Adsorption of charged dendrimers: a Brownian dynamics study

The adsorption of isolated charged dendrimers onto oppositely charged flat surfaces is studied in this work using Brownian dynamics simulations. The dendrimer is modeled as a freely jointed bead-rod chain in which excluded-volume interactions are modeled by a repulsive Lennard-Jones potential and bead-bead and bead-surface electrostatic interactions are described by screened Coulombic potentials. Adsorption behavior is studied as a function of inverse screening length, dendrimer generation, and dendrimer charge distribution. Adsorbed dendrimers adopt a disclike conformation in which they flatten in the direction normal to the surface and expand in the direction parallel to the surface. As the inverse screening length increases, the dendrimer expands in the normal direction and contracts in the parallel direction, adopting a conformation that is more stretched in the normal direction. When the inverse screening length becomes sufficiently large, the dendrimer desorbs and adopts a spherelike conformation. Bead density profiles show that adsorbed dendrimers form a two-layer structure, with one layer corresponding to adsorbed beads and a second, less dense layer corresponding to beads one rod length away from the surface. They also reveal how the distribution of monomers within the dendrimer and near the surface can be tailored by changing various problem parameters. The results presented here are expected to be helpful in providing qualitative guidance for dendrimer design in various applications.     

Brownian dynamics simulation study on the self-assembly of incompatible star-like block copolymers in dilute solution

We study the self-assembly of symmetric star-like block copolymers (A(x))(y)(B(x))(y)C in dilute solution by using Brownian dynamics simulations. In the star-like block copolymer, incompatible A and B components are both solvophobic, and connected to the center bead C of the polymer. Therefore, this star-like block copolymer can be taken as a representative of soft and deformable Janus particles. In our Brownian dynamics simulations, these "soft Janus particles" are found to self-assemble into worm-like lamellar structures, loose aggregates and so on. By systematically varying solvent conditions and temperature, we build up the phase diagram to illustrate the effects of polymer structure and temperature on the aggregate structures. At lower temperatures, we can observe large worm-like lamellar aggregates. Upon increasing the temperature, some block copolymers detach from the aggregate; this phenomenon is especially sensitive for the polymers with less arms. The aggregate structure will be quite disordered when the temperature is high. The incompatibility between the two parts in the star-like block copolymer also affects the self-assembled structures. We find that the worm-like structure is longer and narrower as the incompatibility between the two parts is stronger.     

Effect of temperature on the EPR properties of a rhamnose alkoxy radical: a DFT molecular dynamics study

It has been shown previously that two distinctive variants (called RHop and RO4) exist of the radiation-induced rhamnose alkoxy radical. Density functional theory (DFT) calculations of the electron paramagnetic resonance (EPR) properties were found to be consistent with two separate measurements at different temperatures [E. Pauwels, R. Declerck, V. Van Speybroeck, M. Waroquier, Radiat. Res., in press]. However, the agreement between theory and experiment was only of a qualitative nature, especially for the latter radical. In the present work, it is examined whether this residual difference between theoretical and experimental spectroscopic properties can be explained by explicitly accounting for temperature in DFT calculations. With the aid of ab-initio molecular dynamics, a temperature simulation was conducted of the RO4 variant of the rhamnose alkoxy radical. At several points along the MD trajectory, g and hyperfine tensors were calculated, yielding time (and temperature) dependent mean spectroscopic properties. The effect of including temperature is evaluated but found to be within computational error.     

Silsesquioxane dendrimers as catalysts: a bite-sized molecular dynamics study

A method of calculating the bite (P-M-P) angle for dendritic ligands is reported. Diphenylphosphine terminated dendritic ligands were modified with either a single rhodium or a rhodium complex [HRh(CO)(2)] and molecular dynamics techniques used to run simulations to determine the dynamic bite angle (beta(d)) as a time averaged property. The effects of changing the composition of the dendritic branches is investigated and comparison with experimental hydroformylation data reveals that the dendrimer with the highest linear: branched ratio also has a dynamic bite angle closest to the theoretical ideal value of 120 degrees .     

