Molecular Insights into the Interaction between CD147 and the SARS-CoV‑2 Spike Protein.

Cluster of differentiation 147 (CD147), a transmembrane glycoprotein, has been identified as a potential auxiliary receptor for the SARS-CoV-2 spike protein (SP), contributing to COVID-19 infection. However, the detailed binding characteristics of this interaction remain unclear. Here, we characterized SP-CD147 binding using Enzyme-Linked Immunosorbent Assay (ELISA) and single-molecule force spectroscopy (SMFS) under varying contact times and temperatures.

Molecular insights into supercritical water gasification process of polyoxymethylene plastics.

Effective plastic management is crucial in addressing the growing environmental challenges posed by plastic pollution. Among various plastics, polyoxymethylene (POM) stands out as a widely used engineering thermoplastic with significant applications in industries . Innovative recycling solutions are essential to mitigate its environmental impact.

Thermodynamic Properties of Hydrogen Adsorbed on Graphite Surfaces at Temperatures Above 100 K: A Molecular Dynamics and Classical Density Functional Theory Study.

Improved technological solutions for the transport and storage of hydrogen are crucial for the widespread adoption of hydrogen as a clean energy carrier. Graphite-based materials have been identified as potential candidates due to their high surface area and ability to adsorb hydrogen molecules. In this study, we investigate the adsorption and thermodynamic properties of hydrogen adsorbed on a graphite surface using molecular dynamics (MD) simulation and classical density functional theory (cDFT).

Two-dimensional piezoelectric AlSiX (X = N, P, As) semiconductors with Raman activity, favorable band-gap, and high carrier mobility based on first-principles calculations.

In the present work, we attempt to construct two-dimensional AlSiX (X = N, P, As) monolayers and examine their stabilities, Raman activity, piezoelectricity, as well as electronic/transport properties for various applications, using first-principles calculations. All three - AlSiN, AlSiP and AlSiAs - configurations are confirmed to have good dynamic, thermal, and mechanical stabilities from their phonon spectra, molecular dynamics investigations, and attained elastic constants/cohesive energy results. The Raman spectra of the AlSiX monolayers are performed using the finite displacement technique to assess their vibrational properties and Raman activities.

Thermophysical properties of polyethylene glycol oligomers molecular dynamics simulations.

Polyethylene glycol (PEG) is a versatile chemical with numerous applications in various fields, including biomedical research, pharmaceutical development, and industrial manufacturing. Molecular dynamics (MD) is a powerful tool for investigating the thermophysical properties of PEG molecules. In this study, we employ the General AMBER force field (GAFF) to perform MD simulations on various PEG oligomers, focusing on the calculation of density, self-diffusion coefficients, shear viscosity, and thermal conductivity.

Insights into hydro thermal gasification process of microplastic polyethylene via reactive molecular dynamics simulations.

Microplastics have become a pressing environmental issue due to their widespread presence in our ecosystems. Among various plastic components, polyethylene (PE) is a prevalent and persistent contaminant. Hydrothermal gasification (HTG), a promising technology for converting PE into syngas, holds great promise for mitigating the microplastic problem.

Molecular insights into the interactions between PEG carriers and drug molecules from Celastrus hindsii: a multi-scale simulation study.

Efficient drug delivery is crucial for the creation of effective pharmaceutical treatments, and polyethylene glycol (PEG) carriers have been emerged as promising candidates for this purpose due to their bio-compatibility, enhancement of drug solubility, and stability. In this study, we utilized molecular simulations to examine the interactions between PEG carriers and selected drug molecules extracted from Celastrus hindsii: Hindsiilactone A, Hindsiiquinoflavan B, Maytenfolone A, and Celasdin B. The simulations provided detailed insights into the binding affinity, stability, and structural properties of these drug molecules when complexed with PEG carriers.

Water adsorption on surfaces of calcium aluminosilicate crystal phase of stone wool: a DFT study.

Stone wool is widely used as an efficient thermal insulator within the construction industry; however, its performance can be significantly impacted by the presence of water vapor. By altering the material's characteristics and effective thermo-physical properties, water vapor can reduce overall efficacy in various environmental conditions. Therefore, understanding water adsorption on stone wool surfaces is crucial for optimizing insulation properties.

