OCTP: A Tool for On-the-Fly Calculation of Transport Properties of Fluids with the Order-n Algorithm in LAMMPS

Impact of adsorption on thermal conductivity dynamics of adsorbate and adsorbent: Molecular dynamics study of methane and Cu-BTC

Understanding changes in thermodynamic and transport properties during adsorption is crucial for the thermal management of metal-organic frameworks, which also imposes significant challenges for improved performance and energy density of adsorption system. Because of phase transitions in the intermolecular interactions involved in the adsorption phenomena, transport properties including the thermal conductivity exhibit interesting behaviors, yet fully understood. This study employs detailed molecular dynamics simulations to replicate the methane/Cu-BTC adsorption phenomenon for the evaluation of their thermal conductivities across different pressures and temperatures. The molecular simulations show that the thermal conductivities of both the adsorbent (Cu-BTC) and adsorbate (methane, adsorbed phase) vary notably during adsorption processes. Using the concepts of the change in the degree of free movements of the adsorbate molecules and atomic vibration of adsorbent, the reduction of the adsorbate thermal conductivity (∼70-93%) and increase thermal conductivity of the adsorbent (up to 3 times) in Cu-BTC+CH4 pair are explained.

Thermophysical Properties and Phase Behavior of CO2 with Impurities: Insight from Molecular Simulations

Experimentally determining thermophysical properties for various compositions commonly found in CO2 transportation systems is extremely challenging. To overcome this challenge, we performed Monte Carlo (MC) and Molecular Dynamics (MD) simulations of CO2 rich mixtures to compute thermophysical properties such as densities, thermal expansion coefficients, isothermal compressibilities, heat capacities, Joule-Thomson coefficients, speed of sound, and viscosities at temperatures of (235-313) K and pressures of (20-200) bar. We computed thermophysical properties of pure CO2 and CO2 rich mixtures with N2, Ar, H2, and CH4 as impurities of (1-10) mol % and showed good agreement with available Equations of State (EoS). We showed that impurities decrease the values of thermal expansion coefficients, isothermal compressibilities, heat capacities, and Joule-Thomson coefficients in the gas phase, while these values increase in the liquid and supercritical phases. In contrast, impurities increase the value of speed of sound in the gas phase and decrease it in the liquid and supercritical phases. We present an extensive data set of thermophysical properties for CO2 rich mixtures with various impurities, which will help to design the safe and efficient operation of CO2 transportation systems.

Mutual Diffusivities of Mixtures of Carbon Dioxide and Hydrogen and Their Solubilities in Brine: Insight from Molecular Simulations

H2-CO2 mixtures find wide-ranging applications, including their growing significance as synthetic fuels in the transportation industry, relevance in capture technologies for carbon capture and storage, occurrence in subsurface storage of hydrogen, and hydrogenation of carbon dioxide to form hydrocarbons and alcohols. Here, we focus on the thermodynamic properties of H2-CO2 mixtures pertinent to underground hydrogen storage in depleted gas reservoirs. Molecular dynamics simulations are used to compute mutual (Fick) diffusivities for a wide range of pressures (5 to 50 MPa), temperatures (323.15 to 423.15 K), and mixture compositions (hydrogen mole fraction from 0 to 1). At 5 MPa, the computed mutual diffusivities agree within 5% with the kinetic theory of Chapman and Enskog at 423.15 K, albeit exhibiting deviations of up to 25% between 323.15 and 373.15 K. Even at 50 MPa, kinetic theory predictions match computed diffusivities within 15% for mixtures comprising over 80% H2 due to the ideal-gas-like behavior. In mixtures with higher concentrations of CO2, the Moggridge correlation emerges as a dependable substitute for the kinetic theory. Specifically, when the CO2 content reaches 50%, the Moggridge correlation achieves predictions within 10% of the computed Fick diffusivities. Phase equilibria of ternary mixtures involving CO2-H2-NaCl were explored using Gibbs Ensemble (GE) simulations with the Continuous Fractional Component Monte Carlo (CFCMC) technique. The computed solubilities of CO2 and H2 in NaCl brine increased with the fugacity of the respective component but decreased with NaCl concentration (salting out effect). While the solubility of CO2 in NaCl brine decreased in the ternary system compared to the binary CO2-NaCl brine system, the solubility of H2 in NaCl brine increased less in the ternary system compared to the binary H2-NaCl brine system. The cooperative effect of H2-CO2 enhances the H2 solubility while suppressing the CO2 solubility. The water content in the gas phase was found to be intermediate between H2-NaCl brine and CO2-NaCl brine systems. Our findings have implications for hydrogen storage and chemical technologies dealing with CO2-H2 mixtures, particularly where experimental data are lacking, emphasizing the need for reliable thermodynamic data on H2-CO2 mixtures.

