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Deriving transferable pair potentials from experimental neutron and X-ray scattering measurements has been a longstanding challenge in condensed matter physics. State-of-the-art scattering analysis techniques estimate real-space microstructure from reciprocal-space total scattering data by refining pair potentials to obtain agreement between simulated and experimental results. Prior attempts to apply these potentials with molecular simulations have revealed inaccurate predictions of thermodynamic fluid properties. In this Letter, a machine learning assisted structure-inversion method applied to neutron scattering patterns of the noble gases (Ne, Ar, Kr, and Xe) is shown to recover transferable pair potentials that accurately reproduce both microstructure and vapor-liquid equilibria from the triple to critical point. Therefore, it is concluded that a single neutron scattering measurement is sufficient to predict macroscopic thermodynamic properties over a wide range of states and provide novel insight into local atomic forces in dense monatomic systems.

In order to understand the role of fluorination on the interactions and partitioning of alcohols in aqueous and organic environments, isobaric-isothermal ensemble Monte Carlo simulations are used to determine environmental predictors, such as free energies of hydration and solvation in 1-octanol and n-hexadecane. Calculations are performed with the united-atom Transferable Potentials for Phase Equilibria (TraPPE) force field and compared against available experimental data. TraPPE was found to provide reliable qualitative predictions of trends with respect to the effect of fluorination on partitioning. Investigation of the local solvation environment around the hydroxyl group reveals that fluorination of carbons closest to the hydroxyl group has the greatest effect on solvation free energies for alcohols in water, 1-octanol and n-hexadecane.

The molecular exchange Monte Carlo (MEMC) method is extended to Gibbs ensemble Monte Carlo (GEMC). The utility of the MEMC method is demonstrated through the calculation of the free energies of transfer of n-alkanes from vapor into liquid 1-octanol, n-hexadecane, and 2,2,4-trimethylpentane using isobaric-isothermal GEMC simulations. Calculations are performed for both the Transferable Potentials for Phase Equilibria (TraPPE) and Mie potentials. For all solutes, the Mie potentials predict free energies of transfer that are within 0.1 kcal/mol of experiment for solvation in n-hexadecane and 2,2,4-trimethylpentane. For TraPPE, solutes shorter than n-butane show similar agreement with experiment, but free energies for n-octane in n-hexadencane and 2,2,4-trimethylpentane are over-predicted by approximately 0.25 and 0.5 kcal/mol, respectively.

Histogram reweighting (HR) is a standard approach for converting grand canonical Monte Carlo (GCMC) simulation output into vapor–liquid coexistence properties (saturated liquid density, ρliqsat, sa...

Molecular simulation has emerged as an important sub-field of chemical engineering, due in no small part to the leadership of Keith Gubbins. A characteristic of the chemical engineering molecular simulation community is the commitment to freely share simulation codes and other key software components required to perform a molecular simulation under open-source licenses and distribution on public repositories such as GitHub. Here we provide an overview of open-source molecular modeling software in Chemical Engineering, with focus on the Molecular Simulation Design Framework (MoSDeF). MoSDeF is an open-source Python software stack that enables facile use of multiple open-source molecular simulation engines, while at the same time ensuring maximum reproducibility.

GPU Optimized Monte Carlo (GOMC) is open-source software for simulating molecular systems using the Metropolis Monte Carlo algorithm. It supports simulations in a variety of ensembles, which include canonical, isothermal–isobaric, grand canonical, and Gibbs ensemble. GOMC can be used to study vapor–liquid equilibria, adsorption in porous materials, surfactant self-assembly, and condensed phase structure for complex molecules. GOMC supports a variety of all-atom, united atom, and coarse grained force fields such as OPLS, TraPPE, Mie, and Martini. The software has been written in object oriented C++, and uses OpenMP and NVIDIA CUDA to allow for execution on multi-core CPU and GPU architectures. Keywords: Molecular simulation, Monte Carlo, Gibbs ensemble, Adsorption, Phase equilibrium, GPU

The cell plasma membrane is a highly dynamic organelle governing a wide range of cellular activities including ion transport, secretion, cell division, growth, and development. The fundamental process involved in the addition of new membranes to pre-existing plasma membranes, however, is unclear. Here, we report, using biophysical, morphological, biochemical, and molecular dynamic simulations, the selective incorporation of proteins and lipids from the cytosol into the cell plasma membrane dictated by membrane stretch and composition. Stretching of the cell membrane as a consequence of volume increase following incubation in a hypotonic solution and results in the incorporation of cytosolic proteins and lipids into the existing plasma membrane. Molecular dynamic simulations further confirm that increased membrane stretch results in the rapid insertion of lipids into the existing plasma membrane. Similarly, depletion of cholesterol from the cell plasma membrane selectively alters the incorporation of lipids into the membrane.

