Gabriela Guevara-Carrion

Prediction of self-diffusion coefficient and shear viscosity of water and its binary mixtures with methanol and ethanol by molecular simulation

Density, self-diffusion coefficient, and shear viscosity of pure liquid water are predicted for temperatures between 280 and 373 K by molecular dynamics simulation and the Green-Kubo method. Four different rigid nonpolarizable water models are assessed: SPC, SPC/E, TIP4P, and TIP4P/2005. The pressure dependence of the self-diffusion coefficient and the shear viscosity for pure liquid water is also calculated and the anomalous behavior of these properties is qualitatively well predicted. Furthermore, transport properties as well as excess volume and excess enthalpy of aqueous binary mixtures containing methanol or ethanol, based on the SPC/E and TIP4P/2005 water models, are calculated. Under the tested conditions, the TIP4P/2005 model gives the best quantitative and qualitative agreement with experiments for the regarded transport properties. The deviations from experimental data are of 5% to 15% for pure liquid water and 5% to 20% for the water + alcohol mixtures. Moreover, the center of mass power spectrum of water as well as the investigated mixtures are analyzed and the hydrogen-bonding structure is discussed for different states.

ms2: A molecular simulation tool for thermodynamic properties, new version release

Abstract A new version release (2.0) of the molecular simulation tool ms2 [S. Deublein et al., Comput. Phys. Commun. 182 (2011) 2350] is presented. Version 2.0 of ms2 features a hybrid parallelization based on MPI and OpenMP for molecular dynamics simulation to achieve higher scalability. Furthermore, the formalism by Lustig [R. Lustig, Mol. Phys. 110 (2012) 3041] is implemented, allowing for a systematic sampling of Massieu potential derivatives in a single simulation run. Moreover, the Green–Kubo formalism is extended for the sampling of the electric conductivity and the residence time. To remove the restriction of the preceding version to electro-neutral molecules, Ewald summation is implemented to consider ionic long range interactions. Finally, the sampling of the radial distribution function is added. Program summary Program title: m s 2 Catalogue identifier: AEJF_v2_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEJF_v2_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 50375 No. of bytes in distributed program, including test data, etc.: 345786 Distribution format: tar.gz Programming language: Fortran90. Computer: The simulation program m s 2 is usable on a wide variety of platforms, from single processor machines to modern supercomputers. Operating system: Unix/Linux. Has the code been vectorized or parallelized?: Yes: Message Passing Interface (MPI) protocol and OpenMP Scalability is up to 2000 cores. RAM: m s 2 runs on single cores with 512 MB RAM. The memory demand rises with increasing number of cores used per node and increasing number of molecules. Classification: 7.7, 7.9, 12. External routines: Message Passing Interface (MPI) Catalogue identifier of previous version: AEJF_v1_0 Journal reference of previous version: Comput. Phys. Comm. 182 (2011) 2350 Does the new version supersede the previous version?: Yes. Nature of problem: Calculation of application oriented thermodynamic properties for fluids consisting of rigid molecules: vapor–liquid equilibria of pure fluids and multi-component mixtures, thermal and caloric data as well as transport properties. Solution method: Molecular dynamics, Monte Carlo, various classical ensembles, grand equilibrium method, Green–Kubo formalism, Lustig formalism Reasons for new version: The source code was extended to introduce new features. Summary of revisions: The new features of Version 2.0 include: Hybrid parallelization based on MPI and OpenMP for molecular dynamics simulation; Ewald summation for long range interactions; sampling of Massieu potential derivatives; extended Green–Kubo formalism for the sampling of the electric conductivity and the residence time; radial distribution function. Restrictions: None. The system size is user-defined. Typical problems addressed by m s 2 can be solved by simulating systems containing typically 1000–4000 molecules. Unusual features: Auxiliary feature tools are available for creating input files, analyzing simulation results and visualizing molecular trajectories. Additional comments: Sample makefiles for multiple operation platforms are provided. Documentation is provided with the installation package and is available at http://www.ms-2.de . Running time: The running time of m s 2 depends on the specified problem, the system size and the number of processes used in the simulation. E.g. running four processes on a “Nehalem” processor, simulations calculating vapor–liquid equilibrium data take between two and 12 hours, calculating transport properties between six and 24 hours. Note that the examples given above stand for the total running time as there is no post-processing of any kind involved in property calculations.

