Re: [BlueObelisk-discuss] Proposed amendment to CIP Rule 1b
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 Hansonwrote: > > 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 -- 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
Re: [BlueObelisk-discuss] Proposed amendment to CIP Rule 1b
- John > On 15 May 2017, at 23:47, Robert Hansonwrote: > > 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 -- 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
[BlueObelisk-discuss] Proposed amendment to CIP Rule 1b
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 -- 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