This paper describes computational modeling of interactions between components of organic/inorganic polymer hybrid (OIPH) materials, particularly polymer interactions with colloidal silica particles in aqueous solution. Particle surface models have been developed and molecular dynamics simulations applied to a range of systems representing various separations between the particles and different polymer solution concentrations. The equilibrium structures and specific interactions between the polymer, solvent, and silica surfaces with different surface modifications have been examined and molecular mechanisms of interactions involved in the formation of the nanocomposite materials have been suggested. The results presented in this paper complement our previous study of the interactions between precursors used in the synthesis of the OIPHs, thus providing a more complete picture of the atomistic details and mechanisms of interactions between the components of the OIPH materials at various stages of their formation.