The composition and disposition of active atoms on the surface of a substrate are fully determined in optimal layer synthesis by the molecular layering (ML-ALE) method. As in other epitaxial methods, matrix-substrate interactions determine the structure and the composition of the upper layer. In this work the role of the active oxygen atoms of the upper surface layer in the growth of tin oxide is studied using MOC. It is shown that during the synthesis the cation atoms of the upper monolayer of the oxide on the substrate surface lower their valency. The released oxygen valencies bond to new structural units of tin-containing complexes. Supply of oxidant in the next ML-ALE step restores the oxidation state of the surface atoms and makes it possible to repeat the ML-ALE cycles as often as needed. It was found that a thin buffer layer of transient metal oxides suppresses island-type growth.