Helix formation in linear achiral dendronized polymers: a computer simulation study

We present a molecular simulation study of the structure of linear dendronized polymers. We use excluded volume interactions in the context of a generic coarse grained molecular model whose geometrical parameters are tuned to represent a poly(paraphenylene) backbone with benzyl ether, Frechet-type dendrons. We apply Monte Carlo sampling in order to investigate the formation of packing-induced chiral structures along the polymer backbone of these chemically achiral systems. We find that helical structures can be formed, usually with defects consisting of domains with reversed helical handedness. Clear signs of helical arrangements of the dendrons begin to appear for dendritic generation g=4, while for g=5 these arrangements dominate and perfect helices can be observed as equilibrium structures obtained from certain types of starting configurations.     

Protein adsorption on the hydrophilic surface of a glassy polymer: a computer simulation study

Using atomistic computer simulations, we study the adsorption of different globular protein fragments with different secondary structures on the surface of a hydrophilic glassy polymer, poly(vinyl alcohol), or PVA, and compare the results with our earlier calculations on hydrophobic graphite. The simulations were mainly carried out with implicit solvent in an effective dielectric medium by energy minimizations and molecular dynamics at room temperature. We find that on the hydrophilic PVA surface the fragments basically retain their globular shape with an incomplete denaturation, at variance with our earlier results for the same fragments on graphite. Correspondingly, the interaction energy between the fragments and the surface is significantly smaller than on graphite, both because less residues are in contact with the surface, and because they interact more weakly. Moreover, very few hydrogen bonds are formed between the adsorbate and the PVA surface, since both the protein fragments and the polymer chains separately optimize these interactions. Additional molecular dynamics simulations in explicit solvent were also performed to study the hydration of the adsorbed fragments and to estimate the possible solvation effects.     

Properties of star-branched and linear chains in confined space: a computer simulation study

We studied the properties of simple models of linear and star-branched polymer chains confined in a slit. The polymer chains were built of united atoms and were restricted to a simple cubic lattice. Two macromolecular architectures of the chain linear and star-branched with three branches (of equal length) were studied. The excluded volume was the only potential introduced into the model and thus, the system was athermal. The chains were put between two parallel and impenetrable surfaces. Monte Carlo simulations with a sampling algorithm based on chain’s local changes of conformation were carried out. The differences and similarities in the global size and the structure and of linear and star-branched chains were shown and discussed.     

Wetting properties of passivated metal nanocrystals at liquid-vapor interfaces: a computer simulation study

Molecular dynamics simulations have been employed to determine the contact angles of alkylthiol passivated gold nanocrystals adsorbed at the air-water interface. Simulations were performed using butane-, dodecane-, and octadecanethiol passivated nanoparticles. We demonstrate how the length of the surfactant chain can profoundly influence the wetting behavior of these nanoparticles. All particles were found to be stable at the air-water interface, possessing large, well-defined contact angles. We find that the shape of the dodecane- and octadecanethiol particles is strongly perturbed by the interface. We also present an analysis of the orientational ordering of water molecules at the dodecane-water interface and around butane- and dodecanethiol passivated nanoparticles. The orientational ordering translates into an electrostatic field around the nanoparticles, the magnitude of which corresponds with that of the water liquid-vapor interface.     

Excluded volume effect of linear polymer molecules

An approximate closed expression for the excluded volume effect of linear polymer molecules is developed with the aid of a uniform expansion model of perturbed chains. The linear expansion factor α for the end-to-end distance is given by (α³ ? 1) + (3/8) (α⁵ ? α³) = (5/2)z where z is the excluded volume parameter. This equation is numerically close to the Ptitsyn equation in the ordinary range of α; i.e., for 1 ≤ α ≤ 2.     

