In this work, the mechanism of zinc hydroxide and ammine complexation in caustic and ammonia leaching is investigated by molecular modelling using the density functional theory method. The speciation of zinc complexes is defined based on the thermodynamic data and Pourbiax diagrams. The mechanism of Zn+2 complexation by hydroxide and ammine ligands is simulated by molecular modeling. The structure of reactants in the form of individual clusters is modelled using the density function theory. In order to compare the hydroxide and ammine species structures, the geometry studies are carried out as well. The ammoniacal salt effectiveness to improve the dissolution and stability of the ammine species is studied. The ligand single molecule interaction with a smithsonite molecule is done for a better understanding. Molecular modeling show that the zinc hydroxide species are more stable based on the higher reaction free energies. The reaction free energies decrease by adding the OH- and NH3 ions to the complexes from -30.12 kcal/mol to -16.943 kcal/mol, and -22.590 kcal/mol to 66.516 kcal/mol, respectively. The Zn-OH bonds are shorter than Zn-NH3, and the ammine species show more regular structures in comparison with the hydroxide structures. The change of free energies in the presence of ammoniacal salts indicate that the sulfate ions can significantly improve the dissolution of zinc oxide in ammonia. The smithsonite interaction with ammonia and hydroxide reveal that hydroxide ions lead to a higher interaction energy than ammonia (-36.396 vs. -28.238), which is consistent with the higher stability of hydroxide species. The results obtained well-explain the experimental results obtained before, and can be effectively used to optimize the alkaline leaching of zinc oxide ore.