconstruct can endocytose and partition into the intracellular fatty vacuoles of adipocytes and hydrolyze sequestered OP.

Multi-scale structure and reinforcement mechanisms of multi-element composite ceramic coatings

Ceramic coating is of significant importance for improving metallic materials in terms of mechanical properties or durability, which is commonly encountered in the field of machinery, civil engineering, and aerospace, etc. However, ceramic materials optimization is a great challenge due to the complex multi-scale design from atomic to macro level. This paper investigates the multiscale characteristics of multi-element composite ceramic coating, including electronic properties, 3D pore structure, and engineering performances and gives their bottom-up connections, via first-principles calculations and multiscale experiments. The doping of Ti, Zr, and Ce in the alumina-based ceramic crystal improves the overlap of electronic clouds between oxygen and metal atoms, which modifies the atomic charges and enhances the ionic bonding. In terms of microstructure, it reveals the mechanisms of phase transformation toughening effect of ZrO2 and the grain refinement and grain boundary purification effects of CeO2, which facilitates the amelioration of pore structure and macro mechanical properties. It provides multiscale information on the phase stability of multi-element alumina-based ceramics, shedding light on the fundamental atomic level mechanisms that play a crucial role in customizable functional designs

Unveiling the structural mechanisms behind high affinity and selectivity in phosphorylated epitope-specific rabbit antibodies.

Protein phosphorylation is a crucial process in various cellular functions, and its irregularities have been implicated in several diseases, including cancer. Antibodies are commonly employed to detect protein phosphorylation in research. However, unlike the extensive studies on recognition mechanisms of the phosphate group by proteins such as kinases and phosphatases, only a few studies have explored antibody mechanisms. In this study, we produced and characterized two rabbit monoclonal antibodies that recognize a mono-phosphorylated Akt peptide. Through crystallography, thermodynamic mutational analyses, and molecular dynamics simulations, we investigated the unique recognition mechanism that enables higher binding affinity and selectivity of the antibodies compared to other generic proteins with lower binding affinity to phosphorylated epitopes. Our results demonstrate that molecular dynamics simulations provide novel insights into the dynamic aspects of molecular recognition of post-translational modifications by proteins beyond static crystal structures, highlighting how specific atomic level interactions drive the exceptional affinity and selectivity of antibodies.

Strong Metal–Support Interaction Induces Dual Reaction Sites for Ultrasensitive and Stable NO2 Detection in Extreme Environments

AbstractThe tripartite combination of a high density and stability of surface reaction sites, complemented by the longevity and efficient transfer of interface carriers, along with the effective adsorption and activation of target gas molecules, jointly determines the efficiency of chemiresistors. In this work, the strong metal–support interaction (SMSI) of Pt─Ce3+ is formed by the NaBH4 reduction method and thus prepares metal‐dynamically stable PtNR─CeO2 with Pt─Ce3+ and Pt─Pt reaction sites. The formation of SMSI induces the recombination of the chemical structure of the CeO2 surface causing the localization of electron‐rich Ce3+, which greatly increases the charge concentration at the interface. The experimental findings of the strong interaction of Pt─Ce3+ bonding and the catalytic effect of Pt optimized the adsorption mode of PtNR─CeO2 on target gas, which maintains stable catalytic activity at 20–500 °C and achieving a notable detection response value of 1.43 for 20 ppb NO2. This work offers fresh insights into designing stable oxide chemiresistors with efficiency and stability by customizing reaction sites at the atomic level.

Binary Iron-Manganese Cocatalyst for Simultaneous Activation of C-C and C-O Bonds to Maximally Utilize Lignin for Syngas Generation over InGaN.

Solar-powered lignin reforming offers a carbon-neutral route for syngas production. This study explores a dual non-precious iron-manganese cocatalyst to simultaneously activate both C-C and C-O bonds for maximizing the utilization of various substituents of native lignin to yield syngas. By assembling with InGaN nanowires on a Si wafer, the as-designed dual FeMn cocatalyst affords a measurable syngas evolution rate of 42.4 mol·gcat-1·h-1 from native lignin in distilled water with a high selectivity of 93% and tunable H2/CO ratios under concentrated light, leading to a considerable light-to-fuel efficiency of 11.8%. The high FeMn atom efficiency arising from the 1-dimensional nanostructure of InGaN enables the achievement of a high turnover frequency (TOF) of 220896 mol syngas per mol FeMn per hour. By correlating explorationexperiments,the critical role of the dual FeMn cocatalyst in the evolving mechanism of lignin and water toward syngas is disclosed at the atomic level. It is discovered that the synergetic iron-manganese cocatalyst supported by InGaN nanowires enables simultaneous activation of C-C and C-O bonds with comparable minimized dissociation energies.This work demonstrates a new and earth-abundant bifunctional cocatalyst for utilizing various substituents of lignin to produce syngas powered by sunlight beyond fossil fuels.

