Classical molecular dynamics study of [60]fullerene interactions with silica and polyester surfaces

This study examines the interaction of neutral and charged fullerenes with model silica and polyester surfaces. Molecular dynamics simulations at 298 K indicate that van der Waals forces are sufficiently strong in most cases to cause physisorption of the neutral fullerene particle onto the surfaces. The fullerenes are unable to penetrate the rigid silica surface but are generally able to at least partially infiltrate the flexible polymer surface by opening surface cavities. The introduction of charge to the fullerene generally leads to an increase in both the separation distance and Work of Separation with silica. However, the charged fullerenes generally exhibit significantly closer and stronger interactions with polyester films, with a distinct tendency to absorb into the "bulk" of the polymer. The separation distance and Work of Separation of C60 with each of the surfaces also depend greatly on the sign, magnitude, and localization of the charge on the particle. Cross-linking of the polyester can improve resistance to the neutral fullerene. Functionalization of the polyester surface (F and OH substituents) has been shown to prevent the C60 from approaching as close to the polyester surface. Fluorination leads to improved resistance to positively charged fullerenes, compared to the unmodified polyester. However, hydroxylation generally enables greater adhesion of charged fullerenes to the surface due to H-bonding and electrostatic attraction.     

Thermophoresis in liquids: a molecular dynamics simulation study

Thermophoresis in liquids is studied by molecular dynamics simulation (MD). A theory is developed that divides the problem in the way consistent with the characteristic scales. MD is then conducted to obtain the solution of each problem, which is to be all combined for macroscopic predictions. It is shown that when the temperature gradient is applied to the nonconducting liquid bath that contains neutral particles, there occurs a pressure gradient tangential to the particle surface at the particle-liquid interface. This may induce the flow in the interfacial region and eventually the particle to move. This applies to the material system that interacts through van der Waals forces and may be a general source of the thermophoresis phenomenon in liquids. The particle velocity is linearly proportional to the temperature gradient. And, in a large part of the given temperature range, the particle motion is in the direction toward the cold end and decreases with respect to the temperature. It is also shown that the particle velocity decreases or even reverses its sign in the lowest limit of the temperature range or with a particle of relatively weak molecular interactions with the liquid. The characteristics of the phenomenon are analyzed in molecular details.     

A molecular dynamics simulation of a homogeneous organic-inorganic hybrid silica membrane

A new molecular dynamics simulation method was successfully applied to construct a homogeneous organic-inorganic hybrid silica membrane using the hybrid-pcff (h-pcff) potential function. Analysis suggested that the hybrid BTESE silica membrane provided a looser network and larger cavity size for the enhancement of gas permeability and selectivity.     

Sodium diffusion through amorphous silica surfaces: a molecular dynamics study

We have studied the diffusion inside the silica network of sodium atoms initially located outside the surfaces of an amorphous silica film. We have focused our attention on structural and dynamical quantities, and we have found that the local environment of the sodium atoms is close to the local environment of the sodium atoms inside bulk sodo-silicate glasses obtained by quench. This is in agreement with recent experimental results.     

Implementation of pi-pi interactions in molecular dynamics simulation

No explicit pi-pi interaction term has been incorporated in the conventional molecular dynamics (MD) simulation programs in spite of its significant role in the folding of biomolecules and the clustering of organic chemicals. In this article, we propose a technique to emphasize the effect of pi-pi interactions using a function of energy and implement it into an MD simulation program. Several trial calculations show that the pi-pi incorporated program gives improved results consistent with experimental data on atom geometry and has no unfavorable interference with the conventional computational framework. This indicates an importance of the explicit consideration of pi-pi interactions in MD simulation.     

Interface tension of silica hydroxylated nanoparticle with brine: a combined experimental and molecular dynamics study

We have used molecular dynamics simulations to calculate the interfacial tension of hydroxylated SiO(2) nanoparticles under different temperatures and solutions (helium and brine with monovalent and divalent salts). In order to benchmark the atomistic model, quartz SiO(2) interfacial tension was measured based on inverse gas chromatography under He atmosphere. The experimental interfacial tension values for quartz were found between 0.512 and 0.617 N/m. Our calculated results for the interfacial tension of silica nanoparticles within helium atmosphere was 0.676 N/m, which is higher than the value found for the system containing He∕α-quartz (0.478 N/m), but it is similar to the one found for amorphous silica surface. We have also studied the interfacial tension of the nanoparticles in electrolyte aqueous solution for different types and salts concentrations (NaCl, CaCl(2), and MgCl(2)). Our calculations indicate that adsorption properties and salt solutions greatly influence the interfacial tension in an order of CaCl(2) > MgCl(2) > NaCl. This effect is due to the difference in distribution of ions in solution, which modifies the hydration and electrostatic potential of those ions near the nanoparticle.     