Solvate Suite: A Command-Line Interface for Molecular Simulations and Multiscale Microsolvation Modeling

In this work, we introduce the Solvate Suite, a comprehensive and modular command-line interface designed for molecular simulation and microsolvation modeling. The suite interfaces with widely used scientific software, streamlining computational experiments for liquid systems through the automated creation of simulation boxes and topology with adjustable simulation parameters. Furthermore, it has features for graphical and statistical analysis of simulated properties and extraction of trajectory configurations with various filters. Additionally, it introduces innovative strategies for microsolvation modeling with a multiscale approach, employing equilibrated dynamics to identify favorable solute-solvent interactions and enabling full cluster optimization for free-energy calculations without imaginary frequency contamination.

Ultrasound enhanced diffusion in hydrogels: An experimental and non-equilibrium molecular dynamics study

Focused ultrasound has experimentally been found to enhance the diffusion of nanoparticles; our aim with this work is to study this effect closer using both experiments and non-equilibrium molecular dynamics. Measurements from single particle tracking of 40 nm polystyrene nanoparticles in an agarose hydrogel with and without focused ultrasound are presented and compared with a previous experimental study using 100 nm polystyrene nanoparticles. In both cases, we observed an increase in the mean square displacement during focused ultrasound treatment. We developed a coarse-grained non-equilibrium molecular dynamics model with an implicit solvent to investigate the increase in the mean square displacement and its frequency and amplitude dependencies. This model consists of polymer fibers and two sizes of nanoparticles, and the effect of the focused ultrasound was modeled as an external oscillating force field. A comparison between the simulation and experimental results shows similar mean square displacement trends, suggesting that the particle velocity is a significant contributor to the observed ultrasound-enhanced mean square displacement. The resulting diffusion coefficients from the model are compared to the diffusion equation for a two-time continuous time random walk. The model is found to have the same frequency dependency. At lower particle velocity amplitude values, the model has a quadratic relation with the particle velocity amplitude as described by the two-time continuous time random walk derived diffusion equation, but at higher amplitudes, the model deviates, and its diffusion coefficient reaches the non-hindered diffusion coefficient. This observation suggests that at higher ultrasound intensities in hydrogels, the non-hindered diffusion coefficient can be used.

Force Fields for High Concentration Aqueous KOH Solutions and Zincate Ions

Motivated by increasing interest in electrochemical devices that include highly alkaline electrolytes, we investigated two force fields for potassium hydroxide (KOH) at high concentrations in water. The "FNB" model uses the SPC/E water model, while the "FHM" model uses the TIP4P/2005 water model. We also developed parameters to describe zincate ions in these solutions. The density and viscosity of KOH using the FHM model are in better agreement with experiment than the values from the FNB model. Comparing the properties of the zincate solutions to the available experimental data, we find that both force fields agree reasonably well, although the FHM parameters give a better prediction of the viscosity. The developed force field parameters can be used in future simulations of zincate/KOH solutions in combination with other species of interest.

Effect of the Ion, Solvent, and Thermal Interaction Coefficients on Battery Voltage

In order to increase the adoption of batteries for sustainable transport and energy storage, improved charging and discharging capabilities of lithium-ion batteries are necessary. To achieve this, accurate data that describe the internal state of the cells are essential. Several models have been derived, and transport coefficients have been reported for use in these models. We report for the first time a complete set of transport coefficients to model the concentration and temperature polarization in a lithium-ion battery ternary electrolyte, allowing us to test common assumptions. We include effects due to gradients in chemical potentials and in temperature. We find that the voltage contributions due to salt and solvent polarization are of the same order of magnitude as the ohmic loss and must be taken into account for more accurate modeling and understanding of battery performance. We report new Soret and Seebeck coefficients and find thermal polarization to be significant in cases relevant to battery research. The analysis is suitable for electrochemical systems, in general.

Interfacial Tensions, Solubilities, and Transport Properties of the H2/H2O/NaCl System: A Molecular Simulation Study

Data for several key thermodynamic and transport properties needed for technologies using hydrogen (H2), such as underground H2 storage and H2O electrolysis are scarce or completely missing. Force field-based Molecular Dynamics (MD) and Continuous Fractional Component Monte Carlo (CFCMC) simulations are carried out in this work to cover this gap. Extensive new data sets are provided for (a) interfacial tensions of H2 gas in contact with aqueous NaCl solutions for temperatures of (298 to 523) K, pressures of (1 to 600) bar, and molalities of (0 to 6) mol NaCl/kg H2O, (b) self-diffusivities of infinitely diluted H2 in aqueous NaCl solutions for temperatures of (298 to 723) K, pressures of (1 to 1000) bar, and molalities of (0 to 6) mol NaCl/kg H2O, and (c) solubilities of H2 in aqueous NaCl solutions for temperatures of (298 to 363) K, pressures of (1 to 1000) bar, and molalities of (0 to 6) mol NaCl/kg H2O. The force fields used are the TIP4P/2005 for H2O, the Madrid-2019 and the Madrid-Transport for NaCl, and the Vrabec and Marx for H2. Excellent agreement between the simulation results and available experimental data is found with average deviations lower than 10%.

