Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models.

Thermodynamic data are often used to calibrate or test amomic-level (AL) force fields for molecular dynamics (MD) simulations. In contrast, the majority of coarse-grained (CG) force fields do not rely extensively on thermodynamic quantities. Recently, a CG force field for lipids, hydrocarbons, ions, and water, in which approximately four non-hydrogen atoms are mapped onto one interaction site, has been proposed and applied to study various aspects of lipid systems. To date, no extensive investigation of its capability to describe salvation thermodynamics has been undertaken. In the present study, a detailed picture of vaporization, solvation, and phase-partitioning thermodynamics for liquid hydrocarbons and water was obtained at CG and AL resolutions, in order to compare the two types or models and evaluate their ability to describe thermodynamic properties in the temperature range between 263 and 343 K. Both CG and AL models capture the experimental dependence of the thermodynamic properties on the temperature, albeit a systematically weaker dependence is found for the CG model. Moreover, deviations are found for solvation thermodynamics and for the corresponding enthalpy-entropy compensation for the CG model. Particularly water/oil repulsion seems to be overestimated. However, the results suggest that the thermodynamic properties considered should be reproducible by a CG model provided it is reparametrized on the basis of these liquid-phase properties.     

Thermodynamic and transport properties of carbon dioxide from molecular simulation

Monte Carlo and molecular dynamics simulations have been used in order to test the ability of a three center intermolecular potential for carbon dioxide to reproduce literature experimental thermophysical values. In particular, both the shear viscosity under supercritical conditions and along the phase coexistence line, as well as the thermal conductivity under supercritical conditions, have been calculated. Together with the already reported excellent agreement for the phase coexistence densities, the authors find that the agreement with experimental values is, in general, good, except for the thermal conductivity at low density. Although extended versions of the model were employed, which include an explicit account of bending and vibrational degrees of freedom, a significant difference was still found with respect to the reported experimental value.     

Water in carbon nanotubes: adsorption isotherms and thermodynamic properties from molecular simulation

Grand canonical Monte Carlo simulations are performed to study the adsorption of water in single-walled (6:6), (8:8), (10:10), (12:12), and (20:20) carbon nanotubes in the 248-548 K temperature range. At room temperature the resulting adsorption isotherms in (10:10) and wider single-walled carbon nanotubes (SWCNs) are characterized by negligible water uptake at low pressures, sudden and complete pore filling once a threshold pressure is reached, and wide adsorption/desorption hysteresis loops. The width of the hysteresis loops decreases as pore diameter narrows and it becomes negligible for water adsorption in (8:8) and (6:6) SWCNs. Results for the isosteric heat of adsorption, density profiles along the pore axis and across the pore radii, order parameter across the pore radii, and x-ray diffraction patterns are presented. Layered structures are observed when the internal diameter of the nanotubes is commensurate to the establishment of a hydrogen-bonded network. The structure of water in (8:8) and (10:10) SWCNs is ordered when the temperature is 298 and 248 K, respectively. By simulating adsorption isotherms at various temperatures, the hysteresis critical temperature, e.g., the lowest temperature at which no hysteresis can be detected, is determined for water adsorbed in (20:20), (12:12), and (10:10) SWCNs. The hysteresis critical temperature is lower than the vapor-liquid critical temperature for bulk Simple Point Charge-Extended (SPCE) water model.     

A novel equation of state for the prediction of thermodynamic properties of fluids

This work proposes a new equation of state (EOS) based on molecular theory for the prediction of thermodynamic properties of real fluids. The new EOS uses a novel repulsive term, which gives the correct hard sphere close packed limit and yields accurate values for hard sphere and hard chain virial coefficients. The pressure obtained from this repulsive term is corrected by a combination of van der Waals and Dieterici potentials. No empirical temperature functionality of the parameters has been introduced at this stage. The novel EOS predicts the experimental volumetric data of different compounds and their mixtures better than the successful EOS of Peng and Robinson. The prediction of vapor pressures is only slightly less accurate than the results obtained with the Peng-Robinson equation that is designed for these purposes. The theoretically based parameters of the new EOS make its predictions more reliable than those obtained from purely empirical forms.     