Thermodynamic Properties for Applications in Chemical Industry via Classical Force Fields

Thermodynamic properties of fluids are of key importance for the chemical industry. Presently, the fluid property models used in process design and optimization are mostly equations of state or G (E) models, which are parameterized using experimental data. Molecular modeling and simulation based on classical force fields is a promising alternative route, which in many cases reasonably complements the well established methods. This chapter gives an introduction to the state-of-the-art in this field regarding molecular models, simulation methods, and tools. Attention is given to the way modeling and simulation on the scale of molecular force fields interact with other scales, which is mainly by parameter inheritance. Parameters for molecular force fields are determined both bottom-up from quantum chemistry and top-down from experimental data. Commonly used functional forms for describing the intra- and intermolecular interactions are presented. Several approaches for ab initio to empirical force field parameterization are discussed. Some transferable force field families, which are frequently used in chemical engineering applications, are described. Furthermore, some examples of force fields that were parameterized for specific molecules are given. Molecular dynamics and Monte Carlo methods for the calculation of transport properties and vapor-liquid equilibria are introduced. Two case studies are presented. First, using liquid ammonia as an example, the capabilities of semi-empirical force fields, parameterized on the basis of quantum chemical information and experimental data, are discussed with respect to thermodynamic properties that are relevant for the chemical industry. Second, the ability of molecular simulation methods to describe accurately vapor-liquid equilibrium properties of binary mixtures containing CO(2) is shown.

Mutual diffusion of binary liquid mixtures containing methanol, ethanol, acetone, benzene, cyclohexane, toluene, and carbon tetrachloride

Mutual diffusion coefficients of all 20 binary liquid mixtures that can be formed out of methanol, ethanol, acetone, benzene, cyclohexane, toluene, and carbon tetrachloride without a miscibility gap are studied at ambient conditions of temperature and pressure in the entire composition range. The considered mixtures show a varying mixing behavior from almost ideal to strongly non-ideal. Predictive molecular dynamics simulations employing the Green-Kubo formalism are carried out. Radial distribution functions are analyzed to gain an understanding of the liquid structure influencing the diffusion processes. It is shown that cluster formation in mixtures containing one alcoholic component has a significant impact on the diffusion process. The estimation of the thermodynamic factor from experimental vapor-liquid equilibrium data is investigated, considering three excess Gibbs energy models, i.e., Wilson, NRTL, and UNIQUAC. It is found that the Wilson model yields the thermodynamic factor that best suits the simulation results for the prediction of the Fick diffusion coefficient. Four semi-empirical methods for the prediction of the self-diffusion coefficients and nine predictive equations for the Fick diffusion coefficient are assessed and it is found that methods based on local composition models are more reliable. Finally, the shear viscosity and thermal conductivity are predicted and in most cases favorably compared with experimental literature values.

Molecular Modeling of Hydrogen Bonding Fluids: New Cyclohexanol Model and Transport Properties of Short Monohydric Alcohols

Currently, molecular modeling and simulation gains importance for the prediction ofthermophysical properties of pure fluids and mixtures, both in research and industry.This is due to several reasons: Firstly, the predictive power of molecular models al-lows forresults with technicallyrelevantaccuracyoverwide rangeofstate pointsthatis superior to classical methods. Secondly, a given molecular model provides accessto the full variety of thermophysical properties, such as thermal, caloric, transportor phase equilibrium data. Finally, through the advent of cheaply available powerfulcomputing infrastructure, reasonable execution times for molecular simulations canbe achieved which are of particular importance for industrial applications. Molecu-lar modeling and simulation are based on statistical thermodynamics which directlylinks the intermolecular interactions to the macroscopic thermophysical properties.That sound physical background also supports the increasing acceptance comparedto classical phenomenological modeling.Modeling thermophysical properties of hydrogen bonding systems remains achallenge. Phenomenologicalmodels often fail to describe the interplay between theenergetics of hydrogen bonding and its structural effects. Molecular force field mod-els, however, are much better suited for solving that task as they explicitly considerthis interplay. Most of the presently available molecular models use crude assump-tions for the description of hydrogen bonding which can, for instance, be simplymodeled by point charges eccentrically superimposed to Lennard-Jones (LJ) sites.One benefit of this simple modeling approach for hydrogen bon ding is the compa-rably small number of adjustable model parameters. Furthermore, the approach iscompatible with numerous LJ based models from the literature and it can success-fully be applied to mixtures. This simple modeling approach emerged to be fruitfulin many ways, although many of the molecular models proposed in the literaturelack in the quantitatively sound description of thermophysical properties. The aim

The effect of alcohols as the third component on diffusion in mixtures of aromatics and ketones

With laboratory and numerical work, we demonstrate that one of the main diffusion coefficients and the smaller eigenvalue of the Fick diffusion matrix are invariant to the number of methylene groups of the alcohol in ternary mixtures composed of an aromatic (benzene), a ketone (acetone) and one of three different alcohols (methanol, ethanol or 2-propanol). A critical analysis of the relationship between the kinetic and thermodynamic contributions to the diffusion coefficients allows us to explain this intriguing behaviour of this class of mixture. These findings are reflected by the diffusive behaviour of the according binary subsystems. Our approach provides a promising systematic framework for future investigations into the important and challenging problem of transport diffusion in multicomponent liquids.