Simulation and Data-Driven Modeling of the Transport Properties of the Mie Fluid

This work reports the computation and modeling of the self-diffusivity (D*), shear viscosity (η*), and thermal conductivity (κ*) of the Mie fluid. The transport properties were computed using equilibrium molecular dynamics simulations for the Mie fluid with repulsive exponents (λr) ranging from 7 to 34 and at a fixed attractive exponent (λa) of 6 over the whole fluid density (ρ*) range and over a wide temperature (T*) range. The computed database consists of 17,212, 14,288, and 13,099 data points for self-diffusivity, shear viscosity, and thermal conductivity, respectively. The database is successfully validated against published simulation data. The above-mentioned transport properties are correlated using artificial neural networks (ANNs). Two modeling approaches were tested: a semiempirical formulation based on entropy scaling and an empirical formulation based on density and temperature as input variables. For the former, it was found that a unique formulation based on entropy scaling does not yield satisfactory results over the entire density range due to a divergent and incorrect scaling of the transport properties at low densities. For the latter empirical modeling approach, it was found that regularizing the data, e.g., modeling ρ*D* instead of D*, ln η* instead of η*, and ln κ* instead of κ*, as well as using the inverse of the temperature as an input feature, helps to ease the interpolation efforts of the artificial neural networks. The trained ANNs can model seen and unseen data over a wide range of density and temperature. Ultimately, the ANNs can be used alongside equations of state to regress effective force field parameters from volumetric and transport data.

Efficient single-run implementation of generalized Einstein relation to compute transport coefficients: A binary-based time sampling

A robust and simple implementation of the generalized Einstein formulation using single equilibrium molecular dynamics simulation is introduced to compute diffusion and shear viscosity. The unique features underlying this framework are as follows: (1) The use of a simple binary-based method to sample time-dependent transport coefficients results in a uniform distribution of data on a logarithmic time scale. Although we sample "on-the-fly," the algorithm is readily applicable for post-processing analysis. Overlapping same-length segments are not sampled as they indicate strong correlations. (2) Transport coefficients are estimated using a power law fitting function, a generalization of the standard linear relation, that accurately describes the long-time plateau. (3) The use of a generalized least squares (GLS) fitting estimator to explicitly consider correlations between fitted data points results in a reliable estimate of the statistical uncertainties in a single run. (4) The covariance matrix for the GLS method is estimated analytically using the Wiener process statistics and computed variances. (5) We provide a Python script to perform the fits and automate the procedure to determine the optimal fitting domain. The framework is applied to two fluids, binary hard sphere and a Lennard-Jones near the triple point, and the validity of the single-run estimates is verified against multiple independent runs. The approach should be applicable to other transport coefficients since the diffusive limit is universal to all of them. Given its rigor and simplicity, this methodology can be readily incorporated into standard molecular dynamics packages using on-the-fly or post-processing analysis.

Computation of Shear Viscosity by a Consistent Method in Equilibrium Molecular Dynamics Simulations: Applications to 1-Decene Oligomers

Accurate computation of shear viscosity is fundamental for describing fluid flow and designing and developing new processes. Poly-α-olefins (PAO's), particularly from 1-decene, have been applied to a variety of industrial processes. Recently, these molecules have been applied as carbon dioxide thickeners, enhancing carbon dioxide viscosity, which is important in carbon dioxide injection, either for enhanced oil recovery or sequestration in geological formations. For these applications, knowledge of the pure oligomer viscosity is crucial to design and operate the oligomer upstream pipelines before mixing them with carbon dioxide. Using Green-Kubo formalism with equilibrium molecular dynamics simulations, two methods are presented in the literature to generate the traceless, symmetric pressure tensor. In this work, we show that these two methods provide different values of shear viscosity, from the analysis of how the diagonal components of the traceless, symmetric pressure tensor are computed in each method. Then, we examine the consistency and correctness of each method: one is found to be consistent. The other is corrected by scaling the fluctuations of the diagonal components. Shear viscosities of supercritical carbon dioxide, vapor and liquid n-pentane, and liquid n-decane are computed to illustrate the analysis. We also apply the consistent method to compute the viscosity of 1-decene oligomers, including for the first time larger-than-dimer oligomers (trimer, tetramer, hexamer, and decamer).

