The molecular structures and characteristics of CO and CO2 protonated homogeneous and mixed complexes were studied by theoretical, ab initio calculations. The thermodynamics, vibrational properties, charge distribution, and interaction energy decomposition components are investigated as a function of the increasing size of clusters. The study reveals the similarities and differences between homogeneous protonated carbon oxide and protonated carbon dioxide clusters. In the first-order approximation the structural differences between (CO)(n)H+ and (CO2)(n)H+ clusters are the consequence of the electronic charge distribution in the protonated OCH+ and OCOH+ core fragments. The symmetry of protonated dimers, constituting the cationic core of clusters is the second important factor in determining the overall structure of extended complexes. The OCH+ as well as the OCOH+ fragments are stabilized by cluster formation. The structures and energetics of complexes emerge as a balance between competing electrostatic, exchange, and covalent interactions. The directional covalent forces prevail and enforce the structure of the complexes, however. A universal approach is proposed which allows for the computation of interaction energies for chemical reactions involving significant relaxation of the reactants. (C) 2003 American Institute of Physics.