Isoskeletomerism as an intermediate concept for mediating between stereoisomerism and isomerism. A remedy for conceptual defects of organic chemistry

After isoskeletomerism is introduced as an intermediate concept for mediating between stereoisomerism and isomerism, so-called ‘constitutional isomerism’ is critically discussed as one of the roots of confusion in organic chemistry. The convention that isomerism is subdivided into stereoisomerism and ‘constitutional isomerism’ is concluded to be misleading, because these concepts are conceptually distinct from a viewpoint of the concepts of equivalence relationships and equivalence classes. The indifference toward these concepts is one of the conceptual defects of organic chemistry. A new flowchart for judging enantiomerism, RS-stereoisomerism, stereoisomerism, isoskeletomerism, and isomerism is discussed to generate an isomer-classification diagram, where RS-stereoisomerism and isoskeletomerism are contained as new matters for remedying the conceptual defects. Skeletons are derived from basic skeletons by three operations (the bond operation, the replacement operation, and the substitutive operation), and they are used to examine the action of isoskeletomeric relationships. Equivalent molecular entities under an isoskeletomeric relationship are collected to give a set of isoskeletomers, which is concluded to be an equivalence class. The confusion caused by so-called ‘constitutional isomerism’ and its subcategories (‘skeletal isomerism’, ‘positional isomerism’, and so on) is critically discussed from the viewpoint of isoskeletomerism as a missing link. The double-entendre of the term constitution is examined when applied to both a 3D entity (a set of stereoisomers) and a 2D entity (a graph). Taxonomy of organic compounds and rational formulas, nomenclature of organic compounds, and combinatorial enumeration of chemical compounds are discussed from the viewpoint of isoskeletomerism.