Histogram-reweighting Monte Carlo simulations in the grand canonical ensemble are used to determine saturated liquid and vapor densities, vapor pressures, heats of vaporization, and compressibility factors for radon-222 from the normal boiling point to the critical point. An optimized intermolecular potential is developed by fitting parameters to reproduce experimental vapor pressures and the critical temperature. Vapor pressures are reproduced by simulation to within 2.2% of experiment, while the critical temperature and normal boiling point are reproduced exactly within the combined uncertainty of simulation and experimental data. The predictions of simulation are used to evaluate the reliability of reported experimental liquid densities, and those predicted by equations of state. While the predictions of simulation are in agreement with equations of state for the liquid density, significant differences are observed between the predictions of simulation and experiment. These results suggest that previou...

Because of the widespread use of fluorinated compounds and their subsequent release into the environment, these chemicals have been subjected to a great deal of scrutiny in the past years to determine the extent of their toxicity. In order to better understand the interactions of perfluorinated alcohols and fluorotelomer alcohols in aqueous environments, molecular dynamics simulations are utilized to determine environmental predictors, such as the free energy of hydration. In this work, the predictions of two different force fields, the united-atom Transferable Potentials for Phase Equilibria (TraPPE) and the all-atom Optimized Potentials for Liquid Simulations (OPLS) are compared against available experimental data. Both force fields yield reliable predictions for liquid densities, heats of vaporization and hydration free energies. Investigation of the local solvation environment around the hydroxyl group reveals that fluorination of carbons closest to the hydroxyl group has the greatest effect on the overall hydration free energy.

Transferable united-atom force fields based on Mie potentials are presented for alkenes. Monte Carlo simulations in the grand canonical ensemble, combined with histogram reweighting, are used to determine vapor–liquid coexistence curves, vapor pressures, heats of vaporization, boiling points, and critical properties for 1-alkenes from ethene to 1-octene. To assess the transferability of the optimized parameters, additional calculations are performed for the cis and trans isomers of 2-butene and 2-pentene and the dienes 1,3-butadiene and 1,5-hexadiene. Saturated liquid densities for the 1-alkenes, 2-pentenes, and 1,5-hexadiene are predicted to within 1 % of experimental data, while deviations of (2 to 5) % from experiment were observed for cis-2-butene and 1,3-butadiene, respectively. Vapor pressures for the alkenes are predicted to within (2 to 15) % of experiment, with errors increasing with chain length and at lower temperatures. Critical temperatures are predicted to within 1 % of experiment for all mo...

A transferable united-atom force field, based on Mie potentials, is presented for alkynes. The performance of the optimised Mie potential parameters is assessed for 1-alkynes and 2-alkynes using grand canonical histogram-reweighting Monte Carlo simulations. For each compound, vapour–liquid coexistence curves, vapour pressures, heats of vapourisation, critical properties and normal boiling points are predicted and compared to experiment. Experimental saturated liquid densities are reproduced to within 2% average absolute deviation (AAD), except for 1-hexyne, which are reproduced with 3% AAD. Experimental saturated vapour pressures are reproduced to within 3% AAD, except for 1-pentyne, 2-pentyne and 2-hexyne, where deviations from experiment of up to 20% AAD were observed. Binary phase diagrams, predicted from Gibbs ensemble Monte Carlo simulations, for propane + propyne, propene + propyne and propadiene + propyne, are in close agreement with experiment.

