Towards realistic simulations of polymer networks: tuning vulcanisation and mechanical properties.

Simulations of coarse-grained network models have long been used to test theoretical predictions about rubber elasticity, while atomistic models are still largely unexplored. Here we devise a novel algorithm for the vulcanisation of united-atom poly(cis-1,4-butadiene), characterize the topology of the resulting networks and test their mechanical properties. We observe clear changes in the network structure when using slower vulcanisation, contrary to the traditional view that cross-linking simply freezes the melt configuration. Non-ideality of our networks reverberates on the distribution of strand length and on the strands deformation, which is highly non-affine, especially for short strands. Nevertheless, we do recover some of the trends observed on ideal bead-and-spring networks and controlled laboratory experiments, such as the linear relationships linking the degree of cross-linking and the density. We also compare different deformation methods and find step-equilibrium protocols to be more reliable. Regardless of the adopted method, it is advisable to precede the deformation by a pre-stretching cycle in order to release internal stresses accumulated during the vulcanisation.

Tunable interaction potentials and morphology of polymer-nanoparticle blends.

We present the results of molecular dynamics simulations of a family of polymer nanocomposite systems. The polymer is described by a generic bead-and-spring model, while the polymer chains and the nanoparticles (NPs) interact by Hamaker-style potentials. The potential describing NP-NP interactions is modified by a tuning parameter f, which can be changed continuously between f = 0 (for fully developed van der Waals attractions between the NPs) and f = 1 (for completely repulsive interparticle interactions). We explore systematically the effect of the f parameter on the blend morphologies, for two representative NP sizes. When the polymer-NP attractions are decreased, the systems undergo a transition from dispersed to aggregated morphologies. The sharpness of the transition gradually increases with the interparticle attractions (i.e., decreasing f).

Influence of wall heterogeneity on nanoscopically confined polymers.

We investigate via molecular dynamics simulations the behaviour of a polymer melt confined between surfaces with increasing spatial correlation (patchiness) of weakly and strongly interacting sites. Beyond a critical patchiness, we find a dramatic dynamic decoupling, characterized by a steep growth of the longest relaxation time and a constant diffusion coefficient. This arises from dynamic heterogeneities induced by the walls in the adjacent polymer layers, leading to the coexistence of fast and slow chain populations. Structural variations are also present, but they are not easy to detect. Our work opens the way to a better understanding of adhesion, friction, rubber reinforcement by fillers, and many other open issues involving the dynamics of polymeric materials on rough, chemically heterogeneous and possibly "dirty" surfaces.

Effects of chemically heterogeneous nanoparticles on polymer dynamics: insights from molecular dynamics simulations.

The dispersion of solid nanoparticles within polymeric materials is widely used to enhance their performance. Many scientific and technological aspects of the resulting polymer nanocomposites have been studied, but the role of the structural and chemical heterogeneity of the nanoparticles has just started to be appreciated. For example, simulations of polymer films on planar heterogeneous surfaces revealed unexpected, non-monotonic activation energy to diffusion on varying the surface composition. Motivated by these intriguing results, here we simulate via molecular dynamics a different, fully three-dimensional system, in which the heterogeneous nanoparticles are incorporated in a polymer melt. The nanoparticles are roughly spherical assemblies of strongly and weakly attractive sites, in fractions of f and 1 - f, respectively. We show that the polymer diffusion is still characterized by a non-monotonic dependence of the activation energy on f. The comparison with the case of homogeneous nanoparticles clarifies that the effect of the heterogeneity increases on approaching the polymer glass transition.

Atomistic modelling of entropy driven phase transitions between different crystal modifications in polymers: the case of poly(3-alkylthiophenes).

Polymorphism and related solid-state phase transitions affect the structure and morphology and hence the properties of materials, but they are not-so-well understood. Atomistic computational methods can provide molecular-level insights, but they have rarely proven successful for transitions between polymorphic forms of crystalline polymers. In this work, we report atomistic molecular dynamics (MD) simulations of poly(3-alkylthiophenes) (P3ATs), widely used organic semiconductors to explore the experimentally observed, entropy-driven transition from form II to more common form I type polymorphs, or, more precisely, to form I mesophases. The transition is followed continuously, also considering X-ray diffraction evidence, for poly(3-hexylthiophene) (P3HT) and poly(3-butylthiophene) (P3BT), evidencing three main steps: (i) loss of side chain interdigitation, (ii) partial disruption of the original stacking order and (iii) reorganization of polymer chains into new, tighter, main-chain stacks and new layers with characteristic form I periodicities, substantially larger than those in the original form II. The described approach, likely applicable to other important transitions in polymers, provides previously inaccessible insight into the structural organization and disorder features of form I structures of P3ATs, not only in their development from form II structures but also from melts or solutions.

