Molecular Dynamics of Benzene in Neat Liquid and a Solution Containing Polystyrene. 13C Nuclear Magnetic Relaxation and Molecular Dynamics Simulation Results

Molecular Dynamics Investigation of the Potentiality of Zeolite NaY for Trimethylbenzene Isomer Separation: An Insight in Terms of Structure, Energetics, and Dynamics

Isomers of trimethylbenzene (TMB) are the important constituent chemicals used in a variety of industrial applications, including the production of synthetic resins, insecticides, dyes, pigments, and pharmaceuticals. However, these applications require them in their purest form, mandating them to separate from their mixtures. Due to the similar physicochemical properties of the TMB isomers, traditional methods such as cryogenic distillation are very energy-expensive. Thus, adsorption-based separation methods using nanoporous adsorbents such as zeolite are a cost-effective alternate. Such adsorption-based separation methods, however, require the isomers to exhibit significant differences in their adsorption and diffusion properties. In the present report, we carried out a thorough investigation of the structural, energetic, and dynamical properties of the three isomers of TMB in a faujasite-type zeolite NaY containing cage-like pores. Our results indicate that 1,2,4-TMB exhibits the most facile translational and out-of-plane rotational motions in contrast to the other two isomers. However, the in-plane rotational motions are seen to be more facile in 1,2,3-TMB compared with the other two isomers. It is evident from our analysis that the dynamics are dominantly driven by entropy. These results highlight the importance of the porous material in the case of the separation of a given hydrocarbon mixture.

Systematic bottom-up molecular coarse-graining via force and torque matching using anisotropic particles

We derive a systematic and general method for parametrizing coarse-grained molecular models consisting of anisotropic particles from fine-grained (e.g. all-atom) models for condensed-phase molecular dynamics simulations. The method, which we call anisotropic force-matching coarse-graining (AFM-CG), is based on rigorous statistical mechanical principles, enforcing consistency between the coarse-grained and fine-grained phase-space distributions to derive equations for the coarse-grained forces, torques, masses, and moments of inertia in terms of properties of a condensed-phase fine-grained system. We verify the accuracy and efficiency of the method by coarse-graining liquid-state systems of two different anisotropic organic molecules, benzene and perylene, and show that the parametrized coarse-grained models more accurately describe properties of these systems than previous anisotropic coarse-grained models parametrized using other methods that do not account for finite-temperature and many-body effects on the condensed-phase coarse-grained interactions. The AFM-CG method will be useful for developing accurate and efficient dynamical simulation models of condensed-phase systems of molecules consisting of large, rigid, anisotropic fragments, such as liquid crystals, organic semiconductors, and nucleic acids.

Universal localization transition accompanying glass formation: insights from efficient molecular dynamics simulations of diverse supercooled liquids

The origin of the precipitous dynamic arrest known as the glass transition is a grand open question of soft condensed matter physics. It has long been suspected that this transition is driven by an onset of particle localization and associated emergence of a glassy modulus. However, progress towards an accepted understanding of glass formation has been impeded by an inability to obtain data sufficient in chemical diversity, relaxation timescales, and spatial and temporal resolution to validate or falsify proposed theories for its physics. Here we first describe a strategy enabling facile high-throughput simulation of glass-forming liquids to nearly unprecedented relaxation times. We then perform simulations of 51 glass-forming liquids, spanning polymers, small organic molecules, inorganics, and metallic glass-formers, with longest relaxation times exceeding one microsecond. Results identify a universal particle-localization transition accompanying glass formation across all classes of glass-forming liquid. The onset temperature of non-Arrhenius dynamics is found to serve as a normalizing condition leading to a master collapse of localization data. This transition exhibits a non-universal relationship with dynamic arrest, suggesting that the nonuniversality of supercooled liquid dynamics enters via the dependence of relaxation times on local cage scale. These results suggest that a universal particle-localization transition may underpin the glass transition, and they emphasize the potential for recent theoretical developments connecting relaxation to localization and emergent elasticity to finally explain the origin of this phenomenon. More broadly, the capacity for high-throughput prediction of glass formation behavior may open the door to computational inverse design of glass-forming materials.

An automated approach for the parameterization of accurate intermolecular force-fields: pyridine as a case study

An automated protocol is proposed and validated, which integrates accurate quantum mechanical calculations with classical numerical simulations. Intermolecular force fields, (FF) suitable for molecular dynamics (MD) and Monte Carlo simulations, are parameterized through a novel iterative approach, fully based on quantum mechanical data, which has been automated and coded into the PICKY software, here presented. The whole procedure is tested and validated for pyridine, whose bulk phase, described through MD simulations performed with the specifically parameterized FF, is characterized by computing several of its thermodynamic, structural, and transport properties, comparing them with their experimental counterparts.

