Anisotropic United Atom Research Articles

Self diffusion, viscosity, and surface tension estimations of amines by using AUA4 force field

Accurate and efficient molecular dynamic simulation of amine functional group is crucial for designing improved carbon dioxide absorption processes, as thermodynamic and transport properties can be concurrently calculated with molecular-level insight. The exploration of these properties has been limited, and all-atom force fields have struggled to cope with the dynamic and equilibrium characteristics of amines, especially monoethanolamine, which possess and exceptionally low self-diffusivity. In response to this situation, we propose using an anisotropic united atom (AUA4) force field, which strikes a balance between precision and performance allowing to predict the key transport and equilibrium properties involved in mass transfer units. A total of 7 amines were included in this study. Among the main results observed in this work, there was excellent recreation of density. The surface tension evidenced performance similar to other transferable force fields with a general positive deviation of 20%. Regarding transport properties, methylamine and linear alkylamines shows moderate uniform deviations. Trimethylamne, being the only one tertiary amine, exhibited higher deviations than the other amines. In contrast, excellent results were obtained for ET-DI, while significant deviations were found for MEA. Nevertheless, in light of previous studies on this alkanolamine, these deviations appear promising. Finally, we were able to achieve the best predictions of the currently available force fields for ethanolamine by increasing its torsional barriers. This allowed us to accurately reproduce its low self-diffusion and viscosity while maintaining its main structural features.

Guaiacol and its mixtures: New data and predictive models part 1: Phase equilibrium

In the present work, new experimental data of guaiacol mixture with methane were investigated. The results have been evaluated using several thermodynamic approaches. Predictive calculations using the GC-PPC-SAFT (Group Contribution-Polar Perturbed Chain- Statistical Associating Fluid Theory) equation of state and Molecular Simulation using the Anisotropic United Atoms (AUA4) force field were performed. Data from literature for the binary systems of guaiacol with CO2, ethanol, octanol, acetone, butyl acetate and water were used to evaluate the thermodynamic models. The effect of the association scheme is discussed at length. Predictive phase equilibrium for systems containing small and toxic compounds, such as hydrogen, carbon monoxide, hydrogen sulfide and ammonia were also performed. In GC-PPC-SAFT, two configurations of associative sites for guaiacol were considered. The predicted values showed to be consistent with new experimental data. The effect of conformational structure of guaiacol on phase equilibria was detected.

Physical Absorption of Green House Gases in Amines: The Influence of Functionality, Structure, and Cross-Interactions.

Monte Carlo simulations were performed in the isothermal-isobaric ensemble (NPT) to calculate the Henry constants of methane (CH4), nitrous oxide (N2O), and carbon dioxide (CO2) in pure H2O, amines, and alkanolamines using the classical Lorentz-Berthelot combining rules (L-B). The Henry constants of N2O and CO2 in water are highly overestimated and motivated us to propose a new set of unlike interactions. Contrarily, the Henry constant of N2O in MEA is underestimated by around 40%, and again, a new reoptimized cross unlike parameter is able to reproduce the constant to within 10%. An analysis is given of the relationship between the physical absorption of these gases and the chemical structure or functionality of 12 molecules including amines and alkanolamines using the anisotropic united atom intermolecular potential (AUA4). Finally, the solubility of N2O in an aqueous solution of monoethanolamine (MEA) at 30% (wt) was also studied. A Henry constant within 7% of the experimental value was found by using the reoptimized parameters along with L-B to account for the MEA + H2O unlike interactions. This very good agreement without additional adjustments for the MEA + H2O system may be attributed to the good excess properties predictions found in previous works for the binary mixture (MEA + H2O). However, further work, including additional alkanolamines in aqueous solutions at several concentrations, is required to verify this particular point.

Transferable Anisotropic United-Atom Force Field Based on the Mie Potential for Phase Equilibrium Calculations: n-Alkanes and n-Olefins.