Understanding the Anomalous Diffusion of Water in Aqueous Electrolytes Using Machine Learned Potentials

The diffusivity of water in aqueous cesium iodide solutions is larger than that in neat liquid water and vice versa for sodium chloride solutions. Such peculiar ion-specific behavior, called anomalous diffusion, is not reproduced in typical force field based molecular dynamics (MD) simulations due to inadequate treatment of ion-water interactions. Herein, this hurdle is tackled by using machine learned atomic potentials (MLPs) trained on data from density functional theory calculations. MLP based atomistic MD simulations of aqueous salt solutions reproduce experimentally determined thermodynamic, structural, dynamical, and transport properties, including their varied trends in water diffusivities across salt concentration. This enables an examination of their intermolecular structure to unravel the microscopic underpinnings of the differences in their transport properties. While both ions in CsI solutions contribute to the faster diffusion of water molecules, the competition between the heavy retardation by Na ions and the slight acceleration by Cl ions in NaCl solutions reduces their water diffusivity.

Computation of Electrical Conductivities of Aqueous Electrolyte Solutions: Two Surfaces, One Property

In this work, we computed electrical conductivities under ambient conditions of aqueous NaCl and KCl solutions by using the Einstein-Helfand equation. Common force fields (charge q = ±1 e) do not reproduce the experimental values of electrical conductivities, viscosities, and diffusion coefficients. Recently, we proposed the idea of using different charges to describe the potential energy surface (PES) and the dipole moment surface (DMS). In this work, we implement this concept. The equilibrium trajectories required to evaluate electrical conductivities (within linear response theory) were obtained by using scaled charges (with the value q = ±0.75 e) to describe the PES. The potential parameters were those of the Madrid-Transport force field, which accurately describe viscosities and diffusion coefficients of these ionic solutions. However, integer charges were used to compute the conductivities (thus describing the DMS). The basic idea is that although the scaled charge describes the ion-water interaction better, the integer charge reflects the value of the charge that is transported due to the electric field. The agreement obtained with experiments is excellent, as for the first time electrical conductivities (and the other transport properties) of NaCl and KCl electrolyte solutions are described with high accuracy for the whole concentration range up to their solubility limit. Finally, we propose an easy way to obtain a rough estimate of the actual electrical conductivity of the potential model under consideration using the approximate Nernst-Einstein equation, which neglects correlations between different ions.

Analysis of the Distribution and Influencing Factors of Diffusion Coefficient Model Parameters Based on Molecular Dynamics Simulations

The establishment of mathematical models to predict the diffusion coefficients of gas and liquid systems have important theoretical significance and practical value. In this work, based on the previously proposed diffusion coefficient model D_LV, the distribution and influencing factors of the model parameters characteristic length (L) and diffusion velocity (V) were further investigated using molecular dynamics simulations. The statistical analysis of L and V for 10 gas systems and 10 liquid systems was presented in the paper. New distribution functions were established to describe the probability distributions of molecular motion L and V. The mean values of the correlation coefficients were 0.98 and 0.99, respectively. Meanwhile, the effects of molecular molar mass and system temperature on the molecular diffusion coefficients were discussed. The results show that the effect of molecular molar mass on the diffusion coefficient mainly affects the molecular motion L, and the effect of system temperature on the diffusion coefficient mainly affects V. For the gas system, the average relative deviation of D_LV and D_MSD is 10.73% and that of D_LV and experimental value is 12.63%; for the solution system, the average relative deviation of D_LV and D_MSD is 12.93% and that of D_LV and experimental value is 18.86%, which indicates the accuracy of the new model results. The new model reveals the potential mechanism of molecular motion and provides a theoretical basis for further study of the diffusion process.

Molecular modelling of the thermophysical properties of fluids: expectations, limitations, gaps and opportunities

This manuscript provides an overview of the current state of the art in terms of the molecular modelling of the thermophysical properties of fluids. It is intended to manage the expectations and serve as guidance to practising physical chemists, chemical physicists and engineers in terms of the scope and accuracy of the more commonly available intermolecular potentials along with the peculiarities of the software and methods employed in molecular simulations while providing insights on the gaps and opportunities available in this field. The discussion is focused around case studies which showcase both the precision and the limitations of frequently used workflows.

Charge Transport in Water-NaCl Electrolytes with Molecular Dynamics Simulations

A systematic description of microscopic mechanisms is necessary to understand mass transport in solid and liquid electrolytes. From Molecular Dynamics (MD) simulations, transport properties can be computed and provide a detailed view of the molecular and ionic motions. In this work, ionic conductivity and transport numbers in electrolyte systems are computed from equilibrium and nonequilibrium MD simulations. Results from the two methods are compared with experimental results, and we discuss the significance of the frame of reference when determining and comparing transport numbers. Two ways of computing ionic conductivity from equilibrium simulations are presented: the Nernst-Einstein approximation or the Onsager coefficients. The Onsager coefficients take ionic correlations into account and are found to be more suitable for concentrated electrolytes. Main features and differences between equilibrium and nonequilibrium simulations are discussed, and some potential anomalies and critical pitfalls of using nonequilibrium molecular dynamics to determine transport properties are highlighted.

