Relation between amorphous structure of polymers and penetrant diffusion: A molecular dynamics simulation

Molecular dynamics simulation has been performed for studying the relation between amorphous structure of polymers and penetrant diffusion. The self-diffusion coefficients of O₂ and He in various polymer models, which differ from each other in view of the amorphous structure, were calculated above their glass transition temperatures. The amorphous structure was characterized by considering the percolation of the unoccupied volume. A good correlation was found between the self-diffusion coefficients and the number of clusters in the unoccupied volume at the critical point of the percolation. Based on the simulated cluster size distribution at the critical point, we defined a parameter into which effects of both the amorphous structure and the penetrant size are well incorporated. It was confirmed that the penetrant diffusion is intimately associated with the amorphous structure of polymers.     

Structure,thermodynamics and diffusion in asymmetric binary mixtures: a molecular dynamics simulation study

Structural and thermodynamic properties as well as diffusion coefficients of binary fluid mixtures with asymmetry in mass, size, charge and their combinations have been studied using classical molecular dynamics simulations. The fluid mixture is modelled as spherical particles interacting via the Weeks–Chandler–Andersen and Coulomb potential. The diameter, charge and mass of the fluid particles are in the range 6–60 Å, 1–10e and 1—500 amu, respectively. Systematic variations in pair-correlation functions, thermodynamic properties as well as the self-diffusion coefficient are found with the size, charge and mass ratio of the particles. The self-diffusion coefficient for systems having more than one type of asymmetry is calculated and expressed in terms of diffusion coefficients of systems with only one type of asymmetry.     

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.     

Structure and dynamics of a fluid phase bilayer on a solid support as observed by a molecular dynamics computer simulation

Simulations of a 1-palmitoyl-2-oleoyl- sn-glycero-3-phosphocholine lipid bilayer interacting with a solid surface of hydroxylated nanoporous amorphous silica have been carried out over a range of lipid-solid substrate distances. The porous solid surface allowed the water layer to dynamically adjust its thickness, maintaining equal pressures above and below the membrane bilayer. Qualitative estimates of the force between the surfaces leads to an estimated lipid-silicon distance in very good agreement with the results of neutron scattering experiments. Detailed analysis of the simulation at the separation suggested by experiment shows that for this type of solid support the water layer between surfaces is very narrow, consisting only of bound waters hydrating the lipid head groups and hydrophilic silica surface. The reduced hydration, however, has only minor effects on the head group hydration, the orientation of water molecules at the interface, and the membrane dipole potential. Whereas these structural properties were not sensitive to the presence of the solid substrate, the calculated diffusion coefficient for translation of the lipid molecules was altered significantly by the silica surface.     

Studies of translational diffusion in the smectic A phase of a Gay-Berne mesogen using molecular dynamics computer simulation

Molecular dynamics computer simulations are used to determine the self-diffusion coefficients for a Gay-Berne model mesogen GB (4.4,20,1,1) in the isotropic, nematic and smectic A phases along two isobars. The values of the parallel and perpendicular diffusion coefficients, D(parallel) and D(perpendicular), are calculated and compared in the different phases. For the phase sequence isotropic-smectic A, D(perpendicular)*> or =D(parallel)* over the whole smectic A range with the ratio D(parallel)*/D(perpendicular)* decreasing with decreasing temperature. At a higher pressure, a nematic phase is observed between these two phases and we find that D(parallel)*>D(perpendicular)* throughout the nematic region and the inequality D(parallel)*>D(perpendicular)* remains on entering the smectic A phase. However, the ratio D(parallel)*/D(perpendicular)* decreases with decreasing temperature within the smectic A range and eventually this ratio inverts such that D(perpendicular)*>D(parallel)* at low temperatures. The temperature dependence of the parallel diffusion coefficient in the smectic A phase for this model mesogen is compared to that predicted by a theoretical model for diffusion subject to a cosine potential.     

Structure and dynamics of water at water|Pt interface as seen by molecular dynamics computer simulation

Five molecular dynamics computer simulations were performed to study the structural and dynamical properties of water next to uncharged and charged Pt surfaces. The results show that the structure of a water layer adsorbed on the metal surface is very sensitive to the details of the water–metal potential. While patches of short-living hexagonal ice-like structure are observed in the adsorbed water layer next to the uncharged Pt(111) surface, a square lattice solid-like structure is seen for the layer on top of the uncharged Pt(100) surface. The orientational ordering for the following two layers of water next to uncharged Pt is displaying a preference towards the orientations that are characteristic of hexagonal ice-I, while water is liquid-like in these layers. In the presence of a high value external electric field water reorients and undergoes a layering transition.     