Stability of Ca-montmorillonite hydrates: a computer simulation study

Classic simulations are used to study interlayer structure, swelling curves, and stability of Ca-montmorillonite hydrates. For this purpose, NP(zz)T and muP(zz)T ensembles are sampled for ground level and given burial conditions. For ground level conditions, a double layer hydrate having 15.0 A of basal spacing is the predominant state for relative vapor pressures (p/p0) ranging 0.6-1.0. A triple hydrate counting on 17.9 A of interlaminar distance was also found stable for p/p0 = 1.0. For low vapor pressures, the system may produce a less hydrated but still double layer state with 13.5 A or even a single layer hydrate with 12.2 A of interlaminar distance. This depends on the established initial conditions. On the other hand, the effect of burial conditions is two sided. It was found that it enhances dehydration for all vapor pressures except for saturation, where swelling is promoted.     

Free volume quantities and viscoelasticity of polymer glasses

We have investigated, in terms of the Cohen-Turnbull theory, a relationship for polycarbonate (PC) glasses between average stress relaxation times, <to, and average free volume sizes, 〈v_f〉, obtained from positron annihilation lifetime spectroscopy. This examination suggests that the minimum free volume required for stress relaxation, v*, decreases with decreasing temperature and that, near the glass transition temperature, only a subset of extremely large free volume elements contributes to the stress relaxation of PC glasses. This suggestion is consistent with the idea that near the glass transition temperature, the viscoelastic response is dominated by large-scale, main-chain motion, whereas at lower temperature it is controlled by local motion. Moreover, comparison with the v* value estimated from gas diffusivity through various PC species at room temperature shows that the required free volume size for stress relaxation in the glass transition region is much larger than that for gas diffusion. Previously we showed that the Doolittle equation fails to correlate viscoelastic relaxation times of polymer glasses with changing temperature; determining the free volume fraction, h, from theoretical analysis of volume recovery data and theory, the Doolittle equation is shown to be valid in PC above 135°C (T_g - 14°C) irrespective of temperature and physical aging times. This result supports the idea suggested in the previous article that, as glassy polymers approach the transition region, viscoelastic properties increasingly tend to be controlled by free volume. © 1996 John Wiley & Sons, Inc.     

Free volume studies in miscible polymer blend systems

This paper summarises the currently available literature concerned with measurement of free volume in miscible, amorphous polymer blends using positron annihilation lifetime spectroscopy (PALS) which probes excluded volume at the angstrom level. Previously reported data is compared with new data from a range of different blend systems. Miscible blends tend to show a negative deviation of free volume size (and to a lesser degree free volume fraction) on mixing due to the intimacy of packing of the blend component macromolecules. A largely immiscible system is also reported and shows a different behaviour (positive deviation of free volume size) and this is ascribed to additional free volume at the interface.     

Free volume and mass transport in polymer nanocomposites

This review relates the free volume properties and the morphology to the mass transport coefficients of polymer nanocomposites. Direct, utilising the method of Positron Annihilation Life-time Spectroscopy (PALS), or indirect measurements of the free volume in the nanocomposites are discussed and the influence of spherical or anisometric nanoparticles on its properties is examined.     

Water as a lubricant for graphite: a computer simulation study

The phase state and shear behavior of water confined between parallel graphite sheets are studied using the grand canonical Monte Carlo technique and TIP4P model for water. In describing the water-graphite interaction, two orientation-dependent potentials are tried. Both potentials are fitted to many-body polarizable model predictions for the binding energy and the equilibrium conformation of the water-graphite complex [K. Karapetian and K. D. Jordan in Water in Confining Geometries, edited by V. Buch and J. P. Devlin (Springer, Berlin, 2003), pp. 139-150]. Based on the simulation results, the property of water to serve as a lubricant between the rubbing surfaces of graphitic particles is associated, first, with the capillary condensation of water occurring in graphitic pores of monolayer width and, second, with the fact that the water monolayer compressed between graphite particles retains a liquidlike structure and offers only slight resistance to shear.     

