Coarse-grained molecular dynamics modeling of strongly associating fluids: thermodynamics, liquid structure, and dynamics of symmetric binary mixture fluids

Symmetric binary mixtures capable of strong association via a highly directional and saturable specific interaction between unlike molecules are investigated by canonical molecular dynamics simulations. The specific interaction of the molecules is defined in a new coarse-grained pair potential that can be applied in continuous molecular dynamics as well as in Monte Carlo simulations. The thermodynamic, structural, and dynamic properties of the associating mixture fluids are investigated as a function of density, temperature, and association strength of the specific interaction. Detailed analysis of the simulation data confirms a two-stage mechanism in the formation of specific bonds with increasing interaction strength, including a fast dimerization process and a subsequent stage of perfecting the bonds. A large heat capacity peak is found during the formation or breaking of the bonds, reflecting the large energy fluctuation introduced by the strong association. The fractions of nonbonded molecules obtained from the simulations as a function of density, temperature, and interaction strength are in excellent agreement with the predictions of Wertheim's thermodynamic perturbation theory. The translational and rotational dynamics of the Tmer mixture are effectively retarded with increasing association strength and are analyzed in terms of autocorrelation functions and a non-Gaussian parameter for the translational dynamics. The lifetimes of molecules in bonded and nonbonded states provide detailed information about the transformation of molecules between the bonded state and the nonbonded state. Finally, simulation sampling problems inherent to strongly interacting systems are easily overcome using the parallel tempering simulation technique. This latter result confirms that with the new continuous coarse-grained simulation potential we have a versatile and flexible interaction potential that can be used with many available molecular dynamics and Monte Carlo algorithms under various ensembles.     

Capillary adhesion in the limit of saturation: thermodynamics, self-consistent field modeling and experiment

We introduce a simple thermodynamic argument for capillary adhesion forces, for various geometries, in the limit of saturation of the bulk phase. For one specific geometry (i.e., the sphere-plate geometry such as that found in the colloidal probe AFM technique), we provide evidence of the validity of our model by comparison with experiment and self-consistent field calculations. With this latter numerical technique, we also discuss deviations from the macroscopic argument both when the system is moved away from saturation and when the capillary bridge becomes so small that macroscopic thermodynamics is no longer accurate.     

Transient molecular dynamics simulations of liquid viscosity for nonpolar and polar fluids

A transient molecular dynamics (TMD) method for obtaining fluid viscosity is extended to multisite, force-field models of both nonpolar and polar liquids. The method overlays a sinusoidal velocity profile over the peculiar particle velocities and then records the transient decay of the velocity profile. The viscosity is obtained by regression of the solution of the momentum equation with an appropriate constitutive equation and initial and boundary conditions corresponding to those used in the simulation. The transient velocity decays observed appeared to include both relaxation and retardation effects. The Jeffreys viscoelastic model was found to model accurately the transient responses obtained for multisite models for n-butane, isobutane, n-hexane, water, methanol, and 1-hexanol. TMD viscosities obtained for saturated liquids over a wide range of densities agreed well for the polar fluids, both with nonequilibrium molecular dynamics (NEMD) results using the same force-field models and with correlations based on experimental data. Viscosities obtained for the nonpolar fluids agreed well with the experimental and NEMD results at low to moderate densities, but underpredicted experimental values at higher densities where shear-thinning effects and viscous heating may impact the TMD simulations.     

