Chemical space is a fashionable metaphor for the set of possible chemical structures, which is presumed to be vast but is otherwise only vaguely defined. But how would be go about developing a rigorous definition of the term and what would be the benefit? This talk presents a definition of chemical space as a discrete metric space with a simple metric (distance function). Given a pair of molecules with the same stoichiometry, the distance is simply the length of the shortest path on the (stoichiometry-preserving) reaction network containing them. However, for molecules of different stoichiometry, we first need to find a suitable reaction network using the partial ordering property with respect to inclusion. The distance can then be defined as the Hausdorff metric between the sets of projections of the molecules only the join metric space.<br/><br/>While a metric space has less structure than, for example, the vector space of a molecule's Cartesian coordinates, the proposed definition has a number of attractive properties. It is discrete and, as it turns out, relatively mall. The dimensionality of reaction networks of CHO compounds containing 2--3 carbon atoms, as measured by their fractal dimension, increases only logarithmically with the network size and is about an order of magnitude smaller than the dimension of the space of the Cartesian coordinates (potential energy surface). Low-dimensional spaces are much easier to search than high-dimensional ones, which is valuable for reaction mechanism prediction. Heuristic methods based on simple paths on (stoichiometry-preserving) reaction networks are shown to accurately predict reaction mechanisms of simple polar and sigmatropic organic reactions.

Reaction networks and the metric structure of chemical space(s)

Macromolecular Chemistry: The Second Century

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ACS Spring 2020 National Meeting & Expo

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.