Hi Bob,
Daniel says he'd seen another example in ChEBI essentially the same as this
where if you add Rule 1b it breaks the tie when it shouldn't.
John
On 16 May 2017 at 00:25, John May <john.wilkinson...@gmail.com> wrote:
> I need to think more about it tomorrow, I think your logic is correct but
> I wouldn't say it's critically important. You're conflating two procedures
> - a) finding stereochemistry vs b) naming it. You only need CIP for b, a is
> more efficiently and correctly handled with group theory.
>
> "Everything looks like a nail to a man with a hammer"
>
> - John
>
> On 15 May 2017, at 23:47, Robert Hanson <hans...@stolaf.edu> wrote:
>
> I'm interested in two things. First, feedback on a proposed amendment to
> CIP Rule 1b. Second, suggestions for how to officially propose this.
>
> Current Rule 1:
>
>
> *(1a) higher atomic number precedes lower;*
>
>
> *(1b) a duplicate atom node whose corresponding nonduplicated atom node is
> the root or closer to the root ranks higher than a duplicate atom node
> whose corresponding nonduplicated atom node is farther from the root. *Said
> differently but with the same meaning:
>
>
> *(1a) higher atomic number precedes lower;**(1b) in comparing two
> duplicate nodes, lower root distance precedes higher root distance, where
> "root distance" for a duplicate node is defined as*
> * the distance from its corresponding nonduplicated atom node to the root
> node.*
> Proposed amended rule:
>
>
> *(1a) higher atomic number precedes lower;*
> *(1b) in comparing two duplicate nodes, lower root distance preceded
> higher root distance, where "root distance" is defined: (i) in the case of
> **a duplicate atom for which the atomic number is averaged over two or
> more atoms in applying Rule 1a, *
>
>
> *the distance from the duplicate node itself to the root node; and (ii)
> in all other cases, the distance of its corresponding nonduplicated atom
> node to the root node.*
> If that means nothing to you, ignore this. But it is a critically
> important addition for any algorithm if it is to correctly assign the
> stereochemistry even for very simple compounds based on CIP rules 1-5. For
> example, without that modification, an algorithm following the rules in
> IUPAC BB 2013 will arrive at "S" for the descriptor for in this compound:
>
> [image: Inline image 1]
> C1=CC=CC(O)=C1[C@H](C2=CC=CC=C2O)O
>
> My second question is, having said that, how do I go about officially
> stating this? Publish? Where?
>
>
> Bob
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
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