On the Prediction of Thermodynamic Properties by Atomistic Simulation. from Vapor-Liquid Equilibrium of Alcohols to Self-Assembly in Mixed Solvents
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On the Prediction of Thermodynamic Properties by Atomistic Simulation. From Vapor-Liquid Equilibrium of Alcohols to Self-Assembly in Mixed Solvents Von der Fakult¨atEnergie-, Verfahrens- und Biotechnik der Universit¨at Stuttgart und dem Stuttgart Center for Simulation Science (SC SimTech) zur Erlangung der W¨urdeeines Doktors der Ingenieurwissenschaft (Dr.-Ing.) genehmigte Abhandlung Vorgelegt von J¨orgBaz aus Bietigheim-Bissingen Hauptberichter: Apl. Prof. Dr.-Ing. habil. Niels Hansen Mitberichter: Prof. Dr.-Ing. Ulrich Nieken Prof. Dr. Lars Sch¨afer Tag der m¨undlichen Pr¨ufung:2. April 2020 Institut f¨urTechnische Thermodynamik und Thermische Verfahrenstechnik der Universit¨atStuttgart 2020 Eidesstattliche Erkl¨arung Hiermit versichere ich, dass ich die vorliegende Arbeit mit dem Titel "On the Prediction of Thermodynamic Properties by Atomistic Simulation. From Vapor-Liquid Equilibrium of Alcohols to Self-Assembly in Mixed Solvents" selbstst¨andigverfasst und keine anderen als die angegebenen Quellen und Hilfsmittel benutzt habe, dass alle Stellen der Arbeit, die w¨ortlich oder sinngem¨aßaus anderen Quellen ¨ubernommen wurden, als solche kenntlich gemacht sind. Ich versichere außerdem, dass die vorliegende Dissertation nur in diesem und keinem anderen Promotionsverfahren eingereicht wurde und dass diesem Promotionsverfahren keine endg¨ultiggescheiterten Promotionsverfahren vorausgegangen sind. I herewidth duly declare that I have authored the dissertation "On the Prediction of Thermodynamic Properties by Atomistic Simulation. From Vapor-Liquid Equilibrium of Alcohols to Self-Assembly in Mixed Solvents" independently and only with use of specified aids. I have mentioned all sources used and cited correctly according to scientific rules. Stuttgart, October 6th, 2019 J¨orgBaz Contents 1 Introduction 19 1.1 Molecular Simulations for Condensed Phase Systems . 19 1.2 Force Fields . 23 1.3 Validation . 27 1.4 Purpose of this Work . 30 1.4.1 Supramolecular Complexes . 31 1.4.2 Deep Eutectic Solvents . 33 1.4.3 Transferable Force Fields for n-Alcohols . 36 2 Thermodynamic Characterization of the Dimerization of an Anionic Perylene Bisimide Dye Using Molecular Simulation 39 2.1 Introduction . 40 2.2 Computational Details . 41 2.2.1 Force Field . 41 2.2.2 Simulated Systems . 42 2.2.3 Simulation Parameters . 43 2.2.4 Trajectory Analysis . 43 2.2.5 Modeling the Temperature Dependence of the Potential of Mean Force . 44 2.3 Results and Discussion . 45 2.3.1 Dimerization in Pure Water . 45 2.3.2 Dimerization in an Ethanol/Water Mixture and in Aqueous NaCl Solution . 51 2.4 Conclusion . 55 3 Thermophysical Properties of Glyceline-Water Mixtures Investigated by Molecular Modelling 57 3.1 Introduction . 58 3.2 Computational Details . 59 3.2.1 Molecular Dynamics Simulations . 59 1 3.2.2 Trajectory Analysis . 61 3.2.3 PC-SAFT Calculations . 64 3.3 Results . 66 3.3.1 Volumetric Properties and Liquid Structure . 66 3.3.2 Shear Viscosity . 69 3.3.3 Self-Diffusion Coefficient . 70 3.3.4 Water Activity . 71 3.4 Discussion . 72 3.5 Conclusion . 75 4 On the use of transport properties to discriminate Mie-type molecular models for 1-propanol optimized against VLE data 77 4.1 Introduction . 78 4.2 Force Field . 79 4.2.1 Bonded Energy . 79 4.2.2 Nonbonded Energy . 80 4.2.3 Optimization of Force Field Parameters . 81 4.3 Computational Details . 82 4.3.1 Monte Carlo Simulations . 82 4.3.2 Molecular Dynamics Simulations . 83 4.3.3 Trajectory Analysis . 84 4.4 Results and Discussion . 86 4.4.1 Force Field Optimization . 86 4.4.2 Force Field Assessment . 87 4.5 Conclusion . 93 5 Transferable Anisotropic Mie-Potential Force Field for n-Alcohols: Static and Dynamic Fluid Properties of Pure Substances and Binary Mixtures 95 5.1 Introduction . 96 5.2 Force Field . 97 5.2.1 Bonded Energy . 98 5.2.2 Nonbonded Energy . 98 5.2.3 Optimization of Force Field Parameters . 100 5.3 Simulation Details . 102 5.3.1 Monte Carlo Simulations . 102 5.3.2 Molecular Dynamics Simulations . 104 5.3.3 Trajectory Analysis . 104 5.4 Results and Discussion . 106 5.4.1 Static Pure Component Properties . 106 2 5.4.2 Shear Viscosities of Pure Substance . 108 5.4.3 Self-Diffusion Coefficients of Pure Substance . 110 5.4.4 Mixture Properties . 110 5.5 Conclusion . 113 6 Conclusion 115 6.1 Supramolecular Complexes . 115 6.2 Deep Eutectic Solvents . 116 6.3 Development of a TAMie Force Field for n-Alcohols . 116 Appendices 165 A Supporting Information: Thermodynamic Characterization of the Dimerization of an Anionic Perylene Bisimide Dye Using Molecular Simulation 167 A.1 GROMOS Force Field Parameters for PBI . 168 A.2 Dimerization in Pure Water . 176 A.3 Dimerization in Ethanol/Water Mixtures . 