Origin of repulsive force and structure/dynamics of interfacial water in OEG-protein interactions: a molecular simulation study

Molecular simulations were performed to investigate the origin of the strong repulsive force acting on a protein as the protein approaches an oligo (ethylene glycol) self-assembled monolayer (OEG-SAM) surface. Since the repulsive force is mainly generated from water molecules, the force from the water molecules near the surface was calculated layer by layer to further identify the molecular origin of the repulsive force. Results show that the strong repulsive force acting on the protein near the OEG-SAM surface is dominantly generated by the interfacial water molecules located between the OEG-SAM surface and lysozyme. A hydroxyl-terminated SAM (OH-SAM) surface was used for comparison. No significant repulsive force was observed from the water molecules between the protein and OH-SAM surface. Further studies show that the dipole distribution of the interfacial water molecules is significantly affected by the OEG-SAM surface, as opposed to the negligible impact from the OH-SAM surface. The interfacial water molecules above the OEG-SAM surface stay longer and reorient more slowly than those above the OH-SAM surface. These results from this work support the hypothesis that the OEG-SAM surface interacts strongly with interfacial water molecules and creates a stable hydration layer that prevents proteins from adsorbing to the surface.     

Characterizing hydrophobicity at the nanoscale: a molecular dynamics simulation study

We use molecular dynamics (MD) simulations of water near nanoscopic surfaces to characterize hydrophobic solute-water interfaces. By using nanoscopic paraffin like plates as model solutes, MD simulations in isothermal-isobaric ensemble have been employed to identify characteristic features of such an interface. Enhanced water correlation, density fluctuations, and position dependent compressibility apart from surface specific hydrogen bond distribution and molecular orientations have been identified as characteristic features of such interfaces. Tetrahedral order parameter that quantifies the degree of tetrahedrality in the water structure and an orientational order parameter, which quantifies the orientational preferences of the second solvation shell water around a central water molecule, have also been calculated as a function of distance from the plate surface. In the vicinity of the surface these two order parameters too show considerable sensitivity to the surface hydrophobicity. The potential of mean force (PMF) between water and the surface as a function of the distance from the surface has also been analyzed in terms of direct interaction and induced contribution, which shows unusual effect of plate hydrophobicity on the solvent induced PMF. In order to investigate hydrophobic nature of these plates, we have also investigated interplate dewetting when two such plates are immersed in water.     

Systematic coarse-graining of nanoparticle interactions in molecular dynamics simulation

A recently developed multiscale coarse-graining procedure [Izvekov, S.; Voth, G. A. J. Phys. Chem. B 2005, 109, 2469] is extended to derive coarse-grained models for nanoparticles. The methodology is applied to C(60) and to carbonaceous nanoparticles produced in combustion environments. The coarse-graining of the interparticle force field is accomplished applying a force-matching procedure to data obtained from trajectories and forces from all-atom MD simulations. The CG models are shown to reproduce accurately the structural properties of the nanoparticle systems studied, while allowing for MD simulations of much larger self-assembled nanoparticle systems.     

Structure and dynamics of surfactant and hydrocarbon aggregates on graphite: a molecular dynamics simulation study

We have examined the structure and dynamics of sodium dodecyl sulfate (SDS) and dodecane (C12) molecular aggregates at varying surface coverages on the basal plane of graphite via classical molecular dynamics simulations. Our results suggest that graphite-hydrocarbon chain interactions favor specific molecular orientations at the single-molecule level via alignment of the tail along the crystallographic directions. This orientational bias is reduced greatly upon increasing the surface coverage for both molecules due to intermolecular interactions, leading to very weak bias at intermediate surface coverages. Interestingly, for complete monolayers, we find a re-emergent orientational bias. Furthermore, by comparing the SDS behavior with C12, we demonstrate that the charged head group plays a key role in the aggregate structures: SDS molecules display a tendency to form linear file-like aggregates while C12 forms tightly bound planar ones. The observed orientational bias for SDS molecules is in agreement with experimental observations of hemimicelle orientation and provides support for the belief that an initial oriented layer governs the orientation of hemimicellar aggregates.     

