We describe the intermediate of the reaction between a ruthenium complex and the 1-propen-3-ol in water by an atomistic approach for gaining information about the conformation and dynamics of complex molecules in aqueous solution, which combines DFT based ab initio molecular dynamics (AIMD) and neutron scattering data based on Empirical Potential Structure Refinement (EPSR) simulations. We apply our method to the study of the water soluble h 2-allylic complex [RuCp(exo-h 2-CH2=CH-CH2-OH)(PTA)2] + (2) (PTA = 1,3,5-triaza-7-phosphaadamantane), a significant intermediate in the isomerisation of 1-propen-3-ol into propanal catalysed by {RuCp(H2O-κO)(PTA)2} +. We identify the factors responsible for the stabilisation of a specific conformer of 2 in water solution and, for the first time, we demonstrate the direct involvement of water molecules in the formation of this species. In particular, we show that long-lived (ca. 10 ps) bonded chains of water molecules play a crucial role in influencing the conformation and, potentially, the chemical reactivity of 2.