A new transferable force field parametrization for n-alkanes and n-olefins is proposed in this work. A united-atom approach is taken, where hydrogen atoms are lumped with neighboring atoms to single interaction sites. A comprehensive study is conducted for alkanes, optimizing van der Waals force field parameters in 6 dimensions. A Mie n-6 potential is considered for the van der Waals interaction, where for n-alkanes we simultaneously optimize the energy parameters ϵCH3 and ϵCH2 as well as the size parameters σCH3 and σCH2 of the CH3(sp(3)) and CH2(sp(3)) groups. Further, the repulsive exponent n of the Mie n-6 potential is varied. Moreover, we investigate the bond length toward the terminal CH3 group as a degree of freedom. According to the AUA (anisotropic united-atom) force field, the bond length between the terminal CH3 group and the neighboring interaction site should be increased by Δl compared with the carbon-carbon distance in order to better account for the hydrogen atoms. The parameter Δl is considered as a degree of freedom. The intramolecular force field parametrization is taken from existing force fields. A single objective function for the optimization is defined as squared relative deviations in vapor pressure and in liquid density of propane, n-butane, n-hexane, and n-octane. A similar study is also done for olefins, where the objective function includes 1-butene, 1-hexene, 1-octene, cis-2-pentene, and trans-2-pentene. Molecular simulations are performed in the grand canonical ensemble with transition-matrix sampling where the phase equilibrium properties are obtained with the histogram reweighting technique. The 6-dimensional optimization of strongly correlated parameters is possible, because the analytic PC-SAFT equation of state is used to locally correlate simulation results. The procedure is iterative but leads to very efficient convergence. An implementation is proposed, where the converged result is not affected (disturbed) by the analytic equation of state. The resulting transferable anisotropic Mie-potential (TAMie) force field shows average relative deviations in vapor pressure of 1.1% and in liquid density of 0.9% for alkanes, and 2% and 1.5% for olefins, respectively, in a wide range of (reduced) temperature, Tr = 0.55-0.97. For substances that were not members of the objective function, the TAMie force field enables predictions of phase equilibrium properties with good accuracy.

Conservative and dissipative force field for simulation of coarse-grained alkane molecules: A bottom-up approach

We apply operational procedures available in the literature to the construction of coarse-grained conservative and friction forces for use in dissipative particle dynamics (DPD) simulations. The full procedure rely on a bottom-up approach: large molecular dynamics trajectories of n-pentane and n-decane modeled with an anisotropic united atom model serve as input for the force field generation. As a consequence, the coarse-grained model is expected to reproduce at least semi-quantitatively structural and dynamical properties of the underlying atomistic model. Two different coarse-graining levels are studied, corresponding to five and ten carbon atoms per DPD bead. The influence of the coarse-graining level on the generated force fields contributions, namely, the conservative and the friction part, is discussed. It is shown that the coarse-grained model of n-pentane correctly reproduces self-diffusion and viscosity coefficients of real n-pentane, while the fully coarse-grained model for n-decane at ambient temperature over-predicts diffusion by a factor of 2. However, when the n-pentane coarse-grained model is used as a building block for larger molecule (e.g., n-decane as a two blobs model), a much better agreement with experimental data is obtained, suggesting that the force field constructed is transferable to large macro-molecular systems.

Equilibrium and Transport Properties of Primary, Secondary and Tertiary Amines by Molecular Simulation

Using molecular simulation techniques such as Monte Carlo (MC) and molecular dynamics (MD), we present several simulation results of thermodynamic and transport properties for primary, secondary and tertiary amines. These calculations are based on a recently proposed force field for amines that follows the Anisotropic United Atom approach (AUA). Different amine molecules have been studied, including <i>n<i/>-ButylAmine, di-<i>n<i/>-ButylAmine, tri-<i>n<i/>-ButylAmine and 1,4-ButaneDiAmine for primary, secondary, tertiary and multi-functional amines respectively. For the transport properties, we have calculated the viscosity coefficients as a function of temperature using the isothermal-isobaric (NPT) ensemble. In the case of the pure components, we have investigated different thermodynamic properties using NVT Gibbs ensemble simulations such as liquid-vapor phase equilibrium diagrams, vaporization enthalpies, vapor pressures, normal boiling points, critical temperatures and critical densities. We have also calculated the excess enthalpies for water-<i>n<i/>-ButylAmine and <i>n<i/>-heptane-<i>n<i/>-ButylAmine mixtures using Monte Carlo simulations in the NPT ensemble. In addition, we present the calculation of liquid-vapor surface tensions of <i>n<i/>-ButylAmine using a two-phase NVT simulation as well as the radial distribution functions. Finally, we have investigated the physical Henry constants of nitrous oxide (N<sub>2<sub/>O) and nitrogen (N<sub>2<sub/>) in an aqueous solutions of <i>n<i/>-ButylAmine. In general, we found a good agreement between the available experimental information and our simulation results for all the studied properties, ratifying the predictive capability of the AUA force field for amines.

