Re: [BlueObelisk-discuss] Proposed amendment to CIP Rule 1b

2017-05-15 Thread John May
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  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:
> 
> 
> 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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Re: [BlueObelisk-discuss] Proposed amendment to CIP Rule 1b

2017-05-15 Thread John May


- John

> On 15 May 2017, at 23:47, Robert Hanson  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:
> 
> 
> 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
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Blueobelisk-discuss mailing list
> Blueobelisk-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
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[BlueObelisk-discuss] Proposed amendment to CIP Rule 1b

2017-05-15 Thread Robert Hanson
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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