Molecular Blueprinting by Word Processing

Abstract

In this work, computer-assisted writing techniques for linear expressions of the structure of polycyclic molecules, branched molecules and clusters, based on formal languages, are tested. The techniques used only require the ability to process written texts, even just using a text editor, and one of the many available molecular drawing/optimization programs that accept input in the form of a SMILES string. A few specific syntactic operators acting on strings are characterized in terms of their effect on the corresponding structure, and although they are simply examples, they are already capable of producing non-trivial structures. The aim of this work is to encourage experiments that may lead to potentially interesting molecular schemata, in view of their symmetry and stereochemistry, as revealed by optimization, and to develop insight into the connection between formal expressions and structures. Given the simplicity and availability of the required tools, it can also be useful for education.