An atomistic mechanism has been derived for the initial stages of the adsorption reaction for metal-nitride atomic layer deposition (ALD) from alkylamido organometallic precursors of Ti and Zr on alkyltrichorosilane-based self-assembled monolayers (SAMs). The effect of altering the terminal functional group on the SAM (including -OH, -NH2, -SH, and -NH(CH3)) has been investigated using the density functional theory and the MP2 perturbation theory. Reactions on amine-terminated SAMS proceed through the formation of a dative-bond complex with an activation barrier of 16-20 kcal/mol. In contrast, thick terminated SAMS form weak hydrogen-bonded intermediates with activation barriers between 7 and 10 kcal/mol. The deposition of Ti organometallic precursors on hydroxyl-terminated SAMS proceeds through the formation of stronger hydrogen-bonded complexes with barriers of 7 kcal/mol. Zr-based precursors form dative-bonded adducts with near barrierless transitions. This variety allows us to select a kinetically favorable substrate for a chosen precursor. The predicted order of reactivity of differently terminated SAMS and the temperature dependence of the initial reaction probability have been confirmed for Ti-based precursors by recent experimental resultS.(53) We predict that the replacement of methyl groups by trifluoromethyl groups on the SAM backbone decreases the activation barrier for amine-terminated SAMS by 5 kcal/mol. This opens a route to alter the native reactivities of a given SAM termination, in this case making amine termination energetically viable. The surface distribution of SAM molecules has a strong effect on the adsorption kinetics of Ti-based precursors. Unimolecular side decomposition reactions were found to be kinetically competitive with adsorption at 400 K.