Molecular Distribution Function Research Articles

Molecular Dynamics Simulation of the Viscosity Enhancement Mechanism of P-n Series Vinyl Acetate Polymer-CO2.

Carbon dioxide (CO2) drive is one of the effective methods to develop old oil fields with high water content for tertiary oil recovery and to improve the recovery rate. However, due to the low viscosity of pure CO2, it is not conducive to expanding the wave volume of the mixed phase, which leads to difficulty utilizing the residual oil in vertical distribution and a low degree of recovery in the reservoir. By introducing viscosity enhancers, it is possible to reduce the two-phase fluidity ratio, expanding the degree of longitudinal rippling and oil recovery efficiency. It has been proven that the acetate scCO2 tackifier PVE can effectively tackify CO2 systems. However, little research has been reported on the microscopic viscosity enhancement mechanism of scCO2 viscosity enhancers. To investigate the influence of a vinyl acetate (VAc) functional unit on the viscosity enhancement effect of the CO2 system, PVE (Polymer-Viscosity-Enhance, P-3) was used as the parent, the proportion of VAc was changed, and the molecules P-1 and P-2 were designed to establish a molecular dynamics simulation model for the P-n-CO2 system. The molecules in the system under the conditions of 70 °C-10 MPa, 80 °C-10 MPa, and 70 °C-20 MPa were simulated; the viscosity of the system was calculated; and the error between the theoretical and simulated values of the viscosity in the CO2 system was relatively small. The difference between P-n molecular structure and system viscosity was analyzed at multiple scales through polymer molecular dynamics simulations and used the molecular radial distribution function, system density, accessible surface area, radius of gyration, minimum intermolecular distance, and minimum number of intermolecular contacts as indicators. This study aimed to elucidate the viscosity enhancement mechanism, and the results showed that the higher the proportion of VAc introduced into the molecules of P-n-scCO2 viscosities, the larger the molecular amplitude, the larger the effective contact area, and the greater the viscosity of the system. Improvement in the contact efficiency between the ester group on the P-n molecule and CO2 promotes the onset of solvation behavior. This study on the microscopic mechanism of scCO2 tackifiers provides a theoretical approach for the design of new CO2 tackifiers.

Deciphering the Coarse-Grained Model of Ionic Liquid by Tunning the Interaction Level and Bead Types of Martini 3 Force Field

In recent years, ionic liquids (ILs) have served as potential solvents to dissolve organic, inorganic, and polymer materials. A copolymer (for example, Pluronic) can undergo self-organization by forming a micelle-like structure in pure IL medium, and its assembly depends upon the composition of IL. To evaluate the role of ILs, accurate coarse-grained (CG) modeling of IL is needed. Here, we modeled 1-ethyl-3-methylimidazolium dicyanamide ([EMIM][DCA]) ionic liquid (IL) using a CG framework. We optimized CG parameters for the [DCA]− anion by tuning the non-bonded parameters and selecting different kinds of beads. The molecular density (ρ) and radial distribution function (RDF) of our CG model reveal a good agreement with the all-atom (AA) simulation data. We further validated our model by choosing another imidazolium-based cation. Our modified CG model for the anion shows compatibility with the cation and the obtained density matches well with the experimental data. The strategies for developing the CG model will provide a guideline for accurate modeling of new types of ILs. Our CG model will be useful in studying the micellization of non-ionic Pluronic in the [EMIM][DCA] IL medium.

High adsorption capacities for dyes by a pH-responsive sodium alginate/sodium lignosulfonate/carboxylated chitosan/polyethyleneimine adsorbent