A new force field for sulfur dioxide, capable of predicting accurately the vapor-liquid equilibria, critical properties, vapor pressure, and heats of vaporization is presented. The new force field reproduces the saturated liquid densities, vapor pressures and heats of vaporization to within 0.5, 2, and 2% of experiment, respectively. The predicted critical properties and the normal boiling point are in excellent agreement with experimental results. Pair distribution functions are calculated for the S-S, S-O, and O-O interactions are in close agreement with neutron and X-ray scattering experiments. In addition to the new force field, similar calculations are performed for four SO(2) intermolecular potentials proposed by Sokolic et al. (Sokolic, F.; Guissani, Y. and Guillot, B. J. Phys. Chem. 1985, 89, 3023], which show that these models work reasonably well near the state point where they were originally parametrized, but large errors in the predicted coexistence properties are displayed at higher and lower temperatures. Comparison of the radial distribution functions show the local structure is only weakly affected by the different force field parameters.

Transferable united-atom force fields, based on n - 6 Lennard-Jones potentials, are presented for normal alkanes and perfluorocarbons. It is shown that by varying the repulsive exponent the range of the potential can be altered, leading to improved predictions of vapor pressures while also reproducing saturated liquid densities to high accuracy. Histogram-reweighting Monte Carlo simulations in the grand canonical ensemble are used to determine the vapor liquid coexistence curves, vapor pressures, heats of vaporization, and critical points for normal alkanes methane through tetradecane, and perfluorocarbons perfluoromethane through perfluorooctane. For all molecules studied, saturated liquid densities are reproduced to within 1% of experiment. Vapor pressures for normal alkanes and perfluorocarbons were predicted to within 3% and 6% of experiment, respectively. Calculations performed for binary mixture vapor-liquid equilibria for propane + pentane show excellent agreement with experiment, while slight deviations are observed for the ethane + perfluoroethane mixture.

The effect of torsional potential on the predictions of simulation for vapor–liquid equilibria of n -alkanes is determined. Calculations are performed with histogram-reweighting Monte Carlo simulations in the grand canonical ensemble. Decreasing the magnitude of energy barriers to dihedral rotation or allowing free rotation is found to have no effect on the predicted vapor–liquid equilibria. Restriction of the dihedral angles to a Gaussian distribution around the minimum energy conformation causes an under-prediction of the liquid densities and critical temperatures by a maximum of 7% and 2%, respectively, with discrepancies increasing monotonically with the number of dihedral angles present in a molecule. No significant deviation in vapor pressure is observed for any compound, regardless of torsional potential used. An analysis of the conformational behavior reveals that restriction of the dihedral sampling has a measurable effect on excluded volume of the molecule, and this change of conformational behavior is responsible for the reduction in the predicted saturated liquid densities observed in this work. Similar calculations for force fields employing reduced dihedral potentials or freely jointed chains show little change in the predicted excluded volume compared to the reference force field.

A united-atom force field for ethylene oxide (oxirane) is presented. Parameters for both the dispersive and electrostatic interactions are simultaneously determined by fitting to the experimentally determined critical point, the normal boiling point and two vapor pressures. Vapor and liquid coexistence densities, heats of vaporization and vapor pressures are determined with histogram-reweighting Monte Carlo simulations in the grand canonical ensemble. NpT simulations are used to determine the heat capacity and isothermal compressibility.

Earlier studies using X-ray diffraction, light scattering, photon correlation spectroscopy, and atomic force microscopy, strongly suggest that SNARE-induced membrane fusion in cells proceeds as a result of calcium bridging opposing bilayers. The bridging of phospholipid heads groups in the opposing bilayers by calcium leads to the release of water from hydrated Ca2+ ions as well as the loosely coordinated water at PO-lipid head groups. Local dehydration of phospholipid head groups and the calcium, bridging opposing bilayers, then leads to destabilization of the lipid bilayers and membrane fusion. This hypothesis was tested in the current study by atomistic molecular dynamic simulations in the isobaric–isothermal ensemble using hydrated dimethylphosphate anions (DMP−) and calcium cations. Results from the study demonstrate, formation of DMP–Ca2+ complexes and the consequent removal of water, supporting the hypothesis. Our study further demonstrates that as a result of Ca2+–DMP self-assembly, the distance between anionic oxygens between the two DMP molecules is reduced to 2.92 A, which is in close agreement with the 2.8 A SNARE-induced apposition established between opposing bilayers, reported earlier from X-ray diffraction measurements.

