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In chemical notation, can I safely assume that the notation of

  • a single lower-case latin character
  • followed by a hyphen
  • followed by an Element upper-case latin character (and possibly more characters)

should always be typeset as

  • italic lower-case character
  • hyphen (i.e. never is a bond)
  • element following characters

This question is regarding the further improvement of mhchem.

I know that not all of them stand for the same concept, but I assume they share the same typographical representation. Beware, I am no chemist. And because I don't know the name of these notations, I could not find them in the colored IUPAC books.

The notation is quite rare. There were only 21 usages in 43k \ce calls extracted from chemistry.SE:

(p-NO2Ph)_2CO
t-BuO-
i-Pr
t-Bu
R=i-Pr
n-BuNH2
(c-Hex)2BCl

a-HCl  // should this be \alpha?

1s-H  // what is this?
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migrated from chemistry.meta.stackexchange.com Mar 25 '16 at 21:06

This question came from our discussion, support, and feature requests site for scientists, academics, teachers, and students in the field of chemistry.

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    $\begingroup$ I migrated it to the main site, it will have more traction here and it is a solid question. Notation is something many people struggle with, so having these questions here is very good. $\endgroup$ – Martin - マーチン Mar 25 '16 at 21:10
  • $\begingroup$ Is there a link for the a-HCl one? That looks really weird imo $\endgroup$ – orthocresol Mar 26 '16 at 0:04
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    $\begingroup$ If the a-HCl is from here then it's out if context. That was also another abuse of mhchem as it is easier to write ce than mathrm ;) . The question was about pKa values for HF to HI. :) $\endgroup$ – pH13 - Yet another Philipp Mar 26 '16 at 12:21
  • $\begingroup$ Note that, in the given examples, “Bu” (butyl) and “Pr” (propyl) are not chemical elements. $\endgroup$ – Loong Mar 26 '16 at 12:43
  • $\begingroup$ Regarding the "1s-H" it's the same abuse of mhchem as an easy version of mathrm as with "a-HCl". $\endgroup$ – pH13 - Yet another Philipp Mar 26 '16 at 14:24
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tl;dr: That's probably a good approach.

So, there are at least three different things here. None of these abbreviations are standardised as far as I'm aware[1], so whatever is done is going to be just as non-standard as any other approach.

  1. Specific shorthands for alkyl functional groups: t-Bu, i-Pr, n-Bu, c-Hex

    I've seen the method you've suggested used for these, and also the first three with superscripted initial characters, e.g. $^{\textrm{t}}\textrm{Bu}$ and $^{\textrm{i}}\textrm{Pr}$, and I'd never seen the last one until I read this question. I've also seen them written simply as tBu, iPr, and nBu. They're abbreviations for tert-butyl, isopropyl, n-butyl (straight-chain), and cyclo-hexyl respectively. (Here are links for IUPAC References for non-cyclic and cyclic alkanes.)

  2. Substitution points on a benzene ring: (p-NO2Ph)_2CO

    This example denotes a para- substituted phenyl group (confusingly, benzyl refers to a $\ce{C6H5-CH2 -}$ group). The other options here are ortho- and meta-, which I would personally not find it confusing or uncommon to see abbreviated to o- and m- respectively, and $\ce{{\it p}-NO2Ph}$ seems a perfectly reasonable interpretation of what the person has written here.

  3. Electronic configuration labels: 1s-H

    This seems like using an atomic orbital label (1s) as a hyphenated specifier for the hydrogen: I don't think it's a standard form of writing that at all, but the method you propose would presumably italicise the s, which would be fine -- the atomic orbital labels like this are often italicised.

  4. Whatever the a-HCl is: I don't know.

    I couldn't find anything that looked appropriate for this one.

Most importantly, I can't think of any counter-examples where that wouldn't be a sensible thing to do.


[1] Edit: I defer to @Loong's superior mastery of the ways of IUPAC in their answer.

