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.     

A computer simulation study of water drying at the interface of protein chains

This study investigated the water drying (cavitation) in the interfacial region of two chains of a dimeric protein by nanosecond molecular dynamics simulations using explicit water representation. Separation-induced cavity of water was directly observed in the region. We evaluated the separation length scale of two chains on which the drying transition occurs, and the average number of water molecules that are expelled from the interfacial region during the transition. The obtained values can be rationalized by Kelvin equation for finite lateral size of confinement [K. Lum and A. Luzar, Phys. Rev. E 56, R6283 (1997)]. Also, we found that the drying transition is accompanied by an exponential reduction in the average hydrogen-bond number per interfacial water molecule. The results of this study may deepen the understanding of how hydrophobic interaction drives the assembly of protein chains.     

A Monte Carlo simulation of grafted poly(ethylene oxide) chains

Conformational changes of a simplified model of grafted poly(ethylene oxide) (PEO) chains were simulated using an off-lattice Monte Carlo model. A random-walk scheme was used in our simulations. The initial polymer structure was modeled with molecular mechanics and models of grafted polymer chains were built using programs developed in our laboratory. During the simulation, all bond angles and bond lengths were kept fixed while the dihedral angles of backbones were changed to search for energy-favorite conformations. Torsional energy, van der Waals interaction, and Coulombic interaction were considered. Periodic boundary conditions were implemented. In addition, the solvent quality was simulated implicitly by modifying the Lennard-Jones 12–6 van der Waals expression. Each PEO chain, 50-monomer long, was represented with a united-atom model. Eight series of simulations with varying solvent quality, simulation temperature, and Coulombic interaction were carried out. For each series, nine different initial grafting densities of grafted PEO chains were considered. Five different conformations were simulated at each grafting density. The calculated system energies, scaling properties, and atom density profiles were studied. Changes in solvent quality produced different structural behaviors. As the grafting density increased, there was a mushroom-to-brush transition, and the scaling property of average layer thickness was dependent on the grafting density.     

Self-assembly of amphiphilic molecules: A review on the recent computer simulation results

We provided a short review on the recent progresses in computer simulations of adsorption and self-assembly of amphiphilic molecules. Owing to the extensive applications of amphiphilic molecules, it is very important to understand thoroughly the effects of the detailed chemistry, solid surfaces and the degree of confinement on the aggregate morphologies and kinetics of self-assembly for amphiphilic systems. In this review we paid special attention on (i) morphologies of adsorbed surfactants on solid surfaces, (ii) self-assembly in confined systems, and (iii) kinetic processes involving amphiphilic molecules.     

Properties of rotating nanoalloys formed by cluster collision: a computer simulation study

Results of dynamical simulations of collision-induced formation and properties of bimetallic nanoparticles are presented and analyzed. The analysis includes the effects of the collision energy and the impact parameter. For nonzero impact parameters, the formed (in many cases Janus-type) nanoparticles are rotating. The energy of the rotating nanoparticles is decomposed into the rotational and vibrational components, and the structural effects of these components are analyzed. Comparison is made with the case of the corresponding homoatomic systems, formed by collision of nanoparticles with the same elemental composition.     

Interaction between small colloidal particles and molecular chains with selectively adsorbing groups: computer simulation study

Using the Monte Carlo simulation technique and the method of simulated annealing, we study interactions between small (nanometric) particles and flexible‐chain polymers with sticker groups which selectively adsorb on the particles and also can strongly attract each other. For the chains with two end stickers (telechelic polymers), we find that the colloidal particles adsorbing on the polymers play the role of junction points (locks) which bind together the ends of different chains. This direct or indirect binding leads to the formation of a web‐like structure throughout the sample: colloidal particles and chain stickers group into mixed clusters – “drops of a fog” – which are wrapped by polymer chains and connected by bridges. Analyzing static structure factors, we show that the selectively adsorbing telechelic polymers can affect the equilibrium spatially homogeneous distribution of colloidal particles that results in the appearance of a quasiregular structure on the intermediate scale related to the average intercluster distance. At sufficiently strong attraction between particles and chain end‐groups, most of the telechelic chains (>90%) adopt either a loop‐like or a stretched bridge‐like conformation, the most typical morphology of the system being a combination of these two structural elements. In the mixed clusters, the colloidal particles and the chain ends pack locally on a binary grid corresponding to a local crystal‐like arrangement. For the chains without attracting end‐groups, we observe the formation of elongated, rugby‐ball‐like clusters having alternate layers of particles and adsorbing chain groups.     

