Fig. 5

Two ways to generate the initial configuration of the polyamine (green)-silica octamer (grey)-phosphate (red) aggregate previous to the immersion in the water box. a Silica octamers are added to a previously built polyamine-phosphate cluster in a vacuum, b the resulting aggregate builds the initial structure at t = 0 ns for the MD simulation in a water box, c Snapshot of the final configuration after 40 ns. Although the phosphate ions are dispersed in the aqueous environment, an aggregate of polyamines and octamers remains structurally stable. d–f Similar results for the case that an initial random distribution of the three building blocks (polyamines, silica octamers, and phosphate ions) is used in a vacuum (d) to create the initial configuration for the simulations in water (e). After 40 ns, the phosphate ions are also dispersed in water as for c, but also, in this case, a mostly intact polyamine-octamer aggregate remains, in clear contrast to the simulations with silica dimers, see Fig. 4