Temperature effects on the structure and dynamics of liquid dimethyl sulfoxide: A molecular dynamics study

The molecular dynamics (MD) simulation technique has been employed to investigate the thermodynamic properties and transport coefficients of the neat liquid dimethyl sulfoxide (DMSO). The fluid has been studied at temperatures in the range 298–353 K and at a pressure equal to 1 atm. The simulations employed a nine-site potential model, which is presented for the first time here, and all the available non-polarizable models. The performance of each model is tested using the same statistical mechanical ensemble and simulation method under the same conditions, revealing its weaknesses and strengths. Thermodynamic properties, microscopic structure and dynamic properties, such as transport coefficients, rotational and single-dipole correlation times have been calculated and compared with available experimental results. Estimations of transport coefficients from various theoretical and empirical models are tested against experimental and MD results. Translational and rotational dynamics suggest the existence of the cage effect and agree with the Stokes–Einstein–Debye relation. The dipole relaxation times calculated are discussed in terms of simple and useful approximations, such as the Glarum–Powles and Fatuzzo–Mason models.     

Self-assembly, molecular dynamics, and kinetics of structure formation in dipole-functionalized discotic liquid crystals

The self-assembly, the molecular dynamics, and the kinetics of structure formation are studied in dipole-functionalized hexabenzocoronene (HBC) derivatives. Dipole substitution destabilizes the columnar crystalline phase except for the dimethoxy- and monoethynyl-substituted HBCs that undergo a reversible transformation to the crystalline phase. The disk dynamics are studied by dielectric spectroscopy and site-specific NMR techniques that provide both the time-scale and geometry of motion. Application of pressure results in the thermodynamic phase diagram that shows increasing stability of the crystalline phase at elevated pressures. Long-lived metastability was found during the transformation between the two phases. These results suggest new thermodynamic and kinetic pathways that favor the phase with the highest charge carrier mobility.     

Solvation force, structure and thermodynamics of fluids confined in geometrically rough pores

The effect of periodic surface roughness on the behavior of confined soft sphere fluids is investigated using grand canonical Monte Carlo simulations. Rough pores are constructed by taking the prototypical slit-shaped pore and introducing unidirectional sinusoidal undulations on one wall. For the above geometry our study reveals that the solvation force response can be phase shifted in a controlled manner by varying the amplitude of roughness. At a fixed amplitude of roughness, a, the solvation force for pores with structured walls was relatively insensitive to the wavelength of the undulation, lambda for 2.3/=0.5. The predictions of the superposition approximation, where the solvation force response for the rough pores is deduced from the solvation force response of the slit-shaped pores, was in excellent agreement with simulation results for the structured pores and for lambda/sigma(ff)>/=7 in the case of smooth walled pores. Grand potential computations illustrate that interactions between the walls of the pore can alter the pore width corresponding to the thermodynamically stable state, with wall-wall interactions playing an important role at smaller pore widths and higher amplitudes of roughness.     

Reference interaction site model and molecular dynamics study of structure and thermodynamics of methanol

Thermodynamic and structural properties of various models of liquid methanol are investigated in the framework provided by the reference interaction site model (RISM) theory of molecular fluids. The theoretical predictions are systematically compared with molecular dynamics simulations both at ambient conditions and along a few supercritical isotherms. RISM results for the liquid-vapor phase separation are also obtained and assessed against available Gibbs ensemble Monte Carlo data. At ambient conditions, the theoretical correlations weakly depend on the specific details of the molecular models and reproduce the simulation results with different degrees of accuracy, depending on the pair of interaction sites considered. The position and the strength of the hydrogen bond are quite satisfactorily predicted. RISM results for the internal energy are almost quantitative whereas the pressure is generally overestimated. As for the liquid-vapor phase coexistence, RISM predictions for the vapor branch and for the critical temperature are quite accurate; on the other side, the liquid branch densities, and consequently the critical density, are underestimated. We discuss our results in terms of intrinsic limitations, and suitable improvements, of the RISM approach in describing the physical properties of polar fluids, and in the perspective of a more general investigation of mixtures of methanol with nonpolar fluids of specific interest in the physics of associating fluids.     

Local structure of liquid Ti: Ab initio molecular dynamics study

Local order of liquid Ti is studied by ab initio molecular dynamics to address the unique liquid structure factor in experiments reported recently. The present study reveals that the local order of liquid Ti is in the form of fragments of the distorted icosahedral short range order, where the distortion is induced by strong bond order effects. We show that the fragments in the short-bond rich region separated from the background liquid account for the pronounced feature in structure factor of liquid Ti.     