Dipolar and dispersion interactions in nematogens A computer simulation study

A classical system, consisting of identical cylindrically symmetric particles, with centres fixed on a simple-cubic lattice, may or may not support nematic—like orientational order depending on the interaction potential. For example, a Lebwohl-Lasher potential model produces orientational order, as does an anisotropic London—de Boer dispersion potential restricted to nearest neighbours, although increasing its range destroys the orientational order and brings about a staggered configuration of the system. In consequence, a Maier-Saupe molecular field treatment is appropriate in the first two cases, but not in the last. On the other hand, according to computer simulation results, a purely dipolar interaction produces a low temperature antiferroelectric phase which can be regarded as an extreme case of a nematogen. We carried out Monte Carlo simulations on a potential model defined by a linear combination of dipolar and full ranged London-de Boer dispersion terms, in order to study their competition. To save computer time and yet monitor the physically relevant changes, we have varied their relative weights, while keeping fixed both the temperature and the anisotropy parameter in the dispersion potential. Simulation results show that in energetic terms the two interactions are cooperative, whereas in structural terms their interplay brings about first a weak but recognizable increase of nematic ordering, and then its collapse with the onset of the staggered configuration.     

Coarse-grained simulation of amphiphilic self-assembly

The authors present a computer simulation study of amphiphilic self-assembly performed using a computationally efficient single-site model based on Gay-Berne [J. Chem. Phys. 74, 3316 (1981)] and Lennard-Jones particles. Molecular dynamics simulations of these systems show that free self-assembly of micellar, bilayer, and inverse micelle arrangements can be readily achieved for a single model parametrization. This self-assembly is predominantly driven by the anisotropy of the amphiphile-solvent interaction, amphiphile-amphiphile dispersive interactions being found to be of secondary importance. While amphiphile concentration is the main determinant of phase stability, molecular parameters such as head group size and interaction strength also have measurable affects on system properties.     

Effects of grafted polymer chains on lamellar membranes

We have investigated the effects of grafted polymer chains [poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide)] on the bending modulus and the intermembrane interactions of lamellar membranes (C(12)E(5) water) by means of a neutron spin-echo and a small-angle x-ray scattering technique. In this study the hydrophilic chain takes the mushroom configuration on the membrane. The bending modulus of the polymer-grafted membranes increases in proportion to the square of the end to end distance of the polymer chain, which agrees well with the theoretical prediction of Hiergeist and Lipowsky [J. Phys. II 6, 1465 (1996)]. From the interlamellar interaction point of view, the mushroom layer is renormalized to the membrane thickness, which enhances the repulsive Helfrich interaction. When the size of the decorated polymer chain increases to the interlamellar distance, however, the mushroom is squeezed so as to optimize the interlamellar potential. Further increase of the grafted polymer size brings a lamellar-lamellar phase separation, where the grafted polymer chains are localized in the dilute lamellar phase and the concentrated lamellar phase forms the onionlike texture.     

Properties of liquid crystal molecules from first principles computer simulation

We explore the valence charge distribution, equilibrium geometry and harmonic force fields of the 4-pentyl-4-cyanobiphenyl (5CB) molecule and the benzene (C6H6) molecule, which provides an important mesogenic fragment, using first principles techniques adapted from large scale electronic structure calculations of periodic solids. We present for the first time accurate structural data for the isolated 5CB molecule and observe subtle broken symmetries relative to the constituent mesogenic fragments. The dynamic properties of these molecules are determined by diagonalization of dynamical matrices, the elements of which are obtained directly from quantum mechanical Hellmann-Feynman forces. Results for both molecules are in excellent agreement with available spectroscopic data, and for benzene are comparable to the most accurate quantum chemistry calculations to date. For 5CB we also present values for the molecular dipole and quadrupole moments.     

A computer simulation of trapping electrophoresis

The gel electrophoretic migration of streptavidin-DNA complexes is severely altered by the phenomenon known as “trapping electrophoresis.” We present a first computer simulation study of this process. Our simulations use the very efficient biased reptation algorithm. The steady state is characterized by a large increase in band broadening and interband separation. However, we also find that for a narrow range of molecular sizes, the separation power of gel electrophoresis is greatly increased. We discuss the implications of our findings for the possible improvement of DNA sequencing technologies. © 1992 John Wiley & Sons, Inc.     

