Abstract
Both the automated generation of reaction networks and the automated prediction of synthetic trees require, in one way or another, the definition of possible transformations a molecule can undergo. One way of doing this is by using reaction templates. In view of the expanding amount of known reactions, it has become more and more difficult to envision all possible transformations that could occur in a studied system. Nonetheless, most reaction network generation tools rely on user-defined reaction templates. Not only does this limit the amount of chemistry that can be accounted for in the reaction networks, it also confines the wide-spread use of the tools by a broad public. In retrosynthetic analysis, the quality of the analysis depends on what percentage of the known chemistry is accounted for. Using databases to identify templates is therefore crucial in this respect. For this purpose, an algorithm has been developed to extract reaction templates from various types of chemical databases. Some databases such as the Kyoto Encyclopedia for Genes and Genomes and RMG do not report an atom–atom mapping (AAM) for the reactions. This makes the extraction of a template non-straightforward. If no mapping is available, it is calculated by the Reaction Decoder Tool (RDT). With a correct AAM—either calculated by RDT or specified—the algorithm consistently extracts a correct template for a wide variety of reactions, both elementary and non-elementary. The developed algorithm is a first step towards data-driven generation of synthetic trees or reaction networks, and a greater accessibility for non-expert users.
Highlights
Introduction to methodology and encoding rulesJ Chem Inf Comput Sci 28(1)
An algorithm has been developed to automate the generation of reaction templates from databases
Depending on which database is used, the templates can be used for the prediction of retro-synthetic steps or as input for kinetic model generation tools, such as Genesys
Summary
The continuous increase of our scientific knowledge has led to data quantities that can no longer be processed by the human mind alone: the R eaxys® database contains over 40 million chemical reaction entries and lists over 100 million compounds [1]. Comparing E/Z or R/S configuration of ‘A’ to that of its mapped counterparts further expand all reactive centers by including heteroatoms connected to the reacting atoms This makes the final reactive center more specific and can be useful if surrounding atoms influence or are required in the electronic transitions that occur during the reaction, without changing on a net basis. For each reaction template that has been determined, four input elements are generated; the recipe, the definition of the reactants, molecular constraints for the rulebased algorithm of Genesys and kinetics. The focus of the method is on extracting the reaction template, in order to generate a network, not a kinetic model. An empty block for group additivity based kinetics calculations is added, with the user having to fill out the path to the desired database of ΔGAV0s [42,43,44]
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