{"id":1150,"date":"2015-01-21T16:56:09","date_gmt":"2015-01-21T16:56:09","guid":{"rendered":"http:\/\/nextmovesoftware.com\/blog\/?p=1150"},"modified":"2017-08-01T13:18:03","modified_gmt":"2017-08-01T12:18:03","slug":"r-or-s-lets-vote","status":"publish","type":"post","link":"https:\/\/nextmovesoftware.com\/blog\/2015\/01\/21\/r-or-s-lets-vote\/","title":{"rendered":"R or S? Let’s vote"},"content":{"rendered":"

\"requiresRuleTwoForTwoLigands\"<\/a>
CC[C@](CO)([H])[14CH2]C<\/figcaption><\/figure>The CIP (Cahn-Ingold-Prelog) priority rules are used to assign R and S labels to stereocentres. However it is known to be very prone to mis-implementation:
\nThe CIP System Again:? Respecting Hierarchies Is Always a Must<\/a><\/p>\n

Through our work on OEChem, OPSIN and Centres<\/a> we have independently written 3 different CIP implementations and hence discussion of the corner cases of CIP inevitable becomes a heated coffee time discussion.<\/p>\n

This deceptively simple case on the right turns out to give different results in many implementations.<\/p>\n

Which “ligand” do you think has highest priority?<\/p>\n

If you said [CH2][OH] you’d be right, but the majority of implementations disagree:<\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Toolkit\/application<\/th>\nAssignment<\/th>\n<\/tr>\n
Marvin 2014.11.3.0<\/td>\nS<\/td>\n<\/tr>\n
ChemBioDraw 12<\/td>\nS<\/td>\n<\/tr>\n
RDKit (HEAD)<\/td>\nS<\/td>\n<\/tr>\n
Centres (HEAD)<\/td>\nR<\/td>\n<\/tr>\n
CACTVS (Web Sketcher)<\/td>\nR [updated 23\/02\/2015]<\/td>\n<\/tr>\n
DataWarrior (latest)<\/td>\nS<\/td>\n<\/tr>\n
AccelrysDraw 4.2<\/td>\nS (now R in BIOVIA Draw 2017)<\/td>\n<\/tr>\n
OEChem 2014.Oct.2<\/td>\nS<\/td>\n<\/tr>\n
ChemDoodle 7.0.2<\/td>\nS<\/td>\n<\/tr>\n
OPSIN 1.6<\/td>\nR<\/td>\n<\/tr>\n
CDK 1.5.10<\/td>\nS<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

We can speculate that the cause of the disagreement may be that the left and right side of the molecule are symmetrical by atomic number (rule 1) and that hence rule 2 (atomic mass) is then being erroneously applied to ALL ligands… while correct implementations will only apply rule 2 to split the tie between the two ligands that could not be determined by rule 1 (*). Hence this case should be assigned R.<\/p>\n

* “precedence (priority) of an atom in a group established by a rule
\ndoes not change on application of a subsequent rule.” (IUPAC recommendations)<\/p>\n","protected":false},"excerpt":{"rendered":"

The CIP (Cahn-Ingold-Prelog) priority rules are used to assign R and S labels to stereocentres. However it is known to be very prone to mis-implementation: The CIP System Again:? Respecting Hierarchies Is Always a Must Through our work on OEChem, OPSIN and Centres we have independently written 3 different CIP implementations and hence discussion of … Continue reading R or S? Let’s vote<\/span><\/a><\/p>\n","protected":false},"author":3,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"_links":{"self":[{"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/posts\/1150"}],"collection":[{"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/comments?post=1150"}],"version-history":[{"count":26,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/posts\/1150\/revisions"}],"predecessor-version":[{"id":2586,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/posts\/1150\/revisions\/2586"}],"wp:attachment":[{"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/media?parent=1150"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/categories?post=1150"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/tags?post=1150"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}