Transferrable force fields, based on n-6 Mie potentials, are presented for noble gases. By tuning the repulsive exponent, ni, it is possible to simultaneously reproduce experimental saturated liquid densities and vapor pressures with high accuracy, from the normal boiling point to the critical point. Vapor-liquid coexistence curves for pure fluids are calculated using histogram reweighting Monte Carlo simulations in the grand canonical ensemble. For all noble gases, saturated liquid densities and vapor pressures are reproduced to within 1% and 4% of experiment, respectively. Radial distribution functions, extracted from NVT and NPT Monte Carlo simulations, are in similarly excellent agreement with experimental data. The transferability of the optimized force fields is assessed through calculations of binary mixture vapor-liquid equilibria. These mixtures include argon + krypton, krypton + xenon, methane + krypton, methane + xenon, krypton + ethane, and xenon + ethane. For all mixtures, excellent agreement with experiment is achieved without the introduction of any binary interaction parameters or multi-body interactions.

This paper describes efficient, scalable parallel implementations of the conventional cell list method and a modified cell list method to calculate the total system intermolecular Lennard-Jones force interactions in the Monte Carlo Gibbs ensemble. We targeted this part of the Gibbs ensemble for optimization because it is the most computationally demanding part of the force interactions in the simulation, as it involves all the molecules in the system. The modified cell list implementation reduces the number of particles that are outside the interaction range by making the cells smaller, thus reducing the number of unnecessary distance evaluations. Evaluation of the two cell list methods is done using a hybrid MPI+OpenMP approach and a hybrid MPI+CUDA approach. The cell list methods are evaluated on a small cluster of multicore CPUs, Intel Phi coprocessors, and GPUs. The performance results are evaluated using different combinations of MPI processes, threads, and problem sizes.

Histogram-reweighting Monte Carlo simulations in the grand canonical ensemble are used to determine pressure−composition diagrams for diethylamine + methanol, diethylamine + acetone and diethylamine + acetonitrile. Simulations were unable to predict the polyazeotropy found in the diethylamine + methanol mixture at 398 K or the minimum pressure azeotropy found at 348 and 298 K. Simulation predictions of the pressure−composition behavior of diethylamine + acetone and diethylamine + acetonitrile, however, were found to be in close agreement with experiment. Simulations in the isobaric−isothermal ensemble were used to determine the structure of the liquid phase for each of the mixtures described previously and revealed significant association taking place between unlike species.

Phase diagrams for binary mixtures of H 2 S+ n -alkanes, H 2 S+CO 2 , CO 2 +CH 4 and a ternary mixture containing H 2 S, CH 4 and CO 2 are determined with atomistic simulations. Pressure–composition diagrams for each of the binary mixtures are determined with configurational-bias Monte Carlo simulations in the grand canonical ensemble, combined with histogram-reweighting techniques. Overall, the predicted phase diagrams for the H 2 S+ n -alkanes and CO 2 +CH 4 mixtures are found to be in excellent agreement with experiment, while significant deviations are found between simulation and experiment for the H 2 S+CO 2 mixture. Gibbs ensemble Monte Carlo simulations are used to determine the ternary phase diagram for the H 2 S+CH 4 +CO 2 mixture at 310.93 K and 41.3 bar. Comparison of simulation to experiment shows a close agreement at the temperature and pressure studied in this work.

