In the history of science, the birth of classical chemistry and thermodynamics produced an anomaly within Newtonian mechanical paradigm: force and acceleration were no longer citizens of new cited sciences. Scholars tried to reintroduce them within mechanistic approaches, as the case of the kinetic gas theory. Nevertheless, Thermodynamics, in general, and its Second Law, in particular, gradually affirmed their role of dominant not-reducible cognitive paradigms for various scientific disciplines: more than twenty formulations of Second Law—a sort of indisputable intellectual wealth—are (...) conceived after 1824 Sadi Carnot’s original statement and a multitude of entropy functions are proposed after 1865 Clausius’ former definition. Furthermore, at the end of nineteenth century, thermodynamics extended its cognitive domain to chemistry. Mainly thanks to Gibbs, a brand new discipline—chemical thermodynamics or physical chemistry—gradually affirmed its role inside the scientific community. This paper reports the former results of collaborative research program in the History and Epistemology of Science as well as Nature of Science Teaching aimed at retracing the foundations of the physical chemistry. Specifically, the research is structured in three parts: historical-epistemic reflections on fundamental thermodynamic concepts and principles—such as reversible process, heat, temperature, thermal equilibrium and Clausius’ Second Law—that play a structural role inside modern physical chemistry; panoramic overview on the entropy, whose polysemy makes it one of the most demanding concepts for scholars, teachers and students while approaching thermodynamics; conceptualization of chemical equilibrium as complex entity according to the dual epistemological approach offered by Gibbs’ thermodynamic model and the kinetic standpoint by Guldberg and Waage. In particular, the present work details an original reading of thermodynamic principles with the aim of setting forth a rationalized multidisciplinary substrate whereon the foundational concepts of reversible process and thermal equilibrium can be set. (shrink)