Dual-resolution coarse-grained simulation of the bisphenol-A-polycarbonate/nickel interface

Approaches and Perspective of Coarse-Grained Modeling and Simulation for Polymer-Nanoparticle Hybrid Systems

Molecular modeling and simulations have emerged as effective and indispensable tools to characterize polymeric systems. They provide fundamental and essential insights to design a product of the required properties and to improve the understanding of a phenomenon at the molecular level for a particular system. The polymer-nanoparticle hybrids are materials with outstanding properties and correspondingly large applications whose study has benefited from this new paradigm. However, despite the significant expansion of modern day computational powers, investigation of the long time and large length scale phenomenon in polymeric and polymer-nanoparticle systems is still a challenging task to complete through all-atom molecular dynamics (AA-MD) simulations. To circumvent this problem, a variety of coarse-grained (CG) models have been proposed, ranging from the generic CG models for qualitative properties predictions to more realistic chemically specific CG models for quantitative properties predictions. These CG models have already delivered some success stories in the study of several spatial and temporal evolutions of many processes. Some of these studies were beyond the feasibility of traditional atomistic resolution models due to either the size or the time constraints. This review captures the different types of popular CG approaches that are utilized in the investigation of the microscopic behavior of polymer-nanoparticle hybrid systems. The rationale of this article is to furnish an overview of the popular CG approaches and their applications, to review several important and most recent developments, and to delineate the perspectives on future directions in the field.

Elucidating the co-transport of bisphenol A with polyethylene terephthalate (PET) nanoplastics: A theoretical study of the adsorption mechanism

Polyethylene terephthalate (PET) is a possible key component of nanoplastics in water environments, which can migrate pollutants through co-transport. In this regard, the co-transport of endocrine disruptors (such as bisphenol A, BPA) by nanoplastics is of emergent concern because of its cytotoxicity/bioaccumulation effects in aquatic organisms. In this work, a computational study is performed to reveal the BPA adsorption mechanism onto PET nanoplastics (nanoPET). It is found that the outer surface of nanoPET has a nucleophilic nature, allowing to increase the mass transfer and intraparticle diffusion into the nanoplastic to form stable complexes by inner and outer surface adsorption. The maximum adsorption energy is similar (even higher) in magnitude with respect to nanostructured adsorbents such as graphene, carbon nanotubes, activated carbon, and inorganic surfaces, indicating the worrying adsorption properties of nanoPET. The adsorption mechanism is driven by the interplay of dispersion (38-49%) and electrostatics effects (43-50%); specifically, dispersion effects dominate the inner surface adsorption, while electrostatics energies dominate the outer surface adsorption. It is also determined that π-π stacking is not a reliable interaction mechanism for aromatics on nanoPET. The formed complexes are also highly soluble, and water molecules behave as non-competitive factors, establishing the high risk of nanoPET to adsorb and migrate pollutants in water ecosystems. Furthermore, the adsorption performance is decreased (but not inhibited) at high ionic strength in salt-containing waters. Finally, these results give relevant information for environmental risk assessment, such as quantitative data and interaction mechanisms for non-biodegradable nanoplastics that establish strong interactions with pollutants in water.

Ligand-protein interactions in lysozyme investigated through a dual-resolution model

A fully atomistic (AT) modeling of biological macromolecules at relevant length- and time-scales is often cumbersome or not even desirable, both in terms of computational effort required and a posteriori analysis. This difficulty can be overcome with the use of multiresolution models, in which different regions of the same system are concurrently described at different levels of detail. In enzymes, computationally expensive AT detail is crucial in the modeling of the active site in order to capture, for example, the chemically subtle process of ligand binding. In contrast, important yet more collective properties of the remainder of the protein can be reproduced with a coarser description. In the present work, we demonstrate the effectiveness of this approach through the calculation of the binding free energy of hen egg white lysozyme with the inhibitor di-N-acetylchitotriose. Particular attention is payed to the impact of the mapping, that is, the selection of AT and coarse-grained residues, on the binding free energy. It is shown that, in spite of small variations of the binding free energy with respect to the active site resolution, the separate contributions coming from different energetic terms (such as electrostatic and van der Waals interactions) manifest a stronger dependence on the mapping, thus pointing to the existence of an optimal level of intermediate resolution.

Theory of wavelet-based coarse-graining hierarchies for molecular dynamics

We present a multiresolution approach to compressing the degrees of freedom and potentials associated with molecular dynamics, such as the bond potentials. The approach suggests a systematic way to accelerate large-scale molecular simulations with more than two levels of coarse graining, particularly applications of polymeric materials. In particular, we derive explicit models for (arbitrarily large) linear (homo)polymers and iterative methods to compute large-scale wavelet decompositions from fragment solutions. This approach does not require explicit preparation of atomistic-to-coarse-grained mappings, but instead uses the theory of diffusion wavelets for graph Laplacians to develop system-specific mappings. Our methodology leads to a hierarchy of system-specific coarse-grained degrees of freedom that provides a conceptually clear and mathematically rigorous framework for modeling chemical systems at relevant model scales. The approach is capable of automatically generating as many coarse-grained model scales as necessary, that is, to go beyond the two scales in conventional coarse-grained strategies; furthermore, the wavelet-based coarse-grained models explicitly link time and length scales. Furthermore, a straightforward method for the reintroduction of omitted degrees of freedom is presented, which plays a major role in maintaining model fidelity in long-time simulations and in capturing emergent behaviors.

