The concepts of molecular structure and molecular shape are ubiquitous in the chemical literature, where they are often taken as synonyms, with unavoidable drawbacks in chemistry teaching. A third concept, molecular topology, is less frequent but it is a reference term in molecular research domains such as Quantitative Structure–Activity Relationships. The present paper proposes an epistemological analysis of these three notions, aimed at clarifying the nature of their relationship, as well as the contiguities and differences between them. At first, we (...) discuss the various acceptations of the terms molecular structure and molecular shape. Then, we examine some crucial milestones in the history of these concepts and we analyse the relationship between structure, shape and topology from an epistemological viewpoint. We point out the distinguishing features of each concept and we show that their semantic openness, that may be fruitful in a specialized context, turns into a source of incoherence and inaccuracy in the teaching context, fostered by the misleading use of these terms made by textbooks. Eventually, we propose a criterion fit to discriminate between the conceptual domains of molecular shape, molecular structure and molecular topology. (shrink)

The concept of living has changed in time along the history of biology and its specificity has been associated or to a particular matter, active such as the chemical one, or was considered as a product of the spatial organization of a passive matter. Today, these two paths can be merged in the chemical perspective that takes account of the general reflections on the complexity and on the systemic, in the “systemic complexity” approach.

The philosophical vision of the world and the consequent methodology behind the book are clarified. The perspective used is the systemic one, but since today this term has assumed a wide and diversified meaning in the literature, this introduction will clarify the specific meaning of our approach, starting from the meaning of the term "system". Our idea of system is based on three key assertions that may seem contradictory, but are necessary and complementary to its definition. In particular, we considered (...) the usual idea that the system is more and less than the sum of its juxtaposed parts, highlighting the role of emergencies and constraints. In our idea of a system, however, we must consider a third fundamental characteristic: its dynamism, the dual nature of the system as an entity and as a process, its role as a "dynamic entity". Afterwards, the holistic and reductionist approaches were analysed in detail, and both the specific merits and the fact that these two opposing worldviews, considered individually, cannot give a complete and balanced description of reality, were taken into account. For us, only the systemic approach provides a balanced description of both the parts and the whole and must, therefore, be preferred. Finally, the differences between our approach and the approaches mentioned above have been considered in detail in this introduction. (shrink)

The present work is a comment of a recent paper by Fortin and coauthors in which the authors propose the introduction of Bohmian mechanics in the philosophy of chemistry and the use of standard quantum mechanics as a mere instrument of prediction. This way would allow overcoming the obstacles found in linking molecular chemistry and quantum mechanics. Starting from some remarks on the orbital concept, we highlight and discuss some general issues that need to be taken into account when two (...) scientific theories coexist within the same investigation field, i.e. SQM and BM. (shrink)

The fundamental concept of structured chemical system has been introduced and analysed in this paper. This concept, as in biology but not in physics, is very important in chemistry. In fact, the main chemical concepts (molecule and compound) have been identified as systemic concepts and their use in chemical explanation can only be justified in this approach. The fundamental concept of “environment” has been considered and then the system concept in mechanics, chemistry and biology. The differences and the analogies between (...) the use of the systemic approach in these disciplines have been analyzed and correlated to the general problem of reductionism and complexity perspectives. The inanimate–animate dichotomy can be reconsidered in this new approach. Since the chemical systemic concepts of molecule and compound can be dated to the nineteenth century, chemistry can be considered the first true systemic science and its historical evolution can be a model for other sciences (such as the humanities) where the systemic concepts are important. (shrink)