A molecular simulation study of aqueous solutions of amines and alkanolamines: mixture properties and structural analysis

The behaviour of different aqueous solutions of amines and alkanolamines has been studied in terms of the intermolecular radial distribution function using the anisotropic united atom force field for amines and alkanolamines and the TIP4P/2005 force field for water. We have also calculated the excess volumes and mixture densities at several concentrations, comparing in all cases with available experimental information. Different pair distribution functions have been qualitatively analysed for several molecules, namely methylamine, ethylenediamine, diethylenetriamine, monoethanolamine, diethanolamine and methyldiethanolamine. A qualitative study of the intramolecular structure of multifunctional amines in aqueous solutions has also been included. In general, we have found that amines at all concentrations prefer to be surrounded by water molecules rather than by amine molecules. Although the force field overestimates the excess volumes of alkanolamines in aqueous solutions, their sign and non-monotonic behaviour are well represented for all the studied systems. Finally, a very good numerical agreement has been found for the predictions of the mixture densities.

Overview of MedeA®-GIBBS capabilities for thermodynamic property calculation and VLE behaviour description of pure compounds and mixtures: application to polar compounds generated from ligno-cellulosic biomass

This paper illustrates the use of Monte Carlo (MC) simulations to study a wide range of systems of interest for biomass conversion into high-added value chemicals and biofuels. The interest is focused on the use of molecular simulation to predict the physical–chemical properties of pure compounds and mixtures at a wide range of temperature and pressure conditions, as well as to provide insight on the mechanisms involved and the molecular characteristics that are related to the macroscopic behaviour of such complex systems. A systematic scaling study has been performed in which our implementation of the MC method is scaled well up to 4 to 12 processors. We have automated tasks such as the implementation of default MC frequencies, statistical parameters, convergence analysis and determination of statistical averages. On this basis, we could determine the equilibrium properties for approximately 100 compounds (alcohols, ethers, ketones, aldehydes, esters, glycols) with the TraPPE-UA and the anisotropic united atoms (AUA) forcefields. TraPPE-UA provides a good prediction of liquid density, and AUA provides a better determination of saturation pressures and normal boiling temperature. Liquid–vapour phase diagrams of binary mixtures are also provided to illustrate the predictive capability of MC simulations. Viewing graphs or configurations allows to validate convergence analysis and to understand the hydrogen-bonded systems.

Chemical Potential of Benzene Fluid from Monte Carlo Simulation with Anisotropic United Atom Model

The profile of chemical potential of benzene fluid has been investigated using Anisotropic United Atom (AUA) model. A Monte Carlo simulation in canonical ensemble was done to obtain the isotherm of benzene fluid, from which the excess part of chemical potential was calculated. A surge of potential energy is observed during the simulation at high temperature which is related to the gas-liquid phase transition. The isotherm profile indicates the tendency of benzene to condensate due to the strong attractive interaction. The results show that the chemical potential of benzene rapidly deviates from its ideal gas counterpart even at low density.

Factors influencing properties of interfacial regions in semicrystalline polyethylene: A molecular dynamics simulation study

Molecular dynamics simulations have been used to prepare semicrystalline samples of linear polyethylene (PE) using the anisotropic united atom (AUA4) model. The initial configurations of the simulations were obtained by controlled melting of the pure crystalline system and a unique re-connection method between chain segments in the intercrystalline regions. Systems containing two crystalline slabs and two large intercrystalline regions are built with different defects, introduced to mimic the structure of real PE systems, namely: bridging chains connecting two different crystalline slabs, re-entrant chains emerging and re-entering into the same crystalline slab, and free chains. We observe large structural differences between the different systems. We show that average and local density depend on defect types which in turn affect the dynamical properties. This explicit simulation of a crystalline–amorphous interfacial region thus gives a possible picture of intercrystalline regions that can serve to understand and predict penetrant gases transport in such materials.

A Transferable Force Field for Primary, Secondary, and Tertiary Alkanolamines.

Due to the importance of alkanolamines as solvents in several industrial processes and the absence of a dedicated transferable force field for them, we have developed an anisotropic united-atom (AUA4) force field for primary, secondary, and tertiary alkanolamines. In addition to correctly reproducing the experimental densities, additional properties for six different molecules have been verified at different temperatures including vaporization enthalpies, vapor pressures, normal boiling points, critical temperatures, and critical densities. A qualitative analysis of the radial distribution function of pure monoethanolamine has also been carried out. Furthermore, the viscosity coefficients were also calculated as a function of temperature and found to be in good agreement with experimental data. Finally, and perhaps most strikingly, the prediction of the excess enthalpies of alkanolamines in aqueous solutions has been found to be in excellent qualitative agreement with experimental data.

