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The use of molecular simulation methods to reproduce and predict experimental information has become an excellent option for designing new experiments. The success of these methods depends on the force field used. Their quality depends on the interaction parameters and the target properties used to obtain them. In this work, we review and extend the methodology developed by our group to obtain interaction parameters of polar liquids. In addition, an automated workflow is developed to obtain new force field parameters and the analysis of physical properties. It is applied to small molecules of various functional groups in organic chemistry. The dielectric constant, surface tension, liquid density, self-diffusion coefficient and solubility of a solute in water are used as target properties. The simulations are developed in liquid phase, liquid–vapour and liquid–liquid equilibriums. The procedure can be extended to include other target properties and has the advantage that the parameters can be obtained in shorter times. It also opens the possibility of studying a wide range of problems of scientific and technological interest. [ABSTRACT FROM AUTHOR]

The implementation of the cyclic cluster model (CCM) for molecular mechanics is presented in the framework of the computational chemistry program deMon2k. Because the CCM is particularly well-suited for the description of periodic systems with defects, it can be used for periodic QM/MM approaches where the non-periodic QM part is treated as a defect in a periodic MM surrounding. To this end, we present here the explicit formulae for the evaluation of the Ewald sum and its first- and second-order derivatives as implemented in deMon2k. The outlined implementation was tested in molecular dynamics (MD) simulations and periodic structure optimization calculations. MD simulations of an argon system were carried out using the Nosé-Hoover chain (NHC) thermostat and the Martyna-Tobias-Klein (MTK) barostat to control the temperature and pressure of the system, respectively. For the validation of CCM structure optimization a set of molecular crystals were optimized using the Ewald method for the evaluation of the electrostatic interactions. Two optimization procedures for the determination of the atomic positions and CCM cell parameters were tested. Our results show that the simultaneous optimization of the atomic positions and cell parameters is most efficient. [ABSTRACT FROM AUTHOR]

Direct molecular dynamics simulations on interfaces at constant temperature are performed to obtain the liquid-vapor phase diagram of the two-dimensional soft primitive model, an equimolar mixture of equal size spheres carrying opposite charges. Constant temperature and pressure simulations are also carried out to check consistency with interface simulations results. In addition, an analysis of the cluster formation of mixtures of particles with charge asymmetry in the range 1:1 to 1:36 at low and high densities is performed. The number of free ions, when plotted as a function of the positive ion charge, Z+, has an oscillatory behavior and is independent of the density. The formation of aggregates is analyzed in terms of the attraction and repulsion between ions. [ABSTRACT FROM AUTHOR]

Liquid-vapor interfacial properties of square well chains are calculated. Surface tension, orthobaric densities, and vapor pressures are reported. Spinodal decomposition with a discontinuous molecular dynamics simulation program is used to obtain the results which are compared to previously published data for orthobaric densities and vapor pressures. In order to analyze the effect of the chain stiffness results for near tangent and overlapping linear chains as well as angled chains are obtained. Properties are calculated for linear chains of 2, 4, and 8 spheres for intramolecular distances of 0.97, 0.6, and 0.4 as well as for angled chains of 4 and 8 spheres and intramolecular distances of 0.4. The complete series of fully flexible near tangent square well chains is also studied (chains of 2, 4, 8, 12, and 16 particles with intramolecular distances of 0.97). The corresponding states principle applies to most of the systems considered. Critical properties values are reported as obtained from orthobaric densities, surface tensions, and vapor pressures. For the near tangent chains the critical temperatures increase with chain length but the rate of increment tends to zero for the longest chains considered. When the stiffness of the chain increases (intramolecular distance from 1 , 0.6, and 0.4) this saturation effect is either not present or reverses itself. The surface tension increases with the length of the chain while the width of the interface decreases. [ABSTRACT FROM AUTHOR]