Finding the bulk viscosity of air from Rayleigh-Brillouin light scattering spectra

Spectral line shape models can successfully reproduce experimental Rayleigh-Brillouin spectra, but they need knowledge about the bulk viscosity η_b. Light scattering involves GHz frequencies, but since η_b is only documented at low frequencies, η_b is usually left as a free parameter, which is determined by a fit of the model to an experimental spectrum. The question is whether models work so well because of this freedom. Moreover, for light scattering in air, spectral models view "air" as an effective molecule. We critically evaluate the use of η_b as a fit parameter by comparing η_b obtained from fits of the Tenti S6 model to the result of Direct Simulation Monte Carlo (DSMC) for a mixture of Nitrogen and Oxygen. These simulations are used to compute light scattering spectra, which are then compared to experiments. The DSMC simulation parameters are cross-checked with a molecular dynamics simulation based on intermolecular potentials. At large values of the uniformity parameter y, y ≈ 4, where the Brillouin contribution to spectra is large, fitted η_b are 20% larger than the ones from DSMC, while the quality of the simulated spectra is comparable to that of the Tenti S6 line shape model. At smaller y, the difference between fitted and simulated η_b can be as large as 100%. We hypothesize the breakdown of the bulk viscosity concept to be the cause of this fallacy.

Local Thermodynamic Description of Isothermal Single-Phase Flow in Simple Porous Media

Darcy’s law for porous media transport is given a new local thermodynamic basis in terms of the grand potential of confined fluids. The local effective pressure gradient is determined using non-equilibrium molecular dynamics, and the hydraulic conductivity and permeability are investigated. The transport coefficients are determined for single-phase flow in face-centered cubic lattices of solid spheres. The porosity changed from that in the closest packing of spheres to near unity in a pure fluid, while the fluid mass density varied from that of a dilute gas to a dense liquid. The permeability varied between $$5.7 \times {10^{-20}} \hbox {m}^2$$ 5.7 × 10 - 20 m 2 and $$5.5 \times {10^{-17}} \hbox {m}^2$$ 5.5 × 10 - 17 m 2 , showing a porosity-dependent Klinkenberg effect. Both transport coefficients depended on the average fluid mass density and porosity but in different ways. These results set the stage for a non-equilibrium thermodynamic investigation of coupled transport of multi-phase fluids in complex media.

Valence energy correction for electron reactive force field

Reactive force fields (ReaxFF) are a classical method to describe material properties based on a bond-order formalism, that allows bond dissociation and consequently investigations of reactive systems. Semiclassical treatment of electrons was introduced within ReaxFF simulations, better known as electron reactive force fields (eReaxFF), to explicitly treat electrons as spherical Gaussian waves. In the original version of eReaxFF, the electrons and electron-holes can lead to changes in both the bond energy and the Coulomb energy of the system. In the present study, the method was modified to allow an electron to modify the valence energy, therefore, permitting that the electron's presence modifies the three-body interactions, affecting the angle among three atoms. When a reaction path involving electron transfer is more sensitive to the geometric configuration of the molecules, corrections in the angular structure in the presence of electrons become more relevant; in this case, bond dissociation may not be enough to describe a reaction path. Consequently, the application of the extended eReaxFF method developed in this work should provide an improved description of a reaction path. As a first demonstration this semiclassical force field was parametrized for hydrogen and oxygen interactions, including water and water's ions. With the modified methodology both the overall accuracy of the force field but also the description of the angles within the molecules in presence of electrons could be improved.

Solubilities and Transport Properties of CO2, Oxalic Acid, and Formic Acid in Mixed Solvents Composed of Deep Eutectic Solvents, Methanol, and Propylene Carbonate

Recently, deep eutectic solvents (DES) have been considered as possible electrolytes for the electrochemical reduction of CO₂ to value-added products such as formic and oxalic acids. The applicability of pure DES as electrolytes is hindered by high viscosities. Mixtures of DES with organic solvents can be a promising way of designing superior electrolytes by exploiting the advantages of each solvent type. In this study, densities, viscosities, diffusivities, and ionic conductivities of mixed solvents comprising DES (i.e., reline and ethaline), methanol, and propylene carbonate were computed using molecular simulations. To provide a quantitative assessment of the affinity and mass transport of CO₂ and oxalic and formic acids in the mixed solvents, the solubilities and self-diffusivities of these solutes were also computed. Our results show that the addition of DES to the organic solvents enhances the solubilities of oxalic and formic acids, while the solubility of CO₂ in the ethaline-containing mixtures are in the same order of magnitude with the respective pure organic components. A monotonic increase in the densities and viscosities of the mixed solvents is observed as the mole fraction of DES in the mixture increases, with the exception of the density of ethaline-propylene carbonate which shows the opposite behavior due to the high viscosity of the pure organic component. The self-diffusivities of all species in the mixtures significantly decrease as the mole fraction of DES approaches unity. Similarly, the self-diffusivities of the dissolved CO₂ and the oxalic and formic acids also decrease by at least 1 order of magnitude as the composition of the mixture shifts from the pure organic component to pure DES. The computed ionic conductivities of all mixed solvents show a maximum value for mole fractions of DES in the range from 0.2 to 0.6 and decrease as more DES is added to the mixtures. Since for most mixtures studied here no prior experimental measurements exist, our findings can serve as a first data set based on which further investigation of DES-containing electrolyte solutions can be performed for the electrochemical reduction of CO₂ to useful chemicals.

