Sciencemadness Discussion Board - How often do you really use IUPAC nomenclature?

How often do you really use IUPAC nomenclature?

White Yeti - 5-4-2012 at 09:44

I haven't been acquainted with chemistry for very long, but I can't help but notice how sparingly I use the IUPAC naming system when it comes to organic chemistry.

Perhaps I use this system for looking up obscure chemicals, but other than that, I drop this system in favour of common names.

How often do you really use IUPAC nomenclature when dealing with organic compounds?

gutter_ca - 5-4-2012 at 10:12

Many (especially newer) compounds don't have a common name. Of course, for those that do, why wouldn't one use the simpler name?

arsphenamine - 5-4-2012 at 11:13

The essence of Science is a truthful, accurate, and unambiguous account.

If you collaborate, publish, or wish to write for reproducibility, use IUPAC nomenclature once, followed by a trivial name.

For example:
On the discussion of macrocyclic oligoethers, particularly 1,4,7,10,13,16-hexaoxacyclooctadecane (18-crown-6) ...

...and, having explained it, use 18-crown-6 thereafter.

ziqquratu - 8-4-2012 at 17:30

Quote: Originally posted by arsphenamine

The essence of Science is a truthful, accurate, and unambiguous account.

If you collaborate, publish, or wish to write for reproducibility, use IUPAC nomenclature once, followed by a trivial name.

For example:
On the discussion of macrocyclic oligoethers, particularly 1,4,7,10,13,16-hexaoxacyclooctadecane (18-crown-6) ...

...and, having explained it, use 18-crown-6 thereafter.

That depends... In a significant amount of published organic work, you'll find that the initial reference is to a structure (eg. "As shown in Scheme 5, we prepared ketone 23 by..."), whilst the IUPAC name - if it appears at all - will be later, in the experimental section or supporting information.

IUPAC notation is, of course, absolutely valuable for naming compounds. However, it's often cumbersome, difficult to read and visualise and, for more complex structures, easy to mess up - so simply showing the structure (while often but certainly not always including the name in a later section) is the more common method in the published literature.

When I think about it, that style of "full term once, abbreviate thereafter" is quite rare for ANY type of abbreviations in a chemistry journal. Most common abbreviations (THF, Et, Ac, Ph, m.p., and so forth) are assumed to be understood by readers, and new abbreviations are coined only relatively rarely - so no definition is usually needed. This falls apart in multi-disciplinary articles, to some degree - and in those cases you certainly see the OTHER discipline's abbreviations defined (eg. in med chem, "dopamine (DA)" might be shown, or a code name for a drug lead given, but "EtOAc" is still going to be left to the reader). Also, for journals with a wider readership than just chemists, or articles which contain many abbreviations which may be non-standard, the paper will often contain a small "abbreviations" footnote, which will list all the abbreviations used in that article.

There are three main reasons for the lack of definitions, and the use of generic names ("ketone 23") pointing to an image - necessity, clarity and space. Defining every abbreviation to a skilled audience is pointless (we all KNOW what "THF" stands for!); using IUPAC names makes a paper difficult to read; and it takes a heck of a lot of unnecessary space that journals still don't like to use.

When you get down to it, of course, the requirements fully depend on the journal in which the work is published - but the method you cite is reasonably rare even for English abbreviations, let alone IUPAC names.

White Yeti - 8-4-2012 at 18:21

Quote: Originally posted by ziqquratu

Most common abbreviations (THF, Et, Ac, Ph, m.p., and so forth) are assumed to be understood by readers, and new abbreviations are coined only relatively rarely - so no definition is usually needed. This falls apart in multi-disciplinary articles, to some degree - and in those cases you certainly see the OTHER discipline's abbreviations defined (eg. in med chem, "dopamine (DA)" might be shown, or a code name for a drug lead given, but "EtOAc" is still going to be left to the reader). Also, for journals with a wider readership than just chemists, or articles which contain many abbreviations which may be non-standard, the paper will often contain a small "abbreviations" footnote, which will list all the abbreviations used in that article.

I definately agree, but correct me if I'm wrong, long papers with significant content oftentimes have a list of abbreviations in the beginning that are used often throughout the paper. This eliminates ambiguities to a certain extent.

BromicAcid - 8-4-2012 at 18:32

As a professional chemist in an industrial field... about 50% of the time.

arsphenamine - 8-4-2012 at 21:22

It all started when I made a piss joke about the discovery of phosphorus, but somehow I got drawn into the computational chemistry of Group 15 element clusters. For the moment, our practice is "full term once, abbreviate thereafter", although there may be several overlapping descriptors.

For example, the phosphorus and arsenic tetramers exist in both tetrahedral and tetracyclo forms depending on excitation level (or so it seems). For clarity, we specify the point group symmetry (Td or D2h) when necessary, or the IUPAC (tricyclo[1.1.0.02,4]tetraarsane) for ease of literature searches, or simply as an elemental tetramer for simpler online searches as the NIH WebBook provides.

I guess the answer is "use what you think is prudent" so other people can confirm your work.