The structure of phosphine-functionalised silsesquioxane-based dendrimers: a molecular dynamics study

Molecular dynamics modelling has been used to simulate the structures of phopshine-functionalised, silsesquioxane-based dendrimers whose excellent catalytic properties have been previously demonstrated. The effect of changing the chemical composition of the dendrimer branches is simulated. The results indicate that adding a methylene unit to a branch increases the overall size of the dendrimer but replacing a methylene unit with an oxygen atom decreases the size of the dendrimer. The size and shape of the dendrimers have also been simulated on changing the temperature and polarity of the solvent. The distribution of phosphine groups on the exterior has also been modelled and this suggests that all are available for bonding to catalytic metals in all the compounds.     

Internal structure of dendrimers in the melt under shear: a molecular dynamics study

The molecular structure of fluids composed of dendrimers of different generations is studied using nonequilibrium molecular dynamics (NEMD). NEMD results for dendrimer melts undergoing planar Couette flow are reported and analyzed with particular attention paid to the shear-induced changes in the internal structure of dendrimers. The radii of gyration, pair distribution functions and the fractal dimensionality of the dendrimers are determined at different strain rates. The location of the terminal groups is analyzed and found to be uniformly distributed throughout the space occupied by the molecules. The fractal dimension as a function of strain rate displays crossover behavior analogous to the Newtonian/non-Newtonian transition of shear viscosity.     

Form fluctuations of carbosilane dendrimers in dilute solution: a study using neutron spin echo spectroscopy

A series of carbosilane dendrimers with perfluorinated end groups has been prepared. The structure of these molecules in dilute solution is studied using small angle neutron scattering. For generations g<3 we find a non-spherical shape of the particles and a tendency for aggregation. This result is supported by the analysis of the diffusion coefficient obtained from photon correlation spectroscopy. The overall shape of the molecules is that of a core-shell particle. The generation 4 molecule is obtained as a compact sphere. Neutron spin echo spectroscopy reveals a relaxation time which is attributed to the form fluctuations of this particle.     

A Brownian dynamics study on the self-diffusion of charged tracers in dilute polyelectrolyte solutions

Brownian dynamics simulations with hydrodynamic interactions are conducted to investigate the self-diffusion of charged tracer particles in a dilute solution of charged polymers, which are modeled by bead-spring chains. The Debye-Hückel approximation is used for the electrostatic interactions. The hydrodynamic interactions are implemented by the Ewald summation of the Rotne-Prager tensor. Our simulations find that the difference in short- and long-time diffusivities is very slight in uncharged short-chain solutions. For charged systems, to the contrary, the difference becomes considerable. The short-time diffusivity is found to increase with increasing chain length, while an opposite behavior is obtained for the long-time diffusivity. The former is attributed to the hydrodynamic screening among beads in a same chain due to the bead connectivity. The latter is explained by the memory effect arising from the electrostatic repulsion and chain length. The incorporation of hydrodynamic interactions improves the agreement between the simulation prediction and the experimental result.     

Viscoelastic properties of dendrimers in the melt from nonequlibrium molecular dynamics

The viscoelastic properties of dendrimers of generation 1-4 are studied using nonequilibrium molecular dynamics. Flow properties of dendrimer melts under shear are compared to systems composed of linear chain polymers of the same molecular weight, and the influence of molecular architecture is discussed. Rheological material properties, such as the shear viscosity and normal stress coefficients, are calculated and compared for both systems. We also calculate and compare the microscopic properties of both linear chain and dendrimer molecules, such as their molecular alignment, order parameters and rotational velocities. We find that the highly symmetric shape of dendrimers and their highly constrained geometry allows for substantial differences in their material properties compared to traditional linear polymers of equivalent molecular weight.     

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.     

Comparison of properties of Aib-rich peptides in crystal and solution: a molecular dynamics study.