The transferability of Lennard–Jones parameters in the united-atom force field known as “transferable potentials for phase equilibria” (TraPPE-UA) is assessed through vapor–liquid equilibria calculations performed on carboxylate esters. In the TraPPE-UA force field, non-bonded interactions are governed by a Lennard–Jones plus fixed point charge functional form. Partial charges are borrowed from the optimized potentials for liquid simulations (OPLS) force field [Briggs, Nguyen, Jorgensen, J. Phys. Chem. 95 (1991) 3315]. No reparameterization of pseudo-atoms occurs in this work. Instead, the molecules of interest are built from pseudo-atoms parameterized in previous installments of the TraPPE-UA force field. Configurational-bias Monte Carlo simulations in the grand canonical ensemble, combined with histogram-reweighing techniques, are used to determine the vapor–liquid coexistence curves, vapor pressures and critical points of the esters methyl acetate, ethyl acetate, methyl propionate and vinyl acetate. Pressure-composition diagrams are calculated for methyl acetate + ethyl acetate at 313.15 K and methyl acetate + methanol at 323.15 K. Average deviations in the saturated liquid densities and critical temperatures from experiment vary from 1.8% (methyl acetate) to 4.2% (vinyl acetate), while the critical densities for all four esters are predicted to within 0.8%. The pressure-composition diagrams for methyl acetate + ethyl acetate and methyl acetate + methanol agree qualitatively with experiment, but quantitative differences exist due to the overprediction of the pure component vapor pressures. For the methyl acetate + methanol system the predicted azeotropic composition of x AcOMe = 0.66 is in good agreement with the experimental value of x AcOMe expt = 0.65 . Analysis of the microstructure of the methyl acetate + methanol mixture shows that the addition of methyl acetate has little effect on the self-association of methanol molecules through hydrogen bonding.

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.

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.

Histogram-reweighting Monte Carlo simulations in the grand canonical ensemble are used to determine the effect of quadrupole moment on the phase behavior of binary mixtures containing ethene. Two united-atom force fields for ethene are developed, one with an explicit representation of the quadrupole moment via partial charges, the other without. Simulations demonstrate that the addition of an explicit quadrupole moment results in a slight improvement in the reproduction of pure ethene vapor–liquid equilibria. For mixtures of xenon/ethene, the predictions of simulation are also improved by the use of an explicit quadrupole moment. For CO 2 /ethane mixtures, however, the quadrupole explicit force field fails to predict the maximum pressure azeotrope found experimentally, while the force field without a quadrupole moment is in quantitative agreement with experiment. For n -butane/ethene mixtures the quadrupole moment has little effect on the predicted pressure composition behavior.

The extension of the transferable potentials for phase equilibria−united atom (TraPPE−UA) force field to the ether, glycol, ketone, and aldehyde functionalities is presented. New parameters for the ether oxygen, the carbonyl carbon (ketones), the carbonyl methine (aldehydes), and a special intramolecular hydrogen-bond term were fitted to the vapor−liquid coexistence curves for selected one-component systems. Coupled−decoupled configurational bias Monte Carlo simulations in the Gibbs or grand canonical ensemble were used to compute the vapor−liquid coexistence curves for the neat systems of dimethyl ether, ethyl methyl ether, diethyl ether, dipropyl ether, diisopropyl ether, methyl tert-butyl ether, 1,2-ethanediol, 2-methoxyethan-1-ol, 1,2-dimethoxyethane, 1,3-propanediol, acetone, 2-pentanone, 2-octanone, acetaldehyde, pentanal, and octanal. Additional simulations were performed for the binary mixtures of diethyl ether + ethanol and acetone + hexane. Excellent agreement with experimental results was found...

An improved united-atom force field, based on a Lennard-Jones plus point charge functional form, for carboxylic acids is proposed. Point charges are determined from a Mulliken population analysis of ab initio calculations performed at the MP2 level of theory with the 6-31+g(d,p) basis set. The Lennard-Jones well depth and size parameters for the carboxyl carbon interaction site were determined by fitting to single-component vapor−liquid equilibrium data for acetic acid, while the remaining Lennard-Jones parameters were taken from the TraPPE-UA force field. Histogram-reweighting Monte Carlo simulations in the grand canonical ensemble were used to determine the vapor−liquid coexistence curves, vapor pressures, and critical points predicted by the new force field. The new force field was found to describe accurately the phase equilibria of acetic acid, with mean unsigned errors in the saturated liquid density of less than 1.6%. The critical temperature and density predicted by the new force field were within...