Dyes are indispensable for the rapid development of society, but untreated dye wastewater can threaten human health. In this study, an adsorbent (SA/SL/CCS/PEI@MNPs) was synthesized by one-pot method using magnetic nanoparticles (MNPs), sodium alginate (SA), sodium lignosulfonate (SL), carboxylated chitosan (CCS) and polyethyleneimine (PEI). The adsorbent was mesoporous micrometer-sized particles with pore size of 34.92 nm, which was favorable for dynamic column experiments. SA/SL/CCS/PEI@MNPs possessed pH-responsive performance. Under acidic condition, the maximum adsorption capacities for anionic dyes (tartrazine, reactive black-5, indigo carmine) reached >550 mg/g. Under alkaline condition, those for cationic dyes (methylene blue, methyl violet, neutral red) exceeded 1900 mg/g. The function of the various modifiers was investigated. The results indicated that the incorporation of SL, CCS and PEI was able to provide plenty of sulfonate, carboxylate and amino/imine reactive groups so that adsorption capacities of dyes were improved. The adsorption mechanism was explored by FTIR and XPS. At the same time, the adsorption mechanism was more deeply analyzed using molecular dynamics simulations and radial distribution function. It was demonstrated that the dyes adsorption on the SA/SL/CCS/PEI@MNPs was mainly due to electrostatic attraction and π-π interaction. In addition, the adsorbent had good reusability, and the removal still reached over 90 % after five cycles. In conclusion, the adsorbent displayed a broad prospect for the adsorption of organic dyes.

Insight into the solution thermodynamic properties of cimetidine form A and form B based on experiments and molecular simulations

Cimetidine (CIM) is an antagonist of the type II histamine receptors, and act as a significant agent in the treatment of stomach ulcers. In this work, the effect of polymorphism and solvent type on the thermodynamic properties of CIM was investigated based on experimental results and molecular simulations. The solubility data of two polymorphs for CIM (forms A and B) in organic solvents were measured and correlated with four thermodynamic models. It could be found that the solubility of CIM form A is higher compared to form B. In addition, molecular simulations were adopted to investigate the mechanism of the solubility and stability of the two forms. Hirshfeld surface analysis shows that strong H···N interaction contributes to better stability of form B. Meanwhile, molecular electrostatic potential surface and radial distribution function results indicate that the solubility behavior is significantly influenced by the intensity of the solute–solvent interactions. Finally, the dissolution thermodynamic properties, including the enthalpy change, the Gibbs energy change, and the entropy change, were calculated and the results show that the dissolution process of CIM is endothermic, entropy-driven and spontaneous.

Replacing the Langmuir Isotherm with the Statistical Thermodynamic Fluctuation Theory.

In the age of all-atom simulations, primitive isotherm models, such as Langmuir, BET, and GAB, are still used widely for analyzing experimental data. However, their routine applications to complex materials are not in line with their underlying assumptions (i.e., statistically independent adsorption sites with no interfacial structural changes), which manifests as the temperature dependence of the monolayer capacity. Our proposal is to replace these models with the statistical thermodynamic fluctuation theory because the ABC isotherm derived from it (i) contains these primitive models as its special cases, (ii) is applicable to any interfacial geometry, and (iii) is linked to molecular distribution functions, sharing the same language as simulations. Rectifying the inability of the primitive isotherm models to handle attractive and repulsive interactions consistently leads to a reconsideration of how physical interpretations should be attributed to the isotherms of empirical origin (e.g., Freundlich).

Mesoscopic Kinetic Approach of Nonequilibrium Effects for Shock Waves.

A shock wave is a flow phenomenon that needs to be considered in the development of high-speed aircraft and engines. The traditional computational fluid dynamics (CFD) method describes it from the perspective of macroscopic variables, such as the Mach number, pressure, density, and temperature. The thickness of the shock wave is close to the level of the molecular free path, and molecular motion has a strong influence on the shock wave. According to the analysis of the Chapman-Enskog approach, the nonequilibrium effect is the source term that causes the fluid system to deviate from the equilibrium state. The nonequilibrium effect can be used to obtain a description of the physical characteristics of shock waves that are different from the macroscopic variables. The basic idea of the nonequilibrium effect approach is to obtain the nonequilibrium moment of the molecular velocity distribution function by solving the Boltzmann-Bhatnagar-Gross-Krook (Boltzmann BGK) equations or multiple relaxation times Boltzmann (MRT-Boltzmann) equations and to explore the nonequilibrium effect near the shock wave from the molecular motion level. This article introduces the theory and understanding of the nonequilibrium effect approach and reviews the research progress of nonequilibrium behavior in shock-related flow phenomena. The role of nonequilibrium moments played on the macroscopic governing equations of fluids is discussed, the physical meaning of nonequilibrium moments is given from the perspective of molecular motion, and the relationship between nonequilibrium moments and equilibrium moments is analyzed. Studies on the nonequilibrium effects of shock problems, such as the Riemann problem, shock reflection, shock wave/boundary layer interaction, and detonation wave, are introduced. It reveals the nonequilibrium behavior of the shock wave from the mesoscopic level, which is different from the traditional macro perspective and shows the application potential of the mesoscopic kinetic approach of the nonequilibrium effect in the shock problem.