Discrete perturbation theory (DPT) is a powerful tool to study systems interacting with potentials that are continuous but can be approximated by a piecewise continuous function composed of horizontal segments. The main goal of this work is to analyze the effect of several variables to improve the representation of continuous potentials in order to take advantage of DPT. The main DPT parameters chosen for the purpose are the starting location and size of the horizontal segments used to divide the full range of the potential and its maximum reach. We also studied the effect of having each segment aligned to the left, to the right, or centered on the continuous function. The properties selected to asses the success of this strategy are the orthobaric densities and their corresponding critical points. Critical parameters and orthobaric densities were evaluated by DPT for each of an ample set of variables and compared with their values calculated via discontinuous molecular dynamics. The best sets of DPT parameters are chosen so as to give equations of state that represent accurately the Lennard-Jones and Yukawa fluids. [ABSTRACT FROM AUTHOR]

Surface tensions and liquid-vapor orthobaric densities are calculated for a wide variety of vibrating square well dumbbells using discontinuous molecular dynamics simulations. The size of the vibration well, the elongation or bond distance of the two particles of the dumbbell, the asymmetry in size (and interaction range) of the two particles, and the depth of the interaction well are the variables whose effects are systematically evaluated in this work. Extensive molecular dynamics simulations were carried out and the orthobaric liquid-vapor densities are compared with those obtained previously by other authors using different methods of simulation for rigid and vibrating square well dumbbells. Surface tension values are reported for the first time for homonuclear and heteronuclear vibrating square well dumbbells as well as for all the simulated series. The molecular dynamics results of tangent homonuclear dumbbells are compared with those from Monte Carlo simulations also obtained in this work, as a way of checking the order of magnitude of the molecular dynamics results. The size of the vibration well is shown to have a small influence on the resulting properties. Decreasing elongation and the size of the second particle increase critical temperatures, liquid densities, and surface tensions. Moderate increases in the depth of the interaction well have the same effect. For larger asymmetries of the depth of the interaction well on the dumbbell particles, a strong association phenomenon is observed and the main effects are a maximum on the critical temperature for increasing well depth and a decrease in the surface tension. [ABSTRACT FROM AUTHOR]

The crystal formation of NaCl in water is studied by extensive molecular dynamics simulations. Ionic solutions at room temperature and various concentrations are studied using the SPC/E and TIP4P/2005 water models and seven force fields of NaCl. Most force fields of pure NaCl fail to reproduce the experimental density of the crystal, and in solution some favor dissociation at saturated conditions, while others favor crystal formation at low concentration. A new force field of NaCl is proposed, which reproduces the experimental phase diagram in the solid, liquid, and vapor regions. This force field overestimates the solubility of NaCl in water at saturation conditions when used with standard Lorentz–Berthelot combining rules for the ion-water pair potentials. It is shown that precipitation of ions is driven by the short range interaction between Cl–H pairs, a term which is generally missing in the simulation of ionic solutions. The effects of intramolecular flexibility of water on the solubility of NaCl ions are analyzed and is found to be small compared to rigid models. A flexible water model, extending the rigid SPC/E, is proposed, which incorporates Lennard-Jones interactions centered on the hydrogen atoms. This force field gives liquid-vapor coexisting densities and surface tensions in better agreement with experimental data than the rigid SPC/E model. The Cl–H, Na–O, and Cl–O pair distribution functions of the rigid and flexible models agree well with experiment. The predicted concentration dependence of the electric conductivity is in fair agreement with available experimental data. [ABSTRACT FROM AUTHOR]

The Wolf method for the calculation of electrostatic interactions is applied in a liquid phase and at the liquid-vapor interface of water and its results are compared with those from the Ewald sums method. Molecular dynamics simulations are performed to calculate the radial distribution functions at room temperature. The interface simulations are used to obtain the coexisting densities and surface tension along the coexistence curve. The water model is a flexible version of the extended simple point charge model. The Wolf method gives good structural results, fair coexistence densities, and poor surface tensions as compared with those obtained using the Ewald sums method. [ABSTRACT FROM AUTHOR]

