It has been hypothesized that activation of DMC in the restricted spaces of the internal cavities (super-cages) of NaY occurs by an electric-field-induced polarization of the molecule, which is accompanied by elongation and weakening of the O-CH3 and/or C-OCH3 bonds. To clarify this fundamental point, the aim of this investigation is to shed light on the structural perturbation induced in DMC upon interaction with the positively charged counterions present in the supercages. For this purpose a study of the modification of the IR properties of DMC, induced by the interaction with NaY, has been performed; the experimental results obtained are compared with ab initio simulations. It will be shown that the interaction of DMC with Na+ ions fully explains why NaY is so effective in promoting the methylation and carboxymethylation activity of DMC.