A multi-resolution model to capture both global fluctuations of an enzyme and molecular recognition in the ligand-binding site

In multi-resolution simulations, different system components are simultaneously modeled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is needed in the active site to capture the chemistry of ligand binding. Global properties of the rest of the protein also play an essential role, determining the structure and fluctuations of the binding site; however, these can be modeled on a coarser level. Similarly, in the most computationally efficient scheme only the solvent hydrating the active site requires atomistic detail. We present a methodology to couple atomistic and coarse-grained protein models, while solvating the atomistic part of the protein in atomistic water. This allows a free choice of which protein and solvent degrees of freedom to include atomistically. This multi-resolution methodology can successfully model stable ligand binding, and we further confirm its validity by exploring the reproduction of system properties relevant to enzymatic function. In addition to a computational speedup, such an approach can allow the identification of the essential degrees of freedom playing a role in a given process, potentially yielding new insights into biomolecular function. Proteins 2016; 84:1902-1913. © 2016 Wiley Periodicals, Inc.

Mixing atoms and coarse-grained beads in modelling polymer melts

We present a simple hybrid model for macromolecules where the single molecules are modelled with both atoms and coarse-grained beads. We apply our approach to two different polymer melts, polystyrene and polyethylene, for which the coarse-grained potential has been developed using the iterative Boltzmann inversion procedure. Our results show that it is possible to couple the two potentials without modifying them and that the mixed model preserves the local and the global structure of the melts in each of the case presented. The degree of resolution present in each single molecule seems to not affect the robustness of the model. The mixed potential does not show any bias and no cluster of particles of different resolution has been observed.

Lithography of Polymer Nanostructures on Glass for Teaching Polymer Chemistry and Physics

As nanolithography becomes increasingly important in technology and daily life, a variety of inexpensive and creative methods toward communicating the concepts underpinning these processes in the classroom are necessary. An experiment is described that uses simple CD-Rs, C-clamps, an oven, and a freezer to provide concrete examples and insights into the chemistry and principles of nanolithography. The experiment also has flexibility, making it suitable for a range of classroom levels from high school to more advanced labs in college. Because CD-Rs are composed of grooves of polycarbonate, the experiment provides a basis for discussions and exploration into the chemistry and physics of polymers on the nanoscale.

Adaptive resolution molecular-dynamics simulation: changing the degrees of freedom on the fly

We present a new adaptive resolution technique for efficient particle-based multiscale molecular-dynamics simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially localized domains whereas a lower mesoscopic level of detail is sufficient for the rest of the system. Our method allows an on-the-fly interchange between a given molecule's atomic and coarse-grained levels of description, enabling us to reach large length and time scales while spatially retaining atomistic details of the system. The new approach is tested on a model system of a liquid of tetrahedral molecules. The simulation box is divided into two regions: one containing only atomistically resolved tetrahedral molecules, and the other containing only one-particle coarse-grained spherical molecules. The molecules can freely move between the two regions while changing their level of resolution accordingly. The hybrid and the atomistically resolved systems have the same statistical properties at the same physical conditions.

Interface between platinum(111) and liquid isopropanol (2-propanol): A model for molecular dynamics studies

A molecular dynamics model and its parametrization procedure are devised and used to study adsorption of isopropanol on platinum(111) (Pt(111)) surface in unsaturated and oversaturated coverages regimes. Static and dynamic properties of the interface between Pt(111) and liquid isopropanol are also investigated. The magnitude of the adsorption energy at unsaturated level increases at higher coverages. At the oversaturated coverage (multilayer adsorption) the adsorption energy reduces, which coincides with findings by Panja et al. in their temperature-programed desorption experiment [Surf. Sci. 395, 248 (1998)]. The density analysis showed a strong packing of molecules at the interface followed by a depletion layer and then by an oscillating density profile up to 3 nm. The distribution of individual atom types showed that the first adsorbed layer forms a hydrophobic methyl "brush." This brush then determines the distributions further from the surface. In the second layer methyl and methine groups are closer to the surface and followed by the hydroxyl groups; the third layer has exactly the inverted distribution. The alternating pattern extends up to about 2 nm from the surface. The orientational structure of molecules as a function of distance of molecules is determined by the atom distribution and surprisingly does not depend on the electrostatic or chemical interactions of isopropanol with the metal surface. However, possible formation of hydrogen bonds in the first layer is notably influenced by these interactions. The surface-adsorbate interactions influence the mobility of isopropanol molecules only in the first layer. Mobility in the higher layers is independent of these interactions.

