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Intramolecular reactions have stopped working?
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Lauren

Joined: 15 Jul 2009
Posts: 11

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Link to postPosted: Sat Jul 30, 2016 6:56 pmPost subject: Intramolecular reactions have stopped working? Reply with quote

I am having a problem with an intramolecular cyclization reaction. For the reaction, I am mapping the reactive centers as two different molecules, then highlighting both molecules and selecting "Merge Reactants".

I then select the file with the input molecules, set it to enumerate sequentially, and then when I enumerate it creates zero products every time. I did the same exercise last year with no issue.

I am making fairly large and complex macrocycles, but I tested this also with a simple Williamson ether-type reaction and the same thing occurs - see screenshots below:

Is there an additional option I need to select to make an intramolecular reaction work or has this feature become broken?

Zsolt
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Joined: 11 Jan 2006
Posts: 1163

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Link to postPosted: Mon Aug 01, 2016 10:57 amPost subject: Reply with quote

It seems the R-group notation doesn't work with intramolecular reactions. Replace R1 and R2 groups with carbon atoms (query notation) and it will work.

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