From dioxin to dioxin congeners: understanding the differences in hydrophobic aggregation in water and absorption into lipid membranes by means of atomistic simulations.

Translocation of small molecules through a cell membrane barrier is a fundamental step to explain the response of cells to foreign molecules. Investigating the mechanisms through which this complex process takes place is especially important in the study of the adverse effects of toxicants. In this work, we start from the results of a previous simulation study of the mechanism of dioxin (2,3,7,8-tetrachlorodibenzo-p-dioxin) absorption into a model membrane, and extend it to four structural congeners of dioxin. The new molecules have been chosen taking into consideration the structural features that characterize dioxin: aromaticity, planarity, the presence of chlorine and oxygen atoms, and hydrophobicity. Our results for the absorption mechanism confirm our expectations based on the chemical structures, but also reveal some interesting differences in single-molecules and especially in cooperative actions underlying cluster absorption. The analysis of key parameters, such as free energies of transfer and translocation times, supports the idea that dioxin, more than its congeners investigated here, likely accumulates in cell membranes.

Glassy dynamics of a polymer monolayer on a heterogeneous disordered substrate.

We present molecular dynamics simulations of a polymer monolayer on randomly functionalized surfaces that are characterized by different fractions of weakly and strongly attractive sites. We show that the dynamics slow-down upon cooling resembles that of a strong glass-forming liquid. Indeed, the mean-square displacements show an increasingly lasting subdiffusive behaviour before the diffusive regime, with signs of Fickian yet not Gaussian diffusion, and the dynamic correlation functions exhibit a stretched exponential decay. The glassy dynamics of this relatively dilute system is dominated by the interaction of the polymer with the substrate and becomes more marked when the substrate composition is heterogeneous. Accordingly, the estimated glass transition temperature shows a non-monotic dependence on surface composition, in agreement with previous results for the activation energy and with an analysis of the potential energy landscape experienced by the polymer beads. Our findings are relevant to the description of polymer-surface adhesion and friction and the development of polymer nanocomposites with tailored structural and mechanical properties.

The effect of donor content on the efficiency of P3HT:PCBM bilayers: optical and photocurrent spectral data analyses.

State-of-the-art organic solar cells mostly rely on bulk-heterojunction architectures, where the photoactive layer is cast from a solution containing both the electron donor and acceptor components and subsequently annealed. An alternative route for device preparation is the sequential deposition of the two components using "orthogonal" solvents. The morphology of sequentially deposited bilayers has been extensively studied, but the interplay between optical and electrical properties and its influence on device efficiency is still unclear. Here we present a study of poly(3-hexylthiophene) (P3HT):phenyl-C61-butyric acid methyl ester (PCBM) bilayers with variable P3HT content, including also a standard bulk-heterojunction device for comparison. Measured optical absorption, external quantum efficieny (EQE), and internal quantum efficiency (IQE) data are analysed and interpreted with the aid of numerical models. In agreement with other studies, our results suggest substantial intermixing between the PCBM and P3HT component, regardless of the P3HT content. In the bulk heterojunction and the bilayer devices with an active layer thickness of 100 nm or less, our best fits to both the optical and optoelectronic data highlight a concentration inversion, with an accumulation of PCBM on the anode side. Through the numerical analysis of device performance at short-circuit, we also find that exciton diffusion toward the P3HT:PCBM interface and geminate recombination can be the main IQE loss factors. Additional losses, attributed to bimolecular electron-hole recombination, are also observed upon increasing the P3HT content.

Computational 17O-NMR spectroscopy of organic acids and peracids: comparison of solvation models.

