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I've seen multiple prefixes for naming thiols: mercapto-, sulfanyl-, and -thio. Is there a rule for when specific ones are used? And are they used for IUPAC and/or common naming?

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Mercapto- and sulfanyl- are both prefixes for use with the $\ce{-SH}$ group (known as a thiol), while thio- is used to denote the "sulfur" equivalent of an oxygen-containing functional group.

More details from the IUPAC Blue Book:

  • Mercapto- is mostly abandoned, and only used as a prefix for -SH groups. This quote is from the older edition of the Blue Book. "When -SH is not the principal group, the prefix "mercapto-" is placed before the name of the parent compound to denote an unsubstituted -SH group."
  • Sulfanyl- "In these [1993] recommendations, the prefix "sulfanyl-" is preferred to "mercapto-" which was used in previous editions of the IUPAC Nomenclature of Organic Chemistry."
  • Thio- "In nearly all its applications "thio" denotes replacement of oxygen by sulfur."
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    $\begingroup$ Please note that the links point to obsolete IUPAC recommendations from 1979 and 1993, respectively. However, that does not necessarily mean that names formed according old recommendations are no longer in accordance with current recommendations. $\endgroup$ – Loong Jun 12 '18 at 9:53
  • $\begingroup$ Yeah I forgot to mention that, thanks for adding the clarification. $\endgroup$ – Dennis Cao Jun 12 '18 at 14:23
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If the $\ce{-SH}$ group is the principal characteristic group, the compound is named using the using the suffix ‘thiol’ (e.g. propane-2-thiol).

In presence of another characteristic group having seniority for citation as a suffix, the $\ce{-SH}$ group is cited using the prefix ‘sulfanyl’ (e.g. 3-sulfanylpropanoic acid).

The prefix ‘mercapto’ for ($\ce{-SH}$) is no longer recommended.

The use of the functional replacement prefix ‘thio’ is no longer used to replace oxygen atoms in alcohols etc. (e.g. benzenethiol, not ‘thiophenol’).

The corresponding rule in the current version of Nomenclature of Organic Chemistry – IUPAC Recommendations and Preferred Names 2013 (Blue Book) reads as follows.

P-63.1.5 Sulfur, selenium, and tellurium analogues of hydroxy compounds

Sulfur, selenium, and tellurium analogues of hydroxy compounds are named substitutively using the suffixes ‘thiol’, ‘selenol’, and ‘tellurol’, and the prefixes ‘sulfanyl’, ‘selanyl’, and ‘tellanyl’, respectively; the presence of several of the same kind of ‘ol’ characteristic groups is denoted by the numerical multiplying prefixes ‘di’, ‘tri’, etc. The prefixes ‘mercapto’ ($\ce{-SH}$), and ‘hydroseleno’ or selenyl ($\ce{-SeH}$), etc. are no longer recommended.
Functional class nomenclature is not used.
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