We have performed molecular dynamics simulations of dense liquids using nonconformal and Gaussian potential models. We investigate the effect of the softness of the potential on the pressure tensor of liquids and dense fluids when the simulations are carried out using parallelepiped cells. The combination of periodic boundary conditions and small cross sectional areas induces an anisotropy in the diagonal components of the pressure tensor. This anisotropy results in an artificial stress in the system that has to be taken into account in simulations of explicit interfaces, where the artificial stress introduces errors in the computation of the surface tension. At high liquid densities the stress anisotropy exhibits an oscillatory dependence with the cross sectional area of the simulation box. We find that the softness of the potential has a dramatic effect on the amplitude of the oscillations, which can be significantly reduced in soft potentials, such as those used in the modeling of hydrocarbon liquids or polymers. [ABSTRACT FROM AUTHOR]

An operational procedure to obtain the intrinsic structure of liquid surfaces is applied here to a molecular dynamics simulation of water, with a model of point charges for the molecular interactions. The method, which had been recently proposed and used for simple fluids, is successfully extended to a molecular liquid with the complex bond structure of water. The elimination of the capillary wave fluctuations, in the intrinsic density and orientation profiles, gives a new overall view of the water surface, at the sharpest molecular level, and without the size-dependent broadening observed in the mean profiles. The molecules belonging to the outer liquid layer are clearly identified, and we find that only these molecules exhibit a clear preferential orientation to lie flat on the surface. Moreover, there is a strong correlation between the dipolar structure and the local curvatures of the intrinsic surface, so that at the extrusions of the intrinsic surface the molecular dipoles point preferentially toward the vapor side of the interface. Finally, we have found an intrinsic density layering structure, although the inner structure is strongly damped beyond the second layer. [ABSTRACT FROM AUTHOR]

We report molecular dynamics computer simulations of the surface tension and interfacial thickness of ionic liquid-vapor interfaces modeled with a soft core primitive model potential. We find that the surface tension shows an anomalous oscillatory behavior with interfacial area. This observation is discussed in terms of finite size effects introduced by the periodic boundary conditions employed in computer simulations. Otherwise we show that the thickness of the liquid-vapor interface increases with surface area as predicted by the capillary wave theory. Data on the surface tension of size-asymmetric ionic liquids are reported and compared with experimental data of molten salts. Our data suggest that the surface tensions of size-asymmetric ionic liquids do not follow a corresponding states law. [ABSTRACT FROM AUTHOR]

Monte Carlo and molecular dynamics methods have been used to investigate the influence of chemical association on the structure and thermodynamic properties of the liquid-vapor interface of dimerizing Lennard-Jones fluids. The molecular dynamics simulations have been carried out to obtain the surface tension for the so-called pseudo-mixture model of an associating fluid. The simulation data are also compared with the results of theoretical calculations, based on a density functional approach. [ABSTRACT FROM AUTHOR]

By means of extensive equilibrium molecular dynamics simulations we have investigated the behavior of the interfacial tension γ of two immiscible symmetrical Lennard-Jones fluids. This quantity is studied as function of reduced temperature T* = k[SUBB]T/∈ in the range 0.6 ⩽ T* ⩽ 3.0. We find that, unlike the monotonic decay obtained for the liquid-vapor interracial tension, for the liquid-liquid interface, γ(T) has a maximum at a specific temperature. We also investigate the effect that surfactantlike particles have on the thermodynamic as well as the structural properties of the liquid-liquid interface. It is found that γ decays monotonically as the concentration of the surfactantlike particles increases. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations have been performed to study the liquid–vapor equilibrium of water as a function of temperature. The orthobaric densities and the surface tension of water are reported for temperatures from 316 K until 573 K. The extended simple point charge (SPC/E) interaction potential for water molecules is used with full Ewald summation. The normal and tangential components of the pressure tensor were calculated and are presented at 328 K. The nature of the long-range contribution to the surface tension has been studied in detail. At 328 K the calculated surface tension is 66.0±3.0 mN m-1 in comparison with the experimental value of 67 mN m-1. The simulated surface tensions between 316 K and 573 K are in good agreement with experiment. The orthobaric densities are in better agreement with experimental values than those obtained from the Gibbs ensemble calculation for the SPC model of water. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