Transferable Force Field for Equilibrium and Transport Properties in Linear and Branched Monofunctional and Multifunctional Amines. II. Secondary and Tertiary Amines

Following the same philosophy of our previous force field for primary amines (J. Phys. Chem. B2011, 115, 14617), we present an extension for secondary and tertiary amines using the anisotropic united atom (AUA4) approach. The force field is developed to predict the phase equilibrium and transport properties of secondary and tertiary amines. The transferability was studied for an important set of molecules including as secondary amines dimethylamine, diethylamine, di-n-propylamine, di-iso-propylamine, and di-iso-butylamine. We have also tested diethylenetriamine, a multifunctional molecule which includes two primary and one secondary amino groups. For tertiary amines, we have included simulations for trimethylamine, triethylamine, tri-n-propylamine, and methyldiethylamine. Monte Carlo simulations in the Gibbs ensemble were carried out to study thermodynamic properties such as equilibrium densities, vaporization enthalpies, and vapor pressures. Critical coordinates (critical density and critical temperature) and normal boiling points were also calculated. The shear viscosity coefficients were studied for dimethyl, diethyl, di-n-propyl, trimethyl, triethyl, and tri-n-propylamine at different temperatures using molecular dynamics in the isothermal isobaric ensemble. Our results show a very good agreement with experimental values for all the studied molecules for both thermodynamic and transport properties, demonstrating the transferability of our force field.

Modeling of Mixing Acetone and Water: How Can Their Full Miscibility Be Reproduced in Computer Simulations?

The free energy of mixing of acetone and water is calculated at 298 K by means of thermodynamic integration considering combinations of three acetone and six water potentials. The Anisotropic United Atom 4 (AUA4) and Transferable Potential for phase Equilibria (TraPPE) models of acetone are found not to be miscible with any of the six water models considered, although the free energy cost of the mixing of any of these model pairs is very small, being below the mean kinetic energy of the molecules along one degree of freedom of 0.5RT. On the other hand, the combination of the Pereyra, Asar, and Carignano (PAC) acetone and TIP5P-E water models turns out to be indeed fully miscible, and it is able to reproduce the change of the energy, entropy, and Helmholtz free energy of mixing of the two neat components very accurately (i.e., within 0.8 kJ/mol, 2.5 J/(mol K), and 0.3 kJ/mol, respectively) in the entire composition range. The obtained results also suggest that the PAC model of acetone is likely to be fully miscible with other water models, at least with SPC and TIP4P, as well.

Transferable Force Field for Equilibrium and Transport Properties in Linear, Branched, and Bifunctional Amines I. Primary Amines

A new anisotropic united atom (AUA4) force field is developed to predict the phase equilibrium and transport properties of different primary amines. The force field transferability was studied for an important set of molecules, including linear amines (methyl, ethyl, n-propyl, and n-hexylamine), branched amines (isopropyl and isobutylamine), and bifunctional amines (ethylenediamine, 1,3-propanediamine, and 1,5-pentanediamine). Monte Carlo simulations in the Gibbs ensemble were carried out to study thermodynamic properties such as equilibrium densities, vaporization enthalpies, and vapor pressures. Critical coordinates (critical density, critical temperature, and critical pressure) and normal boiling points were also calculated. The shear viscosity coefficients were studied for methyl, ethyl, and n-propylamine at different temperatures using molecular dynamics. Our results show a very good agreement with experimental values for thermodynamic properties and are an improvement on the models available in the literature, all of which are all-atom. Viscosity coefficients also show a good agreement compared with experimental data, demonstrating the transferability of our force field not only to predict thermodynamic properties but also to predict transport properties.

Prediction of the Surface Tension of the Liquid−Vapor Interface of Alcohols from Monte Carlo Simulations

We report the calculation of the surface tension of the liquid−vapor interface of alcohols by two-phase Monte Carlo simulations. The anisotropic united atom model (AUA4) extended to alcohol is applied here for the prediction of the surface tension for alcohols ranging from methanol to octan-1-ol and phenol. The surface tension is calculated using different mechanical and thermodynamic approaches with specific long-range corrections (LRC) used for each definition. Liquid−vapor coexistence curves are also determined from these two-phase simulations and compared with Monte Carlo simulations carried out in the Gibbs ensemble. These calculations represent a genuine test of transferability for this force field since the surface tension is not a property used in the adjustment procedure for the development of the parameters. The surface tension, saturated liquid densities, and critical points compare very well with experiments along the liquid−vapor saturation curve.

