To investigate the behaviour of poly(propylene imine) dendrimers -- and urea-adamantyl functionalized ones -- in solution using molecular dynamics simulations, we developed a coarse grained model to tackle the relatively large system sizes and time scales needed. Harmonic bond and angle potentials were derived from atomistic simulations using an iterative Boltzmann inversion scheme, modified to incorporate Gaussian fits of the bond and angle distributions. With the coarse grained model and accompanying force field simulations of generations 1 to 7 of both dendrimer types in water were performed. They compare favourably with atomistic simulations and experimental results on the basis of size, shape, monomer density, spacer back-folding and atomic form factor measurements. These results show that the structural dynamics of these dendrimers originate from flexible chains constrained by configurational and spatial requirements. Large dendrimers are more rigid and spherical, while small ones are flexible, alternatively rod-like and globular.
- Molecular dynamics simulations
- coarse graining
- Boltzmann inversion