Chemical nomenclature
Posted: Tue Apr 23, 2019 3:32 pm
Oh I am so frustrated with chemical nomenclature. I'm so frustrated that I'm almost enjoying the process of being frustrated. Natural product chemistry is where it comes into its own, truly antisocial, illogical, unhelpful, self-contradictory and weird self:
(1) Why can't people do a Google search before naming their favourite discovery? If the authors of a 2012 J. Agric. Food Chem. paper had googled for the name they chose for a novel product from Manuka honey, "Leptosin", they would have realised the name had already been in use for decades, for an aurone pigment of snapdragon. There are other examples too; it is unhelpful to have the same trivial name used for multiple products, particularly when they appear in related fields (both Leptosins are plant phenolics).
(2) So perhaps authors shouldn't be allowed to make up their own trivial names? Let's trust IUPAC, the people who decided it was a good idea to reverse the order of numbering on the quinic acid ring of chlorogenic acid, thereby converting 3-caffeoylquinic acid to 5-caffeoylquinic acid. Chlorogenic already had history (having nothing to do with chlorophyll or chlorine). But now it's doomed to a literature where one cannot tell what chemical is being discussed, without knowing whether the authors are aware of the change (Sigma still use the pre-1976 nomenclature). People have written whole papers on the nomenclature of chlorogenic acid.
(3) OK, so if we don't want IUPAC making changes that are probably founded on good logic, but doomed to creating unending chaos, we should stick to the numbering that tradition has handed down. Yes, we've done this with flavonoids, where carbon 1 is an oxygen, and two carbons have no number whatsoever. This doesn't matter, as they're both in positions that can never be substituted, but there are two other carbons that can't be substituted and yet are numbered. Who knows. Go figure (but preferably consistently).
(4) Of course life's safe if we stick to logical computerised naming systems. I'm off to continue working on SVILRWHEUBXRMG-JJRVVBIQSA-N. Oh yes, I love InChI keys too.
(1) Why can't people do a Google search before naming their favourite discovery? If the authors of a 2012 J. Agric. Food Chem. paper had googled for the name they chose for a novel product from Manuka honey, "Leptosin", they would have realised the name had already been in use for decades, for an aurone pigment of snapdragon. There are other examples too; it is unhelpful to have the same trivial name used for multiple products, particularly when they appear in related fields (both Leptosins are plant phenolics).
(2) So perhaps authors shouldn't be allowed to make up their own trivial names? Let's trust IUPAC, the people who decided it was a good idea to reverse the order of numbering on the quinic acid ring of chlorogenic acid, thereby converting 3-caffeoylquinic acid to 5-caffeoylquinic acid. Chlorogenic already had history (having nothing to do with chlorophyll or chlorine). But now it's doomed to a literature where one cannot tell what chemical is being discussed, without knowing whether the authors are aware of the change (Sigma still use the pre-1976 nomenclature). People have written whole papers on the nomenclature of chlorogenic acid.
(3) OK, so if we don't want IUPAC making changes that are probably founded on good logic, but doomed to creating unending chaos, we should stick to the numbering that tradition has handed down. Yes, we've done this with flavonoids, where carbon 1 is an oxygen, and two carbons have no number whatsoever. This doesn't matter, as they're both in positions that can never be substituted, but there are two other carbons that can't be substituted and yet are numbered. Who knows. Go figure (but preferably consistently).
(4) Of course life's safe if we stick to logical computerised naming systems. I'm off to continue working on SVILRWHEUBXRMG-JJRVVBIQSA-N. Oh yes, I love InChI keys too.
