Finite-Size Effects of Binary Mutual Diffusion Coefficients from Molecular Dynamics.
ABSTRACT: Molecular dynamics simulations were performed for the prediction of the finite-size effects of Maxwell-Stefan diffusion coefficients of molecular mixtures and a wide variety of binary Lennard-Jones systems. A strong dependency of computed diffusivities on the system size was observed. Computed diffusivities were found to increase with the number of molecules. We propose a correction for the extrapolation of Maxwell-Stefan diffusion coefficients to the thermodynamic limit, based on the study by Yeh and Hummer ( J. Phys. Chem. B , 2004 , 108 , 15873 - 15879 ). The proposed correction is a function of the viscosity of the system, the size of the simulation box, and the thermodynamic factor, which is a measure for the nonideality of the mixture. Verification is carried out for more than 200 distinct binary Lennard-Jones systems, as well as 9 binary systems of methanol, water, ethanol, acetone, methylamine, and carbon tetrachloride. Significant deviations between finite-size Maxwell-Stefan diffusivities and the corresponding diffusivities at the thermodynamic limit were found for mixtures close to demixing. In these cases, the finite-size correction can be even larger than the simulated (finite-size) Maxwell-Stefan diffusivity. Our results show that considering these finite-size effects is crucial and that the suggested correction allows for reliable computations.
Project description: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. B 2004, 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.
Project description:The main focus of this article is on mixture separations that are driven by differences in intracrystalline diffusivities of guest molecules in microporous crystalline adsorbent materials. Such "kinetic" separations serve to over-ride, and reverse, the selectivities dictated by mixture adsorption equilibrium. The Maxwell-Stefan formulation for the description of intracrystalline fluxes shows that the flux of each species is coupled with that of the partner species. For n-component mixtures, the coupling is quantified by a n × n dimensional matrix of thermodynamic correction factors with elements ? ij ; these elements can be determined from the model used to describe the mixture adsorption equilibrium. If the thermodynamic coupling effects are essentially ignored, i.e., the ? ij is assumed to be equal to ? ij , the Kronecker delta, the Maxwell-Stefan formulation degenerates to yield uncoupled flux relations. The significance of thermodynamic coupling is highlighted by detailed analysis of separations of five different mixtures: N2/CH4, CO2/C2H6, O2/N2, C3H6/C3H8, and hexane isomers. In all cases, the productivity of the purified raffinate, containing the tardier species, is found to be significantly larger than that anticipated if the simplification ? ij = ? ij is assumed. The reason for the strong influence of ? ij on transient breakthroughs is traceable to the phenomenon of uphill intracrystalline diffusion of more mobile species. The major conclusion to emerge from this study is that modeling of kinetic separations needs to properly account for the thermodynamic coupling effects.
Project description:A method is proposed for calculating the shear viscosity of a liquid from finite-size effects of self-diffusion coefficients in Molecular Dynamics simulations. This method uses the difference in the self-diffusivities, computed from at least two system sizes, and an analytic equation to calculate the shear viscosity. To enable the efficient use of this method, a set of guidelines is developed. The most efficient number of system sizes is two and the large system is at least four times the small system. The number of independent simulations for each system size should be assigned in such a way that 50%-70% of the total available computational resources are allocated to the large system. We verified the method for 250 binary and 26 ternary Lennard-Jones systems, pure water, and an ionic liquid ([Bmim][Tf2N]). The computed shear viscosities are in good agreement with viscosities obtained from equilibrium Molecular Dynamics simulations for all liquid systems far from the critical point. Our results indicate that the proposed method is suitable for multicomponent mixtures and highly viscous liquids. This may enable the systematic screening of the viscosities of ionic liquids and deep eutectic solvents.
Project description:Kirkwood-Buff (KB) integrals provide a connection between microscopic properties and thermodynamic properties of multicomponent fluids. The estimation of KB integrals using molecular simulations of finite systems requires accounting for finite size effects. In the small system method, properties of finite subvolumes with different sizes embedded in a larger volume can be used to extrapolate to macroscopic thermodynamic properties. KB integrals computed from small subvolumes scale with the inverse size of the system. This scaling was used to find KB integrals in the thermodynamic limit. To reduce numerical inaccuracies that arise from this extrapolation, alternative approaches were considered in this work. Three methods for computing KB integrals in the thermodynamic limit from information of radial distribution functions (RDFs) of finite systems were compared. These methods allowed for the computation of surface effects. KB integrals and surface terms in the thermodynamic limit were computed for Lennard-Jones (LJ) and Weeks-Chandler-Andersen (WCA) fluids. It was found that all three methods converge to the same value. The main differentiating factor was the speed of convergence with system size L. The method that required the smallest size was the one which exploited the scaling of the finite volume KB integral multiplied by L. The relationship between KB integrals and surface effects was studied for a range of densities.
