Dynamics and thermodynamics of water in PAMAM dendrimers at subnanosecond time scales

Atomistic molecular dynamics simulations are used to study generation 5 polyamidoamine (PAMAM) dendrimers immersed in a bath of water. We interpret the results in terms of three classes of water: buried water well inside of the dendrimer surface, surface water associated with the dendrimer-water interface, and bulk water well outside of the dendrimer. We studied the dynamic and thermodynamic properties of the water at three pH values: high pH with none of the primary or tertiary amines protonated, intermediate pH with only the primary amines protonated, and low pH with all amines protonated. For all pH values we find that both buried and surface water exhibit two relaxation times: a fast relaxation (1 ps) corresponding to the libration motion of the water and a slow (20 ps) diffusional component related to the escaping of water from one domain to another. In contrast for bulk water the fast relaxation is 0.4 ps while the slow relaxation is 14 ps. These results are similar to those found in biological systems, where the fast relaxation is found to be 1 ps while the slow relaxation ranges from 20 to 1000 ps. We used the 2PT MD method to extract the vibrational (power) spectrum and found substantial differences for the three classes of water. The translational diffusion coefficient for buried water is 11-33 % (depending on pH) of the bulk value while the surface water is about 80%. The change in rotational diffusion is quite similar: 21-45 % of the bulk value for buried water and 80 % for surface water. This shows that translational and rotational dynamics of wate