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)

The practice of theoretical research in chemistry largely consists in the construction of models without which experimentation would be impossible. The best-known theoretical models in chemistry are those of the molecular structures of chemical compounds. What is the correspondence between these models and the unobservable entities that they are meant to explain? What is the ontological status of molecular models? The anti-realists question the basis of the realists’ belief in these entities and the truth claims regarding them. Ultimately, the realist/anti-realist (...) debate points to the question of the scope of scientific knowledge. In this paper, I shall show that the description of natural entities offered by the contemporary scientific worldview reveals that molecular modeling presupposes a realistic epistemology that recognizes the limits of scientific objectification. (shrink)

Microstructuralism in the philosophy of chemistry is the thesis that chemical kinds can be individuated in terms of their microstructural properties (Hendry in Philos Sci 73:864–875, 2006 ). Elements provide paradigmatic examples, since the atomic number should suffice to individuate the kind. In theory, Microstructuralism should also characterise higher-level chemical kinds such as molecules, compounds, and macromolecules based on their constituent atomic properties. In this paper, several microstructural theses are distinguished. An analysis of macromolecules such as moonlighting proteins suggests that (...) all the forms of microstructuralism cannot accommodate them. (shrink)

During the past two decades, philosophers of biology have increasingly turned their attention to mechanisms of biological phenomena. Through analyses of mechanistic proposals advanced by biologists, the goal of these philosophers is to understand what a mechanism is and how mechanisms explain. These analyses have generally focused on mechanistic proposals for phenomenon that occur at the cellular or sub-cellular level, such as synapse firing, protein synthesis, or metabolic pathway operation. Little is said about the mechanisms of the macromolecular reactions that (...) underpin these phenomena. These reactions comprise a diverse family of reaction types, and include protein folding, macromolecular complex formation, receptor-ligand interactions, and enzyme catalysis. In this paper, I develop an account of mechanism that focuses exclusively on macromolecular reactions. I begin by reviewing how mechanism is understood in enzymology, and how mechanistic concepts of enzymology apply to macromolecular reactions in general. We will see that the mechanism of a macromolecular reaction is most accurately described as a progression of reaction intermediates, where the evolution of intermediates, from one to the next, is characterized by an energetic coupling between chemistry and protein dynamics. I then make the case that this description necessitates a grounding in a process ontology. To describe the mechanism by which a macromolecular reaction occurs is to describe a process. (shrink)