Decoupling effects in computer simulation of liquid-state molecular dynamics

Decoupling effects in liquid-state molecular dynamics are unambiguously proven by computer simulations. These can be discribed as the weakening of the dissipative interaction between the system if interest (e.g. molecular angular valocity) and its thermal bath caused by an intense external field of force. The new phenomenon may be used to confirm or challenge the validity of simple models of the liquids state of molecular matter and provide information on the microscopic time scale.     

Electrolysis of water in the diffusion layer: first-principles molecular dynamics simulation

With Car-Parrinello molecular dynamics simulations the elementary reaction steps of the electrolysis of bulk water are investigated. To simulate the reactions occurring near the anode and near the cathode, electrons are removed or added, respectively. The study focuses on the reactions in pure water. Effects depending on a particular electrode surface or a particular electrolyte are ignored. Under anodic conditions, the reaction continues till molecular oxygen is formed, under cathodic conditions the formation of molecular hydrogen is observed. In addition the formation of hydrogen peroxide is observed as an intermediate of the anodic reaction. The simulations demonstrate that the electrochemistry of oxygen formation without direct electrode contact can be explained by radical reactions in a solvent. These reactions may involve the intermediate formation of ions. The hydrogen formation is governed by rapid proton transfers between water molecules.     

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.     

Structure and dynamics of water at a clay surface from molecular dynamics simulation

We report a molecular dynamics study of the structure and dynamics of water at a clay surface. The negative charge of the surface and the presence of surface oxygen atoms perturbs water over two to three molecular layers, while the nature of the counterions (Na(+)or Cs(+)) has only a small effect. In the first molecular layer, approximately half of the water molecules are H-bonded to the surface. We also analyze the H-bond network between surface water molecules. The diffusion of water molecules along the surface is slowed down compared to the bulk case. As far as the orientational order and dynamics of the water dipole are concerned, only the component normal to the clay surface is perturbed. We investigate the surface H-bond formation and dissociation dynamics and their coupling to the release of molecules from the first molecular layer. We introduce a simple kinetic model in the spirit of Luzar and Chandler [Nature, 1996, 379, 55] to allow for a comparison with bulk water dynamics. This model semi-quantitatively reproduces the molecular simulation results and suggests that H-bond formation is faster with the surface than in the bulk, while H-bond dissociation is slower.     

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.     

Understanding diffusion in confined systems: methane in a ZK4 molecular sieve. A molecular dynamics simulation study

The equilibrium probability distribution of N methane molecules adsorbed in the interior of n alpha cages of the ZK4 zeolite, the all-silica analogue of zeolite A, is modeled by a modified hypergeometric distribution where the effects of mutual exclusion between particles are extracted from long molecular dynamics simulations. The trajectories are then analyzed in terms of time-correlation functions for the fluctuations in the occupation number of the alpha cages. The analysis digs out the correlations induced by the spatial distribution of the adsorbed molecules coupled with a migration mechanism where a molecule can pass from one alpha cage to another, one-by-one. These correlations lead to cooperative motion, which manifests itself as a nonexponential decay of the correlators. Our results suggest ways of developing improved lattice approaches that may be useful for studying diffusion in much larger systems and for a much longer observation time.     

Molecular dynamics simulation of gas diffusion in polyethylene-clay nanocomposites with different silicate layers configurations

Barrier properties of pristine polyethylene (PE) and polyethylene/montmorillonite-clay (PE/MMT) nanocomposite films with different MMT layers configurations were studied using molecular dynamics simulation within NVT ensemble. The force field parameters were optimized for bond lengths, bond angles and torsion angles of the MMT structure. A special simulation box was designed to simulate the diffusion of oxygen, nitrogen and methane, through pristine PE and PE/MMT nanocomposite films. The diffusion coefficients of these gases and the tortuosity values were calculated and analyzed. Results showed that the configuration of clay nanoparticles has strong effect on the barrier properties of the nanocomposite films. The parallel configuration for layered silicates was predicted to have a low diffusion coefficient and a high tortuosity parameter for gas diffusive molecules. The simulation could also indicate that the diffusion coefficient of oxygen is higher than those of nitrogen and methane gases in the examined systems which can be attributed to the smaller kinetic diameter of oxygen.     