Dynamics of grafted star-branched polymers. A Monte Carlo study

Monte Carlo simulations of simple models of star-branched polymers were carried out. The model chains were confined to simple cubic lattice and consisted of f = 3 branches of equal length and the total number of polymer segments as well as the density of grafted chains on the surface were varied. The chains have had one arm end attached to an impenetrable plate. The simulations were performed by employing the set of local micromodifications of the chain conformations. The model chains were athermal, i.e. good solvent conditions were modeled, the excluded volume effect was present at the model. The density of grafted chains on the surface was varied from a single chain up to 0.3. The static and dynamic properties of the system were studied. The influence of polymer concentration as well as the polymer length on static and dynamic properties of the system studied was shown. The relation between the structure and short-time dynamics (relaxation times) was discussed.     

Langmuir and grafted monolayers of photochromic amphiphilic monodendrons of low generations

Four generations of monodendrons with multiple dodecyl alkyl tails (AA-N, N representing number of alkyl tails from 1 to 8), an azobenzene spacer group, and a carboxylic acid polar head have been studied at the air-water and air-solid interface using AFM, GIXD, X-ray reflectivity, and UV-vis spectrometry. The one and two tail molecules formed orthorhombic lateral packing with long-range intramonolayer ordering. Good agreement between molecular models and thickness measurements indicated that the one and two tail molecules orient along the surface normal. The increase in the cross-sectional mismatch caused by the presence of the multiple chains for the higher generations disrupted the long-range ordering and forced the alkyl tails to adopt quasi-hexagonal structure. The higher generations (AA-4 and AA-8) formed a kinked structure with the alkyl tails oriented perpendicular to the surface with the azobenzene group tilted at a large degree toward the surface. The photoisomerization behavior in dilute solutions, at the air-water interface, and for grafted layers demonstrated that lower generation monodendrons maintained the photochromic behavior after chemical grafting to the silicon substrates, although the confinement of the molecules in monolayers significantly increased the reorganization time.     

A molecular dynamics computer simulation study of room-temperature ionic liquids. II. Equilibrium and nonequilibrium solvation dynamics

The molecular dynamics (MD) simulation study of solvation structure and free energetics in 1-ethyl-3-methylimidazolium chloride and 1-ethyl-3-methylimidazolium hexafluorophosphate using a probe solute in the preceding article [Y. Shim, M. Y. Choi and H. J. Kim, J. Chem. Phys. 122, 044510 (2005)] is extended to investigate dynamic properties of these liquids. Solvent fluctuation dynamics near equilibrium are studied via MD and associated time-dependent friction is analyzed via the generalized Langevin equation. Nonequilibrium solvent relaxation following an instantaneous change in the solute charge distribution and accompanying solvent structure reorganization are also investigated. Both equilibrium and nonequilibrium solvation dynamics are characterized by at least two vastly different time scales--a subpicosecond inertial regime followed by a slow diffusive regime. Solvent regions contributing to the subpicosecond nonequilibrium relaxation are found to vary significantly with initial solvation configurations, especially near the solute. If the solvent density near the solute is sufficiently high at the outset of the relaxation, subpicosecond dynamics are mainly governed by the motions of a few ions close to the solute. By contrast, in the case of a low local density, solvent ions located not only close to but also relatively far from the solute participate in the subpicosecond relaxation. Despite this difference, linear response holds reasonably well in both ionic liquids.     

Controlled synthesis of amphiphilic biodegradable polylactide‐grafted dextran copolymers

The whole controlled synthesis of novel amphiphilic polylactide (PLA)‐grafted dextran copolymers was achieved. The control of the architecture of such biodegradable and potentially biocompatible copolymers has required a three‐step synthesis based on the “grafting from” concept. The first step consisted of the partial silylation of the dextran hydroxyl groups. This protection step was followed by the ring‐opening polymerization of D ,L ‐lactide initiated from the remaining OH functions of the partially silylated polysaccharide. The third step involved the silylether group deprotection under very mild conditions. Based on previous studies, in which the control of the first step was achieved, this study is focused on the last two steps. Experimental conditions were investigated to ensure a controlled polymerization of D ,L ‐lactide, in terms of grafting efficiency, graft length, and transesterification limitation. After polymerization, the final step was studied in order to avoid degradation of both polysaccharide backbone and polyester grafts. The chemical stability of dextran backbone was checked throughout each step of the synthesis. PLA‐grafted dextrans and PLA‐grafted (silylated dextrans) were proved to adopt a core‐shell conformation in various solvents. Furthermore, preliminary experiments on the potential use of these amphiphilic grafted copolymers as liquid/liquid interface stabilizers were performed. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 2577–2588, 2004     