Free energy of liquid water from a computer simulation via cell theory

A method to calculate the free energy of water from computer simulation is presented. Based on cell theory, it approximates the potential energy surface sampled in the simulation by an anisotropic six-dimensional harmonic potential to model the three hindered translations and three hindered rotations of a single rigid water molecule. The potential is parametrized from the magnitude of the forces and torques measured in the simulation. The entropy of these six harmonic oscillators is calculated and summed with a conformational term to give the total entropy. Combining this with the simulation enthalpy yields the free energy. The six water models examined are TIP3P, SPC, TIP4P, SPC/E, TIP5P, and TIP4P-Ew. The results reproduce experiment well: free energies for all models are within 1.6 kJ mol(-1) and entropies are within 3.6 J K(-1) mol(-1). Approximately two-thirds of the entropy comes from translation, a third from rotation, and 5% from conformation. Vibrational frequencies match those in the experimental infrared spectrum and assist in their assignment. Intermolecular quantum effects are found to be small, with free energies for the classical oscillator lying 0.5-0.7 kJ mol(-1) higher than in the quantum case. Molecular displacements and vibrational and zero point energies are also calculated. Altogether, these results validate the harmonic oscillator as a quantitative model for the liquid state.     

Hydrogen bonding in liquid alcohols: a computer simulation study

A series of molecular dynamics simulations has been performed to investigate hydrogen bonding in liquid alcohols. The systems considered have been methanol, ethanol, ethylene glycol and glycerol at 298 K. The hydrogen bonding statistics as well as the mean lifetime of the hydrogen bonds are analyzed. The results are compared with those corresponding to liquid water.     

Arrest of fluid demixing by nanoparticles: a computer simulation study

We use lattice Boltzmann simulations to investigate the formation of arrested structures upon demixing of a binary solvent containing neutrally wetting colloidal particles. Previous simulations for symmetric fluid quenches pointed to the formation of "bijels": bicontinuous interfacially jammed emulsion gels. These should be created when a glassy monolayer of particles forms at the fluid-fluid interface, arresting further demixing and rigidifying the structure. Experimental work has broadly confirmed this scenario, but it shows that bijels can also be formed in volumetrically asymmetric quenches. Here, we present new simulation results for such quenches, compare these to the symmetric case, and find a crossover to an arrested droplet phase at strong asymmetry. We then make extensive new analyses of the postarrest dynamics in our simulated bijel and droplet structures, on time scales comparable to the Brownian time for colloid motion. Our results suggest that, on these intermediate time scales, the effective activation barrier to ejection of particles from the fluid-fluid interface is smaller by at least 2 orders of magnitude than the corresponding barrier for an isolated particle on a flat interface.     

Interaction between light and crystallizing polymer: a simulation study

A study of light transmission through a crystallizing polymer has been carried out by graphic simulations, consisting of sporadic and pre-determinate nucleation and growth of disks (spherulites) in a rectangular area. Interaction between a light beam crossing a sample of polymer has been described by a series of simple graphical rules, accounting for both absorption and scattering. Results of the code well reproduce the experimental behavior observed in the literature of main beam light intensity emerging from a crystallizing polymer sample and allows a better understanding of the interaction between light and nucleating/growing units. Emerging light behavior calculated by the simulation has been adopted as the basis to suggest the dependence of the light scattering coefficient upon crystallization kinetic parameters.     