The Role of Chloride ion in the Silicate Condensation Reaction from ab Initio Molecular Dynamics Simulations.

The comprehension of silicate oligomer formation during the initial stage of zeolite synthesis is of significant importance. In this study, we investigated the effect of chloride ions (Cl) on silicate oligomerization using molecular dynamics simulations with explicit water molecules. The results show that the presence of Cl increases the free energy barriers of all reactions compared to the case without the anion.

Insight into the role of excess hydroxide ions in silicate condensation reactions.

The formation of silicate oligomers in the early stages is key to zeolite synthesis. The pH and the presence of hydroxide ions are important in regulating the reaction rate and the dominant species in solutions. This paper describes the formation of silicate species, from dimers to 4-membered rings, using molecular dynamics simulations in explicit water molecules with an excess hydroxide ion.

How do the doping concentrations of N and B in graphene modify the water adsorption?

Understanding the interaction of water and graphene is crucial for various applications such as water purification, desalination, and electrocatalysis. Experimental and theoretical studies have already investigated water adsorption on N- and B-doped graphene. However, there are no reports available that elucidate the influences of the N and B doping content in graphene on the microscopic geometrical structure and the electronic properties of the adsorbed water.

Impact of Organic Templates on the Selective Formation of Zeolite Oligomers.

Zeolites are essential materials to industry due to their adsorption and catalytic properties. The best current approach to prepare a targeted zeolite still relies on trial and error's synthetic procedures since a rational understanding of the impact of synthesis variables on the final structures is still missing. To discern the role of a variety of organic templates, we perform simulations of the early stages of condensation of silica oligomers by combining DFT, Brønsted-Evans-Polanyi relationships and kinetic Monte Carlo simulations.

Thiosquaramide-Based Supramolecular Polymers: Aromaticity Gain in a Switched Mode of Self-Assembly.

Despite a growing understanding of factors that drive monomer self-assembly to form supramolecular polymers, the effects of aromaticity gain have been largely ignored. Herein, we document the aromaticity gain in two different self-assembly modes of squaramide-based bolaamphiphiles. Importantly, O → S substitution in squaramide synthons resulted in supramolecular polymers with increased fiber flexibility and lower degrees of polymerization.

Elucidating the Role of Tetraethylammonium in the Silicate Condensation Reaction from Molecular Dynamics Simulations.

The understanding of the formation of silicate oligomers in the initial stage of zeolite synthesis is important. The use of organic structure-directing agents (OSDAs) is known to be a key factor in the formation of different silicate species and the final zeolite structure. For example, tetraethylammonium ion (TEA) is a commonly used organic template for zeolite synthesis.

Diffusion of gas mixtures in the sI hydrate structure.

Replacing methane with carbon dioxide in gas hydrates has been suggested as a way of harvesting methane, while at the same time storing carbon dioxide. Experimental evidence suggests that this process is facilitated if gas mixtures are used instead of pure carbon dioxide. We studied the free energy barriers for diffusion of methane, carbon dioxide, nitrogen, and hydrogen in the sI hydrate structure using molecular simulation techniques.

Temperature anisotropy at equilibrium reveals nonlocal entropic contributions to interfacial properties.

Density gradient theory for fluids has played a key role in the study of interfacial phenomena for a century. In this work, we revisit its fundamentals by examining the vapor-liquid interface of argon, represented by the cut and shifted Lennard-Jones fluid. The starting point has traditionally been a Helmholtz energy functional using mass densities as arguments.

Geometrical flexibility of platinum nanoclusters: impacts on catalytic decomposition of ethylene glycol.

Catalytic decomposition of ethylene glycol on the Pt cluster was studied as a model system for hydrogen production from a lignocellulosic material. Ethylene glycol was chosen as a starting material because of two reasons, it is the smallest oxygenate with a 1 : 1 carbon to oxygen ratio and it contains the C-H, O-H, C-C, and C-O bonds also present in biomass. Density functional theory calculations were employed for predictions of reaction pathways for C-H, O-H, C-C and C-O cleavages, and Brønsted-Evans-Polanyi relationships were established between the final state and the transition state for all mechanisms.