Bulk viscosity of gaseous argon from molecular dynamics simulations

The bulk viscosity of dilute argon gas is calculated using molecular dynamics simulations in the temperature range 150-500 K and is found to be proportional to density squared in the investigated range of densities 0.001-1 kg m^{-3}. A comparison of the results obtained using Lennard-Jones and Tang-Toennies models of pair interaction potential reveals that the value of the bulk viscosity coefficient is sensitive to the choice of the pair interaction model. The inclusion of the Axilrod-Teller-Muto three-body interaction in the model does not noticeably affect the values of the bulk viscosity in dilute states, contrary to the previously investigated case of dense fluids.

Interfacial Properties of Hydrophobic Deep Eutectic Solvents with Water

Hydrophobic deep eutectic solvents (DESs) have recently gained much attention as water-immiscible solvents for a wide range of applications. However, very few studies exist in which the hydrophobicity of these DESs is quantified. In this work, the interfacial properties of hydrophobic DESs with water were computed at various temperatures using molecular dynamics simulations. The considered DESs were tetrabutylammonium chloride–decanoic acid (TBAC–dec) with a molar ratio of 1:2, thymol–decanoic acid (Thy–dec) with a molar ratio of 1:2, and dl-menthol–decanoic acid (Men–dec) with a molar ratio of 2:1. The following properties were investigated in detail: interfacial tensions, water-in-DES solubilities (and salt-in-water solubilities for TBAC–dec/water), density profiles, and the number densities of hydrogen bonds. Different ionic charge scaling factors were used for TBAC–dec. Thy–dec and Men–dec showed a high level of hydrophobicity with negligible computed water-in-DES solubilities. For charge scaling factors of 0.7 and 1 for the thymol and decanoic acid components of Thy–dec, the computed interfacial tensions of the DESs are in the following order: TBAC–dec (ca. 4 mN m^–1) < Thy–dec (20 mN m^–1) < Men–dec (26 mN m^–1). The two sets of charge scaling factors for Thy–dec did not lead to different density profiles but resulted in considerable differences in the DES/water interfacial tensions due to different numbers of decanoic acid–water hydrogen bonds at the interfaces. Large peaks were observed for the density profiles of (the hydroxyl oxygen of) decanoic acid at the interfaces of all DES/water mixtures, indicating a preferential alignment of the oxygen atoms of decanoic acid toward the aqueous phase.

Roles of energy dissipation and asymmetric wettability in spontaneous imbibition dynamics in a nanochannel

HYPOTHESIS

The imbibition dynamics is controlled by energy dissipation mechanisms and influenced by asymmetric wettability in a nanochannel. We hypothesize that the imbibition dynamics can be described by a combined model of the Lucas-Washburn equation and the Cox-Voinov law considering velocity-dependent contact angles.

METHODS

Molecular dynamics simulations are utilized to investigate the imbibition dynamics. A wide range of wetting conditions is achieved via adjusting the liquid-solid interaction parameters, and the spontaneous imbibition processes are quantified and compared.

FINDINGS

The critical condition for the occurrence of spontaneous imbibition is analyzed from a surface energy perspective. The analyses of energy conversion and dissipation indicate that the viscous dissipation is dominant during spontaneous imbibition. The classical Lucas-Washburn equation is modified with the Cox-Voinov law considering the effect of the dynamic contact angle and an effective equilibrium contact angle. We show that the proposed theory well captures the imbibition dynamics embodied in the growth of imbibition length as well as the transient interface shape and velocity for both the symmetric and asymmetric wetting conditions. In nanochannels with asymmetric wettability, the imbibition length difference between the sidewalls and interface oscillations increases with wetting disparity. Our findings deepen the understanding of imbibition dynamics on the nanoscale, and provide a theoretical reference for relevant applications.