In order to study the differences of the structural properties of Aib-rich peptides in solution and in the crystalline state, molecular dynamics (MD) simulations of the Aib-containing peptide II (pBrBz-(Aib)5-Leu-(Aib)2-OMe) were performed in the crystalline state, starting from two different conformers obtained experimentally by X-ray diffraction. The structural properties as derived from X-ray crystallography (e.g., torsional angles and hydrogen bonds) are well-reproduced in both constant-volume and constant-pressure simulations, although the force-field parameters used result in a too-high density of the crystals. Through comparison with the results from previous MD and nuclear magnetic resonance (NMR) studies of the very similar peptide I (Z-(Aib)s-Leu-(Aib)2-OMe) in dimethylsulfoxide (DMSO) solution, it is found that, in the crystal simulation, the conformational distribution of peptide II is much narrower than that in the solution simulation of peptide. I. This leads to a significant difference in 3 [symbol: see text] (HN, HC alpha) coupling constant values, in agreement with experimental data, whereas the NOE intensities or proton-proton distance bounds appear insensitive to the difference in conformational distribution. For small peptides the differences between their conformational distribution in the crystalline form and in solution may be much larger than for proteins, a fact which should be kept in mind when interpreting molecular properties in the solution state by using X-ray crystallographic data.     

Molecular dynamics study of charged dendrimers in salt-free solution: effect of counterions

Polyamidoamine dendrimers, being protonated under physiological conditions, represent a promising class of nonviral, nanosized vectors for drug and gene delivery. We performed extensive molecular dynamics simulations of a generic model dendrimer in a salt-free solution with dendrimer's terminal beads positively charged. Solvent molecules as well as counterions were explicitly included as interacting beads. We find that the size of the charged dendrimer depends nonmonotonically on the strength of electrostatic interactions demonstrating a maximum when the Bjerrum length equals the diameter of a bead. Many other structural and dynamic characteristics of charged dendrimers are also found to follow this pattern. We address such a behavior to the interplay between repulsive interactions of the charged terminal beads and their attractive interactions with oppositely charged counterions. The former favors swelling at small Bjerrum lengths and the latter promotes counterion condensation. Thus, counterions can have a dramatic effect on the structure and dynamics of charged dendrimers and, under certain conditions, cannot be treated implicitly.     

Effect of temperature on the diffusion mechanism of xylene isomers in a FAU zeolite: a molecular dynamics study

The diffusion of o-, m-, and p-xylene in a FAU zeolite at 300-900 K was investigated using molecular dynamics simulations. Calculated self-diffusion coefficients of xylene isomers showed that the mobility of p-xylene was the fastest, m-xylene the second fastest, and o-xylene the slowest in the FAU zeolite at the same temperature. The diffusion activation energy of o-xylene, m-xylene and p-xylene was, respectively, determined to be 9.04, 7.45 and 6.44 kJ mol(-1) within the temperature range of 400 to 900 K, while to be 14.12, 13.59 and 15.47 kJ mol(-1) within the temperature range of 300 to 400 K. Xylene density profiles and orientational analysis suggested that this can be attributed to the xylene molecules that diffuse in the FAU zeolite by two different mechanisms at high and low temperatures. The behavior of motion for xylene in the FAU zeolite exhibits a "fluid-like" mode at high temperatures and exhibits a "jump-like" mode at low temperatures.     

Effect of nanostructure on the properties of water at the water-hydrophobic interface: a molecular dynamics simulation

The local structure of water near hydrophobic surfaces of different surface topographies has been analyzed by molecular dynamics simulation. An alkane crystal has been taken as the parent model for a hydrophobic surface. Surface structures were created by placing pits into it, which were half a nanometer deep and several nanometers wide. Around all structures, the water has a lower density, less orientational ordering, fewer water-water hydrogen bonds, and fewer surface contacts than for a flat unstructured surface. This indicates that the structured surfaces are more hydrophobic than the flat surface. Of the structures investigated, pits with a diameter of approximately 2.5 nm were effective in increasing the hydrophobic character of the surface.     

Structural properties of charge-stabilized ferrofluids under a magnetic field: a Brownian dynamics study

We present Brownian dynamics simulations of real charge-stabilized ferrofluids, which are stable colloidal dispersions of magnetic nanoparticles, with and without the presence of an external magnetic field. The colloidal suspensions are treated as collections of monodisperse spherical particles, bearing point dipoles at their centers and undergoing translational and rotational Brownian motions. The overall repulsive isotropic interactions between particles, governed by electrostatic repulsions, are taken into account by a one-component effective pair interaction potential. The potential parameters are fitted in order that computed structure factors are close to the experimental ones. Two samples of ferrofluid differing by the particle diameter and consequently by the intensity of the magnetic interaction are considered here. The magnetization and birefringence curves are computed: a deviation from the ideal Langevin behaviors is observed if the dipolar moment of particles is sufficiently large. Structure factors are also computed from simulations with and without an applied magnetic field H: the microstructure of the repulsive ferrofluid becomes anisotropic under H. Even our simple modeling of the suspension allows us to account for the main experimental features: an increase of the peak intensity is observed in the direction perpendicular to the field whereas the peak intensity decreases in the direction parallel to the field.     

