The main objective of this research was to develop and apply state-of-the-art computational tools to achieve an understanding of intermolecular interactions in molecular imprinting of theophylline into complex polymeric systems. Molecular dynamics (MD) simulations were carried out for different molecular systems in order to predict the interaction energies, the closest approach distances and the active site groups between the simulated molecular systems and different bio-ligands. The minimized structures of five ligands, theophylline and its derivatives (theobromine, theophylline-8-butanoic acid, caffeine and theophylline-7-acetic acid) have been obtained with the use of molecular mechanics approach. NVT MID simulations at room temperature were carried out to obtain equilibrated conformations in all cases. The first simulated molecular systems consisted of a ligand and a commonly used functional monomer, such as acrylic acid, methacrylic acid, acrylamide, acrolein, acrylonitrile, styrene, etc. (a total number of 25 monomers were simulated). For each of the simulated monomer, molecular clusters consisting of 10 monomers were built. For each pair of molecular systems, (10 monomers with a ligand and 10 monomers without a ligand) a total energy difference, (Delta E), was calculated in order to estimate the interaction energy between a ligand and the corresponding monomers. The second simulated molecular systems consisted of a ligand and a polymer. For each of the simulated polymers, a polymeric chain with degree of polymerization (DP) 10 was simulated with theophylline or its derivative and the interaction energy (Delta E) was calculated. From simulated polymer systems it was found that just poly(acrylic acid) and poly(itaconic acid) are selective only for theophylline. The functional groups of monomers interacting with ligands are -COOH or CH2=CH-. The functional groups of polymers are predominantly -COOH. In the case of poly(acrylic acid) and poly(itaconic acid) the distance of closest approach between a polymer and theophylline was between 2.0 and 4.0 angstrom. (c) 2005 Elsevier Ltd. All rights reserved.