Strain induced phase transitions and hysteresis in aluminium nitride: a density functional theory study

Computer atomistic simulations based on density functional theory were carried out to investigate strain induced phase transitions in aluminium nitride (AlN). The wurtzite to graphitic and graphitic to wurtzite transformations were investigated at the atomic level and their physical origins were identified. Both phase transitions were found to be of the first order. The wurtzite to graphitic phase transition takes place in the tensile regime at a strain value of +7%. The driving force for this transformation was identified to be an elastic instability induced by tensile strain. A hysteresis was demonstrated where the graphitic structure is separated from the wurtzite by a kinetic energy barrier. The origin of the observed hysteresis is due to the asymmetry of bond formation and bond breaking associated with the wurtzite to graphitic and graphitic to wurtzite transitions, respectively. A dynamic instability taking place at +3%, along the graphitic path, prevents the hysteresis to fully occur. The possible occurrence of the hysteresis has then to be taken into account when growing the graphitic phase by heteroepitaxy. Otherwise, maintaining the graphitic structure at low strain, through the hysteresis, offers new possibilities in the development of novel future applications.

Binary Iron‐Manganese Cocatalyst for Simultaneous Activation of C‐C and C‐O Bonds to Maximally Utilize Lignin for Syngas Generation over InGaN

Solar‐powered lignin reforming offers a carbon‐neutral route for syngas production. This study explores a dual non‐precious iron‐manganese cocatalyst to simultaneously activate both C‐C and C‐O bonds for maximizing the utilization of various substituents of native lignin to yield syngas. By assembling with InGaN nanowires on a Si wafer, the as‐designed dual FeMn cocatalyst affords a measurable syngas evolution rate of 42.4 mol·gcat‐1·h‐1 from native lignin in distilled water with a high selectivity of 93% and tunable H2/CO ratios under concentrated light, leading to a considerable light‐to‐fuel efficiency of 11.8%. The high FeMn atom efficiency arising from the 1‐dimensional nanostructure of InGaN enables the achievement of a high turnover frequency (TOF) of 220896 mol syngas per mol FeMn per hour. By correlating exploration experiments, the critical role of the dual FeMn cocatalyst in the evolving mechanism of lignin and water toward syngas is disclosed at the atomic level. It is discovered that the synergetic iron‐manganese cocatalyst supported by InGaN nanowires enables simultaneous activation of C‐C and C‐O bonds with comparable minimized dissociation energies. This work demonstrates a new and earth‐abundant bifunctional cocatalyst for utilizing various substituents of lignin to produce syngas powered by sunlight beyond fossil fuels.

Dynamic interplay between a TonB-dependent heme transporter and a TonB protein in a membrane environment.

Gram-negative bacteria import scarce nutrients such as metals and vitamins by an energized mechanism involving a multicomponent protein system that spans the cell envelope. It consists of an outer membrane TonB-dependent transporter (TBDT) and a TonB complex in the inner membrane that provides the proton motive force energy for the nutrient entry. Despite the intense research efforts focused on this system (a) from structural and fundamental microbiology perspectives and (b) for the interest in the development of new antibacterial strategies, the molecular mechanism of the system is not at all well understood. The lack of understanding comes from incomplete structural data and the experimental difficulties of studying an inherently flexible multicomponent complex that resides within the heterogeneous environment of the double membrane bacterial cell envelope. To address these challenges and obtain a comprehensive view of the molecular interactions at atomic level, here, we have used the combined power of advanced molecular simulations and complementary microbiology and biochemical experiments. Our results represent a significant step forward in understanding the structural and molecular bases of this vital mechanism.

Evaluation of All-Atom and Martini 3 Coarse-Grained Force Fields from the Structural Investigation of Nitroxide Spin Probes and Their Confinement in Beta-Cyclodextrin.