Anesthetic molecules embedded in a lipid membrane: a computer simulation study

The effect of four general anesthetic molecules, i.e., chloroform, halothane, diethyl ether and enflurane, on the properties of a fully hydrated dipalmitoylphosphatidylcholine (DPPC) membrane is studied in detail by long molecular dynamics simulations. Furthermore, to address the problem of pressure reversal, the effect of pressure on the anesthetic containing membranes is also investigated. In order to ensure sufficient equilibration and adequate sampling, the simulations performed have been at least an order of magnitude longer than the studies reported previously in the literature on general anesthetics. The results obtained can help in resolving several long-standing contradictions concerning the effect of anesthetics, some of which were the consequence of too short simulation time used in several previous studies. More importantly, a number of seeming contradictions are found to originate from the fact that different anesthetic molecules affect the membrane structure differently in several respects. In particular, halothane, being able to weakly hydrogen bound to the ester group of the lipid tails, is found to behave in a markedly different way than the other three molecules considered. Besides, we also found that two changes, namely lateral expansion of the membrane and increasing local disorder in the lipid tails next to the anesthetic molecules, are clearly induced by all four anesthetic molecules tested here in the same way, and both of these effects are reverted by the increase in pressure.     

Adhesive transitions in Newton black films: a computer simulation study

We report molecular dynamics simulations of Newton black films (NBFs), ultra thin films of aqueous solutions stabilized with two monolayers of ionic surfactants, sodium dodecyl sulfate. We show that at low water content conditions and areas per surfactant corresponding to experimental estimates in NBFs, homogeneous films undergo an adhesion "transition," which results in a very thin adhesive film coexisting with a thicker film. We identify the adhesive film with the equilibrium structure of the Newton black film. We provide here a direct microscopic view of the formation of these important structures, which have been observed in experimental studies of emulsions and foams. We also report a detailed investigation of the structural properties and interfacial fluctuation spectrum of the adhesive film. Our analysis relies on the definition of an "intrinsic surface," which is used to remove the averaging effect that the capillary waves have on the film properties.     

Reaction-induced phase separation of pseudo-interpenetrating polymer networks in polydisperse polymer blends: a simulation study

We develop a minimal model for the process of reaction-induced phase separation in a polydisperse polymer blend. During the reaction, one component undergoes polymerization, leading to phase separation via spinodal decomposition. The effect that changing the final degree of polymerization has on the phase-separation process is studied. Finally an elastic energy term is included mimicking the cross-linking process and the generation of a semi-interpenetrating polymer network. We show that the scaling of the dominant lengthscale with time varies according to the reaction conditions.     

Free energies of molecular crystal surfaces by computer simulation: application to tetrathiophene

We describe a general simulation protocol for the evaluation of the surface free energies of molecular crystals, which are of broad interest for phenomena such as polymorphism and crystal growth. The method has been applied to selected surfaces of two polymorphs of tetrathiophene. The simulations highlight an important temperature-dependent entropic contribution to the surface free energies, which is not included in widely used static simulations of surface structure and energetics.     

Liquid crystal phases of achiral banana-shaped molecules: a computer simulation study

The phase behaviour of achiral banana-shaped molecules was studied by computer simulation. The banana-shaped molecules were described by model intermolecular interactions based on the Gay-Berne potential. The characteristic molecular structure was considered by joining two calamitic Gay-Berne particles through a bond to form a biaxial molecule of point symmetry group C 2v with a suitable bending angle. The dependence on temperature of systems of N =1024 rigid banana-shaped molecules with bending angle ϕ=140° has been studied by means of Monte Carlo simulations in the isobaric-isothermal ensemble ( NpT ). On cooling an isotropic system, two phase transitions characterized by phase transition enthalpy, entropy and relative volume change have been observed. For the first time by computer simulation of a many-particle system of banana-shaped molecules, at low temperature an untilted smectic phase showing a global phase biaxiality and a spontaneous local polarization in the layers, i.e. a local polar arrangement of the steric dipoles, with an antiferroelectric-like superstructure could be proven, a phase structure which recently has been discovered experimentally. Additionally, at intermediate temperature a nematic-like phase has been proved, whereas close to the transition to the smectic phase hints of a spontaneous achiral symmetry breaking have been determined. Here, in the absence of a layered structure a helical superstructure has been formed. All phases have been characterized by visual representations of selected configurations, scalar and pseudoscalar correlation functions, and order parameters.