Amines vs amides and and their glyoxalyl indoles

Issue #8 resolved
Steve Chapman
created an issue

http://opsin.ch.cam.ac.uk/opsin/glyoxalylamine.png http://opsin.ch.cam.ac.uk/opsin/glyoxalylamide.png http://opsin.ch.cam.ac.uk/opsin/indol-3-ylglyoxalylamide.png http://opsin.ch.cam.ac.uk/opsin/2-(indol-3-yl)glyoxalylamine.png

1.Amide has a charge on the nitrogen, the amine does not.

2.The commonplace name for a tryptamine precursor is indol-3-ylglyoxalylamide.which my be imperfect IUPAC but there you go. The structure this name produces is not the one typically desired. Adding a proper locant gives the correct structure.

Comments (7)

  1. Daniel Lowe repo owner

    The problem I think stems from the fact that glyoxalylamide is being used to mean what would be correctly written as glyoxalamide or glyoxylamide. Are you encountering any other issues with names featuring "ylamide"? If not I'm tempted to just add glyoxalylamide as a token with C substitution being used when unspecified. (this is effectively special casing the problem but on the plus side is a one line addition to implement)

    The interpretation as amide meaning [NH2-] is rare in practice so a more heuristic solution is possible but as the IUPAC documents the use of amide meaning [NH2-] even in names like acetylamide I don't like the idea of making such interpretations impossible in the general case.

  2. Steve Chapman reporter

    You are no doubt right, it may be formally incorrect but google glyoxalylamide and let me know if you want to mess with Brandt et al

    If a quick easy workaround will do the trick, great! Thanks Daniel, and I like your parser so much I put a badge on my site for it. PiHKAL info

  3. Daniel Lowe repo owner

    I saw the link on your site, thanks a lot. The fix for glyoxalylamide will appear when the web service is next updated I'm going to add lysergic acid to the grammar (or more specifically the stem lyserg) and have a query regarding its sterochemistry... or more specifically whether Wikipedia has a mistake: http://en.wikipedia.org/wiki/Lysergic_acid Wikipedia has the relationship between the D and L forms as being diasteroisomers whilst your page has them as enantiomers. http://isomerdesign.com/PiHKAL/read.php?domain=tk&id=26#rxa5348 In carbohydrate/amino acid nomenclature they would normally be enantiomers so it would be nice if Wikipedia is wrong.

  4. Steve Chapman reporter

    My pleasure Daniel, I'd been meaning to do it for ages. I really have fun with your parser and it's just so amazingly useful. I'll look forward to future enhancements.

    As for lysergic acid, the diagram of the four stereoisomers, unlike most of the content on that page, was not taken from the book TiHKAL. Rather it was adapted from another review by Shulgin from many years earlier. A poor, large, pdf can be found here: http://bitnest.ca/external.php?id=%250E%253D9%250F%2524G%253A%251FSV%255C%252B%253A%2527UG%250A%250A%2502%255D%2508%2516%2B%25243D%2509%2518%252F%2512%2519%253F%2522u%257DQ%257C See pg 63.

    I believe I've been faithful to the original, and according to my ACD/Labs software, the d-LSD has the requisite 5R,8R configuration, while l-LSD is 5S,8S. So, by definition, they are racemates--enantiomorphs, I think. I should probably mention here I didn't get my degree in chemistry--or in anything else for that matter. David Nichols touches on it somewhat in this review: http://bitnest.ca/external.php?id=%257DbxUgXXC%255DX%25407d%257B%2506 See fig. 11.

    Is it possible this is about d- and l- vs. D- and L-? I've never really learned much about the latter but I think it's based on a convention while the former is derived empirically by optical activity. All I know is they are not interchangeable and I've read the former are now deprecated because of just this kind of confusion. Grabbing at straws here, I know.

    Best wishes,

    /Steve

    -

  5. Daniel Lowe repo owner

    Thank you for the literature sources. ACD's naming is also reliable in my experience. Hence I've gone with the interpretation that they are enantiomers as that seems more consistent. You are right that d/l can mean something quite different from D/L. If Wikipedia is to be trusted the standard stereochemistry for lysergic acid is both D- and d- [meaning (+)] so I don't think this is the cause of the confusion. These updates are now live, let me know if you find any more issues.

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