We examine several computational strategies for the prediction of the (17)O-NMR shielding constants for a selection of organic acids and peracids in aqueous solution. In particular, we consider water (the solvent and reference for the chemical shifts), hydrogen peroxide, acetic acid, lactic acid and peracetic acid. First of all, we demonstrate that the PBE0 density functional in combination with the 6-311+G(d,p) basis set provides an excellent compromise between computational cost and accuracy in the calculation of the shielding constants. Next, we move on to the problem of the solvent representation. Our results confirm the shortcomings of the Polarizable Continuum Model (PCM) in the description of systems susceptible to strong hydrogen bonding interactions, while at the same time they demonstrate its usefulness within a molecular-continuum approach, whereby PCM is applied to describe the solvation of the solute surrounded by some explicit solvent molecules. We examine different models of the solvation shells, sampling their configurations using both energy minimizations of finite clusters and molecular dynamics simulations of bulk systems. Hybrid molecular dynamics simulations, in which the solute is described at the PM6 semiempirical level and the solvent by the TIP3P model, prove to be a promising sampling method for medium-to-large sized systems. The roles of solvent shell size and structure are also briefly discussed.

Numerical simulation of photocurrent generation in bilayer organic solar cells: Comparison of master equation and kinetic Monte Carlo approaches.

Numerical approaches can provide useful information about the microscopic processes underlying photocurrent generation in organic solar cells (OSCs). Among them, the Kinetic Monte Carlo (KMC) method is conceptually the simplest, but computationally the most intensive. A less demanding alternative is potentially represented by so-called Master Equation (ME) approaches, where the equations describing particle dynamics rely on the mean-field approximation and their solution is attained numerically, rather than stochastically. The description of charge separation dynamics, the treatment of electrostatic interactions and numerical stability are some of the key issues which have prevented the application of these methods to OSC modelling, despite of their successes in the study of charge transport in disordered system. Here we describe a three-dimensional ME approach to photocurrent generation in OSCs which attempts to deal with these issues. The reliability of the proposed method is tested against reference KMC simulations on bilayer heterojunction solar cells. Comparison of the current-voltage curves shows that the model well approximates the exact result for most devices. The largest deviations in current densities are mainly due to the adoption of the mean-field approximation for electrostatic interactions. The presence of deep traps, in devices characterized by strong energy disorder, may also affect result quality. Comparison of the simulation times reveals that the ME algorithm runs, on the average, one order of magnitude faster than KMC.

Organic peracids: a structural puzzle for 17O NMR and ab initio chemical shift calculations.

We have applied (17)O NMR spectroscopy to investigate the structure of the organic peracids formed by reaction of acetic acid (AA) or lactic acid (LA) with aqueous hydrogen peroxide (HP), which are used in several "green chemistry" applications. The interpretation of the experimental spectra has been supported by ab initio calculations of the (17)O chemical shifts for several possible species, using a continuum representation of the solvent. The combined use of these tools has also allowed us to discuss the decomposition mechanism of LA/HP solutions. The calculated electric field gradients for water, HP, and CO(2) (a decomposition product of LA) correlate well with the experimental (17)O line widths.

Modeling of the Electrostatic Interaction and Catalytic Activity of [NiFe] Hydrogenases on a Planar Electrode.

Hydrogenases are a group of enzymes that have caught the interest of researchers in renewable energies, due to their ability to catalyze the redox reaction of hydrogen. The exploitation of hydrogenases in electrochemical devices requires their immobilization on the surface of suitable electrodes, such as graphite. The orientation of the enzyme on the electrode is important to ensure a good flux of electrons to the catalytic center, through an array of iron-sulfur clusters. Here we present a computational approach to determine the possible orientations of a [NiFe] hydrogenase (PDB 1e3d) on a planar electrode, as a function of pH, salinity, and electrode potential. The calculations are based on the solution of the linearized Poisson-Boltzmann equation, using the PyGBe software. The results reveal that electrostatic interactions do not truly immobilize the enzyme on the surface of the electrode, but there is instead a dynamic equilibrium between different orientations. Nonetheless, after averaging over all thermally accessible orientations, we find significant differences related to the solution's salinity and pH, while the effect of the electrode potential is relatively weak. We also combine models for the protein adsoption-desorption equilibria and for the electron transfer between the proteins and the electrode to arrive at a prediction of the electrode's activity as a function of the enzyme concentration.

Nonequilibrium simulations of filled polymer networks: searching for the origins of reinforcement and nonlinearity.