Rare event simulations reveal subtle key steps in aqueous silicate condensation.

A replica exchange transition interface sampling (RETIS) study combined with Born-Oppenheimer molecular dynamics (BOMD) is used to investigate the dynamics, thermodynamics and the mechanism of the early stages of the silicate condensation process. In this process, two silicate monomers, of which one is an anionic species, form a negatively charged five-coordinated silicate dimer. In a second stage, this dimer can fall apart again, forming the original monomers, or release a water molecule into the solution.

Chemically accurate energy barriers of small gas molecules moving through hexagonal water rings.

We present chemically accurate potential energy curves of CH4, CO2 and H2 moving through hexagonal water rings, calculated by CCSD(T)/aug-cc-pVTZ with counterpoise correction. The barriers are extracted from a potential energy surface obtained by allowing the water ring to expand while the gas molecule diffuses through. State-of-the-art XC-functionals are evaluated against the CCSD(T) potential energy surface.

The mechanism of the initial step of germanosilicate formation in solution: a first-principles molecular dynamics study.

The condensation reactions between Ge(OH)4 and Si(OH)4 units in solution are studied to understand the mechanism and stable species during the initial steps of the formation process of Ge containing zeolites under basic conditions. The free energy of formation of (OH)3Ge-O-Ge-(OH)2O(-), (OH)3Si-O-Si-(OH)2O(-), (OH)3Ge-O-Si-(OH)2O(-) and (OH)3Si-O-Ge-(OH)2O(-) dimers is calculated with ab initio molecular dynamics and thermodynamic integration, including an explicit description of the water solvent molecules. Calculations show that the attack of the conjugated base (Ge(OH)3O(-) and Si(OH)3O(-)) proceeds with a smaller barrier at the Ge center.

Heat transport through a solid-solid junction: the interface as an autonomous thermodynamic system.

We perform computational experiments using nonequilibrium molecular dynamics simulations, showing that the interface between two solid materials can be described as an autonomous thermodynamic system. We verify the local equilibrium and give support to the Gibbs description of the interface also away from the global equilibrium. In doing so, we reconcile the common formulation of the thermal boundary resistance as the ratio between the temperature discontinuity at the interface and the heat flux with a more rigorous derivation from nonequilibrium thermodynamics.

Coherent description of transport across the water interface: From nanodroplets to climate models.

Transport of mass and energy across the vapor-liquid interface of water is of central importance in a variety of contexts such as climate models, weather forecasts, and power plants. We provide a complete description of the transport properties of the vapor-liquid interface of water with the framework of nonequilibrium thermodynamics. Transport across the planar interface is then described by 3 interface transfer coefficients where 9 more coefficients extend the description to curved interfaces.

Note: A new truncation correction for the configurational temperature extends its applicability to interaction potentials with a discontinuous force.

We present a simple truncation correction for the configurational temperature which, unlike previous corrections, works even at low truncation values for the shifted and truncated Lennard-Jones potential. The success of the new correction suggests that the expression for the configurational temperature is valid also for interaction potentials with a discontinuous force, given that the discontinuity is properly accounted for.

A test on reactive force fields for the study of silica dimerization reactions.

We studied silica dimerization reactions in the gas and aqueous phase by density functional theory (DFT) and reactive force fields based on two parameterizations of ReaxFF. For each method (both ReaxFF force fields and DFT), we performed constrained geometry optimizations, which were subsequently evaluated in single point energy calculations using the other two methods. Standard fitting procedures typically compare the force field energies and geometries with those from quantum mechanical data after a geometry optimization.

Mechanical instability of monocrystalline and polycrystalline methane hydrates.

Despite observations of massive methane release and geohazards associated with gas hydrate instability in nature, as well as ductile flow accompanying hydrate dissociation in artificial polycrystalline methane hydrates in the laboratory, the destabilising mechanisms of gas hydrates under deformation and their grain-boundary structures have not yet been elucidated at the molecular level. Here we report direct molecular dynamics simulations of the material instability of monocrystalline and polycrystalline methane hydrates under mechanical loading. The results show dislocation-free brittle failure in monocrystalline hydrates and an unexpected crossover from strengthening to weakening in polycrystals.