Explorations in chemical space

Chemical space is the collection of all possible chemicals, arranged in some systematic way. I wrote Combimol to generate ‘all’ chemicals as a measure of the widest possible chemical space. However how you define chemical space depends on the circumstances. The space of chemicals in water is smaller than the space of chemicals in liquid nitrogen, because some compounds that are stable in liquid nitrogen are too unstable to exist in water.

Sample of molecules generated from the ‘butanes’ example, with no stability limits

Combimol is a program I wrote to generate a chemical space based on rules that could be adjusted to fit with your constraints on what ‘space’ you wanted to explore. The concept was originally described in Bains and Seager (2012), and the new version (Combimol-B) was described in Petkowski et al (2020).

Combimol is reasonably well documented and easy to use, and is free for non-profit use. This ZIP file contains the Windows executable, documentation, and two sets of example files to get you started. Combimol is written in QB64 Basic. If you want the source code, please e-mail me. If you use Combimol for your research, please cite the two papers above. Thanks.

I wrote Combimol as part of a wider project to explore what corner of chemical space biochemistry occupies, and why. So far only one paper has emerged from this (Bains 2016), but I am continuing with this research in different modes, as described here and here.