Histogram-reweighting Monte Carlo simulations in the grand canonical ensemble were used to obtain vapor−liquid coexistence curves for a series of alkanes physisorbed on a flat gold substrate. The critical temperatures and densities of n-alkanes from methane to decane as well as the branched molecules 2-methylpropane, 2,2-dimethylbutane, and 2,3-dimethylbutane were determined through a mixed-field analysis. The ratio of the 2D (two-dimensional) to the 3D (three-dimensional) critical temperature was found to depend weakly on the chain length for n-alkanes, decreasing from Tc2D/Tc3D = 0.38 for methane to Tc2D/Tc3D = 0.31 for n-decane. In contrast to typical bulk fluid behavior, the branched isomers were found to have higher critical temperatures than their linear counterparts.

New force fields for carbon dioxide and nitrogen are introduced that quantitatively reproduce the vapor–liquid equilibria (VLE) of the neat systems and their mixtures with alkanes. In addition to the usual VLE calculations for pure CO2 and N2, calculations of the binary mixtures with propane were used in the force-field development to achieve a good balance between dispersive and electrostatic (quadrupole–quadrupole) interactions. The transferability of the force fields was then assessed from calculations of the VLE for the binary mixtures with n-hexane, the binary mixture of CO2/N2, and the ternary mixture of CO2 /N2/propane. The VLE calculations were carried out using configurational-bias Monte Carlo simulations in either the grand canonical ensemble with histogram–reweighting or in the Gibbs ensemble.

The transferable potentials for phase equilibria-united atom (TraPPE-UA) force field for hydrocarbons is extended to primary, secondary, and tertiary alcohols by introducing the following (pseudo-)atoms: common hydroxyl O and H for all alcohols, α-CH3, α-CH2, α-CH, and α-C for methanol, primary, secondary, and tertiary alcohols, respectively. In the TraPPE-UA force field, the nonbonded interactions of these sites are governed by Lennard−Jones 12−6 potentials and Coulombic interactions of fixed partial charges. The values of these partial charges were borrowed from the optimized potentials for liquid simulations-united atom (OPLS−UA) force field [Jorgensen, W. L. J. Phys. Chem. 1986, 90, 1276]. The Lennard−Jones well depth and size parameters for the new interaction sites were determined by fitting to the single-component vapor−liquid-phase equilibria of a few selected model compounds. Although the well-depth parameters for the α-carbons could be taken directly from the TraPPE-UA parameters for the corres...

Configurational-bias Monte Carlo simulations in the grand canonical ensemble with histogram reweighting were used to obtain the vapor-liquid coexistence curves of three hexane isomers physisorbed on a flat gold substrate. Examination of the critical ordering operator distributions confirms that these systems exhibit critical behavior consistent with the 2D Ising universality class. The critical temperatures for 2,2-dimethylbutane, 2,3-dimethylbutane, and $n$-hexane were determined as ${T}_{c}^{2\mathrm{D}}\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}195.0$, $161.2$, and $152.4\mathrm{K}$, respectively. This is qualitatively different from the behavior observed for bulk (3D) fluids, where branched alkanes typically exhibit lower critical temperatures than their linear counterparts.

The surface tension of the full three-dimensional Lennard-Jones potential is calculated from grand canonical Monte Carlo simulations with the finite-size scaling methodology outlined by Binder [Phys. Rev. A 25, 1699 (1982)]. Surface tensions are determined for the range of reduced temperatures T*=0.95–1.312 and are found to be in good agreement with molecular-dynamics calculations. A critical temperature Tc*=1.311±0.002 is established by locating the T* where the surface tension of the infinite system size vanishes. In addition, with this method it is possible to determine the critical exponent 2ν. For the Lennard-Jones fluid we found 2ν=1.42±0.08, which differs from the accepted value of 2ν=1.26.

The adiabatic nuclear and electronic sampling Monte Carlo algorithm (ANES-MC) is extended to simulations in the Gibbs ensemble. Whereas the maximum displacements used for translational, rotational, and volume trial moves can be adjusted to foster efficient sampling in the adiabatic limit, the transfer (swap) of particles always causes a major disturbance of the electronic structures of the two phases (supplying and receiving the particle). To reequilibrate the electronic structures requires additional sampling of the electronic degrees of freedom. A simple, distance-dependent criterion for the preferential selection of the electronic degrees of freedom, for which a move is to be attempted, is shown to improve the efficiency of the particle swap move. The ANES-MC algorithm is applied to the polarizable simple point charge-fluctuating charge (SPC−FQ) and transferable intermolecular potential 4 point-fluctuating charge (TIP4P−FQ) models proposed by Rick et al. (J. Chem. Phys. 1994, 101, 6141). For both model...

