The inclusion process involving alpha-cyclodextrin (alpha-CD) and methyl mercury chloride (CH3HgCl) was investigated using the PM3 quantum-mechanical semi-empirical method. Fully unconstrained geometry optimizations were carried out for the free alpha-CD and the complexed forms with CH3HgCl. The inclusion orientation with the methyl mercury chloride passing perpendicular to the center of the cyclodextrin ring was found to be favored over the experimentally hinted parallel structure. It was also observed that the inclusion takes place in a more favored way when solvation water molecules are explicitly included, therefore stabilizing the complex in relation to the free species. The experimentally observed Raman shift for the Hg-Cl stretching mode after the complexation was used in conjunction with the respective PM3 calculated vibrational frequencies for the determination of the preferred structure for the inclusion complex.