Lagrangian steady-state discrete Boltzmann model for non-equilibrium flows at micro–nanoscale

In micro- and nanoscale channels, where the characteristic scale approaches or falls below the mean free path between gas molecules, flow characteristics exhibit pronounced discontinuity. In such scenarios, continuum-based models are inadequate, and adopting kinetic models based on statistical mechanics becomes imperative for accurately describing the gas transport phenomenon. This paper presents a novel steady-state discrete Boltzmann model (DBM) that is specifically tailored for non-equilibrium flows at the micro–nanoscale. Unlike the conventional DBM, the new model focuses on the evolution equation of the non-equilibrium component of the molecular velocity distribution function in the Lagrangian coordinate system, which follows the fluid micro-element. Through numerous numerical simulations, we demonstrate the effectiveness of our model in capturing gas flow characteristics across a wide spectrum of rarefaction parameters, ranging from slip flow to free molecular flow. Utilizing this new model, we initially examine the Onsager reciprocal relationship between heat flux generated by pressure gradients and mass flux resulting from temperature gradients in micro/nanochannels. Subsequently, we calculate higher-order non-equilibrium quantities up to the 10th order and make a comparison of their characteristics. Finally, we present and discuss the features of the non-equilibrium component of the molecular velocity distribution function.

Gas‐kinetic unified algorithm for two‐dimensional planar and axisymmetric nozzle flows

SummaryFor high‐altitude nozzle or micronozzle flows and other gas flows in the slip or transition flow regime, how to solve it reliably has always been a difficult problem. In this paper, a unified gas kinetic expression is presented to describe the two‐dimensional planar and the axisymmetric nozzle flows, and the computable modeling of the Boltzmann equation is developed at the first time for the nozzle flows by introducing the gas molecular collision relaxing parameter and the local equilibrium distribution function integrated in the unified expression with the flow state controlling parameter, including the macroscopic flow variables, the gas viscosity transport coefficient, the thermodynamic effect, the molecular power law, and molecular models, covering a full spectrum of flow regimes. The boundary conditions involved in the nozzle flow have been mathematically expressed at the level of the gas molecular velocity distribution function, and the model equations have been solved uniformly by the gas‐kinetic unified algorithm (GKUA) for rarefied transition to continuum flows. The presented simulated results from the test cases show promising of simulating gas flow from transitional flow to continuum flow in the same flow domain, especially for those flow involving low‐speed gas flow in rarefied regime, which is otherwise practically difficult using direct simulation Monte Carlo (DSMC).

Ultrafast Proton Transfer Pathways Mediated by Amphoteric Imidazole

Imidazole, being an amphoteric molecule, can act both as an acid and as a base. This property enables imidazole, as an essential building block, to effectively facilitate proton transport in high-temperature proton exchange membrane fuel cells and in proton channel transmembrane proteins, enabling those systems to exhibit high energy conversion yields and optimal biological function. We explore the amphoteric properties of imidazole by following the proton transfer exchange reaction dynamics with the bifunctional photoacid 7-hydroxyquinoline (7HQ). We show with ultrafast ultraviolet-mid-infrared pump-probe spectroscopy how for imidazole, in contrast to expectations based on textbook knowledge of acid-base reactivity, the preferential reaction pathway is that of an initial proton transfer from 7HQ to imidazole, and only at a later stage a transfer from imidazole to 7HQ, completing the 7HQ tautomerization reaction. An assessment of the molecular distribution functions and first-principles calculations of proton transfer reaction barriers reveal the underlying reasons for our observations.