Project description:Molecular dynamics simulation data for a variety of binary guest mixtures (H2/CO2, Ne/CO2, CH4/CO2, CO2/N2, H2/CH4, H2/Ar, CH4/Ar, Ar/Kr, Ne/Ar, CH4/C2H6, CH4/C3H8, C2H6C3H8, CH4/nC4H10, and CH4/nC5H11) in zeolites (MFI, BEA, ISV, FAU (all-silica), NaY, NaX, LTA, CHA, DDR) and metal-organic frameworks (MOFs) (IRMOF-1, CuBTC, MgMOF-74) show that the Maxwell-Stefan (M-S) diffusivities, ? 1, ? 2, ? 12, are strongly dependent on the molar loadings. The main aim of this article is to develop a fundamental basis for describing the loading dependence of M-S diffusivities. Using the ideal adsorbed solution theory, a thermodynamically rigorous definition of the occupancy, ?, is derived; this serves as a convenient proxy for the spreading pressure, ?, and provides the correct metric to describe the loading dependence of diffusivities. Configurational-bias Monte Carlo simulations of the unary adsorption isotherms are used for the calculation of the spreading pressure, ?, and occupancy, ?. The M-S diffusivity, ? i , of either constituent in binary mixtures has the same value as that for unary diffusion, provided the comparison is made at the same ?. Furthermore, compared at the same value of ?, the M-S diffusivity ? i of any component in a mixture does not depend on it partner species. The ? i versus ? dependence is amenable to simple interpretation using lattice-models. The degree of correlations, defined by the ratio ? 1/? 12, that characterizes mixture diffusion shows a linear increase with occupancy ?, implying that correlations become increasingly important as pore saturation conditions are approached.
Project description:The quality of stored frozen products such as foods and biomaterials generally degrades in time due to the growth of large ice crystals by recrystallization. While there is ample experimental evidence that recrystallization within such products (or model systems thereof) is often dominated by diffusion-limited Ostwald ripening, the application of Ostwald-ripening theories to predict measured recrystallization rates has only met with limited success. For a model system of polycrystalline ice within an aqueous solution of sugars, we here show recrystallization rates can be predicted on the basis of Ostwald ripening theory, provided (1) the theory accounts for the fact the solution can be nonideal, nondilute and of different density than the crystals, (2) the effect of ice-phase volume fraction on the diffusional flux of water between crystals is accurately described, and (3) all relevant material properties (involving binary Fick diffusion coefficients, the thermodynamic factor of the solution, and the surface energy of ice) are carefully estimated. To enable calculation of material properties, we derive an alternative formulation of Ostwald ripening in terms of the Maxwell-Stefan instead of the Fick approach to diffusion. First, this leads to a cancellation of the thermodynamic factor (a measure for the nonideality of a solution), which is a notoriously difficult property to obtain. Second, we show that Maxwell-Stefan diffusion coefficients can to a reasonable approximation be related to self-diffusion coefficients, which are relatively easy to measure or predict in comparison to Fick diffusion coefficients. Our approach is validated for a binary system of water and sucrose, for which we show predicted recrystallization rates of ice compare well to experimental results, with relative deviations of at most a factor of 2.
Project description:The Maxwell-Stefan (M-S) formulation, that is grounded in the theory of irreversible thermodynamics, is widely used for describing mixture diffusion in microporous crystalline materials such as zeolites and metal-organic frameworks (MOFs). Binary mixture diffusion is characterized by a set of three M-S diffusivities: <i>?</i> <sub>1</sub>, <i>?</i> <sub>2</sub>, and <i>?</i> <sub>12</sub>. The M-S diffusivities <i>?</i> <sub>1</sub> and <i>?</i> <sub>2</sub> characterize interactions of guest molecules with pore walls. The exchange coefficient <i>?</i> <sub>12</sub> quantifies correlation effects that result in slowing-down of the more mobile species due to correlated molecular jumps with tardier partners. The primary objective of this article is to develop a methodology for estimating <i>?</i> <sub>1</sub>, <i>?</i> <sub>2</sub>, and <i>?</i> <sub>12</sub> using input data for the constituent unary systems. The dependence of the unary diffusivities <i>?</i> <sub>1</sub> and <i>?</i> <sub>2</sub> on the pore occupancy, ?, is quantified using the quasi-chemical theory that accounts for repulsive, or attractive, forces experienced by a guest molecule with the nearest neighbors. For binary mixtures, the same occupancy dependence of <i>?</i> <sub>1</sub> and <i>?</i> <sub>2</sub> is assumed to hold; in this case, the occupancy, ?, is calculated using the ideal adsorbed solution theory. The exchange coefficient <i>?</i> <sub>12</sub> is estimated from the data on unary self-diffusivities. The developed estimation methodology is validated using a large data set of M-S diffusivities determined from molecular dynamics simulations for a wide variety of binary mixtures (H<sub>2</sub>/CO<sub>2</sub>, Ne/CO<sub>2</sub>, CH<sub>4</sub>/CO<sub>2</sub>, CO<sub>2</sub>/N<sub>2</sub>, H<sub>2</sub>/CH<sub>4</sub>, H<sub>2</sub>/Ar, CH<sub>4</sub>/Ar, Ne/Ar, CH<sub>4</sub>/C<sub>2</sub>H<sub>6</sub>, CH<sub>4</sub>/C<sub>3</sub>H<sub>8</sub>, and C<sub>2</sub>H<sub>6</sub>/C<sub>3</sub>H<sub>8</sub>) in zeolites (MFI, BEA, ISV, FAU, NaY, NaX, LTA, CHA, and DDR) and MOFs (IRMOF-1, CuBTC, and MgMOF-74).