Anisotropy of the thermal conductivity in a crystalline polymer: reverse nonequilibrium molecular dynamics simulation of the delta phase of syndiotactic polystyrene

The thermal conductivity of the crystalline delta phase of syndiotactic polystyrene has been investigated by reverse nonequilibrium molecular dynamics simulations. The results are in the expected range. An anisotropy is found for the thermal conductivity, with the component in chain direction being 2.5-3 larger than perpendicular to it. Any increase in the density causes an increase also in the thermal conductivity, particularly in the perpendicular directions. As side results, the simulations confirm an earlier finding on the force field dependence of the thermal conductivity: The thermal conductivity has a tendency to decrease when the number of active degrees of freedom in the system is reduced by the introduction of constraints. This dependence is, however, weaker and more erratic than previously found for molecular liquids and amorphous polymers.

Efficient multiparticle sampling in Monte Carlo simulations on fluids: application to polarizable models

A novel Monte Carlo simulation scheme based on biased simultaneous displacements of all particles of the system has been developed. The method is particularly suited for systems with nonadditive interactions and its efficiency is demonstrated by its implementation for the polarizable Stockmayer fluid. Performance of the method is compared with both the standard one-particle move method and an unbiased multiparticle scheme by computing the mean squared displacements, rotation relaxation, and the speed of equilibration (translational order parameter). It is shown that the proposed biased method is about a factor of 10 faster, for the system considered, when compared with the other schemes.

Polarizable empirical force field for aromatic compounds based on the classical drude oscillator

The polarizable empirical CHARMM force field based on the classical Drude oscillator has been extended to the aromatic compounds benzene and toluene. Parameters were optimized for benzene and then transferred directly to toluene, with parameters for the methyl moiety of toluene taken from the previously published work on the alkanes. Optimization of all parameters was performed against an extensive set of quantum mechanical and experimental data. Ab initio data was used for determination of the electrostatic parameters, for the vibrational analysis, and in the optimization of the relative magnitudes of the Lennard-Jones parameters. The absolute values of the Lennard-Jones parameters were determined by comparing computed and experimental heats of vaporization, molecular volumes, free energies of hydration, and dielectric constants. The newly developed parameter set was extensively tested against additional experimental data such as diffusion constants, heat capacities at constant pressure, and isothermal compressibilities including data as a function of temperature. Moreover, the structures of liquid benzene, liquid toluene, and solutions of each in water were studied. In the case of benzene, the computed and experimental total distribution function were compared, with the developed model shown to be in excellent agreement with experiment.

Anisotropic United Atom Model Including the Electrostatic Interactions of Benzene

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

From Mesoscale Back to Atomistic Models: A Fast Reverse-Mapping Procedure for Vinyl Polymer Chains

This paper introduces a systematic procedure to obtain well-relaxed atomistic melt structures from mesocale models of vinyl polymers based on sequences of diads. Following the methodology introduced by Milano and Müller-Plathe [J. Phys. Chem. B. 2005, 109, 18609], coarse-grain models consisting of sequences of superatoms of two different types meso and racemo have been used to relax mesocale melts of atactic and syndiotactic polystyrene. The proposed method, based on a fully geometrical approach, does not involve expensive potential energy and force evaluations and allows a very fast and efficient reconstruction of the atomistic detail. The method, successfully tested against experimental data, allows us to obtain all atom models of both stereoregular and stereoirregular polymers and opens the possibility of relaxing large molecular weight melts of vinyl chains.

Dynamics of Benzene Guest Inside a Self-Assembled Cylindrical Capsule: A Combined Solid-State 2H NMR and Molecular Dynamics Simulation Study

The reorientational dynamics of benzene-d(6) molecules hosted into the cavity of a cavitand-based, self-assembled capsule was investigated by Molecular Dynamics (MD) simulations and temperature-dependent solid-state (2)H NMR spectroscopy. MD simulations were preliminarily performed to assess the motional models of the guest molecules inside the capsules. An in-plane fast reorientation of the benzene guest around the C(6) symmetry axis (B1 motion), characterized by correlation times of the order of picoseconds, was predicted with an activation barrier ( approximately 8 kJ/mol) very similar to that found for neat benzene in the liquid state. An out-of-plane reorientation corresponding to a nutation of the C(6) symmetry axis in a cone angle of 39 degrees (B2 motion, 373 K) with an activation barrier ( approximately 39 kJ/mol) definitely larger than that of liquid benzene was also anticipated. In the temperature range 293-373 K correlation times of the order of a nanosecond have been calculated and a transition from fast to slow regime in the (2)H NMR scale has been predicted between 293 and 173 K. (2)H NMR spectroscopic analysis, carried out in the temperature range 173-373 K on the solid capsules containing the perdeuterated guest (two benzene molecules/capsule), confirmed the occurrence of the B1 and B2 motions found in slow exchange in the (2)H NMR time scale. Line shape simulation of the (2)H NMR spectral lines permitted defining a cone angle value of 39 degrees at 373 K and 35 degrees at 173 K for the nutation axis. The T(1) values measured for the (2)H nuclei of the encapsulated aromatic guest gave correlation times and energetic barrier for the in-plane motion B1 in fine agreement with theoretical calculation. The experimental correlation time for B2 as well as the corresponding energetic barrier are in the same range found for B1. A molecular mechanism for the encapsulated guest accounting for the B1 and B2 motions was also provided.

