Derivation of an Optimized Potential Model for Phase Equilibria (OPPE) for Sulfides and Thiols

TAMie Force Field for Alkanethiols: Multifidelity Gaussian Processes for Dealing with Scarce Experimental Data

This study extends the transferable anisotropic Mie potential (TAMie) to alkanethiols. The force field parameters are optimized by using an analytic equation of state as a surrogate model. Given the lack of experimental density data at elevated temperatures where Monte Carlo simulations have high statistical precision, the equation of state is supplemented by a linear multifidelity Gaussian process approach to bridge the temperature gap. Force field parameters are adjusted by minimizing squared deviations of calculated vapor pressures and liquid densities from experimental data of 1-propanethiol, 1-butanethiol and 1-pentanethiol leading to small mean absolute relative deviations in liquid densities and vapor pressures. The force field is transferable to higher 1-thiols, as shown for 1-hexanethiol and 1-octanethiol. Individual parameter sets are provided for methanethiol and ethanethiol. The shear viscosity of pure substances is predicted in fair agreement with experimental data, considering that it is not included in the parametrization. Further, the phase behavior of binary mixtures of alkanethiols with alkanes is studied, and predictions of the TAMie model are found in excellent agreement with experimental data.

A Kirkwood-Buff derived force field for thiols, sulfides, and disulfides

A force field has been developed for molecular simulations of methanethiol, dimethyl sulfide, and dimethyl disulfide mixtures. The force field specifically attempts to balance the solvation and self-association of these solutes in solution mixtures with methanol. The force field is based on the Kirkwood-Buff (KB) theory of solutions and is parametrized using the KB integrals obtained from the experimental activity coefficients for the solution mixtures. The transferability of the force field was tested and confirmed by the accurate prediction of the activity coefficients for methanethiol/dimethyl sulfide solutions, which were not used in the initial parametrization of the force fields. The ideality of this latter solution is excellently reproduced. The applicability of the force field to simulations in water was corroborated with a reasonably accurate prediction for the low solubility of dimethyl sulfide in water. The aggregation of methanol molecules at low methanol mole fractions displayed by all the mixtures is reproduced and further analyzed.

Effect of partial charge parametrization on the fluid phase behavior of hydrogen sulfide

The effect of partial charge parametrization on the fluid phase behavior of hydrogen sulfide is investigated with grand canonical histogram reweighting Monte Carlo simulations. Four potential models, based on a Lennard-Jones + point charge functional form, are developed. It is shown that Lennard-Jones parameters can be tuned such that partial charges for the sulfur atom in the range -0.40 < q(s) < -0.252 will lead to an accurate reproduction of experimental vapor-liquid equilibria. Each of the parameter sets developed in this work are used to predict the pressure composition behavior H2S-n-pentane at 377.6 K. While the mixture calculation provides a means of reducing the number of candidate parameter sets, multiple parameter sets were found to yield an excellent reproduction of both the pure component and mixture phase behavior.

An Anisotropic United Atoms (AUA) Potential for Thiophenes

The optimization of the parameters of the Lennard-Jones (LJ) 12-6 potential of the sulfur atom in thiophene has allowed the AUA 4 potential to be successfully extended to alkyl and polythiophenes. Monte Carlo Gibbs ensemble and grand canonical simulations combined with histogram reweighting techniques have been performed to investigate the resulting phase equilibrium and the critical region of different molecules of this family in order to test the proposed potential. Excellent agreement with experimental densities, enthalpies of vaporization, and saturation pressures has been obtained in most of the cases. In particular, the critical point of our model for thiophene has been located with a statistical precision of less than 0.1% and is within 1% of the experimental value. The calculation of the critical points has been made through a recently implemented methodology based on the calculation of a fourth order cumulant (Binder parameter) combined with the use of finite size scaling methods, allowing the critical points to be located in a straightforward and accurate way.