Project description:Experimental diffusivities are scarcely available, though their knowledge is essential to model rate-controlled processes. In this work various machine learning models to estimate diffusivities in polar and nonpolar solvents (except water and supercritical CO<sub>2</sub>) were developed. Such models were trained on a database of 90 polar systems (1431 points) and 154 nonpolar systems (1129 points) with data on 20 properties. Five machine learning algorithms were evaluated: multilinear regression, <i>k</i>-nearest neighbors, decision tree, and two ensemble methods (random forest and gradient boosted). For both polar and nonpolar data, the best results were found using the gradient boosted algorithm. The model for polar systems contains 6 variables/parameters (temperature, solvent viscosity, solute molar mass, solute critical pressure, solvent molar mass, and solvent Lennard-Jones energy constant) and showed an average deviation (AARD) of 5.07%. The nonpolar model requires five variables/parameters (the same of polar systems except the Lennard-Jones constant) and presents AARD = 5.86%. These results were compared with four classic models, including the 2-parameter correlation of Magalhães et al. (AARD = 5.19/6.19% for polar/nonpolar) and the predictive Wilke-Chang equation (AARD = 40.92/29.19%). Nonetheless Magalhães et al. requires two parameters per system that must be previously fitted to data. The developed models are coded and provided as command line program.
Project description:Long-range Lennard-Jones (LJ) interactions have a significant impact on the structural and thermodynamic properties of nonpolar systems. While several methods have been introduced for the treatment of long-range LJ interactions in molecular dynamics (MD) simulations, increased accuracy and extended applicability is required for anisotropic systems such as lipid bilayers. The recently refined Lennard-Jones particle-mesh Ewald (LJ-PME) method extends the particle-mesh Ewald (PME) method to long-range LJ interactions and is suitable for use with anisotropic systems. Implementation of LJ-PME with the CHARMM36 (C36) additive and CHARMM Drude polarizable force fields improves agreement with experiment for density, isothermal compressibility, surface tension, viscosity, translational diffusion, and 13C T1 relaxation times of pure alkanes. Trends in the temperature dependence of the density and isothermal compressibility of hexadecane are also improved. While the C36 additive force field with LJ-PME remains a useful model for liquid alkanes, the Drude polarizable force field with LJ-PME is more accurate for nearly all quantities considered. LJ-PME is also preferable to the isotropic long-range correction for hexadecane because the molecular order extends to nearly 20 Å, well beyond the usual 10-12 Å cutoffs used in most simulations.
Project description:Molecular dynamics-based free energy calculations allow the determination of a variety of thermodynamic quantities from computer simulations of small molecules. Thermodynamic integration (TI) calculations can suffer from instabilities during the creation or annihilation of particles. This "singularity" problem can be addressed with "soft-core" potential functions which keep pairwise interaction energies finite for all configurations and provide smooth free energy curves. "One-step" transformations, in which electrostatic and van der Waals forces are simultaneously modified, can be simpler and less expensive than "two-step" transformations in which these properties are changed in separate calculations. Here, we study solvation free energies for molecules of different hydrophobicity using both models. We provide recommended values for the two parameters ?(LJ) and ?(C) controlling the behavior of the soft-core Lennard-Jones and Coulomb potentials and compare one- and two-step transformations with regard to their suitability for numerical integration. For many types of transformations, the one-step procedure offers a convenient and accurate approach to free energy estimates.