Preparation of industrially useful clay-polymer nanocomposite materials often requires the dispersal of clay particles within a polymer matrix. The degree to which the clay particles may be dispersed has an effect on the resultant properties of the material, and the clay is often rendered organophilic using alkylammonium species to facilitate incorporation of polymer. The use of a low molecular weight poly(propylene) oxide diamine is investigated as a reagent for controlling the separation between layers in smectite clays and therefore the extent to which the clay tactoid may be dispersed. The arrangement and interactions of the amine species in the interlayer region are investigated through analysis by both experimental methods and computer simulation, which gives insight into coordination mechanisms within the organoclay. Infrared spectroscopy indicates the presence of extensive hydrogen bonding within the amine-clay interlayer. Some of the amine species were found to intercalate in a nonprotonated state, resulting in strong hydrogen-bonding interactions between amine and ammonium groups. Large-scale classical molecular dynamics simulation shows that the amine groups do not interact strongly with the clay sheets, in contradistinction to ammonium groups. The effect of simulation cell size was considered, and in the limit of zero finite size effects, physically realistic undulations are observed within the individual clay sheets.