How sensitive are physical properties of choline chloride-urea mixtures to composition changes: Molecular dynamics simulations and Kirkwood-Buff theory

Deep eutectic solvents (DESs) have emerged as a cheaper and greener alternative to conventional organic solvents. Choline chloride (ChCl) mixed with urea at a molar ratio of 1:2 is one of the most common DESs for a wide range of applications such as electrochemistry, material science, and biochemistry. In this study, molecular dynamics simulations are performed to study the effect of urea content on the thermodynamic and transport properties of ChCl and urea mixtures. With increased mole fraction of urea, the number of hydrogen bonds (HBs) between cation-anion and ion-urea decreases, while the number of HBs between urea-urea increases. Radial distribution functions (RDFs) for ChCl-urea and ChCl-ChCl pairs shows a significant decrease as the mole fraction of urea increases. Using the computed RDFs, Kirkwood-Buff Integrals (KBIs) are computed. KBIs show that interactions of urea-urea become stronger, while interactions of urea-ChCl and ChCl-ChCl pairs become slightly weaker with increasing mole fraction of urea. All thermodynamic factors are found larger than one, indicating a non-ideal mixture. Our results also show that self- and collective diffusivities increase, while viscosities decrease with increasing urea content. This is mainly due to the weaker interactions between ions and urea, resulting in enhanced mobilities. Ionic conductivities exhibit a non-monotonic behavior. Up to a mole fraction of 0.5, the ionic conductivities increase with increasing urea content and then reach a plateau.

Thermodynamic, transport, and structural properties of hydrophobic deep eutectic solvents composed of tetraalkylammonium chloride and decanoic acid

With the emergence of hydrophobic deep eutectic solvents (DESs), the scope of applications of DESs has been expanded to include situations in which miscibility with water is undesirable. Whereas most studies have focused on the applications of hydrophobic DESs from a practical standpoint, few theoretical works exist that investigate the structural and thermodynamic properties at the nanoscale. In this study, Molecular Dynamics (MD) simulations have been performed to model DESs composed of tetraalkylammonium chloride hydrogen bond acceptor and decanoic acid hydrogen bond donor (HBD) at a molar ratio of 1:2, with three different cation chain lengths (4, 7, and 8). After fine-tuning force field parameters, densities, viscosities, self-diffusivities, and ionic conductivities of the DESs were computed over a wide temperature range. The liquid structure was examined using radial distribution functions (RDFs) and hydrogen bond analysis. The MD simulations reproduced the experimental density and viscosity data from the literature reasonably well and were used to predict diffusivities and ionic conductivities, for which experimental data are scarce or unavailable. It was found that although an increase in the cation chain length considerably affected the density and transport properties of the DESs (i.e., yielding smaller densities and slower dynamics), no significant influence was observed on the RDFs and the hydrogen bonds. The self-diffusivities showed the following order for the mobility of the various components: HBD > anion > cation. Strong hydrogen bonds between the hydroxyl and carbonyl groups of decanoic acid and between the hydroxyl group of decanoic acid and chloride were observed to dominate the intermolecular interactions.

Diffusivity of α-, β-, γ-cyclodextrin and the inclusion complex of β-cyclodextrin: Ibuprofen in aqueous solutions; A molecular dynamics simulation study

Cyclodextrins (CDs) are widely used in drug delivery, catalysis, food and separation processes. In this work, a comprehensive simulation study on the diffusion of the native α-, β- and γ-CDs in aqueous solutions is carried out using Molecular Dynamics simulations. The effect of the system size on the computed self-diffusivity is investigated and it is found that the required correction can be as much as 75% of the final value. The effect of the water force field is examined and it is shown that the q4md-CD/TIP4P/2005 force field combination predicts the experimentally measured self-diffusion coefficients of CDs very accurately. The self-diffusion coefficients of the three native CDs were also computed in aqueous-NaCl solutions using the Joung and Cheatham (JC) and the Madrid-2019 force fields. It is found that Na+ ions have higher affinity towards the CDs when the JC force field is used and for this reason the predicted diffusivity of CDs is lower compared to simulations using the Madrid-2019 force field. As a model system for drug delivery and waste-water treatment applications, the diffusion of the β-CD:Ibuprofen inclusion complex in water is studied. In agreement with experiments for similar components, it is shown that the inclusion complex and the free β-CD have almost equal self-diffusion coefficients. Our analysis revealed that this is most likely caused by the almost full inclusion of the ibuprofen in the cavity of the β-CD. Our findings show that Molecular Dynamics simulation can be used to provide reasonable diffusivity predictions, and to obtain molecular-level understanding useful for industrial applications of CDs.

Machine Learning-Based Upscaling of Finite-Size Molecular Dynamics Diffusion Simulations for Binary Fluids

Molecular diffusion coefficients calculated using molecular dynamics (MD) simulations suffer from finite-size (i.e., finite box size and finite particle number) effects. Results from finite-sized MD simulations can be upscaled to infinite simulation size by applying a correction factor. For self-diffusion of single-component fluids, this correction has been well-studied by many researchers including Yeh and Hummer (YH); for binary fluid mixtures, a modified YH correction was recently proposed for correcting MD-predicted Maxwell-Stephan (MS) diffusion rates. Here we use both empirical and machine learning methods to identify improvements to the finite-size correction factors for both self-diffusion and MS diffusion of binary Lennard-Jones (LJ) fluid mixtures. Using artificial neural networks (ANNs), the error in the corrected LJ fluid diffusion is reduced by an order of magnitude versus existing YH corrections, and the ANN models perform well for mixtures with large dissimilarities in size and interaction energies where the YH correction proves insufficient.