Effect of temperature and pressure on the structure, dynamics, and hydrogen bond properties of liquid N-methylacetamide: a molecular dynamics study

The structure and dynamical properties of liquid N-methylacetamides (NMA) are calculated at five different temperatures and at four different pressures using classical molecular dynamics simulations. Our results are analyzed in terms of pressure-induced changes in structural properties by investigating the radial distribution functions of different atoms in NMA molecule. It is found that the first peak and also the second peak of C-O and N-H are well defined even at higher temperature and pressure. It is also observed that the number of hydrogen bonds increase with application of pressure at a given temperature. On the other hand, the calculated hydrogen bond energy (E(HB)) shows that the stability of hydrogen bond decreases with increasing of pressure and temperature. Various dynamical properties associated with translational and rotational motion of neat NMA are calculated and the self-diffusion coefficient of NMA is found to be in excellent agreement with the experiment and the behavior is non-Arrhenius at low temperatures with application of pressures. The single particle orientational relaxation time for dipole vector and N-C vector are also calculated and it is found that the orientational relaxation time follows Arrhenius behavior with a variation of temperature and pressure.     

Coarse-grained nonequilibrium approach to the molecular modeling of permeation through microporous membranes

We present a modeling technique that combines a statistical-mechanical coarse-graining scheme with a nonequilibrium molecular simulation algorithm to provide an efficient simulation of steady-state permeation across a microporous material. The coarse-graining scheme is based on the mapping of an atomistic model to a lattice using multidimensional free-energy and transition-state calculations. The nonequilibrium simulation algorithm is a stochastic, lattice version of the recently developed atomistic dual-control-volume grand canonical molecular dynamics. We demonstrate the approach on a model of methane permeating through a bulk portion of siliceous zeolite ZK4 at 300 K under imposed fugacity differences. We predict the coarse-grained (cage-level) density profiles and observe the development of nonlinearities as the magnitude of the fugacity difference is increased. From the net flux of methane we also predict a mean permeability coefficient under the various conditions. The simulation results are obtained over time scales on the order of microseconds and length scales on the order of dozens of nanometers.     

Coarse-grained molecular dynamics simulations of the sphere to rod transition in surfactant micelles

Surfactant molecules self-assemble in aqueous solutions to form various micellar structures such as spheres, rods, or lamellae. Although phase transitions in surfactant solutions have been studied experimentally, their molecular mechanisms are still not well understood. In this work, we show that molecular dynamics (MD) simulations using the coarse-grained (CG) MARTINI force field and explicit CG solvent, validated against atomistic MD studies, can accurately represent micellar assemblies of cetyltrimethylammonium chloride (CTAC). The effect of salt on micellar structures is studied for aromatic anionic salts, e.g., sodium salicylate, and simple inorganic salts, e.g., sodium chloride. Above a threshold concentration, sodium salicylate induces a sphere to rod transition in the micelle. CG MD simulations are shown to capture the dynamics of this shape transition and support a mechanism based on the reduction in the micelle-water interfacial tension induced by the adsorption of the amphiphilic salicylate ions. At the threshold salt concentration, the interface is nearly saturated with adsorbed salicylate ions. Predictions of the effect of salt on the micelle structure in different CG solvent models, namely, single-site standard water and three-site polarizable water, show qualitative agreement. This suggests that phase transitions in aqueous micelle solutions could be investigated by using standard CG water models which allow for 3 orders of magnitude reduction in the computational time as compared to that required for atomistic MD simulations.     

