The kaolinite model system was synthesized to investigate the effect of some metal ions on the kaolinite nanostructure. It was found that Mn(II) ions accelerate the polymorphic transformations of metastable alumina and decrease the temperature of its transformation to a stable more form. The phenomenon is explained by a catalytic mechanism, taking into account the Mn(II) electron configuration [d(5) (Mn2+)] and Jahn-Teller effect. The kaolinite layer structure was studied by Diffuse Reflectance Spectroscopy (DRS) and X-ray diffraction (XRD). The energies of electronic levels were calculated and the most probable MO scheme for the synthesized kaolinite model system was proposed.