Stamping patterns of insulated gold nanowires with self-organized ultrathin polymer films

A thermal contact transfer technique is presented for the fabrication of nanoscaled to microscaled patterns of polymer-insulated metal structures on ceramic surfaces using metal-coated, thermoplastic stamps. The thermally activated formation of polymer-metal-polymer (PMP) heterostructures occurs spontaneously when a metal-coated thermoplastic stamp is compressed against a ceramic substrate and subsequently heated. The presented technique exploits the dynamics of ultrathin polymer films localized at interfaces and interfacial forces to prompt local reorganization of polymer stamp materials during processing. Intercalation of polymer stamp materials into the metal-substrate interface yields a cohesive polymer layer that binds the metal layer to the substrate. Disproportionate adhesion between the bulk polymer and the polymer layer at the stamp-metal interface leaves a capping layer upon separation of the stamp from the substrate. Here we demonstrate this technique with single use, bilevel polymer stamps which afford transfer of two distinct general products. The transfer of insulated submicrometer wide wires from the raised stamp features affords patterns of trilayered PMP structures with uniform wire dimensions. Concomitant transfer from the recessed stamp features allows fabrication of multilayered PMP architectures with sub-100 nm spacing from microstructured polymer stamps. Thus, patterns with two different insulated nanowire widths are readily fabricated in a single stamping process. A variety of ceramic substrates, thermoplastic materials, and metals can be used; e.g., inexpensive gold-coated CD or DVD media can be used as stamps, where the combination of materials dictates the relative interfacial forces and the processing parameters.

Adaptive resolution scheme for efficient hybrid atomistic-mesoscale molecular dynamics simulations of dense liquids

The adaptive resolution scheme (AdResS) for efficient hybrid particle-based atomistic/mesoscale molecular dynamics (MD) simulations recently introduced by us, [J. Chem. Phys. 123, 224106 (2005)] is extended to high density molecular liquids with spherical boundaries between the atomistic and mesoscale regions. The key feature of this approach is that it allows for a dynamical change of the number of molecular degrees of freedom during the course of a MD simulation by an on-the-fly switching between the atomistic and mesoscopic levels of detail. Pressure and density variations occurring at the atomistic/mesoscale boundary in the original version are considerably reduced employing the improved methodology presented here.

Coarse-grained interaction potentials for polyaromatic hydrocarbons

Using Kohn-Sham (KS) density-functional theory, we have studied the interaction between various polyaromatic hydrocarbon molecules. The systems range from monocyclic benzene up to hexabenzocoronene (hbc). For several conventional exchange-correlation functionals total potential-energy curves of interaction of the pi-pi stacking hbc dimer are reported. It is found that all pure local density or generalized gradient approximated functionals yield qualitatively incorrect predictions regarding structure and interaction. Inclusion of a nonlocal, atom-centered correction to the KS Hamiltonian enables quantitative predictions. The computed potential-energy surfaces of interaction yield parameters for a coarse-grained potential, which can be employed to study discotic liquid-crystalline mesophases of derived polyaromatic macromolecules.

Flow boundary conditions for chain-end adsorbing polymer blends

Using the phenol-terminated polycarbonate blend as an example, we demonstrate that the hydrodynamic boundary conditions for a flow of an adsorbing polymer melt are extremely sensitive to the structure of the epitaxial layer. Under shear, the adsorbed parts (chain ends) of the polymer melt move along the equipotential lines of the surface potential whereas the adsorbed additives serve as the surface defects. In response to the increase of the number of the adsorbed additives the surface layer becomes thinner and solidifies. This results in a gradual transition from the slip to the no-slip boundary condition for the melt flow, with a nonmonotonic dependence of the slip length on the surface concentration of the adsorbed ends.

BPA-PC on a Ni111 surface: the interplay between adsorption energy and conformational entropy for different chain-end modifications

We extend a previous dual scale modeling approach for the behavior of polymers near a metal surface to a variety of end groups. Our approach combines a coarse-grained polymer model with ab initio DFT calculations. Such a procedure was applied to a melt of phenolic-like terminated Bisphenol A-polycarbonate (BPA-PC) interacting with a (111) nickel surface (Delle Site, L.; Abrams, C. F.; Alavi, A.; Kremer, K. Phys. Rev. Lett. 2002, 89, 156103. Abrams, C. F.; Delle Site, L.; Kremer, K. Phys. Rev. E 2003, 67, 021807). This work extends this study to different chain-end modifications of BPA-PC, p-tert-butylphenolic, p-tetramethylpropylphenolic, and p-cumylphenolic. We show how the interplay between adsorption energies and conformational entropy selects different morphologies for the various melts at the interface. Implications of these results for realistic technical materials are finally discussed.