177 A.4 Dimerization in Aqueous NaCl Solution . 178 B Supporting Information: Thermophysical Properties of Glyceline-Water Mixtures Investigated by Molecular Modelling 181 B.1 Force Field Parameters for the Cholinium Cation . 182 B.2 Force Field Parameters for Chloride Anion . 187 B.3 Force Field Parameters for Glycerol . 187 B.4 Self-Diffusion Coefficients . 190 B.5 Finite Size Effects . 190 B.6 Binary Mixture Glycerol and Water . 191 B.7 Binary Mixture Choline and Water . 192 B.8 Radial Distribution Functions . 193 B.9 Self-Diffusion Coefficients of Choline, Chloride and Glycerol . 196 C Supporting Information: On the use of transport properties to discriminate Mie-type molecular models for 1-propanol optimized against VLE data 199 C.1 Covalent Force Field Parameters . 199 C.2 Self-Diffusion Coefficients - Uncorrected Values . 200 C.3 Radial Distribution Functions . 201 3 D Supporting Information: Transferable Anisotropic Mie-Potential Force Field for n-Alcohols: Static and Dynamic Fluid Properties of Pure Substances and Binary Mixtures205 D.1 Nonbonded Energy Calculation . 205 D.2 Results . 206 4 List of Symbols Latin Letters - Part 1 of 2 a parameter specifying the attractive part of the Mie potential ai Helmholtz energy aW water activity A parameter of Buckingham potential b parameter specifying the repulsive part of the Mie potential B parameter of Buckingham potential c prefactor of potential function C parameter of Buckingham potential or fitting parameter D dimer D0 prefactor of potential energy function Dself self-diffusion coefficient E ethanol f objective function g(r) radial distribution function g(z) cylindrical distribution function kB Boltzmann constant kij mixture parameter kmax maximum number of k-vectors K association constant L liquid or box length m attractive exponent M monomer M molar mass ML molarity n repulsive exponent N number of particles/atoms/molecules Nt computational complexity p pressure p0 pressure of an ideal gas at 1 molar concentration Pα,β pressure tensor components q partial charge r interaction site distance or distance in general ~r atom coordinates in space ri center of mass position of a molecule R ideal gas constant 5 Latin Letters - Part 2 of 2 s(t) time depending standard deviation S salt S solid t time T temperature u dispersion-energy parameter U potential energy V volume V 0 standard state volume V E excess volumina w mass fraction W water x mole fraction 6 Greek Letters α fitting parameter αsc soft-core scaling parameter β fitting parameter ∆G free energy ∆H enthalpy difference of complex formation ∆N window of particle numbers ∆S entropy difference of complex formation potential depth i association parameter 0 vacuum permittivity η shear viscosity γW water activity coefficient κT isothermal compressibility κi association parameter λ coupling parameter µ chemical potential Ω torsional angle Ωn number of observables φ potential energy φW fugacity coefficient of water ρ density σ atom radius σsc soft-core scaling parameter τ fitting parameter or time origin τp coupling constant of barostat τT coupling constant of thermostat ξ dimensionless constant 7 Subscripts a; b indices for interaction sites a and b alc. alcohol angle bond angle bending A; B indices for substances A and B b bound bond covalent bonded box simulation box c cut-off Ci concentration CH2 methylene group electrostatic electrostatic interaction fit fitted H hydrogen H2O water improper improper angle bending i; ii atom specifier j; jj atom specifier ij atom pair specifier m melting max maximum O oxygen PMF corrected potential of mean force raw uncorrected potential of mean force solv solvation torsion torsional angle bending u unbound W water 1 infinity 99 99% limit 8 Superscripts assoc associative c critical disp dispersive exp experimental inter nonbonded potential energy m molar res residual sat saturated seg segments sim simulation species mole fraction considering dissociated choline chloride 9 Abbreviations AAD absolute average deviation ATB automated topology builder AUA anistropic united atom CBMC configurational bias monte carlo ChCl choline chloride COM center of mass DES deep eutectic solvent DNA deoxyribonucleic acid EtOH ethanol exp. experimental GAFF general AMBER force field GCMC grand canonical Monte Carlo Gly glycerol HBA hydrogen bond acceptor HBD hydrogen bond donor IL ionic liquid liq liquid LJ Lennard-Jones MBAR multistate Bennett acceptance ratio MeOH methanol MC Monte Carlo MD molecular dynamics MP2 Møller-Plesset perturbation theory NADES natural deep eutectic solvents NH primary amino group NMR nuclear magnetic resonance NpT isobaric-isothermal ensemble NVT canonical ensemble OH hydroxyl group OPLS optimized potential for liquid simulations OPV organic photovoltaic PBI perylene bismide PC-SAFT perturbed-chain statistical associating fluid theory PME particle-mesh Ewald PMF potential of mean force