Handling isotopomers

Issue #42 new
Anonymous created an issue

I believe that 3-methyl-4-(propyl-2,3-13C)octane is valid IUPAC specification for an isotopomer with 13C at the 2 and 3 atoms of the propyl group. However, OPSIN is not recognizing this.

A lot of stable isotope tracing experiments are generating NMR datasets with assigned isotopomers. Our abililty to utilize IUPAC depends on the ability of tools to process the isotopomer part of the IUPAC standard.

Comments (6)

  1. Daniel Lowe repo owner

    The syntax you are using is a systematic way of specifying isotopes. It is the extended Boughton system and is used in CAS nomenclature. OPSIN currently only implements this system for deuterium.

    The IUPAC currently (1993/2013 recommendations, I don't have the 1979 ones immediately to hand) recommend placing the isotopic specification before the term in brackets e.g. 3-methyl-4-((2,3-13C2)propyl)octane

    Where 13C2 is <sup>13</sup>C<sub>2</sub>.

    I am very unsure whether the IUPAC recommendations require or desire the 2 indicating how many carbons were carbon-13. Re-reading the description below I think it may be optional as the specification is unambiguous without the 2 as obviously at positions 2 and 3 there is only one carbon.

    Relevant IUPAC text: "The name of an isotopically substituted compound is formed by adding or inserting the nuclide symbol(s) enclosed in parenthesis, preceded by any necessary locant(s), letters and/or numerals, before the part of the compound that is isotopically substituted. Immediately after the parentheses there is neither space nor hyphen, except that when the name, or a part of a name, includes a preceding locant, a hyphen is inserted. When two or more nuclide symbols appear at the same place in the name they are cited first in alphabetical order and then by their mass number, if necessary (see P-82.3) When polysubstitution at a single position is possible, the number of atoms substituted is always specified as a right subscript to the atomic symbol(s), even in case of monosubstitution."

  2. Daniel Lowe repo owner

    I've dropped the requirement that the count of replacements be provided so that "4-((2,3-13C)propyl)octane" will now be accepted. Before the next release I'll try adding support for 13C to the Boughton system support, and probably at least the other common organic isotopes e.g. 19F, 15N, 18O. I've been quite conservative about supporting this system as it has the potential to introduce ambiguity as to whether the term is part of the previous or subsequent name component (in your example the brackets make this completely unambiguous). Thanks for letting me know who you are, it's always interesting to know who is using the software.

  3. Hunter Moseley

    Thanks Daniel! This support will really help facilitate our deposition specification plans.

    Also, will we be able to use curly braces instead of parentheses? For example, will the following be parsable by OPSIN as well: 3-methyl-4-({2,3-13C}propyl)octane ?

    Thanks, Hunter

  4. Hunter Moseley

    Daniel, thanks for testing.

    We are thinking of using curly braces to indicate a partial isotopomer assignment for an NMR feature vs a full isotopomer assignment with parentheses. IUPAC has no specification for a partial isotopomer, but it is needed for properly indicating the level of ambiguity of assignment for a particular NMR feature (peak).

    Cheers, Hunter

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