A three-parameter cubic equation of state for prediction of thermodynamic properties of fluids

A new cubic three-parameter equation of state has been proposed for PVT and VLE calculations of simple, high polar and associating fluids. The parameters are temperature dependent in sub-critical region, but temperature independent in super-critical region. The results for 42 simple and 14 associative pure compounds indicate that the calculated saturation properties and volumetric properties over the whole temperature range, up to high pressures, by the proposed equation of state (EOS), were in better agreement with the experimental data, compared with those obtained by the five well-known EOSs (P–R, P–T, Adachi et al., Yu–Lu, and M4). Two derivative properties, molar enthalpy and heat capacity of water and ammonia have been calculated, and demonstrated the thermodynamic consistency of the EOS parameters. Also VLE calculations have been performed for 41 binary mixtures of different type of fluids, including those of interest in petroleum industry. The results indicated the high capability of the proposed EOS for calculating the thermodynamic properties of pure and fluid mixtures.     

Viabilty of atomistic potentials for thermodynamic properties of carbon dioxide at low temperatures

Investigation into volumetric and energetic properties of several atomistic models mimicking carbon dioxide geometry and quadrupole momentum covered the liquid-vapor coexistence curve. Thermodynamic integration over a polynomial and an exponential-polynomial path was used to calculate free energy. Computational results showed that model using GROMOS Lennard-Jones parameters was unsuitable for bulk CO(2) simulations. On the other hand, model with potential fitted to reproduce only correct density-pressure relationship in the supercritical region proved to yield correct enthalpy of vaporization and free energy of liquid CO(2) in the low-temperature region. Except for molar volume at the upper part of the vapor-liquid equilibrium line, the bulk properties of exp-6-1 parametrization of ab initio CO(2) potential were in a close agreement with the experimental results. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1772-1781, 2001     

Polymer translocation through a nanopore induced by adsorption: Monte Carlo simulation of a coarse-grained model

Dynamic Monte Carlo simulation of a bead-spring model of flexible macromolecules threading through a very narrow pore in a very thin rigid membrane are presented, assuming at the cis side of the membrane a purely repulsive monomer-wall interaction, while the trans side is attractive. Two choices of monomer-wall attraction epsilon are considered, one choice is slightly below and the other slightly above the "mushroom to pancake" adsorption threshold epsilon(c) for an infinitely long chain. Studying chain lengths N=32, 64, 128, and 256 and varying the number of monomers N(trans) (time t=0) that have already passed the pore when the simulation started, over a wide range, we find for epsilonepsilon(c) a finite number N(trans)(t=0) suffices that the translocation probability is close to unity. In the case epsilonepsilon(c), we find that the translocation time scales as tau proportional, variant N(1.65+/-0.08). We suggest a tentative scaling explanation for this result. Also the distribution of translocation times is obtained and discussed.     

Thermodynamic properties of carbon dioxide derived from the speed of sound

Thermodynamic properties of CO₂ are derived from speed of sound in the temperature range 300 to 360 K (from 0 to 6 MPa), and 300 to 220 K (from 0 to 90% of the saturation pressure). The density, the specific heat capacity at constant pressure, and the specific heat capacity at constant volume are obtained by numerical integration of differential equations connecting the speed of sound with other thermodynamic properties. The set of differential equations is solved as the initial value problem, with the initial values specified along the isotherm at 300 K in terms of several accurate values of the density and the specific heat capacity at constant pressure. The density, the specific heat capacity at constant pressure and the specific heat capacity at constant volume are derived with the absolute average deviations of 0.018%, 0.19%, and 0.18%, respectively. The results of numerical integration are extrapolated to the saturation line for ρ, c _p , and c _v with the absolute average deviations of 0.056%, 2.31%, and 1.32%, respectively.     