Grand canonical histogram-reweighting Monte Carlo simulations were used to obtain the phase behaviour of several binary mixtures. The main goal of this work was to test the predictive capabilities of recently developed intermolecular potential models that accurately reproduce the phase behaviour of pure components. These united-atom potentials utilize the exponential-6 functional form for repulsive and dispersion interactions and fixed point charges for electrostatic interactions. The mixtures studied were n-pentane—methane, ethane—CO2, propane—CO2, n-pentane-CO2, H2O-ethane, CH3OH-n-hexane and CH3OH-CO2. The conventional Lorentz-Berthelot combining rules, as well as a set of combining rules due to Kong (1973, J. chem. Phys., 59, 2464) were used to obtain unlike-pair potential parameters. The Lorentz—Berthelot rules generally result in more attractive unlike-pair interactions than the Kong rules. For the n-alkane—CO2 systems, predicted phase diagrams are in excellent agreement with experiment when the Kon...

Monte Carlo simulations in the grand canonical ensemble were used to obtain liquid-vapor coexistence curves and critical points of the pure fluid and a binary mixture of Lennard-Jones particles. Critical parameters were obtained from mixed-field finite-size scaling analysis and subcritical coexistence data from histogram reweighting methods. The critical parameters of the untruncated Lennard-Jones potential were obtained as Tc*=1.3120±0.0007, ρc*=0.316±0.001 and pc*=0.1279±0.0006. Our results for the critical temperature and pressure are not in agreement with the recent study of Caillol [J. Chem. Phys. 109, 4885 (1998)] on a four-dimensional hypersphere. Mixture parameters were e1=2e2 and σ1=σ2, with Lorentz–Berthelot combining rules for the unlike-pair interactions. We determined the critical point at T*=1.0 and pressure-composition diagrams at three temperatures. Our results have much smaller statistical uncertainties relative to comparable Gibbs ensemble simulations.

The Transferable Potentials for Phase Equilibria (TraPPE) is extended to zwitterionic and charged lipids including phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), and phosphatidylglycerol (PG). The performance of the force field is validated through isothermal–isobaric ensemble (NPT) molecular dynamics simulations of hydrated lipid bilayers performed with the aforementioned head groups combined with saturated and unsaturated alkyl tails containing 12–18 carbon atoms. The effects of water model and sodium ion parameters on the performance of the lipid force field are determined. The predictions of the TraPPE force field for the area per lipid, bilayer thickness, and volume per lipid are within 1–5% of experimental values. Key structural properties of the bilayer, such as order parameter splitting in the sn-2 chain and X-ray form factors, are found to be in close agreement with experimental data.

United-atom force fields, based on the Transferable Potentials for Phase Equilibria (TraPPE), are developed for twelve nitro-aromatic compounds, which include 2,4-dinitrotoluene (2,4-DNT), 2,6-dinitrotoluene (2,6-DNT), 3-nitrotoluene (3-NT), 4-nitrotoluene (4-NT), 1,3-dinitrobenzene (1,3-DNB), 1,4-dinitrobenzene (1,4-DNB), 2,4-dinitroanisole (DNAN), 1,3,5-trinitrobenzene (TNB), 2,4,6-trinitrotoluene (TNT), 2-nitroanisole (2-NAN), 4-nitroanisole (4-NAN) and n-methyl-p-nitroaniline (MNA). 1-Octanol–water and air–water partition coefficients are predicted for the optimized TraPPE-UA force field with adaptive biasing force molecular dynamics simulations, and compared to available experimental data. Log Kow values are predicted with an average absolute deviation of 0.2 log units, while Henry's law constants are predicted to with an average absolute deviation of 0.5 log units. Two additional models are presented for energetic materials with five membered rings for which no experimental data are available in the open literature: 3,5-dinitropyrazole (DNP) and 3-nitro-1,2,4-triazole-5-one (NTO). Investigation of the local microstructure around each solute reveals that 1-octanol is able to form hydrogen bonded chains around the solute, while little organized microstructure was observed around the solutes in water.