Thermodynamic properties analysis of warm-mix recycled asphalt binders using molecular dynamics simulation

This study aims at investigating the effect of warm-mix recycled on the thermodynamic properties of aged asphalt binders using molecular dynamics simulation. The molecular models of asphalt binders in the virgin, long-term aged, recycled and warm-mix recycled states were developed based on the proportional relationships between the asphalt components as well as oxidation functional indicators. The mean square displacement, molecular radial distribution function and fractional free volume were used to evaluate the molecular structure variations in different asphalt states. Based on this study, it is found that the composite regenerator cannot completely degrade the oxidation functional groups in the aged asphalt, but rather mainly rely on small molecular structures penetrating and filling the intermolecular aggregation spaces of the asphaltene to reduce asphalt brittleness and hardness. The warm mix recycling processes mainly depend on increasing the activity of the lighter components to improve the diffusion properties of the aged asphalt.

Role of the Voltage-Gated Proton Channel Hv1 in Nervous Systems.

Hv1 is the only voltage-gated proton-selective channel in mammalian cells. It contains a conserved voltage-sensor domain, shared by a large class of voltage-gated ion channels, but lacks a pore domain. Its primary role is to extrude protons from the cytoplasm upon pH reduction and membrane depolarization. The best-known function of Hv1 is the regulation of cytosolic pH and the nicotinamide adenine dinucleotide phosphate oxidase-dependent production of reactive oxygen species. Accumulating evidence indicates that Hv1 is expressed in nervous systems, in addition to immune cells and others. Here, we summarize the molecular properties, distribution, and physiological functions of Hv1 in the peripheral and central nervous systems. We describe the recently discovered functions of Hv1 in various neurological diseases, including brain or spinal cord injury, ischemic stroke, demyelinating diseases, and pain. We also summarize the current advances in the discovery and application of Hv1-targeted small molecules in neurological diseases. Finally, we discuss the current limitations of our understanding of Hv1 and suggest future research directions.

Effect of hydrated shell layers on surface tension of electrolyte solutions: Insights from interpretable machine learning

To explore the effects of hydration shell layer on the surface tension of electrolytes solution and to build an effective prediction model, a machine learning based model is proposed to accurately predict and explain the surface tension of electrolytes solution. The model combines machine learning (ML) algorithms, force filed parameters of molecular dynamics simulations and radial distribution function (RDF) to accurately capture the structure feature for electrolytes solution. The prediction performed an extremely low average relative deviation. SHapleyAdditive explanation (SHAP) method is used to indicate the features order of importance from strong to weak. It noted that the second hydration shell on the influence of surface tension may beyond the first hydration shell. This work provides a method for one-step acquisition of surface tension data that not only to accurately predict physical and chemical properties of materials, but also to extend the application of molecular dynamics simulations, providing enlightening insights for detecting underlying physical mechanisms.

Green synthesis, electrochemical, DFT studies and MD simulation of novel synthesized thiourea derivatives on carbon steel corrosion inhibition in 1.0 M HCl

The corrosion inhibiting effect of four new synthesized thiourea derivatives compounds, their structures were identified based on spectral data 1H NMR and FTIR spectra, namely N-((2-aminoethyl)carbamo-thioyl)propionamide (ACP), N-(bis(2-hydroxyethyl)carbamothioyl) propionamide (BCP), N-((2-hydroxy-ethyl)carbamothioyl)propionamide (HCP) and N-((2-((2-((2-((2-aminoethyl)amino)ethyl)amino)ethyl)amino)ethyl)carbamothioyl)propionamide (ECP) as nontoxic corrosion inhibitors for carbon steel in 1.0 M HCl solutions, was evaluated by experimental and theoretical studies. The results of electrochemical frequency modulation, EFM, electrochemical impedance spectroscopy, EIS, and potentiodynamic polarization, PDP at inhibitors concentrations (10−6-10−2M) showed that, the inhibitory efficient of the prepared compounds improves with an increase in their concentrations and the corrosion inhibition performance of ECP was much higher than that of ACP, BCP and HCP. The Langmuir adsorption isotherm model indicated spontaneous adsorption of thiourea derivatives on the carbon steel surface and morphological surface analysis like scanning electron microscopy (SEM), Energy dispersive X-ray spectroscopy (EDX) and atomic force microscopy (AFM) indicated that inhibitors molecules adhere and construct a stronger protective layer on the steel surface. Quantum chemical calculation, Natural Bonding Orbital (NBO) analysis, Molecular Dynamic Simulation (MD) and Radial Distribution Function (RDF) were in perfect agreement with each other suggesting synthesized thiourea derivatives to be environmental friendly corrosion inhibitors.