Polyureas from diamines and carbon dioxide: synthesis, structures and properties

Polyureas were synthesized from diamines and carbon dioxide in the absence of any catalyst or solvent, analogous to the synthesis of urea from condensation of ammonia with carbon dioxide. The method used carbon dioxide as a carbonyl source to substitute highly toxic isocyanates for the synthesis of polyureas. FTIR and DFT calculations confirmed that strong bidentate hydrogen bonds were formed between urea motifs, and XRD patterns showed that the PUas were highly crystalline and formed a network structure through hydrogen bonds, which served as physical cross-links. The long chain PUas presented a microphase separated morphology as characterized by SAXS and showed a high melting temperature above 200 °C. The PUas showed high resistance to solvents and excellent thermal stability, which benefitted from their special network structures. The PUas synthesized by this method are a new kind of functional material and could serve some areas where their analogues with similar functional groups could not be applied.     

MD simulation of the transitions between B-DNA and A-DNA in the framework of a coarse-grained model

Transitions between the B and A forms of a short DNA double helix (12 base pairs) at different salt concentrations in an aqueous solution have been studied by the molecular dynamics method in the framework of a coarse-grained model with explicit ions but without friction. It has been shown that the A-DNA, stable at high salt concentrations, is a dynamic conglomerate of the molecule and the ions coming from the solution into the deep major groove and then leaving it. In such a short helix, in the model without friction, even at low salt concentrations, transitions from B-DNA to A-DNA and back are frequent and fast. Stable ADNA (without transitions to B-DNA) forms at salt concentrations greater than 0.45 mol/L.     

A coarse-grained model and associated lattice Monte Carlo simulation of the coil-helix transition of a homopolypeptide

A new coarse-grained lattice model neglecting atomic details is proposed for the coil-helix transition and a new physical parameter is suggested to characterize a helical structure. In our model, each residue is represented by eight lattice sites, and side groups are not considered explicitly. Chirality and hydrogen bonding are taken into consideration in addition to chain connectivity and the excluded volume effect. Through a dynamic Monte Carlo simulation, the physical properties of the coil-helix transition of a single homopolypeptide have been produced successfully within a short computing time on the PC. We also examined the effects of the variation of chain configurations including chain size and chain shape, etc. A spatial correlation function has been introduced in order to characterize periodicity of a helical chain in a simple way. A propagation parameter and a nucleation parameter have also been calculated, which compares favorably with the results of the Zimm-Bragg theory for the coil-helix transition.     

Molecular simulation of the homogeneous crystal nucleation of carbon dioxide

We report on a molecular simulation study of the homogeneous nucleation of CO2 in the supercooled liquid at low pressure (P = 5 MPa) and for degrees of supercooling ranging from 32% to 60%. In all cases, regardless of the degree of supercooling, the structure of the crystal nuclei is that of the Pa3 phase, the thermodynamically stable phase. For the more moderate degree of supercooling of 32%, the nucleation is an activated process and requires a method to sample states of high free energy. In this work, we apply a series of bias potentials, which promote the ordering of the centers of mass of the molecules and allow us to gradually grow crystal nuclei. The reliability of the results so obtained is assessed by studying the evolution of the nuclei in the absence of any bias potential, and by determining their probability of growth. We estimate that the size of the critical nucleus, for which the probability of growth is 0.5, is approximately 240 molecules. Throughout the nucleation process, the crystal nuclei clearly exhibit a Pa3 structure, in apparent contradiction with Ostwald's rule of stages. The other polymorphs have a much larger free energy. This makes their formation highly unlikely and accounts for the fact that the nucleation of CO2 proceeds directly in the stable Pa3 structure.     

Computation of some thermodynamic properties of nitrogen using a new intermolecular potential from molecular dynamics simulation

A new pair-potential energy function of nitrogen has been determined via the inversion of reduced viscosity collision integrals and fitted to obtain an analytical potential form. The pair-potential reproduces the second virial coefficient, viscosity, thermal conductivity, self-diffusion coefficient, and thermal diffusion factor of nitrogen in a good accordance with experimental data over wide ranges of temperatures and densities. We have also performed the molecular dynamics simulation to obtain pressure, internal energy, heat capacity at constant volume, and self-diffusion coefficient of nitrogen at different temperatures and densities using our calculated pair-potential and some other potentials. The molecular dynamics of the nitrogen molecules has been also used to determine nitrogen equation of state in two (low and high) pressure ranges. Our results are in a good agreement with experiment and literature values.     

