Release 4.4.0
For this update, as a change of pace, attention was turned towards the educational application of the site, namely the modeling of two new reactions: the Benzoin condensation reaction and the Dieckmann condensation reaction. Inspiration for modeling these reactions came directly from an organic chemist and lecturer from the region of West Bengal in India! I am actually very excited about this request and highly encourage other chemists and chemistry teachers to provide similar requests!
Benzoin Condensation Reaction: Modeling of the Benzoin condensation reaction was straightforward. Some work was done to verify that both the interface and search engine could support the molcule benzoin, but after that the work done was primarily to introduce the rules used for the reaction. An example search for a pathway from benzaldehyde to benzoin can be found here: https://www.organicchemmaster.com/Molgen/Reaction/benzaldehyde/benzoin?options=Calc,Reac
Dieckmann condensation reaction: Modeling of the Dieckmann condensation reaction proved more difficult, primarily because support for diesters (and similarly diethers) was a prerequisite. The molecule chosen to model for the reaction was ethyl,methyl hexanedioate. The most difficult implementation challenge of adding support for diesters was to invent a means to distinguish between the two ester radicals, namely the ethyl and methyl radicals, in the model. And to which Oxygen the two radicals were attached. Otherwise, the modeling for the reaction itself was relatively straightforward, though some special care was taken when converting the molecule to a cycloalkane.
As a product of the Dieckmann condensation reaction applied to ethyl,methyl hexanedioate is methyl (1S)-2-oxocyclopentane-1-carboxylate, it was also necessary to introduce support in the interface and search engine for cycloalkanes with an attached ester. This required updates to the nomenclature engine.
An example search for a pathway involving Dieckmann condensation can be found here: https://tinyurl.com/5cet2mpv.
Standards: The usual IUPAC naming standards were followed. In particular, nomenclature support for cycloalkanes with ester side chains was added, e.g., carboxylate and benzoate.
Controls: No new controls were added for this update. However, an auto-scaling feature was added to display the proper size of more complex molecules in the pathways view.
Future Considerations: Hopefully there will be requests for more reactions and more complex molecules from chemists and lecturers in the future!
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