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

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

Molecular Dynamics Simulation on Physical Properties of Liquid Lead, Bismuth and Lead-bismuth Eutectic (LBE)

Molecular dynamics method was applied to simulate the physical properties of liquid metals: lead, bismuth and a binary alloy--lead-bismuth eutectic (LBE). The embedded atom method (EAM), an empirical model rooted in density-functional theory, was used to represent the many-body interaction within the liquid metals. The atomic-scale interactions, structure and thermal physical properties of lead, bismuth and LBE were obtained through the simulation, and then compared to the available experimental results. The theoretical results of the physical properties calculated through the MD simulations are in good agreements with the available experimental data

Origin of Charge Separation at Organic Photovoltaic Heterojunctions: A Mesoscale Quantum Mechanical View

The high efficiency of charge generation within organic photovoltaic blends apparently contrasts with the strong “classical” attraction between newly formed electron–hole pairs. Several factors have been identified as possible facilitators of charge dissociation, such as quantum mechanical coherence and delocalization, structural and energetic disorder, built-in electric fields, and nanoscale intermixing of the donor and acceptor components of the blends. Our mesoscale quantum-chemical model allows an unbiased assessment of their relative importance, through excited-state calculations on systems containing thousands of donor and acceptor sites. The results on several model heterojunctions confirm that the classical model severely overestimates the binding energy of the electron–hole pairs, produced by vertical excitation from the electronic ground state. Using physically sensible parameters for the individual materials, we find that the quantum mechanical energy difference between the lowest interfacial charge transfer states and the fully separated electron and hole is of the order of the thermal energy

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

Chemical Aspect of Ocean Liming for CO2 Removal: Dissolution Kinetics of Calcium Hydroxide in Seawater

Ocean liming is attracting ever-increasing attention as one of the most suitable and convenient ways of removing carbon dioxide from the atmosphere and combating global warming and the acidification of the oceans at the same time. However, the short-term consequences of Ca(OH)2 [slaked lime] dissolution in seawater have been scarcely studied. In this work, we investigate in detail what happens in the initial stages after the dissolution of slaked lime, analyzing the kinetics of the process and the effects on the physicochemical parameters of seawater. A series of experiments, carried out by varying the seawater conditions (like temperature and salinity) or the liming conditions (like the dispersion in the form of slurry or powder and the concentration) allow us to draw conclusions on the ideal conditions for a more efficient and environmentally friendly liming process

Association and diffusion of Li+ in carboxymethylcellulose solutions with application to environmentally friendly Li-ion batteries: a combined Molecular Dynamics and NMR study

Carboxymethylcellulose (CMC) has been proposed as a polymeric binder for the electrodes in environmentally friendly Li-ion batteries. Its physical properties and interaction with Li+ ions in water are interesting 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 MD simulations and variable-time PFGSE-NMR spectroscopy to investigate Li+ transport in CMC-based solutions. Both simulation and experiment show that, at concentrations such that Li-CMC has a gel like consistency, the Li+ diffusion coefficient is still very close to that in water. These ions interact preferentially with CMC’s carboxylate groups, 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

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