A cocrystal is a system with at least two components that can be solids or liquids at room conditions. The molecules in a cocrystal interact by hydrogen bonds producing a new crystal that has different properties than the original compounds and also improved physicochemical properties. In this work, we study by molecular dynamics simulations the formic acid/pyridine and the isonicotinamide/formamide cocrystals at 173 and 150 K, respectively. Except isonicotinamide that is a solid, the rest of molecules are liquids at ambient conditions. The OPLS/AA force field is used with two sets of parameters for the liquids: (a) the original set obtained by matching the simulations results to experimental density and heat of vaporization at room conditions and (b) new values that reproduce the dielectric constant, surface tension and density at different temperatures. The parameters of pyridine and formamide have been published previously by our group (Salas et al. in J Chem Theory Comput 11(2):683, 2015). The liquid formic acid is parameterized in this work using the same procedure. The new parameters improved the predictions of the original values. The isonicotinamide parameters are obtained from those of pyridine and formamide assuming they are transferable. The structure and stability of cocrystals are determined through the calculation of distances and angles of atoms that form hydrogen bonds in different molecules. The simulation results are compared with experimental measurements of X-ray diffraction, and a good agreement is found. Although the new parameters for the liquids give simulation results of thermodynamic properties in better agreement with experimental data at different temperatures and pressures, the cocrystal results are essentially the same as those obtained using the original values. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations are performed to develop new parameters for acetamide using a systematic procedure proposed by Salaset al., where the atomic charges were fitted to reproduce the experimental dielectric constant and the Lennard-Jones parameters to match the surface tension and density. The parameters for formamide recently calculated by Pérezet al.were used to obtain the new parameters of acetamide where atoms of the amine group and carbon kept the same intermolecular parameter values in both molecules. The parameters of the methyl group, taken as united atom, and the oxygen atom were fitted to reproduce the dielectric constant, surface tension and density at 358.15 K. The new set of parameters, based on the optimised potential for liquids simulations with all atoms, was able to predict results of the target properties as a function of temperature as a pure component and the dielectric constant and density of binary mixtures with water and formamide as a function of acetamide concentration at 298.15 K. The polymer chains formed by hydrogen bond interactions were analysed to understand the maximum of dielectric constant in acetamide–water mixtures. [ABSTRACT FROM PUBLISHER]

The static dielectric constant atroom temperature and the temperatureof maximum density are used as target properties to develop, by moleculardynamics simulations, the TIP4P/ε force field of water. TheTIP4P parameters are used as a starting point. The key step, to determinesimultaneously both properties, is to perform simulations at 240 Kwhere a molecular dipole moment of minimum density is found. The minimumis shifted to larger values of μ as the distance between theoxygen atom and site M, lOM, decreases.First, the parameters that define the dipole moment are adjusted toreproduce the experimental dielectric constant and then the Lennard-Jonesparameters are varied to match the temperature of maximum density.The minimum on density at 240 K allows understanding why reportedTIP4P models fail to reproduce the temperature of maximum density,the dielectric constant, or both properties. The new model reproducessome of the thermodynamic and transport anomalies of water. Additionally,the dielectric constant, thermodynamics, and dynamical and structuralproperties at different temperatures and pressures are in excellentagreement with experimental data. The computational cost of the newmodel is the same as that of the TIP4P. [ABSTRACT FROM AUTHOR]

Abstract: Molecular dynamics simulations are performed to analyze the solubility of NaCl and NaI salts from dilute to saturated aqueous solutions. The TIP4Q water model, which reproduces the experimental dielectric constant, is used with ions where the interaction parameters were obtained to reproduce some experimental properties of the crystal and in solution. It is shown the models fail to describe the correct behavior of ions at high concentrations when the Lorentz–Berthelot mixing rules for the cross interactions are used. The hydration of ions at low concentrations and the precipitation of ions at saturated solutions are observed after adding a screening short range function on electrostatic interactions on pairs where the short range repulsion was not taken into account. [Copyright &y& Elsevier]