Performance of a rigid rod statistical mechanical treatment to predict monolayer ordering: a study of chain interactions and comparison with molecular dynamics simulation

A statistical mechanical model that treats hydrocarbon self-assembled monolayer (SAM) chains as rigid rods is examined to interrogate the mechanisms involved in monolayer ordering. The statistical mechanical predictions are compared to fully atomistic molecular dynamics simulations of SAMs with different packing densities. The monolayer chain order is examined as a function of surface coverage, chain-surface interactions, and chain–chain interactions. Reasonable interaction potentials are deduced from ab initio electronic structure calculations of small model systems. It is found that the chain-surface interaction is the most important parameter in formation of flat-lying monolayer phases, while formation of standing phase monolayers is driven most importantly by increased density of molecules at the surface. A brief discussion of the utility and validity of the rigid rod treatment is given in light of the molecular dynamics results.     

Interfacial fluctuations of block copolymers: a coarse-grain molecular dynamics simulation study

The lamellar and cylindrical phases of block copolymers have a number of technological applications, particularly when they occur in supported thin films. One such application is block copolymer lithography, the use of these materials to subdivide or enhance submicrometer patterns defined by optical or electron beam methods. A key parameter of all lithographic methods is the line edge roughness (LER), because the electronic or optical activities of interest are sensitive to small pattern variations. While mean-field models provide a partial picture of the LER and interfacial width expected for the block interface in a diblock copolymer, these models lack chemical detail. To complement mean-field approaches, we have carried out coarse-grain molecular dynamics simulations on model poly(ethyleneoxide)-poly(ethylethylene) (PEO-PEE) lamellae, exploring the influence of chain length and hypothetical chemical modifications on the observed line edge roughness. As expected, our simulations show that increasing chi (the Flory-Huggins parameter) is the most direct route to decreased roughness, although the addition of strong specific interactions at the block interface can also produce smoother patterns.     

Contact angle hysteresis at the nanoscale: a molecular dynamics simulation study

In this paper, the contact angle hysteresis (CAH) of nanodroplets on both rigid and flexible substrates with different wettabilities was studied using molecular dynamics (MD) simulations. The critical shear stress (CSS) that determines the motion of the contact line (CL) was investigated. A theoretical correlation between CAH and CSS was proposed. Both CAH and CSS reflect the energy dissipation at the CL of the droplet in response to the exerted force. MD results of CAH are qualitatively consistent with the theoretical model. Simulation results also show that, for the same liquid–solid interactions, CAH on the flexible substrate is larger than that on the rigid substrate. These findings aim to enhance our understanding of the mechanism of the CAH at the nanoscale.     

Thermal decomposition of a honeycomb-network sheet: A molecular dynamics simulation study

The thermal degradation of a graphene-like two-dimensional honeycomb membrane with bonds undergoing temperature-induced scission is studied by means of Molecular Dynamics simulation using Langevin thermostat. We demonstrate that at lower temperature the probability distribution of breaking bonds is highly peaked at the rim of the membrane sheet whereas at higher temperature bonds break at random everywhere in the hexagonal flake. The mean breakage time τ is found to decrease with the total number of network nodes N by a power law τ ∝ N(-0.5) and reveals an Arrhenian dependence on temperature T. Scission times are themselves exponentially distributed. The fragmentation kinetics of the average number of clusters can be described by first-order chemical reactions between network nodes n(i) of different coordination. The distribution of fragments sizes evolves with time elapsed from initially a δ-function through a bimodal one into a single-peaked again at late times. Our simulation results are complemented by a set of 1st-order kinetic differential equations for n(i) which can be solved exactly and compared to data derived from the computer experiment, providing deeper insight into the thermolysis mechanism.     

IBIsCO: a molecular dynamics simulation package for coarse-grained simulation

IBIsCO is a parallel molecular dynamics simulation package developed specially for coarse-grained simulations with numerical potentials derived by the iterative Boltzmann inversion (IBI) method (Reith et al., J Comput Chem 2003, 24, 1624). In addition to common features of molecular dynamics programs, the techniques of dissipative particle dynamics (Groot and Warren, J Chem Phys 1997, 107, 4423) and Lowe-Andersen dynamics (Lowe, Europhys Lett 1999, 47, 145) are implemented, which can be used both as thermostats and as sources of friction to compensate the loss of degrees of freedom by coarse-graining. The reverse nonequilibrium molecular dynamics simulation method (Müller-Plathe, Phys Rev E 1999, 59, 4894) for the calculation of viscosities is also implemented. Details of the algorithms, functionalities, implementation, user interfaces, and file formats are described. The code is parallelized using PE_MPI on PowerPC architecture. The execution time scales satisfactorily with the number of processors.     

