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.

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.

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.

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.

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.

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).

Evidence of superdiffusive nanoscale motion in anionic polymeric hydrogels: Analysis of PGSE- NMR data and comparison with drug release properties.

Polymeric hydrogels are promising candidates for drug delivery applications, thanks to their ability to encapsulate, transport and release a wide range of chemicals. The successful application of these materials requires a deep understanding of the mechanisms governing solute transport at the nanoscale and its impact on release kinetics. In this work, we investigate the translational diffusion of ibuprofen loaded in anionic agarose-carbomer (AC) hydrogels by 1H high resolution magic angle spinning (HR-MAS) NMR spectroscopy, and compare it to its macroscopic release kinetics. The analysis of the experimental NMR data provides the first evidence of superdiffusion for ibuprofen in AC hydrogels. Superdiffusive transport is observed in the majority of our samples, especially those with the smallest mesh size (7 nm) and highest ibuprofen concentrations (90-120 mg/mL). This outcome is rationalized in terms of heavy-tailed distributions of spatial displacements (Lèvy flights) and of waiting times, which depend on the nanoscopic structural heterogeneity of the gels and the strong but reversible association between ibuprofen and the agarose matrix.

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.

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.

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.

From Nanoscale to Microscale: Crossover in the Diffusion Dynamics within Two Pyrrolidinium-Based Ionic Liquids.

Knowledge of the ion motion in room temperature ionic liquids (RTILs) is critical for their applications in a number of fields, from lithium batteries to dye-sensitized solar cells. Experiments on a limited number of RTILs have shown that on macroscopic time scales the ions typically undergo conventional, Gaussian diffusion. On shorter time scales, however, non-Gaussian behavior has been observed, similar to supercooled fluids, concentrated colloidal suspensions, and more complex systems. Here we characterize the diffusive motion of ionic liquids based on the N-butyl-N-methylpyrrolidinium (PYR14) cation and bis(trifluoro methanesulfonyl)imide (TFSI) or bis(fluorosulfonyl)imide (FSI) anions. A combination of pulsed gradient spin-echo (PGSE) NMR experiments and molecular dynamics (MD) simulations demonstrates a crossover from subdiffusive behavior to conventional Gaussian diffusion at ∼10 ns. The deconvolution of molecular displacements into a continuous spectrum of diffusivities shows that the short-time behavior is related to the effects of molecular caging. For PYR14FSI, we identify the change of short-range ion-counterion associations as one possible mechanism triggering long-range displacements.

Association and Diffusion of Li(+) in Carboxymethylcellulose Solutions for Environmentally Friendly Li-ion Batteries.

Carboxymethylcellulose (CMC) has been proposed as a polymeric binder for electrodes in environmentally friendly Li-ion batteries. Its physical properties and interaction with Li(+) ions in water are interesting not only from the point of view of electrode preparation-processability in water is one of the main reasons for its environmental friendliness-but also for its possible application in aqueous Li-ion batteries. We combine molecular dynamics simulations and variable-time pulsed field gradient spin-echo (PFGSE) NMR spectroscopy to investigate Li(+) transport in CMC-based solutions. Both the simulations and experimental results show that, at concentrations at which Li-CMC has a gel-like consistency, the Li(+) diffusion coefficient is still very close to that in water. These Li(+) ions interact preferentially with the carboxylate groups of CMC, giving rise to a rich variety of coordination patterns. However, the diffusion of Li(+) in these systems is essentially unrestricted, with a fast, nanosecond-scale exchange of the ions between CMC and the aqueous environment.

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.

Surface Reconstructions in Organic Crystals: Simulations of the Effect of Temperature and Defectivity on Bulk and (001) Surfaces of 2,2':6',2″-Ternaphthalene.

2,2':6',2″-Ternaphthalene (NNN) is a novel, blue-emitting material, suitable for preparation of organic light-emitting diodes. Its crystal structure has been solved recently, but its thermal behavior and surface properties have not yet been explored, partly due to the difficulty in obtaining high quality crystals. In the present study we use classical molecular dynamics to investigate the thermal behavior of bulk and (001) surfaces of NNN. Our bulk simulations indicate the occurrence of a phase transition at about 600 K. The transition is facilitated by the presence of a free (001) surface, since a reconstruction leading to a very similar structure occurs around 550 K in our surface models. This holds for both ideal and defective surface models, containing a small number of vacancies (one or two missing molecules in the outermost layer). In all cases, the process is triggered by thermal motion and involves the reorientation of the molecules with respect to the (001) plane. Both the bulk and surface phases share the monoclinic space group P21/a with a herringbone disposition of molecules. These findings and their implications for the use of NNN in organic electronics are discussed.

