Wolfram Mathematica graphical user interface (GUI) for building planar polycyclic aromatic hydrocarbons and analyzing their aromatic sextet structures
The code was developed and tested under
- OS: Microsoft Windows 11 Home
- Mathematica 14.2.1 for Microsoft Windows (64-bit) (March 17, 2025).
This repository contains only a notebook with core functions in .../Core folder.
The GUI distributed in releases does not require installation. It can be run as a regular Mathematica Notebook (.nb), which contains a dynamical content and requires enabling upon the start:
The work with GUI starts from building a planar graph of a hydrocarbon molecule on a canvas by specifying position of atoms with a mouse click anywhere on the canvas. This is the Building mode regime:
The built graphs can be analysed in two other regimes: Gallai-Edmonds' structure and Clar's structure. The idea behind this approach is explained in detail in the LinkedIn article 50 years of Clar's aromatic sextet... and no automation yet? that accompanied v1.0.0 release.
As a quick start, let us build and analyse in the Clar's structure regime a Kekulene molecule studied in J. Am. Chem. Soc. 141, 15488–15493 (2019):
As of v2.0.0. the GUI supports import of carbon skeletons (hydrogens are stripped automatically) from .XYZ, .MOL and .CDXML structure files straight into the canvas, thereby allowing one to avoid manual building. On the other hand, it is possible to export graphs from the canvas into the mentioned structure files with automatic hydrogenation when possible. These two tools can be used interoperably within the GUI.
Consider becoming a paying user on this project. This is how I earn a living, as I am directly user-supported. Moreover, you will get an exclusive content and an early access to new releases. Anyone making a donation is entitled to request a version without watermarks. If you like the free app, you will love the paying user-only version. Such donations are really appreciated for keeping this project going.