We report a biased QM/MM molecular dynamics study of the dissociation process of cytosine-cytosine complexes mediated by Ag⁺ or H⁺ ions in monomeric and dimeric forms. We performed calculations under explicit solvent conditions and obtained the free energy profiles by thermodynamic integration technique to give deep insights on the dissociation process. For all geometries corresponding to key points on energy profiles the noncovalent interaction descriptors were calculated and the details of dissociation mechanism were revealed. Our findings by means of dissociation energy barrier analysis for Ag⁺-mediated cytosines suggested more favorable cis-configuration of C(Ag⁺)C with the energy of 17.8 kcal/mol over trans-configuration with the energy of 12.2 kcal/mol in monomeric form, in contrast to H⁺ mediated cytosines. Also, it is shown that the QM/MM-MD global minimum of dissociation free energy profiles for both monomer isomers (cis- and trans-) doesn't correspond to the geometries found in crystal data and previous theoretical studies of equilibrium geometries. But the addition of an adjacent silver mediated cytosine pair, in which additional stabilizing factors arise such as interplane H-bonding, π-π stacking or argentophilic interaction, leads to a change in the dissociation profiles and improving the agreement with experiment. The trans-configuration of (C(Ag⁺)C)₂ with the energy barrier of 16.6 kcal/mol is more favorable in the dissociation process then cis-configuration with the energy of 15.6 kcal/mol.