AbstractThe interaction of water with alkanethiolate chains is studied from first principles. A detailed analysis is performed by optimizing the structure of small water clusters, one‐dimensional water chains, and ordered and disordered thin water layers adsorbed on hydroxyl(OH)‐ and methyl(CH3)‐terminated alkanethiol monolayers. The hydrophilic/hydrophobic character of these two different substrates is investigated by means of an energetic analysis combined with hydrogen‐bond counting. On the hydrophilic OH‐terminated alkanethiol surface, zigzag, one‐dimensional water chains and disordered thin water layers are the energetically favored structures. The ab initio results can be used to determine the optimal value of the empirical parameters characterizing a suitable force field to be used in classic molecular dynamics simulations.