A new force field for dimethyl ether (DME) based on the Lennard-Jones (LJ) 12-6 plus point charge functional form is presented in this work. This force field reproduces experimental saturated liquid and vapor densities, vapor pressures, heats of vaporization, and critical properties to within the statistical uncertainty of the combined experimental and simulation measurements for temperatures between the normal boiling and critical point. Critical parameters and normal boiling point are predicted to within 0.1% of experiment. This force field is used in grand canonical histogram reweighting Monte Carlo simulations to predict the pressure composition diagrams for the binary mixtures DME + SO(2) at 363.15 K and DME + CO(2) at 335.15 and 308.15 K. For the DME + SO(2) mixture, simulation is able to qualitatively reproduce the minimum pressure azeotropy observed experimentally for this mixture, but quantitative errors exist, suggesting that multibody effects may be important in this system. For the DME + CO(2) mixture, simulation is able to predict the pressure-composition behavior within 1% of experimental data. Simulations in the isobaric-isothermal ensemble are used to determine the microstructure of DME + SO(2) and DME + CO(2) mixtures. The DME + SO(2) shows weak pairing between DME and SO(2) molecules, while no specific pairing or aggregation is observed for mixtures of DME + CO(2).

In an effort to provide insight into the mechanism of Ca(2+)-induced fusion of lipid vesicles, molecular dynamics simulations in the isobaric-isothermal ensemble are used to investigate interactions of Ca(2+) with apposed lipid bilayers in close proximity. Simulations reveal the formation of a Ca(2+)-phospholipid "anhydrous complex" between apposed bilayers, whereas similar calculations performed with Na(+) display only complexation between neighboring lipids within the same bilayer. The binding of Ca(2+) to apposed phospholipids brings large regions of the bilayers into close contact (4 Å), displacing water from phospholipid head groups in the process and creating regions of local dehydration. Dehydration of the apposed bilayers leads to ordering of the phospholipid tails, which is partially disrupted by the presence of Ca(2+)-phospholipid bridges.

The transferable potentials for phase equilibria force field is extended to dimethylmethylphosphonate (DMMP), sarin, and soman by introducing a new interaction site representing the phosphorus atom. Parameters for the phosphorus atom are optimized to reproduce the liquid densities at 303 and 373 K and the normal boiling point of DMMP. Calculations for sarin and soman are performed in predictive mode, without further parameter optimization. Vapor-liquid coexistence curves, critical properties, vapor pressures and heats of vaporization are predicted over a wide range of temperatures with histogram reweighting Monte Carlo simulations in the grand canonical ensemble. Excellent agreement with experiment is achieved for all compounds, with unsigned errors of less than 1% for vapor pressures and normal boiling points and under 5% for heats of vaporization and liquid densities at ambient conditions.

A new all-atom force field capable of accurately predicting the bulk and interfacial properties of 1,1,1,2-tetrafluoroethane (HFA134a) is reported. Parameterization of several force fields with different initial charge configurations from ab initio calculations was performed using the histogram reweighting method and Monte Carlo simulations in the grand canonical ensemble. The 12-6 Lennard-Jones well depth and diameter for the different HFA134a models were determined by fitting the simulation results to pure-component vapor-equilibrium data. Initial screening of the force fields was achieved by comparing the calculated and experimental bulk properties. The surface tension of pure HFA134a served as an additional screening property to help discriminate an optimum model. The proposed model reproduces the experimental saturated liquid and vapor densities, and the vapor pressure for HFA134a within average errors of 0.7%, 4.4%, and 3.1%, respectively. Critical density, temperature, vapor pressure, normal boiling point, and heat of vaporization at 298 K are also in good agreement with experimental data with errors of 0.2%, 0.1%, 6.2%, 0%, 2.2%, respectively. The calculated surface tension is found to be within the experimental range of 7.7-8.1 mN.m(-1). The dipole moment of the different models was found to significantly affect the prediction of the vapor pressure and surface tension. The ability of the HFA134a models in predicting the interfacial tension against water is also discussed. The results presented here are relevant in the development of technologies where the more environmentally friendly HFA134a is utilized as a substitute to the ozone depleting chlorofluorocarbon propellants.