Structure,thermodynamics and diffusion in asymmetric binary mixtures: a molecular dynamics simulation study

Structural and thermodynamic properties as well as diffusion coefficients of binary fluid mixtures with asymmetry in mass, size, charge and their combinations have been studied using classical molecular dynamics simulations. The fluid mixture is modelled as spherical particles interacting via the Weeks–Chandler–Andersen and Coulomb potential. The diameter, charge and mass of the fluid particles are in the range 6–60 Å, 1–10e and 1—500 amu, respectively. Systematic variations in pair-correlation functions, thermodynamic properties as well as the self-diffusion coefficient are found with the size, charge and mass ratio of the particles. The self-diffusion coefficient for systems having more than one type of asymmetry is calculated and expressed in terms of diffusion coefficients of systems with only one type of asymmetry.     

Coarse-grained molecular dynamics simulation of self-assembly of polyacrylamide and sodium dodecylsulfate in aqueous solution

Coarse-grained molecular dynamics simulations have been performed to study the self-assembly of polymer, polyacrylamide (PAM) and surfactant, sodium dodecylsulfate (SDS) in aqueous solution. Our simulations revealed that PAM curled into clusters in the absence of SDS, while it was stretched if SDS was added. For the SDS-PAM complexes, the aggregate formation process can be divided into three stages: firstly, PAM quickly absorbs some SDS monomers until the radius of gyration (Rg) of polymer reaches a minimum; then, PAM stretches and the Rg of PAM increases due to more and more adsorbed SDS; ultimately, the commonly accepted "necklace" structure is formed with PAM located at the interface of the hydrophobic and hydrophilic regions of the SDS micelle. The main driving force for the association was hydrophobic interactions between the polymer backbone and the surfactant hydrophobic tails. As the concentration of SDS increased, the Rg of PAM increased up to a maximum, indicating the polymer was saturated with surfactant.     

Energy dispersive X-ray diffraction and molecular dynamics meet: The structure of liquid pyrrole

In this work, a coupled experimental–theoretical protocol for the study of molecular liquids is reported. Energy dispersive X-ray diffraction results are successfully interpreted with molecular dynamics. Several models, differing for geometry and force field are presented; their behavior in reproducing experimental data is discussed.     

Algorithms for GPU‐based molecular dynamics simulations of complex fluids: Applications to water,mixtures, and liquid crystals

A custom code for molecular dynamics simulations has been designed to run on CUDA‐enabled NVIDIA graphics processing units (GPUs). The double‐precision code simulates multicomponent fluids, with intramolecular and intermolecular forces, coarse‐grained and atomistic models, holonomic constraints, Nosé–Hoover thermostats, and the generation of distribution functions. Algorithms to compute Lennard‐Jones and Gay‐Berne interactions, and the electrostatic force using Ewald summations, are discussed. A neighbor list is introduced to improve scaling with respect to system size. Three test systems are examined: SPC/E water; an n‐hexane/2‐propanol mixture; and a liquid crystal mesogen, 2‐(4‐butyloxyphenyl)‐5‐octyloxypyrimidine. Code performance is analyzed for each system. With one GPU, a 33–119 fold increase in performance is achieved compared with the serial code while the use of two GPUs leads to a 69–287 fold improvement and three GPUs yield a 101–377 fold speedup. © 2015 Wiley Periodicals, Inc.     

Dynamical properties of liquid water from ab initio molecular dynamics performed in the complete basis set limit