Surface tension of water–alcohol mixtures from Monte Carlo simulations

Monte Carlo simulations are reported to predict the dependence of the surface tension of water-alcohol mixtures on the alcohol concentration. Alcohols are modeled using the anisotropic united atom model recently extended to alcohol molecules. The molecular simulations show a good agreement between the experimental and calculated surface tensions for the water-methanol and water-propanol mixtures. This good agreement with experiments is also established through the comparison of the excess surface tensions. A molecular description of the mixture in terms of density profiles and hydrogen bond profiles is used to interpret the decrease of the surface tension with the alcohol concentration and alcohol chain length.

ChemInform Abstract: Self-Diffusion in n-Alkane Fluid Models.

Molecular dynamic simulations of fluid n‐pentane and n‐decane have been performed in order to analyze the self‐diffusion. An isotropic united‐atom (UA) model as well as anisotropic united‐atom (AUA) models have been used to represent the molecular interactions. Self‐diffusion coefficients have been calculated. The sensitivity of the self‐diffusion coefficient to the shape of the intermolecular potential as well as the torsion potential has been analyzed. The simulation results for the diffusion coefficient are in excellent agreement with experimental data when the molecular interaction is represented by an anisotropic United‐Atom model and the internal rotation is governed by a torsion potential proposed in this work.

Modeling of Amorphous Polyaniline Emeraldine Base

Amorphous polyaniline emeraldine base has been investigated using atomistic classical molecular dynamics simulations. Initially, different sets of force-field parameters, which differ in the atomic charges and/or the van der Waals parameters, were tested. The experimental density of polyaniline was satisfactorily reproduced using the following combination: (i) equilibrium bond lengths, equilibrium bond angles, and electrostatic charges derived from quantum mechanical calculations and (ii) van der Waals parameters extrapolated from GROMOS for all atoms with the exception of the CH pseudoparticles of the phenyl ring, which were taken from an anisotropic united atom potential. Next, this force field was used to investigate the structure of the polymer in the amorphous state, the trajectories performed for this purpose allowing accumulation of 750 ns. Analyses of the energies evidence that the interactions between one repeating unit containing an amine nitrogen atom and another unit with an imine nitrogen are favored with respect to those between two identical repeating units. This conclusion is also supported by quantum mechanical and quantum mechanical/molecular mechanics calculations. On the other hand, the partial radial distribution functions indicate that this material only exhibits short-range intramolecular correlation, which is in excellent agreement with experimental evidence.

Extension of a Charged Anisotropic United Atoms Model to Polycyclic Aromatic Compounds

A new potential model for polycyclic aromatic hydrocarbons has been developed on the basis of a charged anisotropic united atoms (AUA) potential with six AUA force centers and three electrostatic point charges per aromatic ring. Using quantum mechanical calculations, quadrupolar moments of several aromatic molecules were computed and a correlation has been observed that links the magnitude of the point charges with respect to the number of aromatic rings. The Lennard-Jones parameters of quaternary carbon atoms bridging two aromatic rings have been optimized with the minimization of a dimensionless error criterion incorporating various thermodynamic data of naphthalene. The new potential model, called ch-AUA, was then evaluated on its abilities to predict thermodynamic and transport properties for a series of polycyclic aromatic compounds in a wide range of temperatures. Although the relative errors with respect to the experimental density, vaporization enthalpy, and vapor pressure data are similar to those computed with the noncharged AUA potential, the new ch-AUA potential noticeably improves the prediction of the shear viscosities of polycyclic aromatic compounds. Comparisons between experimental viscosities of 1-methylnaphthalene at different pressures and those computed using the new ch-AUA and the noncharged AUA potentials show that the new potential improves the prediction of viscosities at high pressures.

Molecular Simulation Prediction of Sound Velocity for a Binary Mixture near Miscible Conditions

The speed of sound was computed via Monte Carlo simulation for a binary mixture of methane and n-butane in the subcritical, near-critical, and supercritical regions at the temperature of 311 K. The technique encompasses a sequential implementation of the isobaric−isothermal and canonical ensembles in a simulation box, in which the (residual) thermodynamic derivative properties are evaluated via the fluctuation method [Escobedo, F. A. J. Chem. Phys. 1998, 108, 8761] during the Monte Carlo moves. A united atom Lennard-Jones potential with parameters proposed by Möller et al. [Möller, D. et al. Mol. Phys. 1992, 75, 363] was chosen to represent methane. In case of n-butane, we employed an optimized anisotropic united atom intermolecular Lennard-Jones description of Ungerer et al. [Ungerer, P. et al. J. Chem. Phys., 2000, 112, 5499]. In decent agreement with the experiment, we find the technique to provide reasonably quantitative estimates for the speed of sound in the thermodynamic regions studied.