Abstract: The Liouville operator approach is employed to derive a new measure-preserving geometric integrator for molecular dynamics simulations in the isothermal–isobaric (NPT) ensemble. Recently, we introduced such a scheme for NPT simulations with isotropic cell fluctuations in the absence of holonomic constraints [M.E. Tuckerman et al., J. Phys. A 39 (2006) 5629]. Here, we extend this approach to include both fully flexible cell fluctuations and holonomic constraints via a new and simpler formulation of the ROLL algorithm of Martyna et al. [Martyna et al., Mol. Phys. 87 (1996) 1117]. The new algorithm improves on earlier schemes in that it possesses a simpler mathematical structure and rigorously preserves the phase space metric. The new algorithm is illustrated on two example systems, ice and liquid n-decane. [Copyright &y& Elsevier]

We report molecular dynamics simulations of the coexistence and interfacial properties of ionic liquids as a function of cation/anion, (z+:z-) = (2:-1), (4:-1), charge asymmetry. Our results correct previous computations of the coexistence curve of (2:-1) charge asymmetric systems, obtained via the fine-lattice discretisation method. In agreement with previous computations we report a reduction in the critical temperature and an increase in the critical density with charge asymmetry. We have quantified the interphase potential resulting from the charge asymmetry, by analysing the charge density across the liquid-vapour interface. We show that the Debye-Huckel theory predicts reasonably well the magnitude and temperature dependence of the interphase potential for moderate charge asymmetries (2:-1) but it underestimates, by about 50, the electrostatic potential of ionic liquids with high charge asymmetries (4:-1). [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations were performed at constant temperature to obtain the surface tension of hydrocarbon chains at the liquid-vapour interface. The Ewald sum was used to calculate the dispersion forces of the Lennard-Jones potential to take into account the full interaction. The NERD and TraPPE_UA flexible force field models were used to simulate molecules from ethane to hexadecane along the coexistence curve. The simulation results for the TraPPE_UA model are in good agreement with experimental data, whereas the NERD model predicts slightly higher values. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations of Lennard-Jones binary mixtures were performed to obtain phase equilibria and thermodynamic properties for the liquid-vapour interface. The dispersion interactions were handled using the lattice sum method where the full interaction is obtained and there is no requirement for any long range correction to the properties. The application of the method using the Lorentz-Berthelot combining rule for unlike interactions is discussed. The coexisting densities, adsorption of molecules at the interface and surface tension are the main results of this work. Coexisting properties were compared with Gibbs ensemble Monte Carlo results and with those of the grand canonical Monte Carlo method combined with the histogram reweighting technique, and good agreement was found. The lattice sum method results were compared with those of the spherically truncated and shifted potential to analyse the truncation effect. The adsorption of molecules at the interface and surface tension increase with interaction. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations of fluids of molecules with extended dipoles were performed, with increasing distance between point charges but with a constant dipole moment, to obtain thermodynamic properties. It was found that the effect of varying the dipole length on the dielectric constant in the liquid phase, the vapor-liquid equilibria, and the surface tension was negligible for dipolar lengths up to half the particle diameter. By comparing thermodynamic properties of the predictions of the extended dipole model with those for the Stockmayer fluid of point dipoles, it was found that extended dipoles are equivalent to point dipoles over a wide range of dipole lengths, and not only near the point dipole limit, when the separation length is very small compared with the mean distance between particles. Finally, phase equilibrium results of extended dipoles were compared to those obtained from the discrete perturbation theory for a Stockmayer potential. [ABSTRACT FROM AUTHOR]