Nitroxide radicals have found wide applications as spin labels or probes, and their guest-host interactions with cyclodextrins exhibit enhanced applications in electron spin resonance (ESR) spectroscopy and imaging due to improved biostability toward reducing agents. Although the computational prediction of the guest-host binding has become increasingly common for small ligands, molecular simulations regarding the conformational preferences of hosted spin probes have not been conducted. Here we present molecular dynamics simulations at an atomistic level for a set of four TEMPO (2,2,6,6-tetramethylpiperidine 1-oxyl) spin probes and thereafter develop coarse-grained models compatible with the recent version of the Martini force field (v 3.0) to tackle their encapsulation in the cavity of β-cyclodextrin (βCD) for which experimental ESR data are available. The results indicate that the atomistic descriptions perform well in relation to the structural parameters derived from X-ray diffraction as well as hydrogen bonding and hydrogen patterns and predict that the guest-host complexation is hydrophobically driven by the presence of a methyl group pair of the spin probe at the cavity center of βCD. The spin probe mobility at the binding site reveals the nitroxide group orientation toward the secondary rim of the cyclodextrin and the alternating presence of the two methyl group pairs inside the cavity, features in agreement with the experimental behavior of the ESR parameters. The coarse-grained parameterizations of TEMPO probes and βCD rely on optimizing the bonded and nonbonded parameters with references to the atomistic simulation results, and they are capable of recovering the orientation and location of the spin probe inside the cyclodextrin cavity predicted by the atomistic guest-host complexes. The results suggest the cyclodextrin host-guest system as a powerful validation suite to evaluate new coarse-grained parameterizations of small ligands and future extensions to functionalized cyclodextrins in inclusion complexes.

High-Density Atomic Level Defect Engineering of 2D Fe-Based Metal-Organic Frameworks Boosts Oxygen and Hydrogen Evolution Reactions.

Electrocatalysts based on metal-organic frameworks (MOFs) attracted significant attention for water splitting, while the transition between MOFs and metal oxyhydroxide poses a great challenge in identifying authentic active sites and long-term stability. Herein, we employ on-purpose defect engineering to create high-density atomic level defects on two-dimensional Fe-MOFs. The coordination number of Fe changes from 6 to 4.46, and over 28% of unsaturated Fe sites are formed in the optimized Fe-MOF. In situ characterizations of the most optimized Fe-MOF0.3 electrocatalyst during the oxygen evolution reaction (OER) process using Fourier transform infrared and Raman spectroscopy have revealed that some Fe unsaturated sites become oxidized with a concomitant dissociation of water molecules, causing generation of the crucial *OH intermediates and Fe oxyhydroxide. Moreover, the presence of Fe oxyhydroxide is compatible with the Volmer and Heyrovsky steps during the hydrogen evolution reaction (HER) process, which lower its energy barrier and accelerate the kinetics. As a result, the optimized Fe-MOF electrodes delivered remarkable OER (259 mV at 10 mA cm-2) and HER (36 mV at 10 mA cm-2) performance. Our study offers comprehensive understanding of the effect of phase transformation on the electrocatalytic process of MOF-based materials.

Synthesis of a 13C/2H Labeled Building Block to Probe the Phosphotyrosine Interactome Using Biomolecular NMR Spectroscopy.

Phosphotyrosine (pTyr) recognition coordinates the assembly of protein complexes, thus controlling key events of cell cycle, cell development and programmed cell death. Although many aspects of membrane receptor function and intracellular signal transduction have been deciphered in the last decades, the details of how phosphorylation alters protein-protein interaction and creates regulating switches of protein activity and localization often remains unclear. We developed a synthetic route to a protected phophotyrosine building block with isolated 13C-1H spins in the aromatic ring. The compound can be used for solid phase peptide synthesis (SPPS) and readily applied to study affinity, dynamics and interactions on an atomic level using NMR spectroscopy. As a first example, we prepared an isotopologue of a pTyr containing 12mer peptide (pY1021) as part of the platelet-derived growth factor to analyze the binding to the phospholipase C-γ (PLCγ-1) SH2 domain.

TOLEDO: enhancing Maestro GUI for non-expert users to perform massive MD simulations

Classical Molecular Dynamics (MD) simulates the dynamical evolution of biological systems at the atomic level. Using MD in conjunction with high-performance computing (HPC) architectures, we can evaluate the possible interactions between a ligand library against one protein target to find a drug that can influence a protein target to cure a disease. Simultaneously, we can also obtain information about their dynamic evolution. One of the primary software packages for MD simulations is Desmond, which employs Maestro for the setup, execution, and analysis of MD through a graphical user interface (GUI), which is suitable even for non-expert users. However, using the GUI, users can typically run only one short (less than 1000 ns) MD each time. Our work aims to create a method/protocol to run several MD simulations simultaneously on a remote HPC cluster within Maestro-Desmond. In this work, we provide TOLEDO (Throughput Optimization of Ligand-Protein Systems Exploration through Dynamics simulation in Optimized HPC systems) to overcome such limitations and run several MD simulations simultaneously. The best feature of TOLEDO is its independence from the usual time constraints of many clusters, with storage space being the only limitation. To run TOLEDO, we prepare/set up the protein-ligand complex before running MD via Maestro GUI. Next, we run the main TOLEDO script for several MD simulations on a supercomputer. When TOLEDO finishes, users obtain reports and graphics. The obtained results are easily interpretable. In essence, TOLEDO significantly enhances MD throughput beyond the capabilities of the Maestro GUI.