Optimized molecular force field for sulfur hexafluoride simulations

An optimized molecular force field for sulfur hexafluoride (SF6) simulations is presented in this work. The new force field for SF6 contains two parts: a Lennard-Jones potential that deals with F-F intermolecular interactions and the second term dealing with the intramolecular forces. In this second part the flexibility of the molecule is explicitly considered by 6 harmonic stretch terms, modeling the S-F chemical bonds, and 12 harmonic bending terms, modeling the F-S-F angular deformations. The parameters of the new force field have been obtained by a multivariable optimization procedure, whose main feature is the simultaneous fitting of all force field parameters, using as reference data several equilibrium properties (vapor pressure, saturated liquid density, and surface tension) and shear viscosity. The new force field clearly improves the description of the phase envelope and the rest of the properties as compared to previous simulations for a rigid model for the same molecule [A. Olivet et al., J. Chem. Phys. 123, 194508 (2005)]. Results for the optimized force field concerning the vapor-liquid coexistence curve, several thermodynamics states at the homogeneous gas and liquid region, and transport coefficients of SF6 are in good agreement with available experimental data.

Anisotropic United Atom Model Including the Electrostatic Interactions of Benzene

An optimization including electrostatic interactions has been performed for the parameters of an anisotropic united atoms intermolecular potential for benzene for thermodynamic and transport property prediction using Gibbs ensemble, isothermal-isobaric (NPT) Monte Carlo, and molecular dynamic simulations. The optimization procedure is based on the minimization of a dimensionless error criterion incorporating various thermodynamic data (saturation pressure, vaporization enthalpy, and liquid density) at ambient conditions and at 350 and 450 K. A comprehensive comparison of the new model is given with other intermolecular potentials taken from the literature. Overall thermodynamic, structural, reorientational, and translational dynamic properties of our optimized model are in very good agreement with experimental data. The new model also provides a good representation of the liquid structure, as revealed by three-dimensional spatial density functions and carbon-carbon radial distribution function. Shear viscosity variations with temperature and pressure are very well reproduced, revealing a significant improvement with respect to nonpolar models.

Transport coefficients and dynamic properties of hydrogen sulfide from molecular simulation

Molecular-dynamics simulation results on thermodynamic and transport properties of pure H2S under conditions of practical interest are presented. Our data are in very good quantitative agreement with the scarce experimental data and estimates on thermophysical properties of this substance. Our results serve as a test of the validity of the intermolecular potential used in the simulations as well as the consistency of the existing data in the studied range. New simulation data on thermal conductivity at low temperature as well as in supercritical states are also reported. Furthermore, we present a comparative analysis between the local order in the liquid phase of pure hydrogen sulfide and water, due to the molecular analogies between both substances, and its relation with the formation of H=S bonds. Our results indicate that under the same corresponding thermodynamic states, H2S is a much less structured substance, with a first solvation shell with a dodecahedral order instead of the tetrahedral order observed in water.

Dynamical and structural properties of benzene in supercritical water

We have employed an anisotropic united atom model of benzene (R. O. Contreras, Ph.D. thesis, Universitat Rovira i Virgili 2002) that reproduces the quadrupolar moment of this molecule through the inclusion of seven point charges. We show that this kind of interaction is required to reproduce the solvation of these molecules in supercritical water. We have computed self-diffusion coefficient and Maxwell-Stefan coefficients as well as the shear viscosity for the mixture water-benzene at supercritical conditions. A strong density and composition dependence of these properties is observed. In addition, our simulations are in qualitative agreement with the experimental evidence that, at medium densities (0.6 g/cm(3) and 673 K), almost half of the benzene molecules have one hydrogen bond with water molecules. We also observe that these bonds are longer lived than the corresponding hydrogen bonds between water molecules. Similarly, we obtain an important reduction of the dielectric constant of the mixture with the increment of the amount of benzene molecules at medium and high densities.

Transferable Potentials for Phase Equilibria. 8. United-Atom Description for Thiols, Sulfides, Disulfides, and Thiophene

