A research program was initiated with both experimental and computational chemistry based molecular modeling components to investigate specific amino acidsurface interactions. The experimental portion of this study, with details reported elsewhere, investigated the adsorption of selected molecular weights of poly(L-lysine) onto silica glass microspheres with the adsorption enthalpy per adsorbed mer determined to be -0.23 ± 0.13 kcal/mol (mean ± 95% confidence interval). Molecular modeling of this system was then conducted using two approaches: an AM1 semiempirical molecular orbital method to predict L-lysine/ glass interaction energy and an MM2 molecular mechanics method to investigate the structural configuration for poly(L-lysine). The modeling predicted a minimum energy configuration of a rotational backbone structure for poly(L-lysine) with approximately one full rotation occurring about every 8 mers, and that the amine side chains of the L-lysine will hydrogen bond with the silica surface with an average adsorption energy of approximately -0.34 kcal/mol/mer. The molecular modeling results are in good agreement with the experimentally measured value and provide insights into possible molecular-level behavior which would be very difficult to determine by experimental analyses alone. This work demonstrates the use of molecular modeling in conjunction with experimental studies to investigate complex molecular interactions.