A molecular dynamics simulation study on polymer networks of end-linked flexible or rigid chains

The differences in formation and structural properties of polymer networks consisting of end-linked flexible or rigid chains were studied by molecular dynamics simulation. Networks were formed from monodisperse, linear, short, flexible or rigid chains with functional end groups and a stoichiometric ratio of trifunctional cross-linkers. The rigid chains had a rodlike shape defined by an angle potential, while the flexible chains had no angle potential. In order to understand the influence of chain rigidity, all parameters of precursor chains (length, reactivity, bond potential, nonbonding potential) were the same, with the exception of the angle potential. The system density rho, corresponding to the concentration of monomer in solvent, was varied from 0.01 to 0.11. Different network structures resulting from the different processes of network formation were observed. Simulations showed that the flexible chains created an inhomogeneous network on a large scale via microgel cluster formation, in agreement with experimental observations, whereas the rigid chains rapidly created a homogeneous network in the entire system volume without first generating microgel clusters, with the additional difference that they gave rise to mutually interpenetrating networks at the local scale.     

Molecular force field investigation for Sulfur Hexafluoride: A computer simulation study

Force fields for Sulfur Hexafluoride (SF₆) from the literature, were investigated by means of their ability to reproduce experimental data in a wide range of thermodynamic conditions, including liquid, gas, vapor–liquid coexistence curve as well as supercritical states. Experimental data include numerous PVT state points, corresponding structural properties in terms of radial distribution functions, diffusion coefficient and shear viscosity. The existing force fields were extensively examined in the framework of molecular dynamics simulations and it is found that they do not accurately reproduce the macroscopic properties of the fluid, especially at high densities. To overcome this problem with the aim to obtain improved potential parameters that better reproduce experimental data, a multi-variable optimization of the force field parameters procedure has been systematically applied based on the “Simplex” method. Finally, it is found that for some common functional forms of these force fields, the new optimized parameters predict better the experimental properties of SF₆ under investigation compared to the original ones.     

A computer simulation study of the ordered phases of some mesogenic fullerene derivatives

We present a Monte Carlo simulation study of the phase behaviour and molecular organization of a system of fullerene-based mesogens, represented by a three-site model composed of a fullerene sphere and two mesogenic moieties rigidly attached to it. It is shown that a combination of suitably modified Lennard-Jones and Gay–Berne attractive–repulsive potentials allows a satisfactory qualitative modeling of the interactions between the fullerene derivatives under investigation. Indeed, simulation results show that, despite the crude representation of the molecular structure, our model generates nematic and smectic phases, thus accounting qualitatively for the basic experimental observations on the class of compounds considered.     

A molecular dynamics computer simulation study of room-temperature ionic liquids. I. Equilibrium solvation structure and free energetics

Solvation in 1-ethyl-3-methylmidazolium chloride and in 1-ethyl-3-methylimidazolium hexafluorophosphate near equilibrium is investigated via molecular dynamics computer simulations with diatomic and benzenelike molecules employed as probe solutes. It is found that electrostriction plays an important role in both solvation structure and free energetics. The angular and radial distributions of cations and anions become more structured and their densities near the solute become enhanced as the solute charge separation grows. Due to the enhancement in structural rigidity induced by electrostriction, the force constant associated with solvent configuration fluctuations relevant to charge shift and transfer processes is also found to increase. The effective polarity and reorganization free energies of these ionic liquids are analyzed and compared with those of highly polar acetonitrile. Their screening behavior of electric charges is also investigated.     

A computer simulation of model discotic dimers

We set up a model for discotic liquid crystal dimers and study, by means of Monte Carlo simulations, their phase behaviour and self–assembling properties, in comparison with the simpler monomeric case. Each discotic dimer is described by two oblate Gay–Berne ellipsoids connected by a flexible spacer, modelled by a harmonic “spring” of three different lengths. We find that dimerization in general yields produces a significant change on the phase behaviour, with an increase of the columnar–nematic transition temperature, a widening of the nematic region and the apparent suppression of the crystalline phase in favour of the columnar phase up to very low temperatures. Longer spacers prove to ease the formation of columns and to increase the orientational order. Contribution to the Fernando Bernardi memorial issue.