Computer simulation study of the phase behavior and structural relaxation in a gel-former modeled by three-body interactions

We report a computer simulation study of a model gel-former obtained by modifying the three-body interactions of the Stillinger-Weber potential for silicon. This modification reduces the average coordination number and consequently shifts the liquid-gas phase coexistence curve to low densities, thus facilitating the formation of gels without phase separation. At low temperatures and densities, the structure of the system is characterized by the presence of long linear chains interconnected by a small number of three coordinated junctions at random locations. At small wave vectors the static structure factor shows a nonmonotonic dependence on temperature, a behavior which is due to the competition between the percolation transition of the particles and the stiffening of the formed chains. We compare in detail the relaxation dynamics of the system as obtained from molecular dynamics with the one obtained from Monte Carlo dynamics. We find that the bond correlation function displays stretched exponential behavior at moderately low temperatures and densities, but exponential relaxation at low temperatures. The bond lifetime shows an Arrhenius behavior, independent of the microscopic dynamics. For the molecular dynamics at low temperatures, the mean squared displacement and the (coherent and incoherent) intermediate scattering function display at intermediate times a dynamics with ballistic character and we show that this leads to compressed exponential relaxation. For the Monte Carlo dynamics we always find an exponential or stretched exponential relaxation. Thus we conclude that the compressed exponential relaxation observed in experiments is due to the out-of-equilibrium dynamics.     

Structure and dynamics of short chain molecules in disordered porous materials: a molecular dynamics simulation study

The static and dynamic properties of short polymer chains in disordered materials are studied using discontinuous molecular dynamics simulations. The polymers are modeled as chains of hard spheres and the matrix is a collection of fixed hard spheres. The simulations show that the chain size is a nonmonotonic function of the matrix concentration for all polymer concentrations. The dependence of polymer diffusion D on the degree of polymerization N becomes stronger as the matrix concentration is increased. At high matrix concentrations we observe a decoupling between translational and rotational diffusion, i.e., the rotational relaxation time becomes very large but the translational diffusion is not affected significantly. We attribute this to the trapping of a small number of polymers. Under these conditions the polymer chains diffuse via a hopping mechanism.     

Reactivity of molecular oxygen with aluminum clusters: Density functional and Ab Initio molecular dynamics simulation study

Dissociative adsorption of molecular oxygen (O₂) on aluminum (Al) clusters has attracted much interest in the field of surface science and catalysis, but theoretical predictions of the reactivity of this reaction in terms of barrier height is still challenging. In this regard, we systematically investigate the reactivity of O₂ with Al clusters using density functional theory (DFT) and atom‐centered density matrix propagation (ADMP) simulations. We also calculate potential energy surfaces (PESs) of the reaction between O₂ and Al clusters to estimate the barrier energy of this reaction. The M06‐2X functional gives the barrier energy in agreement with the one calculated by coupled cluster singles and doubles with perturbed triples (CCSD(T)) while the TPSSh functional significantly underestimates the barrier height. The ADMP simulation using the M06‐2X functional predicts the reactivity of O₂ with the Al cluster in agreement with the experimental findings, that is, singlet O₂ readily reacts with Al clusters but triplet O₂ is less reactive. We found that the ability of a DFT functional to describe the charge transfer appropriately is critical for calculating the barrier energy and the reactivity of the reaction of O₂ with Al clusters. The M06‐2X functional is relevant for investigating chemical reactions involving Al and O₂. © 2016 Wiley Periodicals, Inc.     

Conformational dynamics of the nicotinic acetylcholine receptor channel: a 35-ns molecular dynamics simulation study

The nicotinic acetylcholine receptor (AChR) is the paradigm of ligand-gated ion channels, integral membrane proteins that mediate fast intercellular communication in response to neurotransmitters. A 35-ns molecular dynamics simulation has been performed to explore the conformational dynamics of the entire membrane-spanning region, including the ion channel pore of the AChR. In the simulation, the 20 transmembrane (TM) segments that comprise the whole TM domain of the receptor were inserted into a large dipalmitoylphosphatidylcholine (DPPC) bilayer. The dynamic behavior of individual TM segments and their corresponding AChR subunit helix bundles was examined in order to assess the contribution of each to the conformational transitions of the whole channel. Asymmetrical and asynchronous motions of the M1-M3 TM segments of each subunit were revealed. In addition, the outermost ring of five M4 TM helices was found to convey the effects exerted by the lipid molecules to the central channel domain. Remarkably, a closed-to-open conformational shift was found to occur in one of the channel ring positions in the time scale of the present simulations, the possible physiological significance of which is discussed.