Molecular modeling techniques were applied to predicting binding energies for nanocomposites comprising exfoliated clay layers treated with ammonium salts (usually quaternary) and dispersed in nylon 6,6 resin. For each of 12 selected ammonium ions (quats), a molecular dynamics simulation was performed at 600 K for 100-300 ps with a time step of 0.001 ps on a computer model built from 20 repeating units of nylon 6,6 polymer, six quat molecules and a montmorillonite platelet. Several conformations were selected from the equilibrated time region, energy minimization carried out and binding energies calculated between nylon 6,6 and the clay platelet, between nylon 6,6 and the quat, and between the quat and the platelet. It was found that the binding energy between nylon 6,6 and the clay platelet decreases almost linearly with the volume of adsorbed quat. Consequently, pristine clay yields the highest binding strength to the nylon. Clays partially substituted by long quats were found to be equivalent to those fully substituted with short quats.