Phase Diagram and Glass Transition of Confined Benzene

We used differential scanning calorimetry, neutron scattering, and proton NMR to investigate the phase behavior, the structure, and the dynamics of benzene confined in a series of cylindrical mesoporous materials MCM-41 and SBA-15 with pore diameters, d, between 2.4 and 14 nm. With this multitechnique approach, it was possible to determine the structure and, for the first time to our knowledge, the density of confined benzene as a function of temperature and pore size. Under standard cooling rates, benzene partially crystallizes in SBA-15 matrixes (4.7 <or= d <or= 14 nm) but not in MCM-41 (2.4 <or= d <or= 3.5 nm). Structure factors of the confined phases were recorded at different temperatures and compare to those of the bulk. The confined liquid has the same structure as the bulk above the bulk melting point. In SBA-15, the confined crystals are defective and have the same structure as the bulk. In MCM-41, the liquid undergoes a glass transition at low temperature regardless of the cooling rate or the thermal history of the sample. The density as a function of temperature was measured by neutron scattering contrast matching, and the glass transition temperatures were determined from the density versus temperature curves. The pore size dependence of T(g) does not show any evidence of finite size effects. A temperature versus pore diameter phase diagram of confined benzene is proposed combining liquid, supercooled liquid, crystal states, and glassy states. NMR relaxation time measurements showed that the dynamics of the confined liquids are slower than those of the bulk above its melting point. In the partially crystallized samples, the liquid and the crystal have the same relaxation times. The activation energies of reorientation motions in the confined phases, determined from spin lattice relaxation times, are smaller than the bulk ones.

Molecular Dynamics Study of Translational and Rotational Diffusion in Liquid Ortho-terphenyl

NVT molecular dynamics simulations were performed on liquid o-terphenyl as a function of temperature in the range 320-480 K. Computed translational diffusion coefficients displayed the non-Arrhenius behavior expected of a fragile glass-forming liquid and were in good, semiquantitative agreement with experimental results. Rotational correlation functions calculated for various vectors within the molecule exhibited a very short time (0-1 ps) initial decay, followed by a reversal, which corresponds to free reorientation within the "solvent" cage prior to collision with a wall. Rotational correlation times of three orthogonal vectors fixed on the central benzene were close to equal at all temperatures, indicating nearly isotropic overall molecular reorientation. The average correlation times exhibited a non-Arrhenius temperature dependence and were in very good agreement with experimental values derived from 2D and 1H NMR relaxation times. Correlation times of vectors located on the lateral phenyl rings were used to calculate the "spinning" internal rotation diffusion coefficients, which were approximately twice as great as the overall rotational diffusion constants, indicating rapid internal rotation of the phenyl side groups over wide ranges of angle in the liquid.

Mapping Atomistic Simulations to Mesoscopic Models: A Systematic Coarse-Graining Procedure for Vinyl Polymer Chains

The paper introduces a systematic procedure to coarse-grain atomistic models of the largest family of synthetic polymers into a mesoscopic model that is able to keep detailed information about chain stereosequences. The mesoscopic model consists of sequences of superatoms centered on methylene carbons of two different types according to the kind of diad (m or r) they belong to. The corresponding force-field contains three different bonds, six angle and three nonbonded terms. Recently developed analytical potentials, based on sums of Gaussians for bond and angle terms of the mesoscale force field have been used. For the nonbonded part, numerical potentials optimized by pressure-corrected iterative Boltzmann inversion have been used. As test case we coarse-grained an atomistic all-atom model of atactic polystyrene. The proposed mesoscale model has been successfully tested against structural and dynamical properties for different chain lengths and opens the possibility of relaxing melts of high molecular weight vinyl polymers.

