In this paper I discuss some consequences and manifestations of a mereology of structured wholes in chemistry, with particular reference to the concept of atoms in molecules.

While temporal considerations are of prime importance for chemical reactions, as well as for molecular stability, most chemical concepts are not explicitly formulated on a diachronic basis. It will be argued here that a formulation explicitly incorporating temporal and epistemological considerations enables us to treat chemical reactions and chemical substances on ontologically equivalent terms, instead of assigning a more fundamental status to the latter. After all, in collision theory, a chemical substance is just a collision complex that takes too long. (...) How long qualifies as “too long”, and “too long” in relation to what, are crucial questions that distinguish chemical substances from chemical reactions, and reversible reactions from irreversible ones, thereby introducing anthropocentric considerations into these distinctions. Too long for a lab chemist is very different from too long for an astrochemist studying chemical reactions between chemical substances in inter-stellar space on cosmological timescales. Examining several physical and chemical properties on the basis of which chemical substances are distinguished from one another, the role of temporal and anthropocentric considerations in defining molecular properties is emphasized. I conclude with some observations on the much-debated reduction of chemistry to other disciplines, arguing that such reduction depends on our aesthetic choices as to what kinds of observations demand explanation, and what kinds of explanation are acceptable. (shrink)

The concept of molecular structure is fundamental to the practice and understanding of chemistry, but the meaning of this term has evolved and is still evolving. The Born–Oppenheimer separation of electronic and nuclear motions lies at the heart of most modern quantum chemical models of molecular structure. While this separation introduces a great computational and practical simplification, it is neither essential to the conceptual formulation of molecular structure nor universally valid. Going beyond the Born–Oppenheimer approximation introduces new paradigms, bringing fresh (...) insight into the chemistry of fluxional molecules, proteins, superconductors and macroscopic dielectrics, thus opening up new avenues for exploration. But it requires that our ideas of molecular structure need to evolve beyond simple ball-and-stick-type models. (shrink)