Molecular dynamics simulation of water diffusion inside an amorphous polyacrylate latex film

Molecular dynamics simulations were applied to investigate the diffusion behaviors of water molecules at temperatures ranging from 323 to 443 K inside amorphous polyacrylate. The results showed that the simulated diffusion coefficients and activation energies were similar to those of experiments. Moreover, the activation energy of water molecules at high temperatures was higher than that at low temperatures by 3.16 kcal mol^?1, which was close to the hydrogen‐bonding energy between water and polyacrylate. An analysis of the experimental desorption curves of water molecules and their activation energies has confirmed that there are two forms of water molecules inside rubbery polyacrylate, namely, free water and bound water. In addition, it has been concluded that bound water molecules move from one polar group of polyacrylate to another, and this is followed by occasional jumps. Simulated information is very helpful in designing new polyacrylate latex systems and optimizing existent polyacrylate systems. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 884–891, 2007     

Molecular dynamics simulation study of the mechanisms of water diffusion in a hydrated,amorphous polyamide

Atomistic, molecular dynamics simulations of water diffusion in a hydrated, amorphous polyamide have been carried out to study the effects of polymer dynamics, cross-linking, and hydrogen bonding interactions on the molecular mechanisms of diffusion. This polymer was selected as a model for the discriminating layer of FT-30 reverse osmosis membranes, used commercially for water desalination. Analysis of the configurations generated during the simulations shows that, at the relatively high water content studied, a continuous water phase is formed which permeates the polymer and consists of more than 90% of all waters of hydration. Water diffusion takes place by distinct “jump-like” movements between weakly localized sites in this continuous phase. The jump length is on average ∼3Å, independent of the system studied, and is most likely defined by the local, cooperative rearrangement of water molecules. However, the jump frequency, or equivalently, the rate of water diffusion varies from system to system, and depends on polymer dynamics and cross-linking density, and more significantly, on water–water hydrogen bonding interactions.     

Investigation of vapor-deposited amorphous ice and irradiated ice by molecular dynamics simulation

With the purpose of clarifying a number of points raised in the experimental literature, we investigate by molecular dynamics simulation the thermodynamics, the structure and the vibrational properties of vapor-deposited amorphous ice (ASW) as well as the phase transformations experienced by crystalline and vitreous ice under ion bombardment. Concerning ASW, we have shown that by changing the conditions of the deposition process, it is possible to form either a nonmicroporous amorphous deposit whose density (approximately 1.0 g/cm3) is essentially invariant with the temperature of deposition, or a microporous sample whose density varies drastically upon temperature annealing. We find that ASW is energetically different from glassy water except at the glass transition temperature and above. Moreover, the molecular dynamics simulation shows no evidence for the formation of a high-density phase when depositing water molecules at very low temperature. In order to model the processing of interstellar ices by cosmic ray protons and heavy ions coming from the magnetospheric radiation environment around the giant planets, we bombarded samples of vitreous ice and cubic ice with 35 eV water molecules. After irradiation the recovered samples were found to be densified, the lower the temperature, the higher the density of the recovered sample. The analysis of the structure and vibrational properties of this new high-density phase of amorphous ice shows a close relationship with those of high-density amorphous ice obtained by pressure-induced amorphization.     

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.     

Structure and dynamics of an unfolded protein examined by molecular dynamics simulation

The accurate characterization of the structure and dynamics of proteins in disordered states is a difficult problem at the frontier of structural biology whose solution promises to further our understanding of protein folding and intrinsically disordered proteins. Molecular dynamics (MD) simulations have added considerably to our understanding of folded proteins, but the accuracy with which the force fields used in such simulations can describe disordered proteins is unclear. In this work, using a modern force field, we performed a 200 μs unrestrained MD simulation of the acid-unfolded state of an experimentally well-characterized protein, ACBP, to explore the extent to which state-of-the-art simulation can describe the structural and dynamical features of a disordered protein. By comparing the simulation results with the results of NMR experiments, we demonstrate that the simulation successfully captures important aspects of both the local and global structure. Our simulation was ~2 orders of magnitude longer than those in previous studies of unfolded proteins, a length sufficient to observe repeated formation and breaking of helical structure, which we found to occur on a multimicrosecond time scale. We observed one structural feature that formed but did not break during the simulation, highlighting the difficulty in sampling disordered states. Overall, however, our simulation results are in reasonable agreement with the experimental data, demonstrating that MD simulations can already be useful in describing disordered proteins. Finally, our direct calculation of certain NMR observables from the simulation provides new insight into the general relationship between structural features of disordered proteins and experimental NMR relaxation properties.     

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.