In a recent post ( Chemical names - the challenge) I addressed the question of how to identify chemical names in text and referred to the problem of generic rather than specific names. Here's an example showing how we cannot just lift names out of text and look them up or convert them to connection tables.
I happened to notice that the American Chemical Society had posted a list of its most highly accessed articles. [Which - like all publishers - probably bears little relation to their most highly cited articles]. So I thought I'd use the first one as an example of the use of chemical names. I reproduce the abstract but to avoid charges of violating copyright and remaining within "fair use" have removed all the verbs, replacing them by ellipses.
J. Am. Chem. Soc., 129 (5), 1465 -1469, 2007. 10.1021/ja068047t S0002-7863(06)08047-4
Web Release Date: January 11, 2007 Copyright © 2007 American Chemical Society
Total Synthesis of (+)-Nakadomarin A
Ian S. Young and Michael A. Kerr*
The total synthesis of (+)-nakadomarin A is [...]ed. A three-component cycloaddition of a hydroxylamine, aldehyde, and cyclopropane to form a highly functionalized tetrahydro-1,2-oxazine [...]s as the foundation for this synthesis. The resulting oxazine is [...]ed as a single diastereomer with the absolute configuration being [...]ed by the chirality of the cyclopropane. Other key steps [...] desymmetrization of a malonate by reduction, Heck cyclization and pyrrolidine formation, and ring-closing metathesis to [...] both cycloalkenes. Overall, the synthesis [...]ed 23 linear steps from the cyclopropane, which in turn [...] available (six steps) in optically pure form from commercially available D-mannitol.
So there are 11 different chemical names (one is repeated) of which I judge only 2 represent well defined single identifiable compounds while the other 9 are generic or may represent Synecdoche.
The generic nature of these compounds is not trivial. "aldehyde" could be represented by "R-C(=O)H" but "cyclopropane" would have to be "R1C(R2)1C(R3)(R4)C(R5)(R6)1", unless further indication is given in the text.
[FWIW: (+)-nakadomarin A is not given in Pubchem so is probably of no interest except to synthetic chemists. I can't reproduce the structure as the ACS claim copyright over the graphical abstract. Presumably the high access is mainly from synthetic chemists.
Pubchem does, however, tell us what "D-mannitol" is.
It is listed as having lots of synonyms:
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are these all the same thing? I somewhat doubt it... And some of them are ceritanly generic. Is "mannitol" the same as "D-mannitol"? Without knowing whether they are used synonymously I can't say.