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Set of compounds not handled properly by name->structure
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Nicholas

Joined: 12 Aug 2009
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Link to postPosted: Mon Feb 06, 2012 11:55 pmPost subject: Set of compounds not handled properly by name->structure Reply with quote

I have found a grouping of compounds where the stereochemistry of the molecule does not transfer properly when using name->structure (I ran them through chemicalize.org to ensure newest version was being used).

1-((1S,2S)-1-methoxy-1-phenylpropan-2-yl)pyrrolidine (returns (1R,2S) instead)

1-((1R,2R)-1-methoxy-1-phenylpropan-2-yl)pyrrolidine (enantiomer of first molecule, returns (1S,2R)

(S)-1-(2-methoxy-2-phenylethyl)-4-methylpiperazine (returns compound without stereochemistry)

1-((1S,2S)-1-methoxy-1-phenylpropan-2-yl)-4-methylpiperazine (similar nitrogen based functional group with same problem as first molecule)

1-((1S,2S)-1-methoxy-1-phenylpropan-2-yl)urea (very different nitrogen containing functional group with same problem as first molecule)

(1S,2S)-N,N-diethyl-1-methoxy-1-phenylpropan-2-amine (very similar molecule to the above, but DOES return the correct structure)

Let me know if you need more information to track down the issue.

Nick Reich

dbonniot
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Joined: 20 Mar 2006
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Link to postPosted: Tue Feb 07, 2012 2:32 pmPost subject: Reply with quote

Thank you Nick for your report. You are right about those cases, the stereochemistry is wrong in 5.8. This has been fixed in the 5.9 branch, except for the one case of missing stereochemistry, which I will be looking at.

Do you need a release of the fix urgently?

Daniel

Nicholas

Joined: 12 Aug 2009
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Link to postPosted: Wed Feb 08, 2012 1:21 amPost subject: Reply with quote

Thanks for looking into the issue; I was able to work around it, so no need for an urgent fix here.

Nick

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