An investigation of the interaction between a catalytic system and its substrate (reactant) using neutron diffraction with isotopic substitution (NDIS) is reported. Specifically, the interaction between acetylene and nickel ion exchanged sodium zeolite Y has been investigated using NDIS in situ, revealing the radial distribution of distances at the disordered nickel sites. This is the first time that NDIS has been used for an in situ study, as well as the first time that a catalytic system has been structurally interrogated using this method. The experimental findings are supported and amplified by density functional calculations. Both experiment and theory reveal a Ni-II-(eta(2)-C2H2) complex with small but significant deviation of the geometry exhibited by acetylene in its free state.