Molecular Insight into the Liquid Propan-2-ol + Water Mixture

The hydrogen bonding structure of the mixture propan-2-ol + water is analyzed at ambient conditions of temperature and pressure with molecular modeling and simulation techniques. A new force field for propan-2-ol is developed for this purpose on the basis of quantum chemical calculations and validated for a wide range of macroscopic properties. The basic mixing properties, excess volume and excess enthalpy, as well as the most important transport properties, that is, diffusion coefficients and shear viscosity, are considered to verify the suitability of the employed force fields for studying the complex behavior of this aqueous alcoholic mixture. Radial distribution functions and hydrogen bonding statistics are employed to characterize the hydrogen bond network and molecular clustering. Inhomogeneous mixing on the microscopic level, given by the presence of segregation pockets, is identified. The interrelation between the intriguing macroscopic behavior of this binary mixture and its microscopic structure is revealed.

Interplay of structure and diffusion in ternary liquid mixtures of benzene + acetone + varying alcohols

The Fick diffusion coefficient matrix of ternary mixtures containing benzene + acetone + three different alcohols, i.e., methanol, ethanol, and 2-propanol, is studied by molecular dynamics simulation and Taylor dispersion experiments. Aiming to identify common features of these mixtures, it is found that one of the main diffusion coefficients and the smaller eigenvalue do not depend on the type of alcohol along the studied composition path. Two mechanisms that are responsible for this invariant behavior are discussed in detail, i.e., the interplay between kinetic and thermodynamic contributions to Fick diffusion coefficients and the presence of microscopic heterogeneities caused by hydrogen bonding. Experimental work alone cannot explain these mechanisms, while present simulations on the molecular level indicate structural changes and uniform intermolecular interactions between benzene and acetone molecules in the three ternary mixtures. The main diffusion coefficients of these ternary mixtures exhibit similarities with their binary subsystems. Analyses of radial distribution functions and hydrogen bonding statistics quantitatively evidence alcohol self-association and cluster formation, as well as component segregation. Furthermore, the excess volume of the mixtures is analyzed in the light of intermolecular interactions, further demonstrating the benefits of the simultaneous use of experiment and simulation. The proposed framework for studying diffusion coefficients of a set of ternary mixtures, where only one component varies, opens the way for further investigations and a better understanding of multicomponent diffusion. The presented numerical results may also give an impulse to the development of predictive approaches for multicomponent diffusion.

Molecular Simulation Study of Transport Properties for 20 Binary Liquid Mixtures and New Force Fields for Benzene, Toluene and CCl 4

Nowadays, molecular modeling and simulation is being actively applied in physical, chemical and biological sciences as well as in engineering research and its importance will increase further in the future [31]. In the context of the chemical industry, molecular simulation has emerged as an alternative tool to estimate a wide variety of bulk phase thermodynamic property data, e.g., heat of formation, phase densities, transport coefficients, solubilities, rate constants, as well as to gain a deeper understanding of the subjacent molecular processes. Owing to the rapid increase in computing power and the development of new algorithms, the range of molecules that can be treated and the accuracy of the results is growing rapidly [18]. Traditionally, transport data have played a lesser role than other thermodynamic properties like vapor-liquid equilibria (VLE). Accurate experimental techniques for the measurement of transport properties were only developed around 1970, thus, the availability of such data is still low [52]. Furthermore, experimental measurements alone are not able to meet the demand for transport properties from the industry that may comprise several hundreds of data points for a single technical process [52]. On the other hand, classical theoretical methods are often incapable to accurately predict transport properties, especially when dealing with mixtures of liquids containing associating compounds.

Molecular Modeling of Hydrogen Bonding Fluids: Phase Behavior of Industrial Fluids

Six new rigid models for Hydrogen chloride, Phosgene, Toluene, Benzene, Chlorobenzene and Ortho-Dichlorobenzene, that are based on quantum chemical calculations, are presented. Only the parameters of the dispersive and repulsive interactions are fitted to macroscopic thermodynamic properties to achieve an optimal agreement with experimental vapor-liquid equilibrium data.