Despite the complex phenomena involved in encoding template molecule information within stable synthetic polymers to yield selective and efficient molecular recognition processes, molecularly imprinted polymers (MIP) are increasingly finding broad areas of application. Molecular interactions, both during the polymerization of the functional monomers in the presence of the template and during the processes of specific recognition after template removal, are key determinants of an effective MIP. Covalent and noncovalent template imprinting have been employed to achieve specific recognition sites. In the present study, a molecularly imprinted biocompatible polymer, having a high capacity and affinity for the dye template, nickel(II) phthalocyanine tetrasulfonic acid, has been prepared. UV-visible spectroscopy, FTIR spectroscopy, and ICP analysis were used to investigate the aspects of the synthesis, binding capacity, and adsorption kinetics of the system. Poly(allylamine) cross-linked with epichlorohydrin has been used to represent an amino-functional receptor. Binding isotherms and capacities were correlated with the degree of template removal. Kinetic studies of binding allowed diffusion mechanisms to be evaluated for the fine particulate MIP. Ab initio molecular orbital calculations were performed using Hartree-Fock, MP2, and density functional theory methods to determine the most likely mechanisms of molecular imprinting. Suitable theoretical models have been constructed to mimic the interactions between the template molecule and the polymer. Simulation of the vibrational spectra was also undertaken to make meaningful assignments to experimentally determined spectral bands resulting from these template MIP receptor interactions.