The calculations of the lengths of hydrogen bridge and frequencies of vibrations of bonds in the formation of hydrogen bonds skatole, pyridine and pyrrole with the water molecules in the approximation of B3LYP/6-31G(d,p). The calculations of model potentials of intermolecular interaction of the molecules on the basis of formulas Lennard–Jones and Morse, allowed to account for changes in the length of hydrogen bonds depending on the number of water molecules participating in the formation of complexes.