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Questions about double bond stereochemistry

Asked by , Edited by Robert Kiss

There was a related question about displaying unknown and unspecified double bond stereochemistry in this forum, which initiated a very interesting discussion about the topic. The outcome of that discussion was (at least in my interpretation) that the crossed double bond representation is preferred over wavy bonds next to double bonds to indicate an unspecified or unknown (?) stereochemistry, although this contradicts with the IUPAC recommendations.

I think this is a very important step toward correct double bond stereo representation, but we should also clarify what exactly we want to use the crossed double bonds for. So I also think that we shouldn’t stop here. It would be very important to answer the following questions to distinguish between different double bond stereo types:

1. What are the definitions of unknown and undefined double bond stereochemistries?
2. What would be the correct drawings of unknown and undefined double bond stereochemistry?
3. What would be the correct drawing of mixtures (cis AND trans)?
4. How would you store data in v2000 MOL files for unknown and undefined double bond stereochemistry?
5. How would you store data in v2000 MOL files for mixtures (cis AND trans)?

I tried to describe the problem in more detail here, and I would very much appreciate to hear any answers/suggestions on any of the above questions. Thanks!!  
NN comments
imants
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Thanks for bringing this question up again,!

Unfortunately, very few questions here are discussed until a reasonable conclusion can be made, a consensus is reached. This community is too small. I have asked just a few questions and already I am one of the top contributors. While everybody is complaining about quality of databases, what we should work on is 1) standards that address practical question (IUPAC does not, apparently) and 2) software that supports these standards. I had high hopes for the Pistoia Alliance. But it appears to be too burocratic. Many questions needs to be dealt with ASAP. Databases do this by making their own rules but we can do only so much to deal with poor data coming from data sources. The problem needs to addressed where data are created, not with better database curation.

So how can we get more contributors to BO? People from industry, suppliers, etc? I will ask this question separately. As I feel that a few opinions here in one direction or the other really is not a serious discussion. The loudest of the 5 commenter wins.

robert_kiss
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Thanks for this comment. Posted an answer to your question.

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baoilleach [ Admin ]

It’s important not to conflate IUPAC recommendations on depiction and the best way of storing chemical information in MDL files. Notwithstanding the exact way information is stored in an MDL file, software could depict the structure according to IUPAC recommendations.

NN comments
robert_kiss
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It is definitely important to follow the IUPAC recommendations where they make sense and probably even where they don’t but it is not totally against common sense :) This is important to minimize confusion arising from following different conventions. As for this issue – it looks that the best way to indicate double bond stereochemistry is by flagging the double bond itself rather than the bond next door. The latter gives rise to several problems pointed out by Rich Apodaca here: http://metamolecular.com/blog/2011/06/14/why-chemwriter-doesnt-follow-iupacs-recommendations-for-depicting-unknown-double-bond-stereochemistry/ Your suggestion sounds interesting, but because of the problems described on the above link – the application of the wavy bonds (as IUPAC recommends) is not straightforward. Unfortunately, the IUPAC recommendations also don’t seem to distinguish between the “undefined” and “unknown” cases, as far as I understand.

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