The mechanism of insertion of p-nitroaniline (PNA) and its diffusion behavior in channels of the hexagonal host structure of tris(o-phenylenedioxy)cyclotriphosphazene TPP) was investigated by means of molecular modeling tools. Strong preferential sites in the bulk were found to be due to pi-pi and NH-pi interactions between PNA and channel walls of TPP. MD simulations showed that diffusion can be characterized by jumps from one site to the next, occurring mainly because of the dynamic flexibility of the host structure. Calculations of host-guest interactions between the TPP surface and PNA approaching the entrance of channels with its terminal H2N-first or O2N-first revealed that the H2N-first insertion is clearly preferred. Preferential insertion of PNA is found to be the reason for polar effects, observed experimentally. Because of a distinct guest-host recognition at the surface, guest-guest interactions were found to have a minor influence on polarity.