Dynamical properties of liquid water were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (AIMD) simulations within the Kohn-Sham (KS) density functional theory employing the Becke-Lee-Yang-Parr exchange-correlation functional for the electronic structure. The KS orbitals were expanded in a discrete variable representation basis set, wherein the complete basis set limit can be easily reached and which, therefore, provides complete convergence of ionic forces. In order to minimize possible nonergodic behavior of the simulated water system in a constant energy (NVE) ensemble, a long equilibration run (30 ps) preceded a 60 ps long production run. The temperature drift during the entire 60 ps trajectory was found to be minimal. The diffusion coefficient [0.055 A2/ps] obtained from the present work for 32 D2O molecules is a factor of 4 smaller than the most up to date experimental value, but significantly larger than those of other recent AIMD studies. Adjusting the experimental result so as to match the finite-sized system used in the present study brings the comparison between theory and experiment to within a factor of 3. More importantly, the system is not observed to become "glassy" as has been reported in previous AIMD studies. The computed infrared spectrum is in good agreement with experimental data, especially in the low frequency regime where the translational and librational motions of water are manifested. The long simulation length also made it possible to perform detailed studies of hydrogen bond dynamics. The relaxation dynamics of hydrogen bonds observed in the present AIMD simulation is slower than those of popular force fields, such as the TIP4P potential, but comparable to that of the TIP5P potential.     

Investigation of structure of liquid 2,2,2 trifluoroethanol: neutron diffraction, molecular dynamics, and ab initio quantum chemical study

The molecular conformation and intermolecular H bonding in liquid 2,2,2 trifluoroethanol (TFE) have been studied by neutron diffraction with hydrogen/deuterium isotopic substitution at room temperature. For comparison, conformations of molecules and their dimers in the gas phase have also been calculated, based on the density functional theory. Energies, geometry, and vibrational frequencies of dimers were analyzed. Diffraction data analyzed by the "Monte Carlo determination of g(r)" (MCGR) method resulted in a molecular structure in agreement with the findings from gas phase electron diffraction experiments and density functional calculations. The intermolecular structure functions were compared to the same functions obtained from a molecular dynamics simulation. All of the composite radial distribution functions are in good agreement with the simulation results. According to our calculation the hydrogen-bonded aggregation size is smaller in pure liquid TFE than in pure liquid ethanol.     

Computationally useful bridge diagram series for the structure and thermodynamics of Lennard-Jones fluids

The first two orders of bridge diagrams, those with two and three field points, have been calculated exactly for the Lennard-Jones fluid for several isotherms. The method of calculation was one of expansion in Legendre polynomials, and the dependence of the method on the number of polynomials needed for accurate results was investigated. Thermodynamic and structural properties of the Lennard-Jones fluid calculated from integral equation methods with the inclusion of bridge diagrams were found to be systematically improved. Two attempts at predicting the missing bridge diagrams of even higher order were discussed. The first, which uses the functional form of those diagrams that were calculated exactly, showed no significant improvement. The second, a series sum based on the first two orders of calculated diagrams and motivated by the success of a similar heuristic sum in the case of hard spheres, was extremely successful. When the series sum was employed, thermodynamic and structural quantities were improved to the point where the difference between simulation results and integral equation results was of the same order as the error in the simulations themselves. Received: 9 January 1997 / Accepted 28 January 1997     

On the short-time limit of ring polymer molecular dynamics

We examine the short-time accuracy of a class of approximate quantum dynamical techniques that includes the centroid molecular dynamics (CMD) and ring polymer molecular dynamics (RPMD) methods. Both of these methods are based on the path integral molecular dynamics (PIMD) technique for calculating the exact static equilibrium properties of quantum mechanical systems. For Kubo-transformed real-time correlation functions involving operators that are linear functions of positions or momenta, the RPMD and (adiabatic) CMD approximations differ only in the choice of the artificial mass matrix of the system of ring polymer beads that is employed in PIMD. The obvious ansatz for a general method of this type is therefore to regard the elements of the PIMD (or Parrinello-Rahman) mass matrix as an adjustable set of parameters that can be chosen to improve the accuracy of the resulting approximation. We show here that this ansatz leads uniquely to the RPMD approximation when the criterion that is used to select the mass matrix is the short-time accuracy of the Kubo-transformed correlation function. In particular, we show that the leading error in the RPMD position autocorrelation function is O(t(8)) and the error in the velocity autocorrelation function is O(t(6)), for a general anharmonic potential. The corresponding errors in the CMD approximation are O(t(6)) and O(t(4)), respectively.