Visualizing Generic Reaction Patterns

Uschi Dolfus

doi:10.1021/acs.jcim.2c00992

Visualizing Generic Reaction Patterns

2022-09-28

3

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AI

DOI：10.1021/acs.jcim.2c00992

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Reaction schemes for organic molecules play a crucial role in modern in silico drug design processes. In contrast to the classical drawn reaction diagrams, computational chemists prefer SMARTS based line notations due to a substantially increased expressiveness and precision. They are used to search databases, calculate synthesizability, generate new molecules, or simulate novel reactions. Working with computer-readable representations of reaction schemes can be challenging due to the complexity of the features to be represented. Line representations of reaction schemes can often be cryptic, even to experienced users. To simplify the work with Reaction SMARTS for synthetic, computational, and medicinal chemists, we introduce a visualization technique for reaction schemes and provide a respective tool, called ReactionViewer. ReactionViewer is able to convert reaction schemes encoded as Reaction SMILES, Reaction SMARTS, or SMIRKS into a visual representation. The visualization technique is based on the concept of structure diagrams and follows IUPAC's Compendium of Chemical Terminology definition of chemical reaction equations for the reaction symbols. We demonstrate the applicability of the method using two data sets of organic synthesis reaction schemes taken from recent publications. We discuss various properties of the visualization and highlight its readability and interpretability.

Visualizing Generic Reaction Patterns

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