The Mott-Smith solution to the regular shock reflection problem

The classical Mott-Smith solution for one-dimensional normal shock wave structure is extended to the two-dimensional regular shock reflection problem. The solution for the non-equilibrium molecular velocity distribution function along the symmetry-plane streamline is obtained as a weighted sum of four Maxwellians. An analysis of applicability of the solution has been performed using the results of direct simulation Monte Carlo calculations for a range of incident shock wave intensities. Accuracy of the solution improves with increasing$Ma_n$, the Mach number normal to the shock front, so that the solution becomes rather accurate for strong shocks with$Ma_n>8$.

Revealing the Impact of Cl Substitution on the Crystallization Behavior and Interfacial Stability of Superionic Lithium Argyrodites

AbstractAll‐solid‐state batteries are believed to be the next‐generation energy storage device that can meet the ever‐growing market demand for high energy density and safety. The ionic conductivity and electrochemical stability of the solid electrolyte are two crucial properties that can affect battery performance. Herein, with an optimized crystallization process, the Cl‐rich argyrodite possesses high ionic conductivity, good dendrite inhibition capability, as well as enhanced interfacial stability against decomposition. Ab initio molecular dynamics simulation and radial distribution function analysis are utilized to probe into the interfacial phenomenon between argyrodite electrolyte and lithium metal. LiNi0.8Co0.1Mn0.1O2‐based all‐solid‐state battery using the Cl‐rich argyrodite electrolyte also delivers more stable cyclic performance. This study shows the multiple enhancements of argyrodite electrolyte brought by Cl doping, which provides important guidance in selecting electrolytes for all‐solid‐state batteries.

Two-dimensional kinetic evaporation by direct simulation Monte Carlo (DSMC) with independently controlled downstream boundary conditions

Kinetic evaporation of liquids in a two-dimensional geometry is investigated in this paper by direct simulation Monte Carlo and theoretical analysis. Based on simulations, information such as the spatial distribution of macroscopic vapor properties, the net evaporation mass flux and the molecular velocity distribution functions were obtained. Particularly, the possibility of applying independent downstream vapor pressure and temperature was demonstrated in the two-dimensional configuration. It was found that with the increase of the domain size, the evaporation mass flux approached constant and more importantly, the downstream vapor had a uniform pressure distribution. The downstream vapor was in equilibrium according to the velocity distribution function; its thermodynamic state could be arbitrarily altered. A semi-empirical model was developed for the two-dimensional evaporation; the model followed the conservation law as in the moment method and simultaneously allowed independent inputs of P and T of vapor by introducing one more unknown variable. The model could predict the asymptotic variation trend of relevant quantities with the domain size. Moreover, the simulation data of net evaporation mass flux at different combinations of vapor P and T were captured by the proposed model with good accuracy. The present work is a preliminary attempt to discuss the independent control of downstream vapor properties in kinetic evaporations, based on the two-dimensional geometry.

Orientation Distribution of Molecules in a Smectic Liquid Crystal with a Distorted Director Geometry.

Quantitative determination of the molecular orientation distribution function in samples of liquid crystals with a complex director geometry was performed using the numerical simulation of electron paramagnetic resonance (EPR) spectra of the spin probes in a liquid-crystalline medium. To achieve the quantitative agreement of experimental and simulated EPR spectra, the hierarchy of the orientation order was explicitly taken into account, namely, the local ordering of liquid crystal molecules by the mean-field potential of surrounding molecules, and the partial disordering of local directors within the sample. The samples under study are planar and twist LC cells with liquid crystal 8CB cooled from the nematic into the smectic A phase in the magnetic field. The presence of the magnetic field perpendicular to the cell director leads to distortion of the orientation of the liquid crystal in the cell. The spin probe technique was successfully employed for the reliable measurement of orientation distribution functions of the low nonorthorhombic symmetry. Orientation order parameters up to 12th rank were measured, including nonaxial and nonorthorhombic order parameters. It is shown that the presence of several contradicting aligning forces leads to the tilt of the preferential director toward the direction, which is a compromise between the orienting forces.