Generalized Form for Finite-Size Corrections in Mutual Diffusion Coefficients of Multicomponent Mixtures Obtained from Equilibrium Molecular Dynamics Simulation

The system-size dependence of computed mutual diffusion coefficients of multicomponent mixtures is investigated, and a generalized correction term is derived. The generalized finite-size correction term was validated for the ternary molecular mixture chloroform/acetone/methanol as well as 28 ternary LJ systems. It is shown that only the diagonal elements of the Fick matrix show system-size dependency. The finite-size effects of these elements can be corrected by adding the term derived by Yeh and Hummer (J. Phys. Chem. B2004, 108, 15873–15879). By performing an eigenvalue analysis of the finite-size effects of the matrix of Fick diffusivities we show that the eigenvector matrix of Fick diffusivities does not depend on the size of the simulation box. Only eigenvalues, which describe the speed of diffusion, depend on the size of the system. An analytic relation for finite-size effects of the matrix of Maxwell–Stefan diffusivities was developed. All Maxwell–Stefan diffusivities depend on the system size, and the required correction depends on the matrix of thermodynamic factors.

GEMS-Pack: A Graphical User Interface for the Packmol Program

We present GEMS-Pack, a graphical user interface for Packmol. Since Packmol is largely used by the molecular simulation community, this work provides a complement to it, in the form of a user-friendly and efficient interface. A tool for number/volume/density calculation is provided to make needed calculations faster. Also, a visualization utility is included, which lets the users preview how their systems will look like even before running the packing procedure. This application does not modify the original Packmol code; it works in a complementary way, by generating the input script and running it through the system's terminal. This program is part of a development project and is intended to be further extended. Two examples are described in this paper to illustrate GEMS-Pack usage.

On the transferability of ion parameters to the TIP4P/2005 water model using molecular dynamics simulations

Countless molecular dynamics studies have relied on available ion and water force field parameters to model aqueous electrolyte solutions. The TIP4P/2005 model has proven itself to be among the best rigid water force fields, whereas many of the most successful ion parameters were optimized in combination with SPC/E, TIP3P, or TIP4P/Ew water. Many researchers have combined these ions with TIP4P/2005, hoping to leverage the strengths of both parameter sets. To assess if this widely used approach is justified and to provide a guide in selecting ion parameters, we investigated the transferability of various commonly used monovalent and multivalent ion parameters to the TIP4P/2005 water model. The transferability is evaluated in terms of ion hydration free energy, hydration radius, coordination number, and self-diffusion coefficient at infinite dilution. For selected ion parameters, we also investigated density, ion pairing, chemical potential, and mean ionic activity coefficients at finite concentrations. We found that not all ions are equally transferable to TIP4P/2005 without compromising their performance. In particular, ions optimized for TIP3P water were found to be poorly transferable to TIP4P/2005, whereas ions optimized for TIP4P/Ew water provided nearly perfect transferability. The latter ions also showed good overall agreement with experimental values. The one exception is that no combination of ion parameters and water model considered here was found to accurately reproduce experimental self-diffusion coefficients. Additionally, we found that cations optimized for SPC/E and TIP3P water displayed consistent underpredictions in the hydration free energy, whereas anions consistently overpredicted the hydration free energy.

Structural, Thermodynamic, and Transport Properties of Aqueous Reline and Ethaline Solutions from Molecular Dynamics Simulations

Deep eutectic solvents (DESs) are a new generation of green solvents, which are considered an environmentally friendly alternative to ionic liquids and volatile organic compounds. The addition of controlled amounts of water to DESs has a significant effect on their microscopic structure and thus on their thermodynamic and transport properties. In this way, DESs can be modified, leading to solvents with improved characteristics. In this work, molecular dynamics (MD) simulations are performed to obtain a better understanding of the relation between the microscopic structure, molecular interactions, and thermophysical properties of aqueous reline and ethaline solutions at temperatures ranging from 303.15 to 363.15 K. For both reline and ethaline solutions, the hydrogen bond (HB) networks disappear with increasing mass fraction of water, and the intensity of radial distribution function (RDF) peaks decreases. For a mass fraction of water of 40%, most of the HBs between the compounds of reline and ethaline are broken, and DESs are fully dissolved in water. Consequently, a monotonic decrease in viscosities and an increase in self-diffusion coefficients are observed. Ionic conductivities show a nonmonotonic behavior with increasing water content. Up to 60% water mass fraction, the ionic conductivities increase with increasing water content. A further increase in the mass fraction of water decreases conductivities. For all studied systems, the HB network and the peaks of RDFs show relatively small changes for water mass fractions below 5% and beyond 40%. The MD results show that viscosities decrease with temperature, while diffusivities and ionic conductivities increase. The effect of the temperature on the structure of DES-water mixtures is negligible.