The methodological and ontological issues arising in the organic chemists' explanation of transformations of matter by means of reaction mechanisms are presented based on the general view that chemistry is at the same time an autonomous discipline with its own paradigm and an integral part of the unitary body of science. Among the issues relevant to research is the nature and actual observability of activated complexes, which have by definition a vanishing lifetime. That issue illustrates the interplay of molecular chemistry and quantum physics at the submicroscopic level of sensible reality. A moral concerning the planning and strategy of research is briefly outlined.