Shape persistence and bistability of planar three-fold core polyphenylene dendrimers: a molecular dynamics study

We present an atomistic molecular dynamics investigation of the structural time evolution of isolated polyphenylene dendrimers, carbon based dendrimers with a planar core formed by a 1,3,5 trisubstituted benzene ring. Simulations are carried out at low (80 K) and room temperature. A general classification of the conformations (core conformations) assumed by the three dendrimer branches with respect to the planar core is presented. It is found that out of the six possible core conformations only four are stable, the remaining two being unstable for steric reasons. For second generation dendrimers, two of the four accessible core conformations are associated with an open arrangement of the three branches attached to the planar 3-fold core of the dendrimer, whereas the remaining two are associated with a collapsed arrangement of two branches. At low temperature the initial conformation is generally conserved whereas at room temperature jumps among the four possible core conformations are observed in the nanosecond time range. For second generation dendrimers the core conformation jumps are associated with an oscillation between two global shape states: open and collapsed. The computed bistability of the global shape suggests additional possible functional uses for some of these carbon based dendrimers.     

Proton transport in a binary biomimetic solution revealed by molecular dynamics simulation

We report the simulation results of the proton transport in a binary mixture of amphiphilic tetramethylurea (TMU) molecules and water. We identify different mechanisms that either facilitate or retard the proton transport. The efficiency of these mechanisms depends on the TMU concentration. The overall picture is more complicated than a recent suggestion that the presence of amphiphilic molecules suppresses the proton mobility by slowing down the reorientation of the surrounding water molecules. It has also been suggested that the hydronium ion induces local water orientational order, which results in an ordered region that has to move along with the proton potentially slowing down the proton transport as suggested by experiment. We find that water-wire like structures formed at low amphiphile concentrations facilitate proton transfer, and reduction of the hydrogen bond connectivity induced at high concentrations retards it.     

Polymer dynamics and topology: Extension of stars and dendrimers in external fields

We study the influence of topology on the extension of branched polymers subjected to external forces. Such forces can be applied mechanically (by micromanipulation techniques such as laser tweezers) or electrically (in the case of charged polymers). We focus on the unfold dynamics of star and dendrimer type structures. Some of the dynamical quantities of interest are: (i) the structural average of the mean monomer displacement, (ii) the elastic and the loss moduli and (iii) the mean displacement of a specified monomer. In a Gaussian‐type approach, (i) and (ii) depend only on the eigenvalues of the adjacency matrix whereas (iii) also requires the knowledge of the eigenvectors. Thus one can sometimes dispense with a full diagonalisation and use efficient recursion procedures. We highlight how the dynamic properties depend on topology: the number of branches and their length for stars and the number of generations for dendrimers. The intermediate time (crossover) behavior turns out to be most revealing of the underlying structure. We compare our results to those for fractal structures in external fields.     

Centroid molecular dynamics approach to the transport properties of liquid para-hydrogen over the wide temperature range

Fundamental transport properties of liquid para-hydrogen (p-H(2)), i.e., diffusion coefficients, thermal conductivity, shear viscosity, and bulk viscosity, have been evaluated by means of the path integral centroid molecular dynamics (CMD) calculations. These transport properties have been obtained over the wide temperature range, 14-32 K. Calculated values of the diffusion coefficients and the shear viscosity are in good agreement with the experimental values at all the investigated temperatures. Although a relatively large deviation is found for the thermal conductivity, the calculated values are less than three times the amount of the experimental values at any temperature. On the other hand, the classical molecular dynamics has led all the transport properties to much larger deviation. For the bulk viscosity of liquid p-H(2), which was never known from experiments, the present CMD has given a clear temperature dependence. In addition, from the comparison based on the principle of corresponding states, it has been shown that the marked deviation of the transport properties of liquid p-H(2) from the feature which is expected from the molecular parameters is due to the quantum effect.