Paper Citing NAMD - Abstract
Bertran, Oscar; Zhang, Baozhong; Schlueter, A. Dieter; Halperin, Avraham; Kroeger, Martin; Aleman, Carlos
Computer simulation of dendronized polymers: organization and characterization at the atomistic level
RSC ADVANCES, 3:126-140, 2013
Atomistic molecular dynamics simulations in chloroform and solvent-free environments are used to build and study a homologous series of neutral dendronized linear polymers (DPs), whose repeat units are regularly branched dendrons of generations g = 1-7, excluding g = 5. We find that a DP with g <= 4 displays an elongated conformation, while a DP with g = 6 exhibits a helical backbone. The conformations essentially differ in their alternating (elongated) or regular (helical) twist with respect to the macromolecular axis, at similar average distance between repeat units (2.1-2.3 angstrom). With increasing g the dendrons tend to induce an increasing strain, stiffness and overall cylindrical shape onto the DP; the existence of DPs with g >= 7 is excluded. The fractal dimensionality of the backbone appears similar for DPs with g <= 4, while a discontinuous fractal behavior found for g = 6 is consistent with its helical backbone. Profiles describing the variation of the density as a function of the distance to the molecular backbone are extracted to analyze conformational effects of both backbone and sidegroups. For the solvent-free case the average density grows from 0.97 to 1.11 g cm(-3) upon increasing g, while the radial density profile is basically constant at 1.1-1.2 g cm(-3) and insensitive to g at intermediate distances, where dendrons are able to interpenetrate. The variation of obtained DP thicknesses is successfully compared with experimental estimates deduced from transmission electron microscopy measurements of polymers deposited onto attractive mica surfaces. Finally, we examine and discuss the distribution of solvent molecules inside elongated structures.