Vapor+liquid equilibrium of water, carbon dioxide, and the binary system, water+carbon dioxide, from molecular simulation

NVT- and NpT-Gibbs ensemble Monte Carlo (GEMC) simulations were applied to describe the vapor–liquid equilibrium of water (between 323 and 573 K), carbon dioxide (between 230 and 290 K) and their binary mixtures (between 348 and 393 K). The properties of supercritical carbon dioxide were determined between 310 and 520 K by NpT-MC simulations. Literature data for the effective pair potentials (for water: the SPC-, SPC/E-, and TIP4P potential models; for carbon dioxide: the EPM2 potential model) were used to describe the properties of the pure substances. The vapor pressures of water and carbon dioxide are calculated. For water, the SPC- and TIP4P models give superior results for the vapor pressure when compared to the SPC/E model. The vapor–liquid equilibrium of the binary mixture, carbon dioxide–water, was predicted using the SPC- as well as the TIP4P model for water and the EPM2 model for carbon dioxide. The interactions between carbon dioxide and water were estimated from the pair potentials of the pure components using common mixing rules without any adjustable binary parameter. Agreement of the predicted data for the compositions of the coexisting phases in vapor–liquid equilibrium and experimental results is observed within the statistical uncertainties of the simulation results in the investigated range of state, i.e. at pressures up to about 20 MPa.     

High-throughput prediction of blood-brain partitioning: a thermodynamic approach

A high-throughput in silico screening tool for potentially CNS active compounds was developed on the basis of the correlation of solvation free energies and blood-brain partitioning (log(cbrain/cblood) = log BB) data available from experimental sources. Utilizing a thermodynamic approach, solvation free energies were calculated by the fast and efficient generalized Born/surface area continuum solvation model, which enabled us to evaluate more than 10 compounds/min. Our training set involved a structurally diverse set of 55 compounds and yielded a function of log BB = 0.035Gsolv + 0.2592 (r = 0.85, standard error 0.37). Calculation of solvation free energies for 8700 CNS active compounds (CIPSLINE database) revealed that Gsolv is higher than -50 kJ/mol for the 96% of these compounds which can be used as suitable criteria for the identification of compounds preferable for CNS penetration.     

Dielectric constant and density dependence of the structure of supercritical carbon dioxide using a new modified empirical potential model: a Monte Carlo simulation study

Two modified versions of the Elementary Physical Model (EPM) [J. Phys. Chem. 1995, 99, 12021] for supercritical carbon dioxide have been proposed in this work and their validities are affirmed by computing the thermodynamic properties and dielectric constant up to 910 kg/m3 with use of canonical ensemble Monte Carlo simulation. Simulations performed for 500 molecules with the EPM2-M model reproduce the experimental data accurately at all thermodynamic states. The structural analyses demonstrate that the aggregation is strong at low density while the coordination number is large at high density. In addition, a detailed study on the radial and angular correlation functions reveals that the T-shaped geometry is dominate while a variety of other structures still appear in the first coordination shell. Furthermore, the angular correlation functions show that the probability of a molecule being oriented toward the convex side of another molecule is equal to that pointing toward the concave side since the molecular nonlinearity of carbon dioxide is only marginal. As the distance between two molecules increases, the preferred orientations disappear quickly and all the results are in good agreement with the prior ab initio calculation [J. Chem. Phys. 2004, 120, 9694].     

Interactions of lipid bilayers with supports: a coarse-grained molecular simulation study

The study of lipid structure and phase behavior at the nanoscale is of utmost importance due to implications in understanding the role of the lipids in biochemical membrane processes. Supported lipid bilayers play a key role in understanding real biological systems, but they are vastly underrepresented in computational studies. In this paper, we discuss molecular dynamics simulations of supported lipid bilayers using a coarse-grained model. We first focus on the technical implications of modeling solid supports for biomembrane simulations. We then describe noticeable influences of the support on the systems. We are able to demonstrate that the bilayer system behavior changes when supported by a hydrophilic surface. We find that the thickness of the water layer between the support and the bilayer (the inner-water region in the latter part of this paper) adapts through water permeation on the microsecond time scale. Additionally, we discuss how different surface topologies affect the bilayer. Finally, we point out the differences between the two leaflets induced by the support.