Molecular Dynamics Study of Anisotropic Translational and Rotational Diffusion in Liquid Benzene

Equilibrium NPT and NVT molecular dynamics simulations were performed on liquid benzene over an extended range of temperature (from 260 to 360 K) using the COMPASS force field. Densities and enthalpies of vaporization (from cohesive energy densities) were within 1% of experiment at all temperatures. tumbling and spinning rotational diffusion coefficients, D(perpendicular) and D(parallel), computed as a function of temperature, agreed qualitatively with the results of earlier reported experimental and computational investigations. Generally, it was found that D(parallel)/D(perpendicular) approximately 1.4-2.5 and the activation energy for tumbling was significantly greater than for spinning about the C6 axis [Ea(D(perpendicular)) = 8.1 kJ mol(-1) and Ea(D(parallel)) = 4.5 kJ mol(-1)]. Calculated translational diffusion coefficients were found to be in quantitative agreement with experimental values at all temperatures [deviations were less than the scatter between different reported measurements]. In addition, translational diffusion coefficients were computed in the molecule-fixed frame to yield values for Dxy (diffusion in the plane of the molecule) and Dz (diffusion perpendicular to the plane). It was found that the ratio Dxy/Dz approximately 2.0, and that the two coefficients have roughly equal activation energies. This represents the first atomistic molecular dynamics study of translational diffusion in the molecular frame.

Thermal Conductivities of Molecular Liquids by Reverse Nonequilibrium Molecular Dynamics

The reverse nonequilibrium molecular dynamics method for thermal conductivities is adapted to the investigation of molecular fluids. The method generates a heat flux through the system by suitably exchanging velocities of particles located in different regions. From the resulting temperature gradient, the thermal conductivity is then calculated. Different variants of the algorithm and their combinations with other system parameters are tested: exchange of atomic velocities versus exchange of molecular center-of-mass velocities, different exchange frequencies, molecular models with bond constraints versus models with flexible bonds, united-atom versus all-atom models, and presence versus absence of a thermostat. To help establish the range of applicability, the algorithm is tested on different models of benzene, cyclohexane, water, and n-hexane. We find that the algorithm is robust and that the calculated thermal conductivities are insensitive to variations in its control parameters. The force field, in contrast, has a major influence on the value of the thermal conductivity. While calculated and experimental thermal conductivities fall into the same order of magnitude, in most cases the calculated values are systematically larger. United-atom force fields seem to do better than all-atom force fields, possibly because they remove high-frequency degrees of freedom from the simulation, which, in nature, are quantum-mechanical oscillators in their ground state and do not contribute to heat conduction.

QM/MM Study of the Role of the Solvent in the Formation of the Charge Separated Excited State in 9,9‘-Bianthryl

In this paper the role of the solvent in the formation of the charge-separated excited state of 9,9'-bianthryl (BA) is examined by means of mixed molecular mechanical/quantum mechanical (QM/MM) calculations. It is shown that in weakly polar solvents a relaxed excited state is formed with an interunit angle that is significantly smaller than 90 degrees . This relaxed excited state has a considerable dipole moment even in weakly polar solvents; for benzene and dioxane dipole moments of ca. 6 D were calculated, which is close to experimental data. These dipoles are induced by the solvent in the highly polarizable relaxed excited state of BA, and the dipole relaxation time is governed by solvent reorganizations. In polar solvent the charge separation is driven to completion by the stronger dipoles in the solvent and a fully charged separated excited state is formed with an interunit angle of 90 degrees.

Atomistic Molecular Dynamics Simulation of Benzene as a Solute in a Columnar Discotic Liquid Crystal

A molecular dynamics simulation study on a binary liquid-crystalline mixture, where the solvent is the typical discogen hexakis-pentyloxy-triphenylene in its columnar state, while benzene is the solute, is reported. Both discotic and benzene molecules are modeled employing an atomistic force field. Attention has been paid to the structural and dynamic properties of benzene in this unusual environment, comparing these results with available experiments on the same or similar systems and with computer simulation data on neat liquid benzene.

Computer simulation of solid and liquid benzene with an atomistic interaction potential derived from ab initio calculations

Molecular dynamics atomistic simulations of solid and liquid benzene have been performed, employing a model intermolecular potential derived from quantum mechanical calculations. The ab initio database includes approximately 200 geometries of the benzene dimer with interaction energies computed at the MP2 level of theory. The accuracy of the modeled force field results is satisfactory. The thermodynamic and structural properties, calculated in the condensed phases, are compared with experimental data and previous simulation results. Single particle and collective dynamical properties are also investigated through the calculation of translational and rotational diffusion coefficients, reorientational dynamics, and viscosities. The agreement of these data with experimental measurements confirms the reliability of the proposed force field.