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.

Pyrrolidinium-based ionic liquids doped with lithium salts: how does Li(+) coordination affect its diffusivity?

We present the characterization of LiX-doped room-temperature ionic liquids (ILs) based on the N-butyl-N-methyl pyrrolidinium (PYR14) cation with two fluorinated anions: (trifluoromethanesulfonyl)-(nonafluorobutanesulfonyl)imide (X═IM14) and bis(pentafluoroethanesulfonyl)imide (X═BETI). The new data are also compared with previous results on PYR14TFSI (bis(trifluoromethanesulfonyl)imide). Their local organization has been investigated via NMR nuclear Overhauser effect (NOE) experiments for {(1)H-(19)F} and {(1)H-(7)Li} that give us details on PYR14(+)/X(-) and PYR14(+)/Li(+) contacts. We confirm the presence of [Li(X)2](-) coordinated species in all systems. The long-range, intermolecular NOEs have been detected and provide information on the ions' organization beyond the first solvation sphere. The ionic conductivity, viscosity and self-diffusion coefficients of the ionic mixtures have also been measured. The activation energies for the diffusion of the individual ions and for the fluidity are compared with those for the pure ILs. Finally, density functional calculations on [Li(BETI)2](-), [Li(IM14)2](-), and [Li(TFSI)2](-) complexes demonstrate that the minimum energy structures for all systems correspond to a tetrahedral coordination of the Li-ion by four oxygen atoms of the anions. Assuming very simple key steps for the Li(+) diffusion process (i.e., the concerted breaking and formation of Li-O bonds or the rearrangement around a tetrahedrally coordinated Li(+)), we calculate activation barriers that agree well with the experimental results (approximately 46 kJ/mol, in all systems).

An Effective Two-Orbital Quantum Chemical Model for Organic Photovoltaic Materials.

We present a coarse-grained quantum chemical model of organic photovoltaic materials, which is based on the classic idea that the main physical processes involve the electrons occupying the frontier orbitals (HOMO and LUMO) of each molecule or "site". This translates into an effective electronic Hamiltonian with two electrons and two orbitals per site. The on-site parameters (one- and two-electron integrals) can be rigorously related to the ionization energy, electron affinity, and singlet and triplet first excitation energies of that site. The intersite Hamiltonian parameters are introduced in a way that is consistent with classical electrostatics, and for the one-electron part, we use a simple approximation that could be refined using information from atomistic quantum chemical calculations. The model has been implemented within the GAMESS-US package. This allows the exploration of the physics of these materials using state-of-the art quantum chemical methods on relatively large systems (hundreds of electron-donor and electron-acceptor sites). To illustrate this point, we present ground- and excited-state calculations on dimers and two-dimensional arrays of sites using the Hartree-Fock, configuration interaction, and coupled-cluster methods. The calculations provide evidence for the possibility of low-energy, long-range electron transfer in donor-acceptor heterojunctions characterized by a moderate degree of disorder.

Impact of Interaction Strength and Surface Heterogeneity on the Dynamics of Adsorbed Polymers.

We present molecular dynamics simulations of bead-and-spring polymer chains on chemically heterogeneous, energetically disordered surfaces at near-monolayer coverages. The surfaces consist of random mixtures of weakly (W) and strongly (S) attractive sites. We explore systematically the effect of surface composition on the diffusive dynamics of the chains. The polymer diffusion coefficients have a near-Arrhenius temperature dependence, with activation energies which have a nonmonotonic dependence on the fraction of S sites. In other words, we see a nonmonotonic dependence of the interfacial polymer dynamics on its affinity with the surface, when the latter involves some heterogeneity. The maximum activation energy belongs to the surface containing 75% S and 25% W sites, which combines near-maximum average polymer-surface interactions with near-maximum spread or disorder in these interactions. Our results have interesting implications for polymer adhesion and friction and structure-property relationships in polymer nanocomposites.