We present nonequilibrium dissipative particle dynamics (DPD) simulations of cross-linked elastomers containing solid filler particles at 30% volume fraction. We study systematically the effect of the morphology (dispersed or aggregated particles) and of the effective particle-particle interactions. In addition, we have experimented by replacing the standard harmonic DPD bonds with other potential functions, conceived to deal with the finite extensibility of the polymer chains and the possibility of a slow equilibrium between strongly and weakly adsorbed chains at the rubber-filler interface. The simulation results shed some light on the basic mechanisms of rubber reinforcement, including the nonlinearity and history dependence commonly known as "Payne effect" and "Mullins effect."

Fracture in Silica/Butadiene Rubber: A Molecular Dynamics View of Design-Property Relationships.

Despite intense investigation, the mechanisms governing the mechanical reinforcement of polymers by dispersed nanoparticles have only been partially clarified. This is especially true for the ultimate properties of the nanocomposites, which depend on their resistance to fracture at large deformations. In this work, we adopt molecular dynamics simulations to investigate the mechanical properties of silica/polybutadiene rubber, using a quasi-atomistic model that allows a meaningful description of bond breaking and fracture over relatively large length scales. The behavior of large nanocomposite models is explored systematically by tuning the cross-linking, grafting densities, and nanoparticle concentration. The simulated stress-strain curves are interpreted by monitoring the breaking of chemical bonds and the formation of voids, up to complete rupture of the systems. We find that some chemical bonds, and particularly the S-S linkages at the rubber-nanoparticle interface, start breaking well before the appearance of macroscopic features of fracture and yield.

Identification of viable TCDD access pathways to human AhR PAS-B ligand binding domain.

Unintentionally released in the environment as by-products of industrial activities, dioxins, exemplified by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), represent a primary concern for human health. Exposure to these chemicals is known to produce a broad spectrum of adverse effects, including cancer. The main mechanism of action of TCDD in humans involves binding to the Aryl hydrocarbon Receptor (AhR). Although qualitatively established, TCDD capture by the AhR remains poorly characterized at the molecular level. Starting from a recently developed structural model of the human AhR PAS-B domain, in this work we attempt the identification of viable TCDD access pathways to the human AhR ligand binding domain by means of molecular dynamics. Based on the result of metadynamics simulations, we identify two main regions that may potentially serve as access paths for TCDD. For each path, we characterize the residues closely interacting with TCDD, thereby suggesting a possible mechanism for TCDD capture. Our results are reviewed and discussed in the light of the available information about Human AhR structure and functions.

Blending ionic liquids: how physico-chemical properties change.

Ionic liquids offer the opportunity of tailoring their properties by changing the chemical structure of the cation and anion. Blending of two or more liquids adds a further dimension to this "chemical space". Here we present the results of a study of three binary and one ternary mixture of the ionic liquids formed by the N-butyl-N-methylpyrrolidinium cation with bis(trifluoromethanesulfonyl) imide, bis(pentafluoroethanesulfonyl) imide and (trifluoromethanesulfonyl)(nonafluorobutanesulfonyl) imide. We have collected viscosity and NMR-based data on ionxion correlations (NOE) and diffusion (DOSY). We also attempt to establish a quantitative correlation between mixture and the corresponding pure liquid properties. We find that the binary mixture containing the two very different anions has an intriguing and somewhat anomalous behaviour.

Methodological assessment of kinetic Monte Carlo simulations of organic photovoltaic devices: the treatment of electrostatic interactions.

The kinetic Monte Carlo (KMC) method provides a versatile tool to investigate the mechanisms underlying photocurrent generation in nanostructured organic solar cells. Currently available algorithms can already support the development of more cost-efficient photovoltaic devices, but so far no attempt has been made to test the validity of some fundamental model assumptions and their impact on the simulation result. A meaningful example is given by the treatment of the electrostatic interactions. In most KMC models, electrostatic interactions are approximated by means of cutoff based potentials, irrespective of the long-range nature of the Coulomb interaction. In this paper, the reliability of such approximation is tested against the exact Ewald sum. The results under short-circuit and flat-band conditions show that use of cutoff-based potentials tends to underestimate real device performance, in terms of internal quantum efficiency and current density. Together with this important finding, we formalize other methodological aspects which have been scarcely discussed in the literature.

A Coarse-Grained Force Field for Silica-Polybutadiene Interfaces and Nanocomposites.

