The Need for Systematic Naming Software Tools for Exchange of Chemical Information

The availability of systematic names can enable the simple textual exchange of chemical structure information. The exchange of molecular structures in graphical format or connection tables has become well established in the field of cheminformatics and many structure drawing tools exist to enable this exchange. However, even with the availability of systematic naming rules, software tools to allow the generation of names from structures, and hopefully the reversal of these systematic names back to the original chemical structure, have been sorely lacking in capability and quality. Here we review the need for systematic naming as well as some of the tools and approaches being taken today in this area

Algorithmic Analysis of Cahn-Ingold-Prelog Rules of Stereochemistry: Proposals for Revised Rules and a Guide for Machine Implementation

The most recent version of the Cahn-Ingold-Prelog rules for the determination of stereodescriptors as described in Nomenclature of Organic Chemistry: IUPAC Recommendations and Preferred Names 2013 (the “Blue Book”) were analyzed by an international team of cheminformatics software developers. Algorithms for machine implementation were designed, tested, and cross-validated. Deficiencies in Sequence Rules 1b and 2 were found, and proposed language for their modification is presented. A concise definition of an additional rule (“Rule 6,” below) is proposed, which succinctly covers several cases only tangentially mentioned in the 2013 recommendations. Each rule is discussed from the perspective of machine implementation. The four resultant implementations are supported by validation suites in 2D and 3D SDF format as well as SMILES. The validation suites include all significant examples in Chapter 9 of the Blue Book, as well as several additional structures that highlight more complex aspects of the rules not addressed or not clearly analyzed in that work. These additional structures support a case for the need for modifications of the Sequence Rules. </div

Algorithmic Analysis of Cahn-Ingold-Prelog Rules of Stereochemistry: Proposals for Revised Rules and a Guide for Machine Implementation

<div> <div> <div> <p>The most recent version of the Cahn-Ingold-Prelog rules for the determination of stereodescriptors as described in Nomenclature of Organic Chemistry: IUPAC Recommendations and Preferred Names 2013 (the “Blue Book”) were analyzed by an international team of cheminformatics software developers. Algorithms for machine implementation were designed, tested, and cross-validated. Deficiencies in Sequence Rules 1b and 2 were found, and proposed language for their modification is presented. A concise definition of an additional rule (“Rule 6,” below) is proposed, which succinctly covers several cases only tangentially mentioned in the 2013 recommendations. Each rule is discussed from the perspective of machine implementation. The four resultant implementations are supported by validation suites in 2D and 3D SDF format as well as SMILES. The validation suites include all significant examples in Chapter 9 of the Blue Book, as well as several additional structures that highlight more complex aspects of the rules not addressed or not clearly analyzed in that work. These additional structures support a case for the need for modifications of the Sequence Rules. </p> </div> </div> </div

Nomenclature for boranes and related species (IUPAC Recommendations 2019)

Abstract An appraisal of the current IUPAC recommendations for the nomenclature of boranes and related systems has been undertaken. New developments in the field have been investigated and existing nomenclature systems have been adapted to accommodate these new developments. The principal areas considered are stoichiometric and structural nomenclature (including heteroatom and metal-atom subrogation, as well as substitution of hydrogen), conjoined-cage species, supra-icosahedral systems, and sub-icosahedral non-standard structures. Elements of substitutive, additive, and replacement nomenclature systems have been integrated into individual names to address contentious problems in boron nomenclature that have been around for a long time