The extraction of nitrogen and sulfur compounds from gasoline and diesel, using ionic liquids, is conducted through liquid-liquid molecular dynamics simulations. The novel united atom parameters of pyridine, benzene and thiophene which possess a constant dipole moment successfully reproduce the experimental dielectric constant and solubility in water. These molecular parameters are transferred to simulate toluene and dibenzothiophene. Regarding polar liquids, the coexisting densities and surface tension as functions of temperature align excellently with experimental data. The liquid density and surface tension of modeled diesel and gasoline also match experimental data well although the viscosity is underestimated. Ionic liquids comprise positive ions of imidazolium, pyrrolidinium, pyridinium and trimethyl ammonium varying in hydrocarbon chain length. The anion is bis(trifluoromethylsulfonyl)imide. It has been discovered that the new parameters significantly enhance the extraction of nitrogen and sulfur compounds from hydrocarbon mixtures compared to simulation results from TraPPE-UA force field where the molecules possess zero molecular dipole moment. The extraction efficiency of ionic liquids aligns excellently with experimental results at room temperature. • Extraction of N- and S-compounds is an important issue in industry, since they are related with health and economics. • Molecular dynamics is an important methodology to study extraction and the force field is the most important matter. • Many force fields available are not capable to reproduce miscibility and therefore they have to be re-parameterized. • Polarization of ring-like molecules in the force field is an essential issue to reproduce extraction of N- and S-compounds. [ABSTRACT FROM AUTHOR]

Molecular dynamics (MD) simulations are performed to study benzene extraction from dodecane using polar and ionic liquids solvents in a liquid/liquid equilibrium. Solvents that contain a ring structure with one and two nitrogen atoms are analyzed. Polar solvents are pyrrolidone, N-methylpyrrolidone (NMP) and pyridine while ionic solvents are 1-butyl-1-methylpirrolidonium dicyanamide [BMpyr][DCA], 1-butyl-3-methylimidazolium hexafluorophosphate [BMIM][PF6] and 1-ethyl-3-methylimidazolium hexafluorophosphate [EMIM][PF6]. Results, based on density profiles analysis, show that all polar solvents studied in this work are able to absorb benzene. The [BMpyr][DCA] extracts much more benzene from the non-polar liquid than [BMIM][PF6] and [EMIM][PF6]. The [BMpyr][DCA] has slightly less affinity for benzene than the organic solvents. The partitioning of benzene between the coexisting phases was calculated. [ABSTRACT FROM AUTHOR]

Understanding the role that molecular interactions play on physicochemical properties of ionic solutions is of fundamental importance to design novel electrolytes used in devices to storage energy, such as lithium ion batteries. Several salts containing propylene carbonate are studied. The propylene carbonate and TFSI− anion force fields were previously parametrized by our group. Those of lithium (Li+), hexafluorophosphate (PF 6 −) and tetrafluoroborate (BF 4 −) are developed in this work with ions carrying a charge of ± 1 e. The calculated properties are liquid density, dielectric constant, self-diffusion coefficient and viscosity. The results are in excellent agreement with experimental data at different salt concentrations and temperatures. The dielectric constant of PC/LiBF 4 is greater than that of the other two electrolytes because the ions form large clusters and the solvent molecules behave as a pure liquid. The predictions with the new parameters improve those from a polarizable model for PC/LiTFSI and those from a machine learning force field for PC/LiPF 6. • The [Li+], [PF6-] and [BF4-] force field parameters are developed in this work carrying charges of ±1e. • The dielectric constant of electrolytes at the same salt concentration decreases with molecular size of anions. • Calculated properties are in excellent agreement with experimental data at different salt concentrations and temperatures. • The results show that the used parametrization procedure is helpful to study new electrolytes for lithium-ion batteries. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations for liquid acetone, the pure component and mixed with water, are performed to analyze the effect that the dielectric constant has on the solubility. The CGenFF and OPLS/AA force fields, together with two TraPPE_UA models, are used to simulate acetone, while the TIP4P/∊ model is applied for water. The calculated dielectric constant of acetone models at room conditions follows a linear relation with their molecular dipole moment, allowing us to understand, in simulations, the miscibility problem of acetone in water. The experimental liquid and liquid-vapor properties as the pure component are reasonably well reproduced with those force fields. The TraPPE_UA04 and TraPPE_UA05 models predict dielectric constants for acetone in the liquid phase of 9 and 12, respectively. The experimental value is 21. The values obtained with the OPLS/AA and CGenFF models are 15 and 23, respectively. All of the models used, except CGenFF, give inhomogeneous mixtures at both low and moderate concentrations of acetone. [ABSTRACT FROM AUTHOR]