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  • 1
    $\begingroup$ My answer does not really invalidate your statement. The abbreviations for organic groups may be common, but they are actually not standardized (as you can see, two relevant documents give different recommendations). The author of the IUPAC Recommendations disparagingly calls them “nicknames”. $\endgroup$ – Loong Mar 27 '16 at 12:05
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In the current version of Nomenclature of Organic Chemistry – IUPAC Recommendations and Preferred Names 2013 (Blue Book), single italic lower-case Latin letters are used in some stereodescriptors (such as ‘c’, ‘m’, ‘p’, ‘r’, ‘s’, and ‘t’), in descriptors for fusion sites (e.g. dibenzo[c,g]phenanthrene), in locants (‘o’, ‘m’, and ‘p’ in place of ortho, meta, and para, respectively; however, this usage is strongly discouraged), and in other structural descriptors (e.g. s-indacene).

However, single lower-case Latin letters that are used for numbering are not italicized (e.g. naphthalene-4a,8a-diol).

All these symbols are typically used in names (which are usually not typeset using MathJax/mhchem) and do not necessarily appear in formulas.

Furthermore, common abbreviations for organic structure fragments may be used in formulas, but not in text. According to the Graphical Representation Standards for Chemical Structure Diagrams (IUPAC Recommendations 2008), the permissible abbreviations include:

  • isopropyl: iPr
  • isobutyl: iBu
  • sec-butyl: s-Bu
  • tert-butyl: t-Bu

However, the ACS Style Guide recommends different abbreviations:

  • isopropyl: i-Pr
  • isobutyl: i-Bu
  • sec-butyl: sec-Bu
  • tert-butyl: t-Bu

Furthermore, authors may create their own abbreviations, but any abbreviations not included in the recommendations shall be defined clearly when they are used.

Also note (since the question mentions letters followed by an element) that several structural abbreviations in current usage are identical to an element symbol:

  • Ac (acetyl, actinium)
  • Ar (aryl, argon)
  • Cm (carboxymethyl, curium)
  • Nb (p-nitrobenzyl, niobium)
  • Np (p-nitrophenyl, neptunium)
  • Pr (propyl, praseodymium)
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  • $\begingroup$ Do you know of any counter-example to my proposed formatting rule? $\endgroup$ – mhchem Mar 26 '16 at 18:56
  • $\begingroup$ "Graphical Representation ..." notations are on (printed) page 406. It cannot be found with a full-text search. $\endgroup$ – mhchem Mar 26 '16 at 19:01
  • $\begingroup$ @mhchem 1. see Table II on page 406 (page 130 of the pdf); 2. I haven’t found any counter-examples yet. $\endgroup$ – Loong Mar 26 '16 at 19:01
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I'd like to point out that they are NOT standard notation. t-Bu stands for tert-butyl, i-Pr stands for isopropyl. These are just short hand abbreviations, mostly used in organic chemistry. They are not even abbreviations of standard, systematic names. Isopropyl, for example is a common name.

If you start going down the road of accepting short-hand organic notations, "slangs", you should be prepared for things like TMEDA, py, TsOH, and similar notations too. I suggest you better put a restriction on your input, as I don't see an easy way to standardize the slang.

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  • $\begingroup$ If everyone uses this nomenclature and everyone understands it. Isn't it kind of standard even if it is not written in any important IUPAC book? Also what would TMEDA, py and TsOH change for mhchem? $\endgroup$ – pH13 - Yet another Philipp Mar 26 '16 at 13:48
  • $\begingroup$ It is well-understood, yes. It might be standard, yes. The thing I am trying to say is that they are not official symbols, so they are subjected to nomrul $\endgroup$ – Ezze Mar 26 '16 at 13:49
  • $\begingroup$ ...upps, pressed enter. So they are not subject to any rules whatsoever, one might write them however one pleases. For example, I have no idea what a-HCl is, even tho I am a sort of experienced chemist. The problem is, you can not constructnamset of formatting rules, as there is no rules at all. $\endgroup$ – Ezze Mar 26 '16 at 13:51

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