We present a coarse-grained force field for modelling silica-polybutadiene interfaces and nanocomposites. The polymer, poly(cis-1,4-butadiene), is treated with a previously published united-atom model. Silica is treated as a rigid body, using one Si-centered superatom for each SiO 2 unit. The parameters for the cross-interaction between silica and the polymer are derived by Boltzmann inversion of the density oscillations at model interfaces, obtained from atomistic simulations of silica surfaces containing both Q 4 (hydrophobic) and Q 3 (silanol-containing, hydrophilic) silicon atoms. The performance of the model is tested in both equilibrium and non-equilibrium molecular dynamics simulations. We expect the present model to be useful for future large-scale simulations of rubber-silica nanocomposites.

Magnetic Resonance Imaging and Molecular Dynamics Characterization of Ionic Liquid in Poly(ethylene oxide)-Based Polymer Electrolytes.

Ternary systems consisting of polymers, lithium salts, and ionic liquids (ILs) are promising materials for the development of next-generation lithium batteries. The ternary systems combine the advantages of polymer-salt and IL-salt systems, thus providing media with high ionic conductivity and solid-like mechanical properties. In this work, we apply nuclear magnetic resonance 1H microimaging [magnetic resonance imaging (MRI)] techniques and molecular dynamics (MD) simulations to study the translational and rotational dynamics of the N-butyl-N-methylpyrrolidinium (PYR14) cation in poly(ethylene oxide) (PEO) matrices containing the lithium bis(trifluoromethanesulfonyl) imide salt (LiTFSI) and the PYR14TFSI IL. The analysis of diffusion-weighted images in PEO/LiTFSI/PYR14TFSI samples with varying mole ratios (10:1:x, with x = 1, 2, 3, and 4) shows, in a wide range of temperatures, a spatially heterogeneous distribution of PYR14 diffusion coefficients. Their weight-averaged values increase with IL content but remain well below the values estimated for the neat IL. The analysis of T2 (spin-spin relaxation) parametric images shows that the PEO matrix significantly hinders PYR14 rotational freedom, which is only partially restored by increasing the IL content. The MD simulations, performed on IL-filled cavities within the PEO matrix, reveal that PYR14 diffusion is mainly affected by Li/TFSI coordination within the IL phase. In agreement with MRI experiments, increasing the IL content increases the PYR14 diffusion coefficients. Finally, the analysis of MD trajectories suggests that Li diffusion mostly develops within the IL phase, although a fraction of Li cations is strongly coordinated by PEO oxygen atoms.

Structural organization and transport properties of novel pyrrolidinium-based ionic liquids with perfluoroalkyl sulfonylimide anions.

Room-temperature ionic liquids (RTILs) based on the N-butyl-N-methyl pyrrolidinium cation (PYR(14)(+)) combined with three different fluorinated anions have been prepared and characterized by NMR, conductivity, and rheological measurements. The anions are (trifluoromethanesulfonyl)(nonafluorobutanesulfonyl)imide (IM(14)(-)), bis(pentafluoroethanesulfonyl)imide (BETI(-)), and bis(trifluoromethanesulfonyl)imide (TFSI(-)). Intermolecular anion-cation nuclear Overhauser enhancements (NOEs) have been experimentally observed in all titled compounds. These findings indicate the formation of long-lived aggregates in the bulk liquids. The NOE patterns show marked selectivity and can be rationalized assuming that the perfluorinated moieties of the anions tend to adopt a preferential orientation with respect to the cations, with possible formation of mesoscopic fluorous domains. Self-diffusion coefficients D for the anion and the cation have been measured by DOSY NMR. Diffusion data show similar but not identical values for cation and anion, consistent with local ordering at the molecular level. The observed trend in diffusion coefficients, D(cation) > D(anion) for all compounds, is compatible with a higher degree of intermolecular organization of the anions. This nanoscale organization is connected to rather strong deviations of the experimental conductivities from those estimated from the ion diffusion coefficients through the Nernst-Einstein relationship. The measured viscosities and ion diffusion coefficients in PYR(14)IM(14) and in PYR(14)TFSI have similar temperature dependencies, leading to very close values of the activation energies for these processes. Ab initio density functional calculations on models of a PYR(14)TFSI ion pair lead to the identification of several local minima, whose structure and energy can be qualitatively related to the experimental NOE signals and activation energies.