A structural study has been carried out involving geometry optimization of different capsules and encapsulated complexes of single monomers, homodimers and heterodimers of benzoic acid and benzamide and substituted dimers, as well as hydrogen-bonded networks of benzamide addressing experimental observation, where cages offering similar cavities but made up of slightly different cavitands result in strikingly different dimer distributions. This is attributed, according to the present results, mainly to the fact that the two cages have different formation energy and different dimer encapsulation energy. The generation of hydrogen-bonded networks of the amide in solution acts competitively to encapsulation. In addition, the trends of the different quantities associated with encapsulation such as dimerization energy, % dimer distribution and encapsulation energies, as the size of the dimers is increased, are examined. Furthermore, the efficacy of the ONIOM(DFT or MP2 and CCSD:PM6) method with respect to the calculation of % distribution of encapsulated dimers in limited cavities is studied. The results show that when the interaction of the guests with the cage is significant, the ONIOM % distributions do not agree with the experimental finding, as full DFT does, due to PM6 method, where the use of semi-empirical PM6 method changes the ordering of the low in energy encapsulated complexes.