An extension of the transferable potentials for phase equilibria united-atom (TraPPE-UA) force field to thiol, sulfide, and disulfide functionalities and thiophene is presented. In the TraPPE-UA force field, nonbonded interactions are governed by a Lennard-Jones plus fixed point charge functional form. Partial charges are determined through a CHELPG analysis of electrostatic potential energy surfaces derived from ab initio calculations at the HF/6-31g+(d,p) level. The Lennard-Jones well depth and size parameters for four new interaction sites, S (thiols), S(sulfides), S(disulfides), and S(thiophene), were determined by fitting simulation data to pure-component vapor-equilibrium data for methanethiol, dimethyl sulfide, dimethyl disulfide, and thiophene, respectively. Configurational-bias Monte Carlo simulations in the grand canonical ensemble combined with histogram-reweighting methods were used to calculate the vapor-liquid coexistence curves for methanethiol, ethanethiol, 2-methyl-1-propanethiol, 2-methyl-2-propanethiol, 2-butanethiol, pentanethiol, octanethiol, dimethyl sulfide, diethyl sulfide, ethylmethyl sulfide, dimethyl disulfide, diethyl disulfide, and thiophene. Excellent agreement with experiment is achieved, with unsigned errors of less than 1% for saturated liquid densities and less than 3% for critical temperatures. The normal boiling points were predicted to within 1% of experiment in most cases, although for certain molecules (pentanethiol) deviations as large as 5% were found. Additional calculations were performed to determine the pressure-composition behavior of ethanethiol+n-butane at 373.15 K and the temperature-composition behavior of 1-propanethiol+n-hexane at 1.01 bar. In each case, a good reproduction of experimental vapor-liquid equilibrium separation factors is achieved; both of the coexistence curves are somewhat shifted because of overprediction of the pure-component vapor pressures.

Molecular Modeling of Phase Behavior and Microstructure of Acetone−Chloroform−Methanol Binary Mixtures

Force fields based on a Lennard-Jones (LJ) 12-6 plus point charge functional form are developed for acetone and chloroform specifically to reproduce the minimum pressure azeotropy found experimentally in this system. Point charges are determined from a CHELPG population analysis performed on an acetone-chloroform dimer. The required electrostatic surface for this dimer is determined from ab initio calculations performed with MP2 theory and the 6-31g++(3df,3pd) basis set. LJ parameters are then optimized such that the liquid-vapor coexistence curve, critical parameters, and vapor pressures are well reproduced by simulation. Histogram-reweighting Monte Carlo simulations in the grand canonical ensemble are used to determine the phase diagrams for the binary mixtures acetone-chloroform, acetone-methanol, and chloroform-methanol. The force fields developed in this work reproduce the minimum pressure azeotrope in the acetone-chloroform mixture found in experiment. The predicted azeotropic composition of x(CHCl3) = 0.77 is in fair agreement with the experimental value of x(CHCl3)expt = 0.64. The new force fields were also found to provide improved predictions of the pressure-composition behavior of acetone-methanol and chloroform-methanol when compared to other force fields commonly used for vapor-liquid equilibria calculations. NPT simulations were conducted at 300 K and 1 bar for equimolar mixtures of acetone-chloroform, acetone-methanol, and methanol-chloroform. Analysis of the microstructure reveals significant hydrogen bonding occurring between acetone and chloroform. Limited interspecies hydrogen bonding was found in the acetone-methanol or chloroform-methanol mixtures.

CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations

A first-generation fluctuating charge (FQ) force field to be ultimately applied for protein simulations is presented. The electrostatic model parameters, the atomic hardnesses, and electronegativities, are parameterized by fitting to DFT-based charge responses of small molecules perturbed by a dipolar probe mimicking a water dipole. The nonbonded parameters for atoms based on the CHARMM atom-typing scheme are determined via simultaneously optimizing vacuum water-solute geometries and energies (for a set of small organic molecules) and condensed phase properties (densities and vaporization enthalpies) for pure bulk liquids. Vacuum solute-water geometries, specifically hydrogen bond distances, are fit to 0.19 A r.m.s. error, while dimerization energies are fit to 0.98 kcal/mol r.m.s. error. Properties of the liquids studied include bulk liquid structure and polarization. The FQ model does indeed show a condensed phase effect in the shifting of molecular dipole moments to higher values relative to the gas phase. The FQ liquids also appear to be more strongly associated, in the case of hydrogen bonding liquids, due to the enhanced dipolar interactions as evidenced by shifts toward lower energies in pair energy distributions. We present results from a short simulation of NMA in bulk TIP4P-FQ water as a step towards simulating solvated peptide/protein systems. As expected, there is a nontrivial dipole moment enhancement of the NMA (although the quantitative accuracy is difficult to assess). Furthermore, the distribution of dipole moments of water molecules in the vicinity of the solutes is shifted towards larger values by 0.1-0.2 Debye in keeping with previously reported work.