DFT periodic, ONIOM, and cluster studies with all-electron basis sets are applied to Cu(I) exchanged zeolites and silicoalumino-phosphate analogs with faujasite and chabazite topology. The reactivity of the cations at different cation positions is probed by NO adsorption. In the ONIOM approach, the cation center and the nearest framework environment are described by DFT, whereas a larger part of the structure is modeled at the semiempirical PM6 level. The importance of including all electrons explicitly in the periodic model computations is outlined by comparison of the results with those from ONIOM and previous plane-wave studies. The Cu(I) cations reside at distinct extraframework cation sites in the vicinity of the double six-membered rings (D6R) and upon adsorption they experience a displacement from their previous position. A full optimization with all-electron basis set is a prerequisite for proper elucidation of the coordination of the transition metal cations by the framework oxygen atoms. © 2012 Wiley Periodicals, Inc.