Zn/Pt dual-site single-atom driven difunctional superimposition-augmented sonosensitizer for sonodynamic therapy boosted ferroptosis of cancer

Sonodynamic therapy (SDT) as a non-invasive antitumor strategy has been widely concerned. However, the rapid electron (e-) and hole (h+) recombination of traditional inorganic semiconductor sonosensitizers under ultrasonic (US) stimulation greatly limits the production of reactive oxygen species (ROS). Herein, we report a unique Zn/Pt dual-site single-atom driven difunctional superimposition-augmented TiO2-based sonosensitizer (Zn/Pt SATs). Initially, we verify through theoretical calculation that the strongly coupled Zn and Pt atoms can assist electron excitation at the atomic level by increasing electron conductivity and excitation efficiency under US, respectively, thus effectively improving the yield of ROS. Additionally, Zn/Pt SATs can significantly enhance ferroptosis by producing more ROS and sonoexcited holes under US stimuli. Therefore, the establishment of dual-site single-atom system represents an innovative strategy to enhance SDT in cancer model of female mice and provides a typical example for the development of inorganic sonosensitizer in the field of antitumor therapy.

Ab Initio Simulation of Raman Fingerprints of Sulfur/Carbon Copolymer Cathodes During Discharge of Li-S Batteries.

Sulfur/carbon copolymers have emerged as promising alternatives for conventional crystalline sulfur cathodes for lithium-sulfur batteries. Among these, sulfur--n--1,3--diisopropenylbenzene (S/DIB) copolymers, which present a 3D network of DIB molecules interconnected via sulfur chains, have particularly shown a good performance and, therefore, have been under intensive experimental and theoretical investigations. However, their structural complexity and flexibility have hindered a clear understanding of their structural evolution during redox reactions at an atomistic level. Here, by performing state-of-the-art ab initiomolecular dynamics-based Raman spectroscopy simulations, we investigate the spectral fingerprints of S/DIB copolymers arising from local structures during consecutive reactions with lithium. We discuss Raman spectral changes in particular frequency ranges which are common in S/DIB copolymers having shortand those consisting of longer sulfur chains. We also highlight those spectroscopic fingerprints specific to local S/DIB structures containing only short or long sulfur chains. This could help distinguish them experimentally during discharge. Our theoretically predicted results are in a good agreement with experimental Raman measurements on cells at different discharge stages. This work representsan attempt to compute Raman fingerprints ofcopolymer cathodes during battery operationincluding quantum-chemical and finite-temperature effects, and provides a guideline for Raman spectral changes of arbitrary electrodes during discharge.

Enhanced water splitting on (010) facet-exposed BiVO4 photoanode with improved carrier injection efficiency

Transition metal oxide semiconductors, noted for their stability and suitable bandgap, are promising photoanodes for water splitting. Surface engineering is critical to tackle issues like low carrier mobility and charge recombination, stemming from atomic arrangement and Fermi level differences. While exposing dominant crystal facets boosts photocatalytic capability, it can hinder carrier injection into the electrolyte. In this study, BiVO4 films with various facet exposures were synthesized and characterized using scanning electron microscopy and x-ray diffraction to confirm their morphology and crystalline structure. Mott–Schottky analysis was employed to investigate changes in the band structure near the semiconductor–electrolyte interface, revealing that high (010)-BiVO4 facet exposure enhances carrier separation but reduces injection efficiency. The results from photoconductive atomic force microscopy tests demonstrated that enhanced band bending at the semiconductor interface improves hole transfer. Coating the (010)-BiVO4 photoanode with MoS2 and an amorphous ZrO2 interlayer yielded a photocurrent density of 0.6 mA cm−2 at 1.2 V (vs RHE) under AM 1.5 G illumination, tripling the pristine photoanode's performance and nearly tripling water splitting efficiency. Mechanism revealing the improved photoelectrochemical performance is attributed to a greater band bending on the BiVO4 surface, enhancing hole injection dynamics. This work provides a feasible strategy for a deeper understanding of the intrinsic mechanisms of facet engineering and improving the activity of photoanodes.