Solid-liquid equilibrium of ropivacaine in fourteen organic solvents: An experimental and molecular simulation study

The solubility of ropivacaine in fourteen pure solvents at 283.15 K to 323.15 K was determined via the gravimetric method and was well correlated with three thermodynamic models, including the Apelblat, λh, and NRTL models. Among all experimental solvents, the solubility of ropivacaine was found to be highest in pure THF and lowest in acetonitrile. In alcohol solvents, the maximum solubility was observed in amyl alcohol followed by 1-butanol, while the minimum value was observed in 1-propanol. The thermodynamic properties of mixing were calculated based on the NRTL equation, indicating that the mixing processes are spontaneous and entropy-driven. In addition, the crystal structure of ropivacaine was obtained and investigated by Hirshfeld surface analysis and molecular electrostatic potential surface analysis. The physicochemical properties of solvents, such as polarity, cohesive energy density and dielectric constant, were analyzed to explain the solid–liquid behavior of ropivacaine. Finally, a molecular dynamics simulation and radial distribution function analysis were performed. The results indicated that ropivacaine could interact with organic solvents via van der Waals interactions, electrostatic interactions, and hydrogen bonding.

Making High-Dimensional Molecular Distribution Functions Tractable through Belief Propagation on Factor Graphs.

Molecular dynamics (MD) simulations provide a wealth of high-dimensional data at all-atom and femtosecond resolution but deciphering mechanistic information from this data is an ongoing challenge in physical chemistry and biophysics. Theoretically speaking, joint probabilities of the equilibrium distribution contain all thermodynamic information, but they prove increasingly difficult to compute and interpret as the dimensionality increases. Here, inspired by tools in probabilistic graphical modeling, we develop a factor graph trained through belief propagation that helps factorize the joint probability into an approximate tractable form that can be easily visualized and used. We validate the study through the analysis of the conformational dynamics of two small peptides with five and nine residues. Our validations include testing the conditional dependency predictions through an intervention scheme inspired by Judea Pearl. Second, we directly use the belief propagation-based approximate probability distribution as a high-dimensional static bias for enhanced sampling, where we achieve spontaneous back-and-forth motion between metastable states that is up to 350 times faster than unbiased MD. We believe this work opens up useful ways to thinking about and dealing with high-dimensional molecular simulations.

Experimental measurement and thermodynamic modelling of ethenzamide solubility in three binary solvent systems

The solid–liquid phase equilibrium of ethenzamide (ETZ), a classic anti-inflammatory drug, in binary solvent systems was experimentally investigated and simulated. The equilibrium solubility of ETZ in binary solvent mixtures of methanol + acetonitrile, ethanol + acetonitrile, and isopropanol + acetonitrile was determined via a gravimetric method at temperatures ranging from 293.15 K to 323.15 K at atmospheric pressure (0.1 MPa). In all binary solvent systems, the solubility of ETZ increases with the increasing of temperature at a given solvent composition, but it initially increased and then decreased with the increase in alcohol composition (good solvent). Additionally, the Jouyban-Acree, van’t Hoff-Jouyban-Acree, Apelblat-Jouyban-Acree, and Ma models were utilized to correlate the experimental data. Results showed that the Jouyban-Acree model achieved the best correlation performance. Molecular dynamic simulation and radial distribution function analysis revealed the cooperation effect originating from solute-solvent and solvent–solvent interactions, which explained the dissolution behaviors of ETZ in various solvent mixtures. Calculations of dissolution thermodynamic properties, including enthalpy, Gibbs free energy, and entropy, revealed that the dissolution behavior of ETZ was an endothermic and entropy-driven process. This study provides insights into modulating ETZ crystallization and in understanding solid–liquid phase equilibrium behaviors in mixed solvent systems.