Molecular dynamics studies of the size, shape, and internal structure of 0% and 90% acetylated fifth-generation polyamidoamine dendrimers in water and methanol

We have performed molecular dynamics simulations of 0% and 90% acetylated fifth-generation (G5) polyamidoamine (PAMAM) dendrimers in water and methanol and obtained radii of gyration of 2.51-2.57 and 2.11-2.33 nm, respectively, similar to those measured experimentally in methanol by Prosa et al. (J. Polym. Sci. 1997, 35, 2913-2924) and in water by Choi et al. (Nano Lett. 2004, 4, 391-397). Calculation of the moments of inertia and the relative shape anisotropy show that both 0% and 90% acetylated G5 are modestly ellipsoidal. The distribution of branch points relative to the center of the dendrimer and penetration of solvent show that the core and surface of the dendrimer are more exposed to water than is the region between the core and the surface due to the interactions between monomers, including hydrogen bonds that rapidly break and re-form as solvent molecules compete for hydrogen-bonding sites on the monomers. The water and methanol solvents seem to produce similar numbers of hydrogen bond interactions between monomers.