Since molecules are inaccessible to immediate observation, our conception of the molecule is brought about by transdiction which entails invention of various transcendental ideas. In organic chemistry we think that molecules consist of atoms, bonds, functional groups, etc. This is, however, not the unique description of the molecule as is shown by quantum mechanical calculations, for example. Then, what description represents the real molecule? Before asking this question, we have to consider what the real molecule is in the first place. (...) Constructive realism distinguishes our cognitive world and the world just given, and claims that we should accept the former as reality. Understanding our cognitive world is possible only through construction of micro-worlds. Atoms, bonds, functional groups, etc., are micro-worlds which make sense in a theoretical framework of organic chemistry. In this study we translate a micro-world to an affordance and paraphrase it as a context-relative dispositional attribute of an {agent-world} complex. Then, we can understand that it is what we take as molecular structure, not what might be out there to be found, that we should accept as reality. Excluding metaphysical fictions from scientific arguments, constructive realism makes science a meaningful activity. Constructive realism claims that, for getting knowledge of the world, we have to integrate information into our own linguistic frame, i.e., to translate it. Strangification is a technique of intentionally taking an accepted proposition out of one scientific system and putting it into a completely different context. As is the case with translation, strangification brings about deeper understanding of philosophical as well as scientific grounds on which the proposition system holds. We apply this method to molecular structure and reveal that it is an ingenious model to describe molecular behavior in multi-molecular systems with strong interactions between molecules. Information provided by strangification is essential to claim the legitimacy of a proposition system. As far as strangification is properly applied, relativism is irrelevant to constructive realism. (shrink)

Abstract‘Structure’ is the term whose proper use is exemplified by an expression like ‘the structure of a diesel-engine,’ in which what is referred to is accessible to immediate observation. It is also used figuratively like ‘social structure.’ While unobservable, what is referred to is empirically accessible. By contrast, molecules are neither observable nor empirically accessible. What philosophical grounds enable us to design invisible structure of molecules? Our cognition of objects becomes realized as phenomena when objects are given to our phenomenal (...) fields. (Ochiai, Found Chem 22:77–86, 2020a, Found Chem 22:457–465, 2020b, A philosophical essay on molecular structure, Cambridge Scholars Publishing, Newcastle upon Tyne, pp 147–174, 2021) A phenomenal field is a pictorial representation of the mind’s self-transcending character and shows the relation between ‘self’ and ‘world.’ Molecular structure becomes realized as an affordance of molecules in a phenomenal field proper to organic chemists. It is a context-sensitive dispositional attribute of an {organic chemist-world} complex. Although designing molecules presupposes molecular structure, the latter is not sufficient for the former to make sense. Molecules must be designable as well. Designing molecules aims to create or modify molecular structure in order to provide compounds with certain chemical and/or physical properties. That is, designable molecules make sense in contexts in which they serve as a means to achieve this purpose and become realized as an affordance. Given that molecular structure and designable molecules are affordances of molecules, the fact that there are contexts in which they make sense provides grounds for conceiving and designing invisible structure of molecules. Heidegger’s arguments in Being and Time about characteristics of the being of beings corroborate our argument that what becomes realized as an affordance exists as what he calls a useful thing for us. (shrink)

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)